Citrus Sinensis ID: 008117

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------
Protein Sequence
MNEYTVRKVGRLQILHKRTTSTTPFLQQTMLATECSLALFKVICSAGDSCHACGAISIMLLMCGLPRYPAPYPSMVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEHDYHDDSIRENHMEIRLHKMVMGMNQPMCR
Secondary Structure (PSIPRED)
cccccHHccccEEEEEccccccccHHHccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEccccccccHHHHHHHHHHccccccccccccccccccccEEEEEcccHHHHHHHHHHHccccccccEEEEcccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHcccccccHHHHHHcHHHHccccccccccccccccccccccccccccccHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHcccHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
ccccEHHHccHEEEEEcccccccHHHHHHHHHHHHHHHHHHHHEccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccHHHHHHHHHHcccEEEEEEEcccccccccccEEEccccHHHHHHHHHHHccccccccEEEEEEcHHHHHHHHHHHHHHHccccccccccccccccHcccHHHHHHHHHcccHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHcccccccccccccHcccccccHHHccccccccccccccccccccHccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHcHHccHcccccccccccEEEEHHHHHccccccccc
Coil and Loop (DISEMBL)
MNEYTVRKVGRLQIlhkrttsttpflQQTMLATECSLALFKVICSagdschacGAISIMLLmcglprypapypsmvrpafpprppgpvgvlpsvarppvpgipgvrpimppvvrpvplptvtpaekpqtkvyvgkiaptadsDFVLSVLKVCGTvkswkraqypsngtpkgfgfcefESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKEtqdagagkedesvqsvekneptkspenlkdnetgnkeshdptnfgvvteeDRKADQEALEKLTCMVEerlktnplpppppqttadgsgisnselpakardgdsdvDMIRNDiaedklddettsdtkasdhdrpetsspdrsrvhdrrgrdkerDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEilydeeededdsRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLsdnavngslaeesaveskgmdvehdyhddsirENHMEIRLHKMvmgmnqpmcr
Flexible Loop (DISEMBL)
mneytvrkvgrlqilhkrttsttpflQQTMLATECSLALFKVICSAGDSCHACGAISIMLLMCGLPRYPAPYPSMVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPtvtpaekpqtkvYVGKiaptadsdfVLSVLKVCGTVKswkraqypsngtpkgFGFCEFESAEGVLRALRLLNKFnidgqelmlkVDQATREYLERyvdkktentkklketqdagagkedesvqsvekneptkspenlkdnetgnkeshdptnfgvvteEDRKADQEALEKLTCMVEErlktnplpppppqttadgsgisnselpakardgdsdVDMIRNDiaedklddettsdtkasdhdrpetsspdrsrvhdrrgrdkerdlkrekereidryereaerervrkereqrrkieeaereyerclkdweyrererekerqyekekekererkrkkeilydeeededdsrkrwrrsvleekrrkrirekeedladevreeEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEesaveskgmdvEHDYHDDSIRENHMEIRLHKmvmgmnqpmcr
Low Complexity Region (SEG)
MNEYTVRKVGRLQILHKRTTSTTPFLQQTMLATECSLALFKVICSAGDSCHACGAISIMLLMCGLPRYPAPYpsmvrpafpprppgpvgvlpsvaRppvpgipgvrpimppvvrpvplptvtpAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDkktentkklketQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNplpppppQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHdrrgrdkerdlkrekereidryereaerervrkereqrrkieeaereYERCLKDWeyrererekerqyekekekererkrkkeILYdeeededdSRKRWRRSVLeekrrkrirekeedladevreeeeiavakrraeeeqlqqqqrdalklLSDNAVNGSLAEESAVESKGMDVEHDYHDDSIRENHMEIRLHKMVMGMNQPMCR
Disordered region (IsUnstruct)
*****VRKVGRLQILHKRTTSTTPFLQQTMLATECSLALFKVICSAGDSCHACGAISIMLLMCGLPRYPAPYP**********************************IM*PVVRPV************TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYV*************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
****TVRKVGRLQILHKRTTSTTPFLQQTMLATECSLALFK****************************************************************************************KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATRE***********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************GMNQP***
Disordered Region (DISEMBL)
MNEYTVRKVGRLQILHKRTTSTTPFLQQTMLATECSLALFKVICSAGDSCHACGAISIMLLMCGLPRYPAPYPSMVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKL*****************************LKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKL********************************************EIDRY************************EYERCLKDWEYR*********************RKKEILY************WRRSVLEEKRRKRIRE************EEIAVAK*************DALKLLSDNAVNGS*************VEHDYHDDSIRENHMEIRLHKMVMGMNQPMCR
Disordered Region (DISPRO)
*NEYTVRKVGRLQILHKRTTSTTPFLQQTMLATECSLALFKVICSAGDSCHACGAISIMLLMCGLPRYPAPYPSMVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMP***************KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTE*****************ESVQSVEKNEPTKSPENLKDNETGNKESHDPTNF*V******KADQEALEKLTCMVEERLK***************************************************************************************************************RKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDN*V*********************HDDSIRENHMEIRLHKMVMGMNQPMCR
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MNEYTVRKVGRLQILHKRTTSTTPFLQQTMLATECSLALFKVICSAGDSCHACGAISIMLLMCGLPRYPAPYPSMVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxWExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxDDSRKRWRRSVLEEKRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxNAVNGSLAEESAVESKGMDVEHDYHDDSIRENHMEIRLHKMVMGMNQPMCR
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	577	2.2.26 [Sep-21-2011]
B2RY56	838	RNA-binding protein 25 OS	yes	no	0.218	0.150	0.355	9e-14
P49756	843	RNA-binding protein 25 OS	yes	no	0.201	0.137	0.359	3e-13
Q8IDX6	3130	Reticulocyte-binding prot	yes	no	0.211	0.038	0.299	3e-06

>sp|B2RY56|RBM25_MOUSE RNA-binding protein 25 OS=Mus musculus GN=Rbm25 PE=1 SV=2

 Score = 79.0 bits (193), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 53/149 (35%), Positives = 70/149 (46%), Gaps = 23/149 (15%)

Query: 102 IPGVRPIMPPVVRPVPLPTVTPAEK---------------------PQTKVYVGKIAPTA 140
           IP    IM P    V +PTV+   K                     P T V+VG I+  A
Sbjct: 40  IPVPMSIMAPAPT-VLVPTVSMVGKHLGARKDHPGLKLKENDENCGPTTTVFVGNISEKA 98

Query: 141 DSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL 200
               +  +L  CG V SWKR Q  S G  + FGFCE++  E  LRALRLL+   I  ++L
Sbjct: 99  SDMLIRQLLAKCGLVLSWKRVQGAS-GKLQAFGFCEYKEPESTLRALRLLHDLQIGEKKL 157

Query: 201 MLKVDQATREYLERYVDKKTENTKKLKET 229
           ++KVD  T+  L+ +  KK  N     ET
Sbjct: 158 LVKVDAKTKAQLDEWKAKKKANGNARPET 186

RNA-binding protein that acts as a regulator of alternative pre-mRNA splicing. Involved in apoptotic cell death through the regulation of the apoptotic factor BCL2L1 isoform expression. Modulates the ratio of proapoptotic BCL2L1 isoform S to antiapoptotic BCL2L1 isoform L mRNA expression. When overexpressed, stimulates proapoptotic BCL2L1 isoform S 5'-splice site (5'-ss) selection, whereas its depletion caused the accumulation of antiapoptotic BCL2L1 isoform L. Promotes BCL2L1 isoform S 5'-ss usage through the 5'-CGGGCA-3' RNA sequence. Its association with LUC7L3 promotes U1 snRNP binding to a weak 5' ss in a 5'-CGGGCA-3'-dependent manner. Binds to the exonic splicing enhancer 5'-CGGGCA-3' RNA sequence located within exon 2 of the BCL2L1 pre-mRNA.
Mus musculus (taxid: 10090)

>sp|P49756|RBM25_HUMAN RNA-binding protein 25 OS=Homo sapiens GN=RBM25 PE=1 SV=3

 Score = 77.0 bits (188), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 50/139 (35%), Positives = 67/139 (48%), Gaps = 23/139 (16%)

Query: 102 IPGVRPIMPPVVRPVPLPTVTPAEK---------------------PQTKVYVGKIAPTA 140
           IP    IM P    V +PTV+   K                     P T V+VG I+  A
Sbjct: 40  IPVPMSIMAPAPT-VLVPTVSMVGKHLGARKDHPGLKAKENDENCGPTTTVFVGNISEKA 98

Query: 141 DSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL 200
               +  +L  CG V SWKR Q  S G  + FGFCE++  E  LRALRLL+   I  ++L
Sbjct: 99  SDMLIRQLLAKCGLVLSWKRVQGAS-GKLQAFGFCEYKEPESTLRALRLLHDLQIGEKKL 157

Query: 201 MLKVDQATREYLERYVDKK 219
           ++KVD  T+  L+ +  KK
Sbjct: 158 LVKVDAKTKAQLDEWKAKK 176

RNA-binding protein that acts as a regulator of alternative pre-mRNA splicing. Involved in apoptotic cell death through the regulation of the apoptotic factor BCL2L1 isoform expression. Modulates the ratio of proapoptotic BCL2L1 isoform S to antiapoptotic BCL2L1 isoform L mRNA expression. When overexpressed, stimulates proapoptotic BCL2L1 isoform S 5'-splice site (5'-ss) selection, whereas its depletion caused the accumulation of antiapoptotic BCL2L1 isoform L. Promotes BCL2L1 isoform S 5'-ss usage through the 5'-CGGGCA-3' RNA sequence. Its association with LUC7L3 promotes U1 snRNP binding to a weak 5' ss in a 5'-CGGGCA-3'-dependent manner. Binds to the exonic splicing enhancer 5'-CGGGCA-3' RNA sequence located within exon 2 of the BCL2L1 pre-mRNA.

Homo sapiens (taxid: 9606)

>sp|Q8IDX6|RBP2A_PLAF7 Reticulocyte-binding protein 2 homolog a OS=Plasmodium falciparum (isolate 3D7) GN=PF13_0198 PE=3 SV=1

 Score = 54.3 bits (129), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/137 (29%), Positives = 80/137 (58%), Gaps = 15/137 (10%)

Query: 387  KEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEK 446
            K +E +R ++E E +R  +ER +R K E+ ++E E   ++ E  ++E   +RQ ++  +K
Sbjct: 2740 KRQEQERLQKEEELKRQEQERLEREKQEQLQKEEELKRQEQERLQKEEALKRQEQERLQK 2799

Query: 447  ERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIR-EKEEDLADEVREEEEIAVAK 505
            E E KR+++   + E+ E   ++       E KR+++ R +KEE L    R+E+E     
Sbjct: 2800 EEELKRQEQERLEREKQEQLQKEE------ELKRQEQERLQKEEALK---RQEQE----- 2845

Query: 506  RRAEEEQLQQQQRDALK 522
            R  +EE+L++Q+++ L+
Sbjct: 2846 RLQKEEELKRQEQERLE 2862

Involved in reticulocyte adhesion.

Plasmodium falciparum (isolate 3D7) (taxid: 36329)

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	577
255568764	948	conserved hypothetical protein [Ricinus	0.837	0.509	0.681	1e-144
224111298	894	predicted protein [Populus trichocarpa]	0.852	0.550	0.642	1e-134
296086551	828	unnamed protein product [Vitis vinifera]	0.852	0.594	0.607	1e-132
225424679	958	PREDICTED: uncharacterized protein LOC10	0.849	0.511	0.603	1e-131
357485911	771	RNA-binding protein [Medicago truncatula	0.778	0.582	0.633	1e-126
356497763	927	PREDICTED: uncharacterized protein LOC10	0.845	0.526	0.625	1e-113
356501735	765	PREDICTED: uncharacterized protein LOC10	0.826	0.623	0.622	1e-111
449513686	968	PREDICTED: uncharacterized LOC101214372	0.863	0.514	0.611	1e-108
449434915	770	PREDICTED: uncharacterized protein LOC10	0.840	0.629	0.613	1e-102
42562828	899	RNA-binding protein 25 [Arabidopsis thal	0.778	0.499	0.570	3e-94

>gi|255568764|ref|XP_002525353.1| conserved hypothetical protein [Ricinus communis] gi|223535316|gb|EEF36991.1| conserved hypothetical protein [Ricinus communis]

 Score =  517 bits (1332), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 342/502 (68%), Positives = 405/502 (80%), Gaps = 19/502 (3%)

Query: 62  MCGLPRYPAPYPSMVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTV 121
           + G+ RYP+PYP+MVRP FPPRP G +G+LP+ +R  VPGIPGVRP+  P+VRP  +P+V
Sbjct: 173 ITGIQRYPSPYPAMVRPMFPPRPLGALGILPAASRLLVPGIPGVRPV--PIVRPG-VPSV 229

Query: 122 TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 181
           TPAEKP T VYVGKIAPT D+DF+LS+L+ CG VKSWKR Q P++GTP+GFGFCEFESAE
Sbjct: 230 TPAEKPLTTVYVGKIAPTVDNDFMLSLLRFCGPVKSWKRPQDPNDGTPRGFGFCEFESAE 289

Query: 182 GVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESV 241
           GVLRALRLL+KFNIDGQEL+L V+QATREYLERYV+KKTEN K LKE Q  GA KED   
Sbjct: 290 GVLRALRLLSKFNIDGQELVLNVNQATREYLERYVEKKTENLKNLKENQAPGAAKED--- 346

Query: 242 QSVEKNEPTK--SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLK 299
            + EK+EP K    ++ KD +  NKE++DP NFG+VT+ED++ D+EALEKLT M+EERLK
Sbjct: 347 GTAEKSEPPKIIGEDSNKDGDKVNKENNDPANFGIVTDEDKEGDKEALEKLTSMIEERLK 406

Query: 300 TNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSD-TKASDH 358
           TNPLPPPPPQT A GSG +NSE PAK+RDGDSD D  R   AEDK DDET SD   A++ 
Sbjct: 407 TNPLPPPPPQTPAHGSG-TNSEFPAKSRDGDSDADTTRQ--AEDKNDDETISDHIPATEQ 463

Query: 359 DRPETSSPDRSR---VHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEE 415
           DRP T SPDRS        R RD+ERDLKREKEREI+RYEREAERER+RKEREQRRKIEE
Sbjct: 464 DRPGTCSPDRSSRKYDRRSRERDRERDLKREKEREIERYEREAERERIRKEREQRRKIEE 523

Query: 416 AEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSV 475
           AEREYE  LKDWEYRERE+EK+RQY+KEK+KER+RKR+KEILYDEE D+DDSRK+WRRS 
Sbjct: 524 AEREYEERLKDWEYREREKEKQRQYDKEKDKERDRKRRKEILYDEEGDDDDSRKKWRRSA 583

Query: 476 LEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGS--- 532
           L++KRRK+ REKE+D+AD ++EEEE+A AKRRAEEE++QQQQ DA KL  D  +NG+   
Sbjct: 584 LDDKRRKKQREKEDDMADRLKEEEEMAEAKRRAEEERIQQQQTDAFKLSFDQVMNGTEMK 643

Query: 533 -LAEESAVESKGMDVEHDYHDD 553
            L EE  VESK   VE D   D
Sbjct: 644 VLVEEVYVESKDKVVEQDNEGD 665

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224111298|ref|XP_002315807.1| predicted protein [Populus trichocarpa] gi|222864847|gb|EEF01978.1| predicted protein [Populus trichocarpa]

 Score =  484 bits (1245), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 325/506 (64%), Positives = 408/506 (80%), Gaps = 14/506 (2%)

Query: 64  GLPRYPAPYPSMVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTP 123
           G+ RYP+PYP+MVRP FPPRPPG + V+P+V RP VPGIPGVRP+M P++RPV +P+VTP
Sbjct: 116 GIMRYPSPYPAMVRPLFPPRPPGALSVVPAVPRPLVPGIPGVRPVMYPIIRPV-IPSVTP 174

Query: 124 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 183
           AEKPQT VY+GKIAP+ ++DF++S+L+ CG VKSWKR Q P+NGTP+GFGFCEFESAEGV
Sbjct: 175 AEKPQTTVYIGKIAPSVENDFMMSLLQFCGPVKSWKRPQDPANGTPRGFGFCEFESAEGV 234

Query: 184 LRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQS 243
           LRALRLL KFNIDGQELML V+QAT+EYLERYV+KKTEN+K  KETQ A  GKED +   
Sbjct: 235 LRALRLLTKFNIDGQELMLNVNQATKEYLERYVEKKTENSKNFKETQVADTGKEDGTGID 294

Query: 244 VEKNEPTKSP--ENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTN 301
            +K E +KS   ++  D++ GNKE+HD  NFG+VT+ED+  D+EA+EKLT M+EERLKT 
Sbjct: 295 GKKGEFSKSSAEDSNNDSDKGNKENHDLANFGIVTDEDKAGDREAIEKLTSMIEERLKTK 354

Query: 302 PLPPPPPQTTA--DGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKA-SDH 358
           PLPPPPP + A  DGSG SN ELP+K+RDGD+D D++R+   E K DDET+SD KA S+ 
Sbjct: 355 PLPPPPPPSLAPADGSGNSNLELPSKSRDGDTDADIMRS--VEGKNDDETSSDNKAASEQ 412

Query: 359 DRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRR--KIEEA 416
           DRPETSSPDRSR +DRR RD++R+   ++E+E +    E E ER R  +E+ +  KIEEA
Sbjct: 413 DRPETSSPDRSRGYDRRSRDRDRERDLKREKEREIERYERETERERVRKEREQRRKIEEA 472

Query: 417 EREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVL 476
           EREYE  L+DWEYRERE+EK+RQYEKE++KERERKR+KEIL+DEE+++DDSRKRWRRS L
Sbjct: 473 EREYEERLRDWEYREREKEKQRQYEKERDKERERKRRKEILHDEEDEDDDSRKRWRRSAL 532

Query: 477 EEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGS---- 532
           E++RRKR+REKE+DLAD ++EEEEIA +KRR EEE+LQ++Q+D LKLLS + +N S    
Sbjct: 533 EDRRRKRLREKEDDLADRLKEEEEIAESKRRDEEEKLQEKQKDELKLLSGHVLNESEMTN 592

Query: 533 LAEESAVESKGMDVEHDYHDDSIREN 558
           LAE   VESK   +E DY  DS  EN
Sbjct: 593 LAEGPIVESKDEAIEKDYDGDSGNEN 618

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296086551|emb|CBI32140.3| unnamed protein product [Vitis vinifera]

 Score =  477 bits (1227), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 311/512 (60%), Positives = 389/512 (75%), Gaps = 20/512 (3%)

Query: 64  GLPRYPAPYPSMVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTP 123
           G+PRYP+PY +MVRPAFPPRPPG +G+LP+++RPPVPG+PGVRPIMPPVVRP  +P   P
Sbjct: 42  GVPRYPSPYATMVRPAFPPRPPGAIGMLPALSRPPVPGMPGVRPIMPPVVRPAIVPVAAP 101

Query: 124 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 183
            EKPQT VYVGKIA T ++DF+LS+L+VCG VKSWK AQYP +GTP+G GFCEFES EGV
Sbjct: 102 TEKPQTTVYVGKIASTVENDFILSLLQVCGPVKSWKHAQYPIDGTPRGLGFCEFESPEGV 161

Query: 184 LRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQS 243
           LRALRLL KFN+DGQEL+L V+QATREYLERYV+KKTEN+KK +E+   G+ KE ESV  
Sbjct: 162 LRALRLLTKFNVDGQELVLNVNQATREYLERYVEKKTENSKKPQESDIEGSEKEQESVPG 221

Query: 244 VEKNEPTK-SPENLK--DNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKT 300
           VE+NE  K S E+ K   NE  NKE+ D  +FG+VT+EDR+AD+EALEKLT M+EER+KT
Sbjct: 222 VEQNEILKPSLEDSKKDGNELVNKENQDNASFGIVTDEDREADREALEKLTSMMEERIKT 281

Query: 301 NPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTK-ASDHD 359
            PLPPPP Q  ADGS  +NSELP K+R  DSDVD++RND AE   DDETTS+ K  SD +
Sbjct: 282 KPLPPPPAQGAADGSENTNSELPTKSR--DSDVDVMRNDAAE---DDETTSENKPKSDQE 336

Query: 360 RPETSSP--DRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAE 417
           R E SSP   R      R RD++R+LKREKERE DR ERE ERERVR+E+E+  KIE AE
Sbjct: 337 RLERSSPDRSRRYDRRSRERDRDRELKREKEREFDRLERERERERVRREKEREIKIERAE 396

Query: 418 REYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEED--EDDSRKRWRRSV 475
             Y   +K+WEYRERE+E +RQ+EKE+EKERER+R++EI   E ++  +D  ++R R S 
Sbjct: 397 NLYRERVKEWEYREREKEYQRQHEKEREKERERERRREISNQERDNDEDDSRKRRRRSSE 456

Query: 476 LEEKRRKRIREKEEDLADEVREEEEIAVAKRRAE---EEQLQQQQRDALKLLSDNAVNGS 532
           +EEKR+KR REKEEDLAD ++E EEIA   RRA    ++Q Q+QQ +A+KLL+ +A  GS
Sbjct: 457 VEEKRKKRQREKEEDLADRLKEVEEIAETNRRASEEEQQQQQEQQNNAVKLLALHATTGS 516

Query: 533 ----LAEESAVESKGMDVEHDYHDDSIRENHM 560
               L +E+  ++K   VE  Y  DS  +NH+
Sbjct: 517 EKEVLTDETDAQNKDKAVEQAYEGDSSHQNHI 548

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225424679|ref|XP_002264457.1| PREDICTED: uncharacterized protein LOC100263874 [Vitis vinifera]

 Score =  476 bits (1226), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 310/514 (60%), Positives = 389/514 (75%), Gaps = 24/514 (4%)

Query: 64  GLPRYPAPYPSMVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTP 123
           G+PRYP+PY +MVRPAFPPRPPG +G+LP+++RPPVPG+PGVRPIMPPVVRP  +P   P
Sbjct: 172 GVPRYPSPYATMVRPAFPPRPPGAIGMLPALSRPPVPGMPGVRPIMPPVVRPAIVPVAAP 231

Query: 124 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 183
            EKPQT VYVGKIA T ++DF+LS+L+VCG VKSWK AQYP +GTP+G GFCEFES EGV
Sbjct: 232 TEKPQTTVYVGKIASTVENDFILSLLQVCGPVKSWKHAQYPIDGTPRGLGFCEFESPEGV 291

Query: 184 LRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQS 243
           LRALRLL KFN+DGQEL+L V+QATREYLERYV+KKTEN+KK +E+   G+ KE ESV  
Sbjct: 292 LRALRLLTKFNVDGQELVLNVNQATREYLERYVEKKTENSKKPQESDIEGSEKEQESVPG 351

Query: 244 VEKNEPTKSPENLKD-----NETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERL 298
           VE+NE  K   +L+D     NE  NKE+ D  +FG+VT+EDR+AD+EALEKLT M+EER+
Sbjct: 352 VEQNEILKP--SLEDSKKDGNELVNKENQDNASFGIVTDEDREADREALEKLTSMMEERI 409

Query: 299 KTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKA-SD 357
           KT PLPPPP Q  ADGS  +NSELP K+R  DSDVD++RND AE   DDETTS+ K  SD
Sbjct: 410 KTKPLPPPPAQGAADGSENTNSELPTKSR--DSDVDVMRNDAAE---DDETTSENKPKSD 464

Query: 358 HDRPETSSP--DRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEE 415
            +R E SSP   R      R RD++R+LKREKERE DR ERE ERERVR+E+E+  KIE 
Sbjct: 465 QERLERSSPDRSRRYDRRSRERDRDRELKREKEREFDRLERERERERVRREKEREIKIER 524

Query: 416 AEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEED--EDDSRKRWRR 473
           AE  Y   +K+WEYRERE+E +RQ+EKE+EKERER+R++EI   E ++  +D  ++R R 
Sbjct: 525 AENLYRERVKEWEYREREKEYQRQHEKEREKERERERRREISNQERDNDEDDSRKRRRRS 584

Query: 474 SVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAE---EEQLQQQQRDALKLLSDNAVN 530
           S +EEKR+KR REKEEDLAD ++E EEIA   RRA    ++Q Q+QQ +A+KLL+ +A  
Sbjct: 585 SEVEEKRKKRQREKEEDLADRLKEVEEIAETNRRASEEEQQQQQEQQNNAVKLLALHATT 644

Query: 531 GS----LAEESAVESKGMDVEHDYHDDSIRENHM 560
           GS    L +E+  ++K   VE  Y  DS  +NH+
Sbjct: 645 GSEKEVLTDETDAQNKDKAVEQAYEGDSSHQNHI 678

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357485911|ref|XP_003613243.1| RNA-binding protein [Medicago truncatula] gi|355514578|gb|AES96201.1| RNA-binding protein [Medicago truncatula]

 Score =  458 bits (1178), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 294/464 (63%), Positives = 367/464 (79%), Gaps = 15/464 (3%)

Query: 75  MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVG 134
           MVRP +PPR PG + VLP V+RPPV GIP +RPI+PPVVRPV  P+VTPAEK  T VY+G
Sbjct: 1   MVRPVYPPRLPGAINVLP-VSRPPVAGIPSIRPIIPPVVRPVVPPSVTPAEKQHTTVYIG 59

Query: 135 KIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN 194
           KIAPT +++F+LS+LK+CG +KSWKR Q  S+GTPK FGF EF++AEGVLRALRLL K N
Sbjct: 60  KIAPTVENEFMLSLLKLCGNIKSWKRPQDLSSGTPKSFGFYEFDTAEGVLRALRLLTKLN 119

Query: 195 IDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPE 254
           IDGQEL++ VD+A R YLERYV KKT+N+K+ KETQ A  GK D+  ++ + NE  K   
Sbjct: 120 IDGQELVINVDEAMRNYLERYVQKKTDNSKE-KETQAAEVGK-DQVAKTSDVNEEAKPDV 177

Query: 255 NLKDNETGN----KESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQT 310
              + E GN    K++HD   FG+VT+EDR+ D++ALEK+  M+EERL + PLPPPPP  
Sbjct: 178 EHSNKEEGNDSVNKKTHDVATFGIVTDEDREVDRDALEKIKQMIEERLNSRPLPPPPPLP 237

Query: 311 TADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTK-ASDHDRPETSSPDRS 369
           T DGS  S SE P K R+GDSDVD  +N+  E+K + ET  D K  S+HDRPET  PDR 
Sbjct: 238 TGDGSVDSTSEQPTKTREGDSDVD-TKNESGEEKNERETNGDKKPTSEHDRPET--PDRR 294

Query: 370 RVHDR--RGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDW 427
             HDR  R RD+ER+LKREKER ++RYEREAER+R+RKEREQ+R+IEE ER++E  LK+W
Sbjct: 295 --HDRKSRERDRERELKREKERVLERYEREAERDRIRKEREQKRRIEEVERQFELQLKEW 352

Query: 428 EYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREK 487
           EYRERE+EKERQYEKEKEK+RERKR+KEILYDEE+D+ DSRKRWRR+ +EEKR KR+REK
Sbjct: 353 EYREREKEKERQYEKEKEKDRERKRRKEILYDEEDDDGDSRKRWRRNAIEEKRNKRLREK 412

Query: 488 EEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNG 531
           E+DLAD+ +EEEEIA AK+R EE+Q  ++QRDALKLL+++ VNG
Sbjct: 413 EDDLADKQKEEEEIAEAKKRTEEDQQLKRQRDALKLLTEHIVNG 456

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356497763|ref|XP_003517728.1| PREDICTED: uncharacterized protein LOC100809428 [Glycine max]

 Score =  414 bits (1064), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 318/508 (62%), Positives = 389/508 (76%), Gaps = 20/508 (3%)

Query: 63  CGLPRYPAPYPSMVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVT 122
            G+PRYP PY +MVRP FP RPPG V + P+++RPPV GIP VRPI+PPVVRPV  P+VT
Sbjct: 148 AGIPRYPPPYGTMVRPVFPARPPGAVNI-PTISRPPVAGIPAVRPIIPPVVRPVVAPSVT 206

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
           PAEKPQ  VY+GKIAPT +++F+LS+L++CGT+K+WKR Q  S GTP  FGF EFESAEG
Sbjct: 207 PAEKPQNTVYIGKIAPTVENEFMLSLLQLCGTIKTWKRPQDLSTGTPTSFGFYEFESAEG 266

Query: 183 VLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQ 242
           VLRALRLL K NIDGQEL + V+QA +E LE YV  KTEN K  KETQ+ G   E E  Q
Sbjct: 267 VLRALRLLTKLNIDGQELKVNVNQAMKEILELYVKTKTENLKN-KETQEVGEKNEGE--Q 323

Query: 243 SVEKNEPTK---SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLK 299
               NE  K    P N + +E+ NKESHD  NFG+VT+EDR+AD EALEK+T M+EERLK
Sbjct: 324 PSNANEDAKVDTEPSNKEASESSNKESHDVANFGIVTDEDREADCEALEKITKMIEERLK 383

Query: 300 TNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTK-ASDH 358
           T PLP PP Q T DGS    SE P KARDGDS VD  +N+ AE+K + ET +D K  S+H
Sbjct: 384 TRPLPTPPAQPTGDGSVNLTSEQPVKARDGDSVVDTEKNESAENKNEKETNNDNKPTSEH 443

Query: 359 DRPETSSPDRSRVHDR--RGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEA 416
           +R  T SPDR   HDR  R RD++R+LKREK+RE++RYEREAERERVRKEREQRR++EEA
Sbjct: 444 ER--TESPDRR--HDRKSRERDRDRELKREKDRELERYEREAERERVRKEREQRRRVEEA 499

Query: 417 EREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVL 476
           ER+YE  LKDWEYRERE+EKERQYEKEKEKERERKR+KEILYDEE++++DSRKRWRRSV+
Sbjct: 500 ERQYETYLKDWEYREREKEKERQYEKEKEKERERKRRKEILYDEEDEDEDSRKRWRRSVI 559

Query: 477 EEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGS---- 532
           EEKR+KR+REKE+DL D  R++EE  +A+ + + E+ Q++QRDALKLLS++ VNG     
Sbjct: 560 EEKRKKRLREKEDDLVD--RQKEEEEIAEAKKKAEEEQKRQRDALKLLSEHVVNGGKENM 617

Query: 533 LAEESAVESKGMDVEHDYHDDSIRENHM 560
           + EE   E K + VE D   D  RE+H+
Sbjct: 618 ITEEITNEVKSIVVEQDTVADYSREDHI 645

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356501735|ref|XP_003519679.1| PREDICTED: uncharacterized protein LOC100803051 [Glycine max]

 Score =  410 bits (1053), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 309/496 (62%), Positives = 380/496 (76%), Gaps = 19/496 (3%)

Query: 75  MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVG 134
           MVRP FP RPPG V + P+++RPPV GIP VRPI+PPVVRPV  P+VTPAEKPQ  VY+G
Sbjct: 1   MVRPVFPARPPGAVNI-PTISRPPVAGIPAVRPIIPPVVRPVVAPSVTPAEKPQNTVYIG 59

Query: 135 KIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN 194
           KIAPT +++F+LS+L++CGT+K+WKR Q  S GTP  FGF EFESAEGVLRALRLL K N
Sbjct: 60  KIAPTVENEFMLSLLQLCGTIKTWKRPQDLSTGTPTSFGFYEFESAEGVLRALRLLTKLN 119

Query: 195 IDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKS-- 252
           IDGQEL + V+QA +E LERY   KTEN K  K+TQ AG G+++E  Q    N+  K+  
Sbjct: 120 IDGQELKVNVNQAMKENLERYDKTKTENLKN-KKTQ-AGVGEKNEGEQPSNANKDAKADT 177

Query: 253 -PENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTT 311
            P N +  E+ NKESHD  NFG+VT+EDR+AD+EALEK++ M+EERLK  PLP P  Q T
Sbjct: 178 EPSNKEVLESSNKESHDVANFGIVTDEDREADREALEKISKMIEERLKIRPLPAPSAQLT 237

Query: 312 ADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTK-ASDHDRPETSSPDRSR 370
            DGS    SE P KARDGDS VD  +N+ AE+K + ET +D K  S+H+R  T SPDR  
Sbjct: 238 GDGSVNLTSEQPVKARDGDSVVDTEKNESAENKNEKETNNDNKPTSEHER--TESPDRR- 294

Query: 371 VHDR--RGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWE 428
            HDR  R RD++R+LKREK+RE++RYEREAERERVRKEREQRR++EE ER+YE  LKDWE
Sbjct: 295 -HDRKSRERDRDRELKREKDRELERYEREAERERVRKEREQRRRVEETERQYETYLKDWE 353

Query: 429 YREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKE 488
           YRERE+EKERQYEKEKEKERERKR+KEILYDEE++++DSRKRWRRSV+E+KR+KR+REKE
Sbjct: 354 YREREKEKERQYEKEKEKERERKRRKEILYDEEDEDEDSRKRWRRSVIEDKRKKRLREKE 413

Query: 489 EDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGS----LAEESAVESKGM 544
           +DL D  +EEEEIA  K++AEEE  Q+QQRDALKLLS++ VN      + EE  +E K +
Sbjct: 414 DDLVDRQKEEEEIAETKKKAEEE--QKQQRDALKLLSEHVVNAGKENMITEEITIEVKSI 471

Query: 545 DVEHDYHDDSIRENHM 560
             E D   D   E H+
Sbjct: 472 VAEQDTVADYHHEYHI 487

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449513686|ref|XP_004164394.1| PREDICTED: uncharacterized LOC101214372 [Cucumis sativus]

 Score =  399 bits (1024), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 310/507 (61%), Positives = 391/507 (77%), Gaps = 9/507 (1%)

Query: 62  MCGLPRYPAPYPSMVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTV 121
           + G+PR+P+PYP M+R  FPPRPPG +G++P + RPP+PGIPGVRPI+PPVVRP  LP++
Sbjct: 186 LPGVPRFPSPYPGMIRTPFPPRPPGAMGMVPGMPRPPIPGIPGVRPIIPPVVRPAILPSI 245

Query: 122 TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 181
           TPAEKPQT +Y+G+IA + D+DF+LS+L++CG VKSWKRAQ PS+GTP+ FGFCEFESAE
Sbjct: 246 TPAEKPQTTIYIGRIAQSVDNDFMLSLLQLCGPVKSWKRAQDPSDGTPRTFGFCEFESAE 305

Query: 182 GVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESV 241
           GVLRALRLL K NIDGQEL LK  QATR+YL+RYV+KK EN+KKLKETQ +   +E+   
Sbjct: 306 GVLRALRLLTKLNIDGQELGLKGTQATRDYLKRYVEKKAENSKKLKETQASETKEEETDT 365

Query: 242 QSVEKNEPTK-SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKT 300
            +V K E +K S E+ K++    ++  D     V+++EDR AD+EA EKLT  +EER+K+
Sbjct: 366 TNVAKKETSKPSAEDSKEDHDSGEKDFDIACSAVLSDEDRDADREAKEKLTNALEERMKS 425

Query: 301 NPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTK-ASDHD 359
            PLPPPP  TT D S  S+ E  AK +DG++D D  + D A+D+ D++TTSD K AS+HD
Sbjct: 426 RPLPPPPLLTTTDVSDNSSVEPSAKPKDGEADGDTSKPDAADDRNDEDTTSDHKQASEHD 485

Query: 360 RPETSSP--DRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAE 417
           +PETSSP   R      R RD+ERDLKR+KEREI+RYERE ERER RKEREQRRK EEAE
Sbjct: 486 KPETSSPERSRRYDRRSRERDRERDLKRDKEREIERYERETERERARKEREQRRKFEEAE 545

Query: 418 REYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLE 477
           R+YE CLK+WEYREREREK+RQYEKE+EKE+ERKRKKEILYDE++++DDSR++WRR  LE
Sbjct: 546 RQYEECLKEWEYREREREKQRQYEKEREKEKERKRKKEILYDEDDEDDDSRRKWRRGALE 605

Query: 478 EKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGS----L 533
           EKR+KR REKE+D  D  REEEEIA AKR+AEEEQL Q+ RD  KLL    ++ S     
Sbjct: 606 EKRKKRSREKEDDSFDRQREEEEIAEAKRKAEEEQL-QKLRDPPKLLPSQTISVSEKTVT 664

Query: 534 AEESAVESKGMDVEHDYHDDSIRENHM 560
           AEES +E K +  E +   DS  +NH+
Sbjct: 665 AEESTIEIKVVASERESEIDSSCDNHI 691

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434915|ref|XP_004135241.1| PREDICTED: uncharacterized protein LOC101214372 [Cucumis sativus]

 Score =  380 bits (976), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 303/494 (61%), Positives = 380/494 (76%), Gaps = 9/494 (1%)

Query: 75  MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVG 134
           M+R  FPPRPPG +G++P + RPP+PGIPGVRPI+PPVVRP  LP++TPAEKPQT +Y+G
Sbjct: 1   MIRTPFPPRPPGAMGMVPGMPRPPIPGIPGVRPIIPPVVRPAILPSITPAEKPQTTIYIG 60

Query: 135 KIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN 194
           +IA + D+DF+LS+L++CG VKSWKRAQ PS+GTP+ FGFCEFESAEGVLRALRLL K N
Sbjct: 61  RIAQSVDNDFMLSLLQLCGPVKSWKRAQDPSDGTPRTFGFCEFESAEGVLRALRLLTKLN 120

Query: 195 IDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTK-SP 253
           IDGQEL LK  QATR+YL+RYV+KK EN+KKLKETQ +   +E+    +V K E +K S 
Sbjct: 121 IDGQELGLKGTQATRDYLKRYVEKKAENSKKLKETQASETKEEETDTTNVAKKETSKPSA 180

Query: 254 ENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTAD 313
           E+ K++    ++  D     V+++EDR AD+EA EKLT  +EER+K+ PLPPPP  TT D
Sbjct: 181 EDSKEDHDSGEKDFDIACSAVLSDEDRDADREAKEKLTNALEERMKSRPLPPPPLLTTTD 240

Query: 314 GSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTK-ASDHDRPETSSP--DRSR 370
            S  S+ E  AK +DG++D D  + D A+D+ D++TTSD K AS+HD+PETSSP   R  
Sbjct: 241 VSDNSSVEPSAKPKDGEADGDTSKPDAADDRNDEDTTSDHKQASEHDKPETSSPERSRRY 300

Query: 371 VHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYR 430
               R RD+ERDLKR+KEREI+RYERE ERER RKEREQRRK EEAER+YE CLK+WEYR
Sbjct: 301 DRRSRERDRERDLKRDKEREIERYERETERERARKEREQRRKFEEAERQYEECLKEWEYR 360

Query: 431 EREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEED 490
           EREREK+RQYEKE+EKE+ERKRKKEILYDE++++DDSR++WRR  LEEKR+KR REKE+D
Sbjct: 361 EREREKQRQYEKEREKEKERKRKKEILYDEDDEDDDSRRKWRRGALEEKRKKRSREKEDD 420

Query: 491 LADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGS----LAEESAVESKGMDV 546
             D  REEEEIA AKR+AEEEQL Q+ RD  KLL    ++ S     AEES +E K +  
Sbjct: 421 SFDRQREEEEIAEAKRKAEEEQL-QKLRDPPKLLPSQTISVSEKTVTAEESTIEIKVVAS 479

Query: 547 EHDYHDDSIRENHM 560
           E +   DS  +NH+
Sbjct: 480 ERESEIDSSCDNHI 493

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42562828|ref|NP_176226.3| RNA-binding protein 25 [Arabidopsis thaliana] gi|18377662|gb|AAL66981.1| unknown protein [Arabidopsis thaliana] gi|25055015|gb|AAN71971.1| unknown protein [Arabidopsis thaliana] gi|332195545|gb|AEE33666.1| RNA-binding protein 25 [Arabidopsis thaliana]

 Score =  352 bits (903), Expect = 3e-94,   Method: Compositional matrix adjust.
 Identities = 270/473 (57%), Positives = 356/473 (75%), Gaps = 24/473 (5%)

Query: 64  GLPRYPAPYPSMVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTP 123
           GL RYP+PYP+MVRP F  RPPG +G +    RP +PG+PG+RP+MPP+VRP  LP VTP
Sbjct: 139 GLLRYPSPYPTMVRPGFIMRPPGTIGAVQLAPRPLIPGMPGLRPVMPPMVRPASLPFVTP 198

Query: 124 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 183
           AEKPQT +Y+GKIA T ++DF++S+L+ CG VKS  RA+ P+   PKGFGF EFESAEG+
Sbjct: 199 AEKPQTTIYIGKIA-TVENDFMMSILEFCGHVKSCLRAEDPTTKKPKGFGFYEFESAEGI 257

Query: 184 LRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQS 243
           LRA+RLL +  IDGQEL++ V+QAT+EYL +YV+KK E  KK KE+Q     KE+++   
Sbjct: 258 LRAIRLLTQRTIDGQELLVNVNQATKEYLLKYVEKKIETAKKAKESQGT---KENQAEGP 314

Query: 244 VEKNEPTKSPEN--LKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTN 301
             + +  +S +N   KD E+  KE+ D  N  V+T+E+R+AD+EA+EK+   +EERLK+N
Sbjct: 315 ESEQDKLESADNETGKDGESKIKENIDIANSAVLTDEEREADREAMEKIETAIEERLKSN 374

Query: 302 PLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRP 361
              PPPP   ADGSG+   E   K++DGDS+ D+ R+D A +  D ET+      +H+RP
Sbjct: 375 -PLPPPPPPPADGSGM---EFAFKSKDGDSNTDVARSDAAAN--DVETS-----GEHNRP 423

Query: 362 ETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYE 421
           +TSSPD S+ +DRR R+     + EKE+E+DRYEREAERER RKEREQRRK+E+AER Y+
Sbjct: 424 DTSSPDWSKRNDRRSRE-----RGEKEQEMDRYEREAERERSRKEREQRRKLEDAERAYQ 478

Query: 422 RCLKDWEYREREREKERQYEKEKEKERERKRKKEILY--DEEEDEDDSRKRWRRSVLEEK 479
             L+ WE RERE+EKERQYEKEKEKE+ERKRKKEI Y  +EEED+DDSR+RW R+ L+E+
Sbjct: 479 TRLRQWERREREKEKERQYEKEKEKEKERKRKKEIRYEEEEEEDDDDSRRRWHRAALDER 538

Query: 480 RRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGS 532
           RR+++REKE+DLAD ++EEEE+A AKR AEE+ LQQQQ DAL++LS  A  GS
Sbjct: 539 RRRQLREKEDDLADRLKEEEEVAEAKRSAEEQNLQQQQLDALRILSGQAAIGS 591

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	577
TAIR|locus:2195568	899	AT1G60200 [Arabidopsis thalian	0.402	0.258	0.453	7.7e-50
WB|WBGene00012245	707	W04D2.6 [Caenorhabditis elegan	0.415	0.339	0.259	1.8e-13
UNIPROTKB|E2RQR0	211	RBM25 "Uncharacterized protein	0.152	0.417	0.426	2.5e-13
UNIPROTKB|E9PQU5	243	RBM25 "RNA-binding protein 25"	0.152	0.362	0.426	2.5e-13
DICTYBASE|DDB_G0269926	724	DDB_G0269926 "splicing factor	0.287	0.229	0.335	5.3e-13
RGD|1565486	494	RGD1565486 "similar to RNA bin	0.152	0.178	0.426	2.1e-12
UNIPROTKB|I3LLA0	513	RBM25 "Uncharacterized protein	0.152	0.171	0.426	1.3e-11
ZFIN|ZDB-GENE-030131-5547	833	rbm25 "RNA binding motif prote	0.202	0.140	0.369	1.3e-11
MGI|MGI:1914289	838	Rbm25 "RNA binding motif prote	0.152	0.105	0.426	2.3e-11
UNIPROTKB|E1BHM5	843	RBM25 "Uncharacterized protein	0.152	0.104	0.426	6e-11

TAIR|locus:2195568 AT1G60200 [Arabidopsis thaliana (taxid:3702)]

 Score = 493 (178.6 bits), Expect = 7.7e-50, Sum P(3) = 7.7e-50
 Identities = 113/249 (45%), Positives = 162/249 (65%)

Query:   124 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 183
             AEKPQT +Y+GKIA T ++DF++S+L+ CG VKS  RA+ P+   PKGFGF EFESAEG+
Sbjct:   199 AEKPQTTIYIGKIA-TVENDFMMSILEFCGHVKSCLRAEDPTTKKPKGFGFYEFESAEGI 257

Query:   184 LRALRLLNKFNIDGQELMLKVDQATREYLERYVDXXXXXXXXXXXXQDAGAGKEDESVQS 243
             LRA+RLL +  IDGQEL++ V+QAT+EYL +YV+            Q     KE+++   
Sbjct:   258 LRAIRLLTQRTIDGQELLVNVNQATKEYLLKYVEKKIETAKKAKESQGT---KENQAEGP 314

Query:   244 VEKNEPTKSPENL--KDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTN 301
               + +  +S +N   KD E+  KE+ D  N  V+T+E+R+AD+EA+EK+   +EERLK+N
Sbjct:   315 ESEQDKLESADNETGKDGESKIKENIDIANSAVLTDEEREADREAMEKIETAIEERLKSN 374

Query:   302 XXXXXXXQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRP 361
                       ADGSG+   E   K++DGDS+ D+ R+D A +  D ET+ +     H+RP
Sbjct:   375 PLPPPP-PPPADGSGM---EFAFKSKDGDSNTDVARSDAAAN--DVETSGE-----HNRP 423

Query:   362 ETSSPDRSR 370
             +TSSPD S+
Sbjct:   424 DTSSPDWSK 432

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM

GO:0006397 "mRNA processing" evidence=IEA

WB|WBGene00012245 W04D2.6 [Caenorhabditis elegans (taxid:6239)]

 Score = 205 (77.2 bits), Expect = 1.8e-13, P = 1.8e-13
 Identities = 66/254 (25%), Positives = 114/254 (44%)

Query:   125 EKPQTK-VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 183
             +KP +  V+VG I+     +F+  +L  CG V SWKR +  SNG  +GFGFC F   EG 
Sbjct:    42 QKPDSSPVFVGNISDKCSDEFIRKILNECGNVASWKRIK-GSNGKLQGFGFCHFTDLEGT 100

Query:   184 LRALRLLNKFNIDGQELMLKVDQATREYLERYV--DXXXXXXXXXXXXQDAGAGKEDESV 241
             LRALR+L++F++  ++L +K D+  R+ L +    +             D     ED+  
Sbjct:   101 LRALRILHEFHLGDKKLTVKPDEKVRDDLRKNAIENRKRQGKKELKLKHDELPADEDD-- 158

Query:   242 QSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKAD--QEALEKLTCMVEERLK 299
               ++K+E  +  + L   ET +KE    T  G +++E +K       +EK T        
Sbjct:   159 --LKKDEEIRL-KILHWMETDHKELFSITEDGELSDETKKVKGHDSKIEKQTVPSSSSNP 215

Query:   300 TNXXXXXXXQTTADGSGISNSELPAKARDGDSDVDMI--RNDIAEDKLDDETTSDTKASD 357
                         +     S      ++R  +S       R+  + +   +  +S +++S 
Sbjct:   216 KKDEHKRNRNRRSRSRTRSRERTSRRSRSKESPRSKRSRRSRSSSNSSSESDSSSSRSSS 275

Query:   358 HD-RPETSSPDRSR 370
             +  R  + +P RSR
Sbjct:   276 YSSRSRSRTPQRSR 289

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0018991 "oviposition" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0048477 "oogenesis" evidence=IMP

GO:0002009 "morphogenesis of an epithelium" evidence=IMP

UNIPROTKB|E2RQR0 RBM25 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 180 (68.4 bits), Expect = 2.5e-13, P = 2.5e-13
 Identities = 38/89 (42%), Positives = 53/89 (59%)

Query:   127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
             P T V+VG I+  A    +  +L  CG V SWKR Q  S G  + FGFCE++  E  LRA
Sbjct:    47 PTTTVFVGNISEKASDMLIRQLLAKCGLVLSWKRVQGAS-GKLQAFGFCEYKEPESTLRA 105

Query:   187 LRLLNKFNIDGQELMLKVDQATREYLERY 215
             LRLL+   I  ++L++KVD  T+  L+ +
Sbjct:   106 LRLLHDLQIGEKKLLVKVDAKTKAQLDEW 134

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E9PQU5 RBM25 "RNA-binding protein 25" [Homo sapiens (taxid:9606)]

 Score = 180 (68.4 bits), Expect = 2.5e-13, P = 2.5e-13
 Identities = 38/89 (42%), Positives = 53/89 (59%)

Query:   127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
             P T V+VG I+  A    +  +L  CG V SWKR Q  S G  + FGFCE++  E  LRA
Sbjct:    85 PTTTVFVGNISEKASDMLIRQLLAKCGLVLSWKRVQGAS-GKLQAFGFCEYKEPESTLRA 143

Query:   187 LRLLNKFNIDGQELMLKVDQATREYLERY 215
             LRLL+   I  ++L++KVD  T+  L+ +
Sbjct:   144 LRLLHDLQIGEKKLLVKVDAKTKAQLDEW 172

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

DICTYBASE|DDB_G0269926 DDB_G0269926 "splicing factor PWI domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 201 (75.8 bits), Expect = 5.3e-13, P = 5.3e-13
 Identities = 61/182 (33%), Positives = 88/182 (48%)

Query:   129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
             T  Y+GKI    +  F+ S+L  CG V  W RA   +NG  K FG CEFE AEG + ALR
Sbjct:   246 TTAYIGKIPQFVEDSFIRSLLNQCGKVSKWNRAS-DTNGKLKQFGLCEFEHAEGAVTALR 304

Query:   189 LLNKFNID--GQELMLKVDQATREYLERYVDXXXXXXXXXXXX-QDAGAGKEDESVQS-V 244
             +LN   +D  G +L++KVD+  +++   Y+D             QD       ES+++ V
Sbjct:   305 VLNDLEVDRDGGKLVVKVDKG-QKFFSDYLDKKGGLTDQSSDSPQDIILR---ESIKAMV 360

Query:   245 EKN----EPTKSPENLKDNETGNKESHDPTN---FGVVTEEDRKADQEALEKLTCMVEER 297
             EKN       K  E+ + N+  NK+  D T      ++ +E  K  Q   E+     E  
Sbjct:   361 EKNFINIYEKKKMESNEINDFYNKDRRDLTKEEKIKIIEKEKEKEKQRHKERELKNKERD 420

Query:   298 LK 299
             LK
Sbjct:   421 LK 422

GO:0006397 "mRNA processing" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

RGD|1565486 RGD1565486 "similar to RNA binding motif protein 25" [Rattus norvegicus (taxid:10116)]

 Score = 180 (68.4 bits), Expect = 2.1e-12, Sum P(2) = 2.1e-12
 Identities = 38/89 (42%), Positives = 53/89 (59%)

Query:   127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
             P T V+VG I+  A    +  +L  CG V SWKR Q  S G  + FGFCE++  E  LRA
Sbjct:    85 PTTTVFVGNISEKASDMLIRQLLAKCGLVLSWKRVQGAS-GKLQAFGFCEYKEPESTLRA 143

Query:   187 LRLLNKFNIDGQELMLKVDQATREYLERY 215
             LRLL+   I  ++L++KVD  T+  L+ +
Sbjct:   144 LRLLHDLQIGEKKLLVKVDAKTKAQLDEW 172

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|I3LLA0 RBM25 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 180 (68.4 bits), Expect = 1.3e-11, Sum P(2) = 1.3e-11
 Identities = 38/89 (42%), Positives = 53/89 (59%)

Query:   127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
             P T V+VG I+  A    +  +L  CG V SWKR Q  S G  + FGFCE++  E  LRA
Sbjct:    85 PTTTVFVGNISEKASDMLIRQLLAKCGLVLSWKRVQGAS-GKLQAFGFCEYKEPESTLRA 143

Query:   187 LRLLNKFNIDGQELMLKVDQATREYLERY 215
             LRLL+   I  ++L++KVD  T+  L+ +
Sbjct:   144 LRLLHDLQIGEKKLLVKVDAKTKAQLDEW 172

GO:0016607 "nuclear speck" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003729 "mRNA binding" evidence=IEA

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

ZFIN|ZDB-GENE-030131-5547 rbm25 "RNA binding motif protein 25" [Danio rerio (taxid:7955)]

 Score = 192 (72.6 bits), Expect = 1.3e-11, Sum P(2) = 1.3e-11
 Identities = 44/119 (36%), Positives = 63/119 (52%)

Query:   127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
             P T V+VG I+  A    +  +L  CG V SWKR Q  S G  + FGFCE++  E  LRA
Sbjct:    85 PTTTVFVGNISEKASDMLIRQLLAKCGLVLSWKRVQGAS-GKLQAFGFCEYKEPESTLRA 143

Query:   187 LRLLNKFNIDGQELMLKVDQATREYLERYVDXXXXXXXXXXXXQDAGAGKEDESVQSVE 245
             LRLL++  +  ++L++KVD  T+  L+ +               D  AG+E+E V   E
Sbjct:   144 LRLLHELQVGEKKLLVKVDAKTKAQLDEWKAKKKSTSANGNGKAD-DAGEEEEEVLDEE 201

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

MGI|MGI:1914289 Rbm25 "RNA binding motif protein 25" [Mus musculus (taxid:10090)]

 Score = 180 (68.4 bits), Expect = 2.3e-11, Sum P(2) = 2.3e-11
 Identities = 38/89 (42%), Positives = 53/89 (59%)

Query:   127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
             P T V+VG I+  A    +  +L  CG V SWKR Q  S G  + FGFCE++  E  LRA
Sbjct:    85 PTTTVFVGNISEKASDMLIRQLLAKCGLVLSWKRVQGAS-GKLQAFGFCEYKEPESTLRA 143

Query:   187 LRLLNKFNIDGQELMLKVDQATREYLERY 215
             LRLL+   I  ++L++KVD  T+  L+ +
Sbjct:   144 LRLLHDLQIGEKKLLVKVDAKTKAQLDEW 172

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=ISO

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006915 "apoptotic process" evidence=ISO

GO:0008380 "RNA splicing" evidence=IEA

GO:0016607 "nuclear speck" evidence=ISO

UNIPROTKB|E1BHM5 RBM25 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 180 (68.4 bits), Expect = 6.0e-11, Sum P(2) = 6.0e-11
 Identities = 38/89 (42%), Positives = 53/89 (59%)

Query:   127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
             P T V+VG I+  A    +  +L  CG V SWKR Q  S G  + FGFCE++  E  LRA
Sbjct:    85 PTTTVFVGNISEKASDMLIRQLLAKCGLVLSWKRVQGAS-GKLQAFGFCEYKEPESTLRA 143

Query:   187 LRLLNKFNIDGQELMLKVDQATREYLERY 215
             LRLL+   I  ++L++KVD  T+  L+ +
Sbjct:   144 LRLLHDLQIGEKKLLVKVDAKTKAQLDEW 172

GO:0016607 "nuclear speck" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003729 "mRNA binding" evidence=IEA

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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	577
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	1e-35
smart00360	73	smart00360, RRM, RNA recognition motif	3e-12
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-10
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	9e-10
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-08
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	5e-08
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	5e-08
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	2e-07
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	4e-07
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-07
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-06
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	2e-06
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-06
PRK12678	672	PRK12678, PRK12678, transcription termination fact	5e-06
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	5e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	6e-06
PRK12705	508	PRK12705, PRK12705, hypothetical protein; Provisio	6e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	7e-06
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	7e-06
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	8e-06
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	8e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	9e-06
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	1e-05
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-05
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	1e-05
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-05
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-05
pfam09756	189	pfam09756, DDRGK, DDRGK domain	2e-05
COG3064	387	COG3064, TolA, Membrane protein involved in colici	3e-05
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	3e-05
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	5e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	6e-05
pfam13904	261	pfam13904, DUF4207, Domain of unknown function (DU	6e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	7e-05
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	7e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	8e-05
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	8e-05
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	8e-05
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	8e-05
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	9e-05
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	1e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	1e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	1e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	1e-04
COG1390	194	COG1390, NtpE, Archaeal/vacuolar-type H+-ATPase su	1e-04
TIGR02794	346	TIGR02794, tolA_full, TolA protein	1e-04
pfam05557	722	pfam05557, MAD, Mitotic checkpoint protein	1e-04
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	2e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	2e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	2e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	2e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	2e-04
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-04
COG2268	548	COG2268, COG2268, Uncharacterized protein conserve	2e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-04
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	2e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-04
PTZ00266	1021	PTZ00266, PTZ00266, NIMA-related protein kinase; P	2e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-04
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	3e-04
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	3e-04
PRK12585	197	PRK12585, PRK12585, putative monovalent cation/H+	3e-04
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	3e-04
PRK07735	430	PRK07735, PRK07735, NADH dehydrogenase subunit C;	3e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	4e-04
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	4e-04
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	4e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	5e-04
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	6e-04
COG4942	420	COG4942, COG4942, Membrane-bound metallopeptidase	7e-04
pfam12128	1198	pfam12128, DUF3584, Protein of unknown function (D	8e-04
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	8e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	9e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.001
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.001
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.001
PRK12705	508	PRK12705, PRK12705, hypothetical protein; Provisio	0.001
pfam09756	189	pfam09756, DDRGK, DDRGK domain	0.001
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	0.001
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	0.001
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	0.001
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	0.001
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	0.001
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.002
PTZ00266	1021	PTZ00266, PTZ00266, NIMA-related protein kinase; P	0.002
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	0.002
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	0.002
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	0.002
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.002
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	0.002
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.003
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.003
TIGR02794	346	TIGR02794, tolA_full, TolA protein	0.003
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	0.003
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.003
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	0.003
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	0.003
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	0.003
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	0.003
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.004
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.004
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.004
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.004
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	0.004
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	0.004
pfam02841	297	pfam02841, GBP_C, Guanylate-binding protein, C-ter	0.004
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	0.004

>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score =  128 bits (323), Expect = 1e-35
 Identities = 44/84 (52%), Positives = 55/84 (65%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
           T V+VG I      DF+  +L+ CG V SWKR + PS G  K FGFCEFE  EG LRALR
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 189 LLNKFNIDGQELMLKVDQATREYL 212
           LLN   + G++L++KVD  TR+ L
Sbjct: 61  LLNGLELGGKKLLVKVDAKTRKLL 84

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|214636 smart00360, RRM, RNA recognition motif

 Score = 61.8 bits (151), Expect = 3e-12
 Identities = 23/71 (32%), Positives = 35/71 (49%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
            ++VG + P    + +  +    G V+S +  +    G  KGF F EFES E   +AL  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 190 LNKFNIDGQEL 200
           LN   +DG+ L
Sbjct: 61  LNGKELDGRPL 71

Length = 73

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 62.1 bits (150), Expect = 7e-10
 Identities = 62/305 (20%), Positives = 135/305 (44%), Gaps = 32/305 (10%)

Query: 218  KKTENTKKLKETQDAGAGKEDESVQSVE---KNEPTKSPENLKDNETGNKESHDPTNFGV 274
            KK +  KK +E + A   K+ E  +  +   K E  K  E  K  E   K   D      
Sbjct: 1522 KKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALR 1581

Query: 275  VTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVD 334
              EE +KA++  +E++  + EE  K                    +E   KA +     +
Sbjct: 1582 KAEEAKKAEEARIEEVMKLYEEEKKMK------------------AEEAKKAEEAKIKAE 1623

Query: 335  MIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRY 394
             ++    E K  ++             +  + ++ +  + +  ++E  +K  +E +    
Sbjct: 1624 ELKKAEEEKKKVEQL-----------KKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEE 1672

Query: 395  EREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKK 454
            +++   E  + E ++++  E  ++E E   K  E +++E E++++ E+ K+ E E K K 
Sbjct: 1673 DKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKA 1732

Query: 455  EILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQ 514
            E    E E++    +  ++   E+K+   ++++EE  A+E+R+E+E  + +   EE++ +
Sbjct: 1733 EEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKR 1792

Query: 515  QQQRD 519
            + + D
Sbjct: 1793 RMEVD 1797

Length = 2084

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

 Score = 54.6 bits (132), Expect = 9e-10
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
           ++VG + P    + +  +    G ++S  R     +G  KGF F EFES E   +AL  L
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESV-RIVRDKDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 191 NKFNIDGQELMLK 203
           N   +DG++L + 
Sbjct: 60  NGKELDGRKLKVS 72

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

>gnl|CDD|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 = 54.6 bits (132), Expect = 1e-09
 Identities = 28/80 (35%), Positives = 40/80 (50%), Gaps = 8/80 (10%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
           V+VG I   A  + ++ +    G V S++       G PKG+GFCEFE  E    A+R  
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIR-- 58

Query: 191 NKFNIDGQELM---LKVDQA 207
              N++G E     L+VD A
Sbjct: 59  ---NLNGYEFNGRALRVDFA 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|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 60.2 bits (145), Expect = 3e-09
 Identities = 41/184 (22%), Positives = 92/184 (50%), Gaps = 6/184 (3%)

Query: 378  DKERDLKREKEREIDRYEREAERERVRKEREQRRKIEE-AEREYERCLKDWEYREREREK 436
            ++E+ +K E+ ++ +  E + + E ++K  E+++K+E+  ++E E   K  E ++ E E 
Sbjct: 1602 EEEKKMKAEEAKKAE--EAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEEN 1659

Query: 437  ERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEED---LAD 493
            + +  +E +K  E K+K E     EEDE  + +  ++   E K+ + +++KE +    A+
Sbjct: 1660 KIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAE 1719

Query: 494  EVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEHDYHDD 553
            E+++ EE    K    +++ ++ ++ A +   D      +A     E K  +      + 
Sbjct: 1720 ELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEA 1779

Query: 554  SIRE 557
             I E
Sbjct: 1780 VIEE 1783

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 55.9 bits (134), Expect = 4e-08
 Identities = 63/313 (20%), Positives = 140/313 (44%), Gaps = 28/313 (8%)

Query: 218  KKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTE 277
            +K +  KK +E + A   K+ E  +  +  E  K  E  K  +   K++          E
Sbjct: 1278 RKADELKKAEEKKKADEAKKAEEKKKAD--EAKKKAEEAKKADEAKKKA----------E 1325

Query: 278  EDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIR 337
            E +K    A +K     EE  K         +  AD      +E  A+A +   +    +
Sbjct: 1326 EAKKKADAAKKK----AEEAKKAAEAAKAEAEAAADE--AEAAEEKAEAAEKKKEEAKKK 1379

Query: 338  NDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYERE 397
             D A+ K +++  +D      +  +  + +  +    + +  E   K E++++ D  +++
Sbjct: 1380 ADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKK 1439

Query: 398  AERER----VRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRK 453
            AE  +     +K+ E+ +K EEA+++ E   K  E +++  E ++  E +K+ E  +K+ 
Sbjct: 1440 AEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKA 1499

Query: 454  KEILYDEEEDE--DDSRKRWRRSVLEEKRRKRIREKEEDL--ADEVREEEEIAVAK--RR 507
             E     E  +  D+++K       +E ++    +K ++   A+E ++ +E+  A+  ++
Sbjct: 1500 DEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKK 1559

Query: 508  AEEEQLQQQQRDA 520
            AEE++  ++ + A
Sbjct: 1560 AEEKKKAEEAKKA 1572

Length = 2084

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

 Score = 50.0 bits (120), Expect = 5e-08
 Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
            ++YV  + P    D + SV +  G +KS   A  P  G  KG+GF E+E+ +    A+ 
Sbjct: 1   NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 189 LLNKFNIDGQELMLKVDQA 207
            +N F++ GQ   L+V +A
Sbjct: 61  SMNLFDLGGQ--QLRVGKA 77

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|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 = 49.8 bits (119), Expect = 5e-08
 Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 2/77 (2%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
           V+VG I   A  + +  +    G V S++       G PKG+GFCE++  E  L A+R L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 191 NKFNIDGQELMLKVDQA 207
           N + ++G++  L+VD A
Sbjct: 61  NGYELNGRQ--LRVDNA 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|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 48.5 bits (116), Expect = 2e-07
 Identities = 21/63 (33%), Positives = 30/63 (47%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
           VYV  +   A  +++ +V    GTV      +Y   G  KGF F EFE+ E   +A + L
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 191 NKF 193
           N  
Sbjct: 62  NNP 64

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|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 52.5 bits (127), Expect = 4e-07
 Identities = 42/179 (23%), Positives = 80/179 (44%), Gaps = 31/179 (17%)

Query: 371 VHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWE-- 428
           V  +    K ++ + E +R ++  ++EAE  +       +  + EA+ E  +   ++E  
Sbjct: 24  VRKKIAEAKIKEAEEEAKRILEEAKKEAEAIK-------KEALLEAKEEIHKLRNEFEKE 76

Query: 429 YREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRW---------RRSVLEEK 479
            RER  E ++  ++  +KE    RK E+L   EE+ +   K           +   LEE 
Sbjct: 77  LRERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEEL 136

Query: 480 RRKRIREKE-----------EDLADEVREE--EEIAVAKRRAEEEQLQQQQRDALKLLS 525
             ++++E E           E L ++V EE   E AV  +  EEE  ++  + A ++L+
Sbjct: 137 IEEQLQELERISGLTAEEAKEILLEKVEEEARHEAAVLIKEIEEEAKEEADKKAKEILA 195

Length = 520

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

 Score = 46.8 bits (112), Expect = 5e-07
 Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 1/71 (1%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
           ++VG + P    + +  +    G ++S +       G  KGF F EFE  E   +AL  L
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIV-RDETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 191 NKFNIDGQELM 201
           N   + G+EL 
Sbjct: 60  NGKELGGRELR 70

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

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 52.5 bits (125), Expect = 6e-07
 Identities = 67/315 (21%), Positives = 128/315 (40%), Gaps = 18/315 (5%)

Query: 218  KKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTE 277
            KK E  KK  E +      + ++ ++ +  E  K  +  K  E   K            E
Sbjct: 1477 KKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKK-----AE 1531

Query: 278  EDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIR 337
            E +KAD+    +     +E  K   L     +  A+ +  +  +     R  +       
Sbjct: 1532 EAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEE 1591

Query: 338  NDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVH-DRRGRDKERDLKREKEREIDRYE- 395
              I E     E     KA +  + E +      +      + K   LK+++  E  + E 
Sbjct: 1592 ARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEE 1651

Query: 396  -REAERERVRKEREQRRKIEEAEREYERCLKDWEYR-------EREREKERQYEKEKEKE 447
             ++AE E   K  E+ +K EE +++ E   K  E         ++E E+ ++ E+ K+KE
Sbjct: 1652 LKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKE 1711

Query: 448  RERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRK---RIREKEEDLADEVREEEEIAVA 504
             E K+K E L   EE+     +  ++   E+K++    +  E+E+     +++EEE    
Sbjct: 1712 AEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAE 1771

Query: 505  KRRAEEEQLQQQQRD 519
            + R E+E + +++ D
Sbjct: 1772 EIRKEKEAVIEEELD 1786

Length = 2084

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

 Score = 51.1 bits (122), Expect = 1e-06
 Identities = 28/115 (24%), Positives = 46/115 (40%), Gaps = 11/115 (9%)

Query: 375 RGRDKERDLKREKEREIDRYEREAERERVR-KEREQRRKIEEAEREYERCLKDWEYRERE 433
           R RD+ER   R   R       +  RER R + R + R     +R+Y R       R R 
Sbjct: 1   RYRDRERGRLRNDTRR-----SDKGRERSRRRSRSRDRSRRRRDRDYYR---GRRGRSRS 52

Query: 434 REKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKE 488
           R   R Y    ++   R  ++     +E   +   +R  R+V   +   + RE++
Sbjct: 53  RSPNRYYRPRGDRSYRRDDRRSGRNTKEPLTEA--ERDDRTVFVLQLALKARERD 105

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|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 50.4 bits (120), Expect = 2e-06
 Identities = 24/153 (15%), Positives = 61/153 (39%), Gaps = 6/153 (3%)

Query: 380 ERDLKREKEREIDRYEREAERERVRKEREQRRKI------EEAEREYERCLKDWEYRERE 433
           +    + KE+     E    +E++  E E    +      EE     +  L+D +     
Sbjct: 197 KLQELKLKEQAKKALEYYQLKEKLELEEENLLYLDYLKLNEERIDLLQELLRDEQEEIES 256

Query: 434 REKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLAD 493
            ++E + E+E   +  ++ K+E    + ++E+          L+ +  K  R K +D   
Sbjct: 257 SKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEK 316

Query: 494 EVREEEEIAVAKRRAEEEQLQQQQRDALKLLSD 526
               E+E+   ++  ++E+ + ++ +      +
Sbjct: 317 LKESEKELKKLEKELKKEKEEIEELEKELKELE 349

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 49.5 bits (119), Expect = 2e-06
 Identities = 38/142 (26%), Positives = 77/142 (54%), Gaps = 2/142 (1%)

Query: 379 KERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDW-EYREREREKE 437
           +ER+ +R++E E    ERE   E + + +E+     + +RE ++ L++  +    ER + 
Sbjct: 81  EEREKRRQEEYEERLQEREQMDEIIERIQEEDEAEAQEKREKQKKLREEIDEFNEERIER 140

Query: 438 RQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVRE 497
           ++ EKE+E+E E K  +      E +E+   +R  R   +E+   R+R ++E+  DE  E
Sbjct: 141 KEEEKEREREEELKILEYQREKAEREEEREAERRERKEEKEREVARLRAQQEEAEDEREE 200

Query: 498 EEEIAVAKRRAEEEQLQQQQRD 519
            +E+  A    EE + +++Q++
Sbjct: 201 LDEL-RADLYQEEYERKERQKE 221

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

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

 Score = 44.5 bits (106), Expect = 4e-06
 Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 4/71 (5%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGT-PKGFGFCEFESAEGVLRALRL 189
           +YV  + P+   + +       G V+     +   N   P+GF F EF S E    AL+ 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEG---VRLVRNKDRPRGFAFVEFASPEDAEAALKK 57

Query: 190 LNKFNIDGQEL 200
           LN   +DG+ L
Sbjct: 58  LNGLVLDGRTL 68

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

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 49.3 bits (118), Expect = 5e-06
 Identities = 31/155 (20%), Positives = 67/155 (43%), Gaps = 12/155 (7%)

Query: 382 DLKREKEREIDRYEREAERERVRKEREQRR----------KIEEAEREYERCLKDWEYRE 431
           DL  E E+++++ ER+AE+    +E +             K++E  +E E   ++    E
Sbjct: 193 DLLEELEKQLEKLERQAEKAERYQELKAELRELELALLLAKLKELRKELEELEEELSRLE 252

Query: 432 REREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDL 491
            E E+ ++  +E EKE E  + +     EE +E        +  +EE   +    +E   
Sbjct: 253 EELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEIEELEGEISLLRER-- 310

Query: 492 ADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSD 526
            +E+  E E    +    +E+++  + +  +  + 
Sbjct: 311 LEELENELEELEERLEELKEKIEALKEELEERETL 345

Length = 1163

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

 Score = 49.1 bits (118), Expect = 5e-06
 Identities = 37/241 (15%), Positives = 67/241 (27%), Gaps = 18/241 (7%)

Query: 259 NETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGIS 318
             T    +             R+A+Q A E      E             +  +      
Sbjct: 67  AATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQ 126

Query: 319 NSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRD 378
             E   +                E   +   T     +     E    +R R  DR  R 
Sbjct: 127 ARERRERGEAARRGA---ARKAGEGG-EQPATEARADAAERTEEEERDERRRRGDREDRQ 182

Query: 379 KERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKER 438
            E +      RE    ER  + +   +   + +      RE        + R R R ++R
Sbjct: 183 AEAERGERGRRE----ERGRDGDDRDRRDRREQ---GDRREERGRRDGGDRRGRRRRRDR 235

Query: 439 QYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREE 498
           +  +  +   +R  +     D ++ E    +R RR    ++ R+  R  +     E    
Sbjct: 236 RDARGDDNREDRGDR-----DGDDGEGRGGRRGRRF--RDRDRRGRRGGDGGNEREPELR 288

Query: 499 E 499
           E
Sbjct: 289 E 289

Length = 672

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 48.8 bits (117), Expect = 5e-06
 Identities = 44/170 (25%), Positives = 76/170 (44%), Gaps = 21/170 (12%)

Query: 371 VHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYR 430
           +  R    K    +   +R I+  ++EAE  +     E + ++ +   E ER     E +
Sbjct: 18  LRKRIAEKKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELER-----ELK 72

Query: 431 EREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEED 490
           ER  E +R   +  ++E    RK E L  +EE+              EK+ K +  KE++
Sbjct: 73  ERRNELQRLERRLLQREETLDRKMESLDKKEEN-------------LEKKEKELSNKEKN 119

Query: 491 LADEVREEEEIAVAKRRAEEEQLQQ-QQRDALKLLSDNAVNGSLAEESAV 539
           L DE  EE E  +A++R E E++    Q +A ++L +  V      E+A 
Sbjct: 120 L-DEKEEELEELIAEQREELERISGLTQEEAKEILLEE-VEEEARHEAAK 167

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

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

 Score = 48.9 bits (116), Expect = 6e-06
 Identities = 25/95 (26%), Positives = 45/95 (47%), Gaps = 1/95 (1%)

Query: 106 RPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPS 165
           RP   P  +P+ +  V    K   ++YV  + P      + SV +  G +   + A+ P+
Sbjct: 183 RPSNMPQAQPI-IDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPT 241

Query: 166 NGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL 200
               KG+GF E+ + +    A+  +N F++ GQ L
Sbjct: 242 GRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYL 276

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|237178 PRK12705, PRK12705, hypothetical protein; Provisional

 Score = 48.6 bits (116), Expect = 6e-06
 Identities = 37/170 (21%), Positives = 79/170 (46%), Gaps = 11/170 (6%)

Query: 373 DRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRER 432
           +R  ++ +++ + + E  +   +    RER ++ +E RR+ EE +RE ER ++      +
Sbjct: 36  ERILQEAQKEAEEKLEAALLEAKELLLRERNQQRQEARREREELQREEERLVQ------K 89

Query: 433 EREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLA 492
           E + + + EK    E + + +++ L   E  E +  ++   + L         +  + L 
Sbjct: 90  EEQLDARAEKLDNLENQLEEREKALSAREL-ELEELEKQLDNELYRVAGLTPEQARKLLL 148

Query: 493 DEVREE--EEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVE 540
             +  E  EE A   ++ EEE   + +R A  +L+  A+    A E+A +
Sbjct: 149 KLLDAELEEEKAQRVKKIEEEADLEAERKAQNILA-QAMQRI-ASETASD 196

Length = 508

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 48.9 bits (117), Expect = 7e-06
 Identities = 29/161 (18%), Positives = 60/161 (37%), Gaps = 1/161 (0%)

Query: 367 DRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKD 426
                       +E + +     E+++   E E  +   E +    +EE E  +E   ++
Sbjct: 325 LEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREE 384

Query: 427 WEYREREREK-ERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIR 485
               E E  +   + E+ K +    + + E L +  ED  +  K     + E +      
Sbjct: 385 LAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQTELEEL 444

Query: 486 EKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSD 526
            +E +  +E  EE    + +   E  +LQ++ +   K LS 
Sbjct: 445 NEELEELEEQLEELRDRLKELERELAELQEELQRLEKELSS 485

Length = 1163

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

 Score = 43.9 bits (104), Expect = 7e-06
 Identities = 23/72 (31%), Positives = 36/72 (50%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
           ++VG ++  AD D +       G + S +    P +G PKGFG+ EF S E    AL  L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 191 NKFNIDGQELML 202
              ++ G+ + L
Sbjct: 61  GGTDLLGRPVRL 72

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

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

 Score = 43.8 bits (104), Expect = 8e-06
 Identities = 20/60 (33%), Positives = 30/60 (50%)

Query: 132 YVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN 191
           ++G + P  D  ++ S    CG V S K  +    G   G+GF EF + E   +AL+ LN
Sbjct: 3   WMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLN 62

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

 Score = 43.7 bits (104), Expect = 8e-06
 Identities = 21/71 (29%), Positives = 36/71 (50%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
           ++VGK+    + D +  +    GTVK            P+G+ + EFES E   +A++ +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 191 NKFNIDGQELM 201
           +   IDGQE+ 
Sbjct: 61  DGGQIDGQEVT 71

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

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 48.4 bits (115), Expect = 9e-06
 Identities = 29/156 (18%), Positives = 61/156 (39%), Gaps = 16/156 (10%)

Query: 372 HDRRGRDKERDLKREKER----------EIDRYEREAERERVRKEREQRRKIEEAEREYE 421
             R+ +++ + L  E E              +  +  E+ +   E  Q ++  E E E  
Sbjct: 168 EKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEENL 227

Query: 422 RCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRR 481
               D+     ER    Q     E  R+ + + E    E E E++   +  +   EE++ 
Sbjct: 228 L-YLDYLKLNEERIDLLQ-----ELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKE 281

Query: 482 KRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQ 517
           K+++E+E  L  +  EE +  + K    +   +++ 
Sbjct: 282 KKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKL 317

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 47.2 bits (113), Expect = 1e-05
 Identities = 47/159 (29%), Positives = 79/159 (49%), Gaps = 15/159 (9%)

Query: 368 RSRVHDRRGRDKERDLKREKERE---IDRYEREAERERVRKEREQRRKIEEAEREYERCL 424
           + R   R    +E      +E +    D Y+ E ER+  +KE+E+  K    ++E     
Sbjct: 180 KEREVARLRAQQEEAEDEREELDELRADLYQEEYERKERQKEKEEAEKRRRQKQE---LQ 236

Query: 425 KDWEYREREREKERQYEK-EKEKERERKRKKEILYDEEEDEDDSRKRWRR--------SV 475
           +  E +  E+E+  Q E+ E+E ERER  +K+   +E E E+  ++R +R          
Sbjct: 237 RAREEQIEEKEERLQEERAEEEAERERMLEKQAEDEELEQENAEKRRMKRLEHRRELEQQ 296

Query: 476 LEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQ 514
           +EEK  +R  E+EE+L +  R  EE A  + R EEE+ +
Sbjct: 297 IEEKEERRAAEREEELEEGERLREEEAERQARIEEERQR 335

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

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

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 129 TKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRAL 187
           T VY+  + P T D D    + +  G + S K          KG+GF +F+S E  L+A+
Sbjct: 1   TNVYIRGLPPNTTDEDLEK-LCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAI 59

Query: 188 RLLNKFNIDGQ 198
             LN   +  Q
Sbjct: 60  EGLNGRGVQAQ 70

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

 Score = 48.0 bits (114), Expect = 1e-05
 Identities = 29/134 (21%), Positives = 45/134 (33%), Gaps = 30/134 (22%)

Query: 377 RDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREK 436
           RD+E D +REK R  DR   +   ER R+    R                  +R+R R  
Sbjct: 1   RDEEPDREREKSRGRDR---DRSSERPRRRSRDR----------------SRFRDRHRRS 41

Query: 437 ERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVR 496
             +  +E  + R+R+R     YD            RRS      R R R +   +    +
Sbjct: 42  RERSYREDSRPRDRRR-----YDSRSPRSLRYSSVRRS------RDRPRRRSRSVRSIEQ 90

Query: 497 EEEEIAVAKRRAEE 510
               +       + 
Sbjct: 91  HRRRLRDRSPSNQW 104

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

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 47.8 bits (114), Expect = 1e-05
 Identities = 41/154 (26%), Positives = 73/154 (47%), Gaps = 10/154 (6%)

Query: 377 RDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREK 436
           + K  +L+ +    ++  E   E   + +E ++ +K+EE + E E    +   +E E  +
Sbjct: 184 KAKIEELEGQLSELLEDIEDLLEA--LEEELKELKKLEEIQEEQEEEELE---QEIEALE 238

Query: 437 ERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRR-KRIREKEEDLADEV 495
           ER  E E+EKER  + K  +L  E   E ++ K     + E +R  + + EK E L +  
Sbjct: 239 ERLAELEEEKERLEELKARLLEIESL-ELEALKIREEELRELERLLEELEEKIERLEELE 297

Query: 496 RE--EEEIAVAKRRAEEEQLQQQQRDALKLLSDN 527
           RE  E E  +   RA  E+  ++  + LK L + 
Sbjct: 298 REIEELEEELEGLRALLEE-LEELLEKLKSLEER 330

Length = 908

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

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 4/78 (5%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
           ++VG ++ +A+ D +    K CG V    R     +G  KGFG  EF + EG  +AL   
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVD-VRIAQDDDGRSKGFGHVEFATEEGAQKALEKS 60

Query: 191 NKFNIDGQELMLKVDQAT 208
               + G+E  ++VD AT
Sbjct: 61  G-EELLGRE--IRVDLAT 75

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|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 47.1 bits (111), Expect = 2e-05
 Identities = 35/172 (20%), Positives = 82/172 (47%), Gaps = 2/172 (1%)

Query: 342  EDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERE 401
            E K D E     +   ++       +    H  R +   +  +  K  E+ + E + + +
Sbjct: 1234 EAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKAD 1293

Query: 402  RVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEE 461
              +K  E+++K +EA+++ E   K  E +++  E +++ +  K+K  E K+  E    E 
Sbjct: 1294 EAKKA-EEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEA 1352

Query: 462  E-DEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQ 512
            E   D++     ++   EK+++  ++K +    +  E+++   AK++AEE++
Sbjct: 1353 EAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDK 1404

Length = 2084

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 47.3 bits (112), Expect = 2e-05
 Identities = 26/158 (16%), Positives = 64/158 (40%), Gaps = 15/158 (9%)

Query: 374 RRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCL------KDW 427
               +   +L  + E    +  +  E+ +   E  Q ++  E E E    L      ++ 
Sbjct: 180 IEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEENLLYLDYLKLNEER 239

Query: 428 EYREREREKERQYEKEKEKERERKRKKEI-----LYDEEEDEDDSRKRWRRSVLEEKRRK 482
               +E  ++ Q E E  K+   K ++ +        EEE E   ++     +L ++  +
Sbjct: 240 IDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEEL-KLLAKEEEE 298

Query: 483 RIREKEEDLADEVREEEEIAVAK---RRAEEEQLQQQQ 517
              E  +    +V +EE++  ++   ++ E+E  ++++
Sbjct: 299 LKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKE 336

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 47.3 bits (112), Expect = 2e-05
 Identities = 39/170 (22%), Positives = 76/170 (44%), Gaps = 5/170 (2%)

Query: 377 RDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREK 436
             +E   K+ +E E+    +E E E   +  +  R+  + E + +   K+ +  E+E +K
Sbjct: 275 NKEEEKEKKLQEEELKLLAKE-EEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKK 333

Query: 437 ERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVR 496
           E++  +E EKE +    K    +EEE++ +  +     + EE   K+  E E   +    
Sbjct: 334 EKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKL 393

Query: 497 EEEEIAVA----KRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESK 542
           +EEE+ +     K      +L +Q+ D LK      +      E ++E+K
Sbjct: 394 KEEELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEELEESLETK 443

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

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

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 5/77 (6%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
           +YVG +  T   D +  +    G +KS K  +   N     + F E+        AL+ +
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP---YAFVEYYDHRSAAAALQTM 57

Query: 191 NKFNIDGQELMLKVDQA 207
           N   I GQE  +KV+ A
Sbjct: 58  NGRLILGQE--IKVNWA 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|220383 pfam09756, DDRGK, DDRGK domain

 Score = 45.1 bits (107), Expect = 2e-05
 Identities = 23/85 (27%), Positives = 50/85 (58%), Gaps = 3/85 (3%)

Query: 395 EREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKK 454
            ++  +   ++ R Q+R+ EE ERE  + L++    ER+ E+E + E+EK+KE E ++++
Sbjct: 5   AKKRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKER 64

Query: 455 EILYDEEEDEDDSRKRWRRSVLEEK 479
           E   ++   E +  ++ + S + E+
Sbjct: 65  E---EQARKEQEEYEKLKSSFVVEE 86

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 46.5 bits (110), Expect = 3e-05
 Identities = 31/156 (19%), Positives = 68/156 (43%), Gaps = 19/156 (12%)

Query: 368 RSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDW 427
           +S+    +  +++R  K E+  E  + ++ AE+ER+++  ++R K +E +++ E      
Sbjct: 68  QSQQSSAKKGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAE------ 121

Query: 428 EYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREK 487
                E EK+ Q E+++++E+ RK   E     E          +     E  + +   +
Sbjct: 122 -----EAEKQAQLEQKQQEEQARKAAAEQKKKAEAA--------KAKAAAEAAKLKAAAE 168

Query: 488 EEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKL 523
            +  A+E  +  E A AK  A   + + +       
Sbjct: 169 AKKKAEEAAKAAEEAKAKAEAAAAKKKAEAEAKAAA 204

Length = 387

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 46.6 bits (111), Expect = 3e-05
 Identities = 34/157 (21%), Positives = 72/157 (45%), Gaps = 13/157 (8%)

Query: 378 DKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKE 437
           + E DL + +E  ++  E      R+ + + +  K+EE     E  L++ E +      E
Sbjct: 769 ELEEDLHKLEE-ALNDLEARLSHSRIPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLE 827

Query: 438 RQYEKEKEKERERK------RKKEILYDEEEDEDDSRKRWRRSVLEEKRR--KRIREKEE 489
           ++Y +++ +E + +      + K I  ++E +  + +K      LEE     + +  +  
Sbjct: 828 KEYLEKEIQELQEQRIDLKEQIKSI--EKEIENLNGKKEELEEELEELEAALRDLESRLG 885

Query: 490 DLADEVRE-EEEIAVAKRRAEEEQLQ-QQQRDALKLL 524
           DL  E  E E ++   +R+ EE + Q +++R  L  L
Sbjct: 886 DLKKERDELEAQLRELERKIEELEAQIEKKRKRLSEL 922

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 46.2 bits (110), Expect = 5e-05
 Identities = 40/222 (18%), Positives = 83/222 (37%), Gaps = 12/222 (5%)

Query: 320 SELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDK 379
           SEL  +  +   ++  + N+I+  +   +   +  A+   + E        +  +     
Sbjct: 277 SELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELA 336

Query: 380 ERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQ 439
           E   + E++ E  + E E+    + +   +  ++E    E E      E  E  R K  Q
Sbjct: 337 EELAELEEKLEELKEELESLEAELEELEAELEELESRLEELE------EQLETLRSKVAQ 390

Query: 440 YEKEKEKERERKRKKEILYDEEEDEDDSRKRWR---RSVLEEKRRKRIREKEEDLADEVR 496
            E +           E L    E  +D R+R +     +L++     ++E + +L +   
Sbjct: 391 LELQIASLNNEI---ERLEARLERLEDRRERLQQEIEELLKKLEEAELKELQAELEELEE 447

Query: 497 EEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESA 538
           E EE+     R EE   + ++       + +A    LA+  A
Sbjct: 448 ELEELQEELERLEEALEELREELEEAEQALDAAERELAQLQA 489

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 45.7 bits (108), Expect = 6e-05
 Identities = 32/169 (18%), Positives = 72/169 (42%), Gaps = 4/169 (2%)

Query: 376 GRDKERDLKREKEREIDR-YEREAERERV-RKEREQRRKIEEAEREYERCLKDWEYRERE 433
              +E+  K+E+ +++    E  AE      + + Q  K++E  ++     +  E  E E
Sbjct: 164 AGSREKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELE 223

Query: 434 REKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLAD 493
            E     +  K  E      +E+L DE+E+ + S++   +      +  +  ++EE    
Sbjct: 224 EENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKK 283

Query: 494 EVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESK 542
              +EEE+ +  +  EE + +  + +  K+  +  +  S  E   +E +
Sbjct: 284 L--QEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKE 330

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207)

 Score = 44.7 bits (106), Expect = 6e-05
 Identities = 45/198 (22%), Positives = 92/198 (46%), Gaps = 8/198 (4%)

Query: 327 RDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKRE 386
            D   +     +D+ E   D E++S++  S       SS   S  + R    KE  L+R+
Sbjct: 27  EDCSEESTDSWSDMYEGLKDSESSSNSVPSLSLSSTASSLSDSSTYSRS--LKEVKLERQ 84

Query: 387 KEREID---RYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKE 443
            +   +     ++   +++++K  E+++K E  +   E  L+    +E+  E  RQ  ++
Sbjct: 85  AQEAYENWLSAKQAQRQKKLQKLLEEKQKQEREKEREEAELRQRLAKEKYEEWCRQKAQQ 144

Query: 444 KEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIRE--KEEDLADEVREEEEI 501
             K+R  K KKE           S K  R  V +E+ +KR++E   ++    + + EEE 
Sbjct: 145 AAKQRTPKHKKEAAESASSSLSGSAKPERN-VSQEEAKKRLQEWELKKLKQQQQKREEER 203

Query: 502 AVAKRRAEEEQLQQQQRD 519
              +++ +EE+ ++Q+ +
Sbjct: 204 RKQRKKQQEEEERKQKAE 221

This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known. Length = 261

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

 Score = 45.3 bits (107), Expect = 7e-05
 Identities = 32/120 (26%), Positives = 49/120 (40%), Gaps = 13/120 (10%)

Query: 366 PDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLK 425
           PDR R    RGRD++R  +R + R  DR      R R R  R + R   E  R  +R   
Sbjct: 5   PDRER-EKSRGRDRDRSSERPRRRSRDR-----SRFRDRHRRSRERSYREDSRPRDR--- 55

Query: 426 DWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIR 485
              Y  R     R     + ++R R+R + +   E+      R R R    + ++  + R
Sbjct: 56  -RRYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRR---RLRDRSPSNQWRKDDKKR 111

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

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 45.4 bits (108), Expect = 7e-05
 Identities = 41/185 (22%), Positives = 73/185 (39%), Gaps = 25/185 (13%)

Query: 374 RRGRDKERDLKREKEREIDRYEREAERERVRKEREQ-RRKIEEAEREYERCLKDWEYRER 432
           +R R++   LKRE            E  R+    ++  +++ +A R+     K+ E  E+
Sbjct: 677 QRLRERLEGLKRELSSLQS------ELRRIENRLDELSQELSDASRKIGEIEKEIEQLEQ 730

Query: 433 EREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLA 492
           E       EK KE+  E +     L  E E+     K             RI E EEDL 
Sbjct: 731 EE------EKLKERLEELEEDLSSLEQEIENVKSELKEL---------EARIEELEEDLH 775

Query: 493 DEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEHDYHD 552
              + EE +   + R    ++ + Q +  KL  + +   +   E   +   + +E +Y +
Sbjct: 776 ---KLEEALNDLEARLSHSRIPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLE 832

Query: 553 DSIRE 557
             I+E
Sbjct: 833 KEIQE 837

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 45.5 bits (108), Expect = 8e-05
 Identities = 40/186 (21%), Positives = 69/186 (37%), Gaps = 16/186 (8%)

Query: 380 ERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQ 439
           E  L+ ++E E    E E E   +R+  E+     E   E    LK+ +    + E E +
Sbjct: 288 EELLELKEEIE----ELEGEISLLRERLEELENELEELEERLEELKE-KIEALKEELEER 342

Query: 440 YEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEE 499
               +E E+     +E   + EE         + S L E+  +      E+LA+   E  
Sbjct: 343 ETLLEELEQLLAELEEAKEELEE---------KLSALLEELEELFEALREELAELEAELA 393

Query: 500 EIAVAKR--RAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEHDYHDDSIRE 557
           EI       + E E L+++     + L D        E    E +    E +   + + E
Sbjct: 394 EIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQTELEELNEELEELEE 453

Query: 558 NHMEIR 563
              E+R
Sbjct: 454 QLEELR 459

Length = 1163

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 45.1 bits (107), Expect = 8e-05
 Identities = 39/168 (23%), Positives = 70/168 (41%), Gaps = 4/168 (2%)

Query: 379 KERDLKREKEREIDRYERE-AERERVRKEREQRRKIEEAEREYERCL--KDWEYRERERE 435
            E++L    E E++  E E +  +   + RE+  ++E+  RE E  L          + E
Sbjct: 471 HEKELLELYELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALKEE 530

Query: 436 KERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIR-EKEEDLADE 494
            E + EK +    E +  KE L  ++  E+  +   R   L+E   +       ++  +E
Sbjct: 531 LEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEE 590

Query: 495 VREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESK 542
           +RE  +    K +  EE+L Q +     L    A N     E  +ES+
Sbjct: 591 LRERLKELKKKLKELEERLSQLEELLQSLELSEAENELEEAEEELESE 638

Length = 908

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

 Score = 44.6 bits (104), Expect = 8e-05
 Identities = 30/133 (22%), Positives = 54/133 (40%), Gaps = 2/133 (1%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
            +++    ++VG +      + +  + K  G VK  +  +    G  +GF F EFES E 
Sbjct: 110 KSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEES 169

Query: 183 VLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQ 242
             +A+  LN   ++G+   L+V +A      R       +    K+     A   ++S  
Sbjct: 170 AEKAIEELNGKELEGRP--LRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDN 227

Query: 243 SVEKNEPTKSPEN 255
               N P K+ E 
Sbjct: 228 LYVGNLPLKTAEE 240

Length = 306

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 45.4 bits (107), Expect = 8e-05
 Identities = 66/350 (18%), Positives = 124/350 (35%), Gaps = 58/350 (16%)

Query: 217  DKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVT 276
            +   E+  + ++  +  +   +ES   V K +  K+ E+ KD +    E     + G+  
Sbjct: 3910 EPNEEDLLETEQKSNEQSAANNES-DLVSKEDDNKALED-KDRQEKEDEEEMSDDVGI-D 3966

Query: 277  EEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMI 336
            +E +   QE   +               PPP     D     + +L  K  D   D D+ 
Sbjct: 3967 DEIQPDIQENNSQ---------------PPPENEDLDLP--EDLKLDEKEGDVSKDSDLE 4009

Query: 337  RNDIA---EDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDR 393
              D+    E+K + +   D    D D  E ++     + +   +D   DL  + E+    
Sbjct: 4010 DMDMEAADENKEEADAEKDEPMQDEDPLEENNT----LDEDIQQDDFSDLAEDDEKM--- 4062

Query: 394  YEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRK 453
                                EE  +E E   +D    + E E+    E +      +   
Sbjct: 4063 ---------------NEDGFEENVQENEESTEDGVKSDEELEQGEVPEDQAIDNHPKMDA 4107

Query: 454  KEILYDEEEDEDDSRKRWRRSVLEEKRRKRIR-------EKEEDLADEVREEEEIAVAKR 506
            K      E DE+++ K       E      +R       E E+   D    +E ++ A R
Sbjct: 4108 KSTFASAEADEENTDKGIVGENEELGEEDGVRGNGTADGEFEQVQEDTSTPKEAMSEADR 4167

Query: 507  RAEE--EQLQQ-QQRDALKLLSDNAVNGSLAEESAVESKGMDVEHDYHDD 553
            + +   + L++ QQ + +    D   + S A +   +S+ M V+ D  +D
Sbjct: 4168 QYQSLGDHLREWQQANRIHEWEDLTESQSQAFD---DSEFMHVKEDEEED 4214

Length = 4600

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 45.1 bits (107), Expect = 9e-05
 Identities = 35/155 (22%), Positives = 66/155 (42%), Gaps = 11/155 (7%)

Query: 373 DRRGRDKERDLKREKEREIDRYEREAERERVRKEREQ----RRKIEEAEREYERCLKDWE 428
           +   R+ E   +  +       E E   E+++   E+      K+E+ E E E   ++  
Sbjct: 294 EELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKN 353

Query: 429 YR-----EREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKR 483
                  ER +E E + E E EKE E+  ++    +E   E         S   E+ ++ 
Sbjct: 354 ELAKLLEERLKELEERLE-ELEKELEKALERLKQLEEAIQELKEELA-ELSAALEEIQEE 411

Query: 484 IREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQR 518
           + E E++L +  RE EE+    ++ EE+  Q + +
Sbjct: 412 LEELEKELEELERELEELEEEIKKLEEQINQLESK 446

Length = 908

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 44.1 bits (105), Expect = 1e-04
 Identities = 39/152 (25%), Positives = 67/152 (44%), Gaps = 17/152 (11%)

Query: 377 RDKERDLKREKEREIDRYEREAERERVR----KEREQRRKIEEAEREYERCLKDWEYRER 432
            ++ + L  E+ERE  R E   E   V     +ERE+RR+ E  ER  ER        + 
Sbjct: 49  EERLKALAEEEERERKRKEERREGRAVLQEQIEEREKRRQEEYEERLQER-------EQM 101

Query: 433 EREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKR------IRE 486
           +   ER  E+++ + +E++ K++ L +E ++ ++ R   +    E +R +        RE
Sbjct: 102 DEIIERIQEEDEAEAQEKREKQKKLREEIDEFNEERIERKEEEKEREREEELKILEYQRE 161

Query: 487 KEEDLADEVREEEEIAVAKRRAEEEQLQQQQR 518
           K E   +   E  E    K R       QQ+ 
Sbjct: 162 KAEREEEREAERRERKEEKEREVARLRAQQEE 193

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 45.1 bits (107), Expect = 1e-04
 Identities = 39/155 (25%), Positives = 70/155 (45%), Gaps = 5/155 (3%)

Query: 373 DRRGRDKERDLKREKEREIDRYEREAE-RERVRKEREQRRKIEEAEREYERCLKDWEYR- 430
             R  + E +L+  +E      E   E  E+ +  +E+  ++EE   E ER L   E   
Sbjct: 757 QERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALEREL 816

Query: 431 EREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLE--EKRRKRIREKE 488
           E   ++  + E+E E+  E   + E   DE E+E +  ++    + E  E+      E E
Sbjct: 817 ESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELE 876

Query: 489 EDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKL 523
           ++L  E+ EE+E    + R  E +L + + +  KL
Sbjct: 877 DELK-ELEEEKEELEEELRELESELAELKEEIEKL 910

Length = 1163

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 44.8 bits (106), Expect = 1e-04
 Identities = 44/156 (28%), Positives = 69/156 (44%), Gaps = 7/156 (4%)

Query: 379 KERDLKREKEREIDRYEREAER--ERVRKEREQRRKIEEAEREYERCLKDWEYREREREK 436
           +ER  + E+E+E  R E    R  E    E E  +  EE  RE ER L++ E  + ER +
Sbjct: 238 EERLAELEEEKE--RLEELKARLLEIESLELEALKIREEELRELERLLEELE-EKIERLE 294

Query: 437 ERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEE--DLADE 494
           E + E E+ +E     +  +   EE  E       R   LEEK  K   E EE  +  +E
Sbjct: 295 ELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKNE 354

Query: 495 VREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVN 530
           + +  E  + +     E+L+++   AL+ L      
Sbjct: 355 LAKLLEERLKELEERLEELEKELEKALERLKQLEEA 390

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 44.8 bits (106), Expect = 1e-04
 Identities = 29/171 (16%), Positives = 65/171 (38%), Gaps = 12/171 (7%)

Query: 375 RGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEE-AEREYERCLKDWEYRERE 433
           +  +  +++ +E + +I+  E +        E       EE  E +    +++ +  E  
Sbjct: 171 KLSELLKEVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEEQEEEEL 230

Query: 434 REKERQYE---KEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEED 490
            ++    E    E E+E+ER  + +    E E  +    +         R + +RE E  
Sbjct: 231 EQEIEALEERLAELEEEKERLEELKARLLEIESLELEALK--------IREEELRELERL 282

Query: 491 LADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVES 541
           L +   + E +   +R  EE + + +   AL    +  +    + E  +E 
Sbjct: 283 LEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEK 333

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 44.8 bits (106), Expect = 1e-04
 Identities = 36/149 (24%), Positives = 60/149 (40%), Gaps = 9/149 (6%)

Query: 386 EKEREIDRYEREAE--RERVRKEREQRRKIEEAEREYERCLKDWEYREREREKE--RQYE 441
           E ERE++  E E +   E++ +   +   I E     E+C    +    E EKE    YE
Sbjct: 421 ELERELEELEEEIKKLEEQINQLESKELMIAELAGAGEKCPVCGQELPEEHEKELLELYE 480

Query: 442 KEKEKERERKRKKEILYDEEEDEDDSRKRWR-----RSVLEEKRRKRIREKEEDLADEVR 496
            E E+  E   +++   +  E+ ++  K  R        L E       E EE L     
Sbjct: 481 LELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALKEELEEKLEKLEN 540

Query: 497 EEEEIAVAKRRAEEEQLQQQQRDALKLLS 525
             EE+   K + + +QL+++ R     L 
Sbjct: 541 LLEELEELKEKLQLQQLKEELRQLEDRLQ 569

Length = 908

>gnl|CDD|224308 COG1390, NtpE, Archaeal/vacuolar-type H+-ATPase subunit E [Energy production and conversion]

 Score = 43.1 bits (102), Expect = 1e-04
 Identities = 39/182 (21%), Positives = 74/182 (40%), Gaps = 8/182 (4%)

Query: 377 RDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREK 436
               + + RE E E +    EA  E  + + E +R+ EEA  E  R  +    RER+R  
Sbjct: 5   EKLIKKILREAEEEAEEILEEAREEAEKIKEEAKREAEEAIEEILRKAEKEAERERQRII 64

Query: 437 ERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVR 496
                + + K  E   K+EIL    E   ++ +   R++  +   + ++E   +  +++ 
Sbjct: 65  SSALLEARRKLLE--AKEEIL----ESVFEAVEEKLRNIASDPEYESLQELLIEALEKLL 118

Query: 497 EEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEHDYHDDSIR 556
             E +     + +   L +Q    LK+  +      +     VES+   +  D   +SI 
Sbjct: 119 GGELVVYLNEKDKA--LVEQILRELKIGVELGEGIDIIGGVVVESRDGKIRLDNTFESIL 176

Query: 557 EN 558
           E 
Sbjct: 177 ER 178

Length = 194

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 44.1 bits (104), Expect = 1e-04
 Identities = 34/146 (23%), Positives = 71/146 (48%), Gaps = 7/146 (4%)

Query: 375 RGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRERER 434
             +++ER  K E++ E    +R AE+ R +KE EQR   E+A ++ E      +  ++  
Sbjct: 63  AKKEQERQKKLEQQAEEAEKQRAAEQAR-QKELEQRAAAEKAAKQAE------QAAKQAE 115

Query: 435 EKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADE 494
           EK++Q E+ K K+    + K     E++ +++++K+       +   +  ++  E     
Sbjct: 116 EKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKA 175

Query: 495 VREEEEIAVAKRRAEEEQLQQQQRDA 520
             E +  A AK +A+ E+ + +   A
Sbjct: 176 EAEAKAKAEAKAKAKAEEAKAKAEAA 201

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|218636 pfam05557, MAD, Mitotic checkpoint protein

 Score = 44.5 bits (105), Expect = 1e-04
 Identities = 36/165 (21%), Positives = 66/165 (40%), Gaps = 16/165 (9%)

Query: 388 EREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKE 447
           E E+ + E E +R ++  ER+     E  ERE +R L+     +   E E++ E E  + 
Sbjct: 74  ENELMQKELEHKRAQIELERKASTLAENYERELDRNLELEVRLKALEELEKKAENEAAEA 133

Query: 448 RERKRKKEILYDEEE-----DEDDSRKRWRRSV------LEEKRRKRIREK-----EEDL 491
            E  +  +   D E      +++D  K  + S+      L E + +           E  
Sbjct: 134 EEEAKLLKDKLDAESLKLQNEKEDQLKEAKESISRIKNDLSEMQCRAQNADTELKLLESE 193

Query: 492 ADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEE 536
            +E+RE+ E    +    E++LQ    +      ++     L EE
Sbjct: 194 LEELREQLEECQKELAEAEKKLQSLTSEQASSADNSVKIKHLEEE 238

This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated. Length = 722

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 43.4 bits (103), Expect = 2e-04
 Identities = 36/152 (23%), Positives = 73/152 (48%), Gaps = 10/152 (6%)

Query: 379 KERDLKREKEREIDRYEREAERERVRKERE----QRRKIEEAEREY-ERCLKDWEYRERE 433
           + R+ K EKERE+ R   + E     +E           EE ER+  ++  ++ E R R+
Sbjct: 172 ERRERKEEKEREVARLRAQQEEAEDEREELDELRADLYQEEYERKERQKEKEEAEKRRRQ 231

Query: 434 REKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLAD 493
           +++ ++  +E+ +E+E + ++E   +E E E    K+     LE++  ++ R K  +   
Sbjct: 232 KQELQRAREEQIEEKEERLQEERAEEEAERERMLEKQAEDEELEQENAEKRRMKRLEHRR 291

Query: 494 EVRE-----EEEIAVAKRRAEEEQLQQQQRDA 520
           E+ +     EE  A  +    EE  + ++ +A
Sbjct: 292 ELEQQIEEKEERRAAEREEELEEGERLREEEA 323

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 44.3 bits (105), Expect = 2e-04
 Identities = 42/215 (19%), Positives = 80/215 (37%), Gaps = 23/215 (10%)

Query: 377 RDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREK 436
             +      + E E+   + E  R       E RR++EE ER+ E   ++    E E E+
Sbjct: 676 LAELEAQLEKLEEELKSLKNEL-RSLEDLLEELRRQLEELERQLEELKRELAALEEELEQ 734

Query: 437 ERQYEKEKEKERERKRKKEILYDEE-----------EDEDDSRK------RWRRSVLEEK 479
            +   +E E+E E   ++     E            E+     K        +R  L+E+
Sbjct: 735 LQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEE 794

Query: 480 R---RKRIREKEEDLADEVREEEEIAVAKRRAEEE--QLQQQQRDALKLLSDNAVNGSLA 534
                + + E E  L    RE E +   + R E+E  +L+++  +  + L +        
Sbjct: 795 LEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEEL 854

Query: 535 EESAVESKGMDVEHDYHDDSIRENHMEIRLHKMVM 569
           E+   E K    E +   + + +   E+   K  +
Sbjct: 855 EKELEELKEELEELEAEKEELEDELKELEEEKEEL 889

Length = 1163

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 44.4 bits (105), Expect = 2e-04
 Identities = 37/173 (21%), Positives = 73/173 (42%), Gaps = 25/173 (14%)

Query: 379 KERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKER 438
            E  LK E E ++++ E   E     KE+ Q ++++E  R+ E  L++ +    E    R
Sbjct: 523 LEEALKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLR 582

Query: 439 QYEKEKEKERERKR----------KKEILYDEEEDEDDSRKRWR-----RSVLEEKRRKR 483
             ++E E+ RER +          ++    +E     +  +           LE +  K 
Sbjct: 583 TRKEELEELRERLKELKKKLKELEERLSQLEELLQSLELSEAENELEEAEEELESELEKL 642

Query: 484 ---------IREKEEDLADEVRE-EEEIAVAKRRAEEEQLQQQQRDALKLLSD 526
                    ++   E+L ++V E E EI    +R E E+  +++ + L+ L +
Sbjct: 643 NLQAELEELLQAALEELEEKVEELEAEIRRELQRIENEEQLEEKLEELEQLEE 695

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 44.0 bits (104), Expect = 2e-04
 Identities = 36/160 (22%), Positives = 73/160 (45%), Gaps = 13/160 (8%)

Query: 370 RVHDRRGRDKERDLKREKEREIDRYER-EAERERVRKEREQRRKIEEAEREYERCLKDWE 428
            + ++    + ++  R+ E  +   +    E   +R  +E+  ++ E  +E ++ LK+ E
Sbjct: 547 ELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEELRERLKELKKKLKELE 606

Query: 429 YREREREKERQYEKEKEKERERKRKKEILYDEEE--DEDDSRKRWRRSVLEEKRRKRIRE 486
            R  + E+  Q  +  E E E +  +E L  E E  +     +   ++ LEE     + E
Sbjct: 607 ERLSQLEELLQSLELSEAENELEEAEEELESELEKLNLQAELEELLQAALEE-----LEE 661

Query: 487 KEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSD 526
           K E+L  E+R E +     R   EEQL+++  +  +L  +
Sbjct: 662 KVEELEAEIRRELQ-----RIENEEQLEEKLEELEQLEEE 696

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 44.0 bits (104), Expect = 2e-04
 Identities = 40/165 (24%), Positives = 75/165 (45%), Gaps = 5/165 (3%)

Query: 367 DRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKD 426
           +  R  +R   + E  ++R +E E +  E E E E +R   E+  ++ E  +  E  L+ 
Sbjct: 274 EELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEK 333

Query: 427 WE--YREREREKERQYEKEKEKERE-RKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKR 483
            E    + E E E   E++ E  +   +R KE+    EE E +  K   R    E+  + 
Sbjct: 334 LEEKLEKLESELEELAEEKNELAKLLEERLKELEERLEELEKELEKALERLKQLEEAIQE 393

Query: 484 IREKEEDLADEVRE--EEEIAVAKRRAEEEQLQQQQRDALKLLSD 526
           ++E+  +L+  + E  EE   + K   E E+  ++  + +K L +
Sbjct: 394 LKEELAELSAALEEIQEELEELEKELEELERELEELEEEIKKLEE 438

Length = 908

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 43.9 bits (104), Expect = 2e-04
 Identities = 42/178 (23%), Positives = 69/178 (38%), Gaps = 19/178 (10%)

Query: 382 DLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYE 441
           D+  E ER++   ER+AE+       E+ ++++   RE E  L      E   E E   E
Sbjct: 193 DILNELERQLKSLERQAEKA------ERYKELKAELRELELALLVLRLEELREELEELQE 246

Query: 442 KEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKR----------RKRIREKEEDL 491
           + KE E E +     L  +E +E     R   S LEE+              I   E+  
Sbjct: 247 ELKEAEEELEELTAEL--QELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQK 304

Query: 492 ADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEHD 549
              +RE       +    E QL++ +    +L  + A      EE   E + ++ E +
Sbjct: 305 Q-ILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELE 361

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 2/78 (2%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
            +YVG +      + +  +    G V S +       G  +GFGF E E+AE    A+  
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 190 LNKFNIDGQELMLKVDQA 207
           LN  +  G+   L V++A
Sbjct: 61  LNGTDFGGRT--LTVNEA 76

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|225177 COG2268, COG2268, Uncharacterized protein conserved in bacteria [Function unknown]

 Score = 44.1 bits (104), Expect = 2e-04
 Identities = 28/164 (17%), Positives = 60/164 (36%), Gaps = 14/164 (8%)

Query: 386 EKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREK----ERQYE 441
           E E E+  ++ E  RE  + E    + I+E + + E+ ++  +  E    +    ERQ E
Sbjct: 273 ETEAEVAAWKAETRREAEQAEILAEQAIQEEKAQAEQEVQHAKALEAREMRVGLIERQKE 332

Query: 442 -----KEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVR 496
                +E+       +++     +           +     E  R+    +  + A  V 
Sbjct: 333 TELEPQERSYFINAAQRQAQEEAKAAANIAEAIGAQAEAAVETARETEEAERAEQAALVA 392

Query: 497 -----EEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAE 535
                E+E++ +A R    +   + Q   +K  ++       AE
Sbjct: 393 AAEAAEQEQVEIAVRAEAAKAEAEAQAAEIKAEAEAIREKGKAE 436

Length = 548

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 7/73 (9%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSN---GTPKGFGFCEFESAEGVLRAL 187
           ++VG +      + +    K CGT+    R     +   G PKGF + EF     V  AL
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTIN---RITILCDKFTGQPKGFAYIEFLDKSSVENAL 58

Query: 188 RLLNKFNIDGQEL 200
            LLN+    G+++
Sbjct: 59  -LLNESEFRGRQI 70

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|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 43.9 bits (104), Expect = 2e-04
 Identities = 34/178 (19%), Positives = 72/178 (40%), Gaps = 21/178 (11%)

Query: 357 DHDRPETSSPDRSRVHDRRGRDKERDLKREKEREI--DRYEREAERERVRKEREQRRKIE 414
           D +    +  +R+R   R  R++ R  +R+ +++    R  ++AE     + ++++++  
Sbjct: 616 DRNERRDTRDNRTRREGRENREENRRNRRQAQQQTAETRESQQAEVTEKARTQDEQQQAP 675

Query: 415 EAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRK---RW 471
             ER+          R R  EK +  ++ K    E +        E E E+  ++   R 
Sbjct: 676 RRERQ----------RRRNDEKRQAQQEAKALNVEEQSV-----QETEQEERVQQVQPRR 720

Query: 472 RRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAV 529
           ++  L +K R      EE +A  V EE   A    +       +  +  L +++  A 
Sbjct: 721 KQRQLNQKVRIEQSVAEEAVAPVV-EETVAAEPVVQEVPAPRTELVKVPLPVVAQTAP 777

Length = 1068

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

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 7/78 (8%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSN---GTPKGFGFCEFESAEGVLR 185
           TK++VG +      D +       G ++    A   ++   G  +G+GF  F+  E   R
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIE---EAVVITDRQTGKSRGYGFVTFKDKESAER 57

Query: 186 ALRLLNKFNIDGQELMLK 203
           A +  N   IDG++  + 
Sbjct: 58  ACKDPNP-IIDGRKANVN 74

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|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional

 Score = 44.0 bits (103), Expect = 2e-04
 Identities = 30/102 (29%), Positives = 52/102 (50%), Gaps = 4/102 (3%)

Query: 360 RPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERV---RKEREQRRKIEEA 416
           R +    +R+R+       K  ++K  +++ I+R ERE ERER+   R ER +R ++E  
Sbjct: 429 RVDKDHAERARIEKENAHRKALEMKILEKKRIERLERE-ERERLERERMERIERERLERE 487

Query: 417 EREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILY 458
             E ER  +D   R+R    ER+     E++R  K ++   +
Sbjct: 488 RLERERLERDRLERDRLDRLERERVDRLERDRLEKARRNSYF 529

Length = 1021

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 43.6 bits (102), Expect = 3e-04
 Identities = 57/295 (19%), Positives = 115/295 (38%), Gaps = 17/295 (5%)

Query: 218  KKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTE 277
            +K E  +K +E + A   K+ E+V+  E        E  KD E   K   +  N  +   
Sbjct: 1206 RKAEEERKAEEARKAEDAKKAEAVKKAE--------EAKKDAEEAKKAEEERNNEEIRKF 1257

Query: 278  EDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIR 337
            E+ +    A  +     EE  K + L     +  AD      +E   KA +     +  +
Sbjct: 1258 EEARMAHFARRQAAIKAEEARKADELKKAEEKKKADE--AKKAEEKKKADEAKKKAEEAK 1315

Query: 338  NDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYERE 397
                  K  +E      A+     E      +   +      E +   E++ E    ++E
Sbjct: 1316 KADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAE-AAEEKAEAAEKKKE 1374

Query: 398  AERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEIL 457
              +   +K    ++K EE ++  E   K  E +++  E ++    +K+ +  +K+ +E  
Sbjct: 1375 EAK---KKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEK- 1430

Query: 458  YDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQ 512
              ++ DE   +    +   E K++    +K E+   +  E ++   AK++AEE +
Sbjct: 1431 --KKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAK 1483

Length = 2084

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 43.0 bits (102), Expect = 3e-04
 Identities = 37/154 (24%), Positives = 72/154 (46%), Gaps = 23/154 (14%)

Query: 380 ERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQ 439
           ER+ +RE ER   + E+E E  R+R ++E   + E+   E +    D    E ER++ ++
Sbjct: 164 EREEEREAERRERKEEKEREVARLRAQQE---EAEDEREELDELRADLYQEEYERKERQK 220

Query: 440 YEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLA------D 493
            ++E EK   R+R+K+ L           +R R   +EEK  +   E+ E+ A      +
Sbjct: 221 EKEEAEK---RRRQKQEL-----------QRAREEQIEEKEERLQEERAEEEAERERMLE 266

Query: 494 EVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDN 527
           +  E+EE+          +  + +R+  + + + 
Sbjct: 267 KQAEDEELEQENAEKRRMKRLEHRRELEQQIEEK 300

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 43.9 bits (104), Expect = 3e-04
 Identities = 38/169 (22%), Positives = 69/169 (40%), Gaps = 17/169 (10%)

Query: 384 KREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKE 443
            + + +   + +R   R+  R++R +RR      R         E RE  R   RQ +++
Sbjct: 594 PKAEAKPERQQDRRKPRQNNRRDRNERRD-TRDNRTRRE---GRENREENRRNRRQAQQQ 649

Query: 444 KEKERERKRKKEILYDEEEDEDDSRKRW----RRSVLEEKRRKRIREK----EEDLADEV 495
             + RE ++ +       +DE     R     RR+  +EKR+ +   K    EE    E 
Sbjct: 650 TAETRESQQAEVTEKARTQDEQQQAPRRERQRRRN--DEKRQAQQEAKALNVEEQSVQET 707

Query: 496 REEEEIAVAKRRAEEEQLQQQQR---DALKLLSDNAVNGSLAEESAVES 541
            +EE +   + R ++ QL Q+ R      +      V  ++A E  V+ 
Sbjct: 708 EQEERVQQVQPRRKQRQLNQKVRIEQSVAEEAVAPVVEETVAAEPVVQE 756

Length = 1068

>gnl|CDD|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter subunit G; Reviewed

 Score = 42.0 bits (98), Expect = 3e-04
 Identities = 31/108 (28%), Positives = 58/108 (53%), Gaps = 4/108 (3%)

Query: 362 ETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYE 421
           +T  P   R+ D+    K+ D+K++K   I    R+ + E+ R+ERE+  +  E ER  E
Sbjct: 94  DTGVPLAIRIRDQLRSVKKDDIKKKKSLII----RQEQIEKARQEREELEERMEWERREE 149

Query: 422 RCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRK 469
           +  +  +  E+ERE+E Q  +E+  + E +  ++   + E D+D + K
Sbjct: 150 KIDEREDQEEQEREREEQTIEEQSDDSEHEIIEQDESETESDDDKTEK 197

Length = 197

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

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 3/77 (3%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKR---AQYPSNGTPKGFGFCEFESAEGVLRA 186
           ++++G +        +L +    G +K +        P  G P+G+ F  FE+ E   +A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 187 LRLLNKFNIDGQELMLK 203
           L+ LN     G++L+++
Sbjct: 61  LKSLNGKTALGKKLVVR 77

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

>gnl|CDD|236081 PRK07735, PRK07735, NADH dehydrogenase subunit C; Validated

 Score = 43.0 bits (101), Expect = 3e-04
 Identities = 32/133 (24%), Positives = 61/133 (45%)

Query: 378 DKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKE 437
           D E+DL+  K+    R + EA +  V K   +  K+EE  RE E+ L   +    E  K 
Sbjct: 2   DPEKDLEDLKKEAARRAKEEARKRLVAKHGAEISKLEEENREKEKALPKNDDMTIEEAKR 61

Query: 438 RQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVRE 497
           R     K K     ++K    +E  +E+ ++ + + +   + +   + +++ +  +EV E
Sbjct: 62  RAAAAAKAKAAALAKQKREGTEEVTEEEKAKAKAKAAAAAKAKAAALAKQKREGTEEVTE 121

Query: 498 EEEIAVAKRRAEE 510
           EE+ A   + A  
Sbjct: 122 EEKAAAKAKAAAA 134

Length = 430

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 43.2 bits (101), Expect = 4e-04
 Identities = 33/143 (23%), Positives = 65/143 (45%), Gaps = 4/143 (2%)

Query: 374  RRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAER-EYERCLKDWEYRER 432
            R+     +  +  K  E  + E   + E V+K  E ++  EEA++ E ER  ++    E 
Sbjct: 1200 RKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEE 1259

Query: 433  EREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRW--RRSVLEEKRRKRIREKEED 490
             R       +   K  E ++  E+   EE+ + D  K+   ++   E K++    +K ++
Sbjct: 1260 ARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADE 1319

Query: 491  LADEVREEEEIA-VAKRRAEEEQ 512
               +  E ++ A  AK++AEE +
Sbjct: 1320 AKKKAEEAKKKADAAKKKAEEAK 1342

Length = 2084

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 43.2 bits (102), Expect = 4e-04
 Identities = 30/145 (20%), Positives = 64/145 (44%), Gaps = 2/145 (1%)

Query: 373 DRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRER 432
           ++R    ++   +E E E+   E + E +   + +  + ++   E   E   +  E  ER
Sbjct: 658 NKRSSLAQKRELKELEEELAELEAQLE-KLEEELKSLKNELRSLEDLLEELRRQLEELER 716

Query: 433 EREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLA 492
           + E+ ++     E+E E+ + +    +EE +E +      +  LEE     +   EE LA
Sbjct: 717 QLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEE-ELESLEEALA 775

Query: 493 DEVREEEEIAVAKRRAEEEQLQQQQ 517
               E EE+   ++  +EE  + ++
Sbjct: 776 KLKEEIEELEEKRQALQEELEELEE 800

Length = 1163

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 43.1 bits (102), Expect = 4e-04
 Identities = 33/152 (21%), Positives = 65/152 (42%), Gaps = 7/152 (4%)

Query: 373 DRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRER 432
           +R+    E +L++  E   +  +R  E E++ +E  ++ K +  E E  R  +     E 
Sbjct: 243 ERQLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIK-DLGEEEQLRVKEKIGELEA 301

Query: 433 EREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKR------IRE 486
           E     +   EKE+E E   ++    + E D+  +        +EE+R++R        E
Sbjct: 302 EIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAE 361

Query: 487 KEEDLADEVREEEEIAVAKRRAEEEQLQQQQR 518
            +E+L D   E EE+        +E    +++
Sbjct: 362 LKEELEDLRAELEEVDKEFAETRDELKDYREK 393

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

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

 Score = 38.9 bits (91), Expect = 4e-04
 Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 2/52 (3%)

Query: 153 GTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV 204
           G VK+ K  +    G   GFGF +++SAE   RA+R LN   +  Q   +KV
Sbjct: 25  GPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQL--QNKRIKV 74

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|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 40.6 bits (95), Expect = 4e-04
 Identities = 31/115 (26%), Positives = 52/115 (45%), Gaps = 7/115 (6%)

Query: 355 ASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIE 414
                R    S  R R   R  R++ R+  R +ER+  R  R     R R+ R  RR   
Sbjct: 2   GRSRSRSPRRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRH-R 60

Query: 415 EAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRK 469
              R   R       R+R+RE+++   + K++ER++  K+E L  + ++E +  K
Sbjct: 61  SRSRSPSR------RRDRKRERDKDAREPKKRERQKLIKEEDLEGKSDEEVEMMK 109

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

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

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 5/58 (8%)

Query: 152 CGTVKSWKRAQYPSNGTPK-----GFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV 204
           CG V+S   A+      P      G+GF EF+S E   +AL+ L    +DG  L LK+
Sbjct: 24  CGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKALKRLQGTVLDGHALELKL 81

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

 Score = 38.2 bits (89), Expect = 6e-04
 Identities = 21/71 (29%), Positives = 31/71 (43%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
           +VYVG I+     D +       G +KS   +  P     KGF F E+E  E    AL  
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 190 LNKFNIDGQEL 200
           +N   + G+ +
Sbjct: 62  MNGVMLGGRNI 72

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|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division and chromosome partitioning]

 Score = 42.0 bits (99), Expect = 7e-04
 Identities = 28/171 (16%), Positives = 64/171 (37%), Gaps = 22/171 (12%)

Query: 373 DRRGRDKERDLKR-EKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRE 431
           D++ +  ++++   EK+    + +R    ++++    +   +E    E    LK  + R+
Sbjct: 37  DKQLKQIQKEIAALEKKIREQQDQRAKLEKQLKSLETEIASLEAQLIETADDLK--KLRK 94

Query: 432 REREKERQYEKEKEKERERKRKKEILYD------------EEEDEDDSRKRWRRSVLEEK 479
           +  +   +    + +ERE++R+                       +D+++  R ++    
Sbjct: 95  QIADLNARLNALEVQEREQRRRLAEQLAALQRSGRNPPPALLVSPEDAQRSVRLAIYYGA 154

Query: 480 ----RRKRIREKEEDLADEVREEEEIAVAK---RRAEEEQLQQQQRDALKL 523
               R +RI   +  L        EIA  +        EQ  QQ + A  L
Sbjct: 155 LNPARAERIDALKATLKQLAAVRAEIAAEQAELTTLLSEQRAQQAKLAQLL 205

Length = 420

>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584)

 Score = 42.4 bits (100), Expect = 8e-04
 Identities = 33/173 (19%), Positives = 66/173 (38%), Gaps = 19/173 (10%)

Query: 357 DHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRR-KIEE 415
             D       D  R ++R     ++ +K + ER++++         +R+E+++++  IEE
Sbjct: 367 RLDALTGKHQDVQRKYERL----KQKIKEQLERDLEK--NNERLAAIREEKDRQKAAIEE 420

Query: 416 AEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDED----DSRKRW 471
             +  E  L+      +    E +YE E    R ++R        EE E     D     
Sbjct: 421 DLQALESQLRQQLEAGKLEFNEEEYELELRLGRLKQRLDSATATPEELEQLEINDEALEK 480

Query: 472 RRSVLEEKRRKRIREKEE--------DLADEVREEEEIAVAKRRAEEEQLQQQ 516
            +   E+      + + E        D A E  +  E  + + R   ++L+ Q
Sbjct: 481 AQEEQEQAEANVEQLQSELRQLRKRRDEALEALQRAERRLLQLRQALDELELQ 533

This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. This family contains a P-loop motif suggesting it is a nucleotide binding protein. It may be involved in replication. Length = 1198

>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 = 38.0 bits (89), Expect = 8e-04
 Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 2/81 (2%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
            K++V  ++       + ++    G V+     + P  G  +GFGF  FES E    A+R
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 189 LLNKFNIDGQELMLKVDQATR 209
            LN   ++G+  ++KV++A R
Sbjct: 62  DLNGKELEGR--VIKVEKAKR 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|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 42.1 bits (98), Expect = 9e-04
 Identities = 44/191 (23%), Positives = 83/191 (43%), Gaps = 30/191 (15%)

Query: 374  RRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIE----------------EAE 417
            R+  D +R     K  +  + E   + E  +K    R+  E                EA 
Sbjct: 1146 RKAEDAKRVEIARKAEDARKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKAEAA 1205

Query: 418  REYERCLKDWEYREREREKE----RQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRR 473
            R+ E   K  E R+ E  K+    ++ E+ K+   E K+ +E    E  +E+  +    R
Sbjct: 1206 RKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEE----ERNNEEIRKFEEAR 1261

Query: 474  SVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQR--DALKLLSDNAVNG 531
                 +R+  I+ +E   ADE+++ EE    K++A+E +  ++++  D  K  ++ A   
Sbjct: 1262 MAHFARRQAAIKAEEARKADELKKAEE----KKKADEAKKAEEKKKADEAKKKAEEAKKA 1317

Query: 532  SLAEESAVESK 542
              A++ A E+K
Sbjct: 1318 DEAKKKAEEAK 1328

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 41.3 bits (96), Expect = 0.001
 Identities = 35/175 (20%), Positives = 77/175 (44%), Gaps = 14/175 (8%)

Query: 362  ETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYE 421
            E    D ++  + + +  E   K E+ ++ D  +++AE E  +K    ++K EEA++   
Sbjct: 1288 EKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAE-EAKKKADAAKKKAEEAKK--- 1343

Query: 422  RCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRR 481
                    +        + E  +EK    ++KKE    E + + D+ K+      +    
Sbjct: 1344 ---AAEAAKAEAEAAADEAEAAEEKAEAAEKKKE----EAKKKADAAKKKAEEKKKADEA 1396

Query: 482  KRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEE 536
            K+  E+++  ADE+++      AK++A+E + + +++         A     A+E
Sbjct: 1397 KKKAEEDKKKADELKKAAA---AKKKADEAKKKAEEKKKADEAKKKAEEAKKADE 1448

Length = 2084

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

 Score = 41.0 bits (96), Expect = 0.001
 Identities = 23/97 (23%), Positives = 36/97 (37%), Gaps = 6/97 (6%)

Query: 429 YREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKE 488
           YR+RER + R   +  +K RER R++         +   R+R R      + R R R   
Sbjct: 2   YRDRERGRLRNDTRRSDKGRERSRRR-----SRSRDRSRRRRDRDYYRGRRGRSRSRSPN 56

Query: 489 E-DLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLL 524
                   R          R  +E L + +RD   + 
Sbjct: 57  RYYRPRGDRSYRRDDRRSGRNTKEPLTEAERDDRTVF 93

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|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 41.9 bits (98), Expect = 0.001
 Identities = 38/195 (19%), Positives = 81/195 (41%), Gaps = 4/195 (2%)

Query: 383 LKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEK 442
                +   +R +   E  R  +E  +  K E  + E        E +E E+EK+ Q E+
Sbjct: 229 YLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEE 288

Query: 443 EKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIA 502
            K   +E +  K  L   E  + D  ++ + S  E K+ ++  +KE++  +E+ +E +  
Sbjct: 289 LKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKEL 348

Query: 503 VAKR----RAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEHDYHDDSIREN 558
             KR      EE+  + Q++         A     +E  +  +K  + E +  ++  +E 
Sbjct: 349 EIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELELKNEEEKEA 408

Query: 559 HMEIRLHKMVMGMNQ 573
            + + L +    + +
Sbjct: 409 KLLLELSEQEEDLLK 423

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional

 Score = 41.2 bits (97), Expect = 0.001
 Identities = 37/166 (22%), Positives = 71/166 (42%), Gaps = 17/166 (10%)

Query: 393 RYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKR 452
           R  +EAER     ++E   K+E A  E +  L     ++R+  +  + E ++E+ER   +
Sbjct: 30  RLAKEAERILQEAQKEAEEKLEAALLEAKELLLRERNQQRQEARREREELQREEER-LVQ 88

Query: 453 KKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQ 512
           K+E L    E  D+   +       E+R K +  +E +L +  ++ +           EQ
Sbjct: 89  KEEQLDARAEKLDNLENQ------LEEREKALSARELELEELEKQLDNELYRVAGLTPEQ 142

Query: 513 LQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEHDYHDDSIREN 558
            ++       LL    ++  L EE A   K +  E +   ++ R+ 
Sbjct: 143 ARKL------LLKL--LDAELEEEKAQRVKKI--EEEADLEAERKA 178

Length = 508

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 40.1 bits (94), Expect = 0.001
 Identities = 33/105 (31%), Positives = 57/105 (54%), Gaps = 11/105 (10%)

Query: 380 ERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQ 439
            +   + +E++  R +REAE E    ERE+R+K+EE +RE ER  ++    ERE++KE +
Sbjct: 5   AKKRAKLEEKQARRQQREAEEE----EREERKKLEE-KREGERKEEEELEEEREKKKEEE 59

Query: 440 YEKEKEKERER------KRKKEILYDEEEDEDDSRKRWRRSVLEE 478
             KE+E++  +      K K   + +EE  +  S       +LE+
Sbjct: 60  ERKEREEQARKEQEEYEKLKSSFVVEEEGTDKLSADEESNELLED 104

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 41.6 bits (98), Expect = 0.001
 Identities = 37/127 (29%), Positives = 63/127 (49%), Gaps = 7/127 (5%)

Query: 378 DKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKE 437
              +D++R K   I  Y       +V++E   R K E  E E  R +    Y +R ++ E
Sbjct: 372 GIWKDVERIKALVIRGYPLAEALSKVKEEERPREK-EGTEEEERREITV--YEKRIKKLE 428

Query: 438 RQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKR-IREKE---EDLAD 493
              E+ +E+  E KR+ E L  E E  +   +R+RR V ++ R+ R IR ++   E L  
Sbjct: 429 ETVERLEEENSELKRELEELKREIEKLESELERFRREVRDKVRKDREIRARDRRIERLEK 488

Query: 494 EVREEEE 500
           E+ E+++
Sbjct: 489 ELEEKKK 495

Length = 652

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 41.3 bits (97), Expect = 0.001
 Identities = 32/150 (21%), Positives = 68/150 (45%), Gaps = 11/150 (7%)

Query: 391 IDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRER--EREKERQYEKEKEKER 448
           +++Y R+ ++++  K  E++RK +E ++  E   K    +ER  + EKER   +E++K+ 
Sbjct: 61  VEQYNRQQQQQKSAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQA 120

Query: 449 ERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRA 508
           E   K+  L  ++ +E         +      + +   + +  A   ++      AK++A
Sbjct: 121 EEAAKQAALKQKQAEE-------AAAKAAAAAKAKAEAEAKRAAAAAKKAAA--EAKKKA 171

Query: 509 EEEQLQQQQRDALKLLSDNAVNGSLAEESA 538
           E E  ++   +A K     A   + AE   
Sbjct: 172 EAEAAKKAAAEAKKKAEAEAAAKAAAEAKK 201

Length = 387

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 35/170 (20%), Positives = 76/170 (44%), Gaps = 13/170 (7%)

Query: 373 DRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRER 432
             +  +++R  K +++ E  + ++ AE+ER+++  ++R   +E +++ E      E  ++
Sbjct: 73  SAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAE------EAAKQ 126

Query: 433 EREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLA 492
              K++Q E+   K     + K       E E        +    E ++K   E  +  A
Sbjct: 127 AALKQKQAEEAAAKAAAAAKAK------AEAEAKRAAAAAKKAAAEAKKKAEAEAAKKAA 180

Query: 493 DEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESK 542
            E +++ E A A  +A  E  ++ + +A K  +  A   + AE  A  +K
Sbjct: 181 AEAKKKAE-AEAAAKAAAEAKKKAEAEAKKKAAAEAKKKAAAEAKAAAAK 229

Length = 387

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

 Score = 37.8 bits (88), Expect = 0.001
 Identities = 19/78 (24%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
            ++VG ++ + D +++ +  +  GTV   +       G  +GFG+ +FES E   +A+  
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 190 LNKFNIDGQELMLKVDQA 207
           ++   +DG+   + VD +
Sbjct: 61  MDGKELDGR--PINVDFS 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|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 41.4 bits (97), Expect = 0.001
 Identities = 29/126 (23%), Positives = 45/126 (35%), Gaps = 20/126 (15%)

Query: 428 EYREREREKERQYEKEKEKERERKRKKEI--------LYDEEEDEDDSRKRWRRSVLEEK 479
           +YRE+++EK     K       R R + I        L+ E  +   +R   +    E K
Sbjct: 293 QYREKQKEK-----KAFLWTLRRNRLRMIITPWRAPELHAENAEIKKTRTAEKN---EAK 344

Query: 480 -RRKRIREKE---EDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAE 535
            R+K I +K    E   +    +E  A   R        + ++  L   S N    S  E
Sbjct: 345 ARKKEIAQKRRAAEREINREARQERAAAMARARARRAAVKAKKKGLIDASPNEDTPSENE 404

Query: 536 ESAVES 541
           ES    
Sbjct: 405 ESKGSP 410

Length = 429

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 35/174 (20%), Positives = 66/174 (37%), Gaps = 1/174 (0%)

Query: 379 KERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKER 438
           + ++   E E EI       E      E  + R +EE + + E   ++ E RE   E+  
Sbjct: 292 ELKEEIEELEGEISLLRERLEELENELEELEER-LEELKEKIEALKEELEERETLLEELE 350

Query: 439 QYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREE 498
           Q   E E+ +E   +K     EE +E     R   + LE +  +   E EE   +    E
Sbjct: 351 QLLAELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLE 410

Query: 499 EEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEHDYHD 552
           E +     R E+ + + ++ +A        +     E   +E +  ++     +
Sbjct: 411 ERLERLSERLEDLKEELKELEAELEELQTELEELNEELEELEEQLEELRDRLKE 464

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 31/143 (21%), Positives = 63/143 (44%), Gaps = 8/143 (5%)

Query: 384 KREKEREIDRYEREAE--RERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYE 441
             E E+EI+  + E E  RE + + +E+  +++E   E E  +     R  E E E +  
Sbjct: 262 LEEAEKEIEELKSELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEEL 321

Query: 442 KEKEKERE-----RKRKKEILYDEEEDEDDSRKRWRRSV-LEEKRRKRIREKEEDLADEV 495
           +E+ +E +      K + E      E+ +        +    E++   + E+ E+L + +
Sbjct: 322 EERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEAL 381

Query: 496 REEEEIAVAKRRAEEEQLQQQQR 518
           REE     A+      +L++ +R
Sbjct: 382 REELAELEAELAEIRNELEELKR 404

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 40/188 (21%), Positives = 83/188 (44%), Gaps = 10/188 (5%)

Query: 348 ETTSDTKASDHDRPETSS--PDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRK 405
              ++ ++ +    E      +  R  +   R+     +  ++ +    E E E E + +
Sbjct: 692 SLKNELRSLEDLLEELRRQLEELERQLEELKRELAALEEELEQLQSRLEELEEELEELEE 751

Query: 406 EREQRR----KIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERK-RKKEILYDE 460
           E E+ +    ++EE     E  L   +    E E++RQ  +E+ +E E +  + E   D 
Sbjct: 752 ELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDA 811

Query: 461 EEDEDDSRKRWRRSVLEE--KRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQR 518
            E E +S ++ R  + +E  +  + I E EE L DE+ EE E    +    +E+L++ + 
Sbjct: 812 LERELESLEQRRERLEQEIEELEEEIEELEEKL-DELEEELEELEKELEELKEELEELEA 870

Query: 519 DALKLLSD 526
           +  +L  +
Sbjct: 871 EKEELEDE 878

Length = 1163

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 29/174 (16%), Positives = 68/174 (39%), Gaps = 10/174 (5%)

Query: 381 RDLKREKEREIDRYERE-----AERERVRKE-REQRRKIEEAEREYERCLKDWEYRERER 434
           R    E E EI+  ++E      E  R+ ++ +  R ++   ER+ E    + +  E E 
Sbjct: 273 RLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEE--LEAQLEELES 330

Query: 435 EKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSV-LEEKRRKRIREKEEDLAD 493
           + +   E+  E E + +  KE L   E + ++            E+  +++      +A 
Sbjct: 331 KLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQ 390

Query: 494 EVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVE 547
              +   +   +    E +L++ +    +L  +        EE+ ++    ++E
Sbjct: 391 LELQIASLN-NEIERLEARLERLEDRRERLQQEIEELLKKLEEAELKELQAELE 443

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional

 Score = 40.5 bits (94), Expect = 0.002
 Identities = 34/91 (37%), Positives = 49/91 (53%), Gaps = 4/91 (4%)

Query: 398 AERERVRKEREQRRKIEEAEREYERCLKDWEYRERER-EKERQYEKEKEK-ERERKRKKE 455
           AER R+ KE   R+ +E    E +R ++  E  ERER E+ER    E+E+ ERER  ++ 
Sbjct: 435 AERARIEKENAHRKALEMKILEKKR-IERLEREERERLERERMERIERERLERERLERER 493

Query: 456 ILYDE-EEDEDDSRKRWRRSVLEEKRRKRIR 485
           +  D  E D  D  +R R   LE  R ++ R
Sbjct: 494 LERDRLERDRLDRLERERVDRLERDRLEKAR 524

Length = 1021

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

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 16/39 (41%), Positives = 22/39 (56%)

Query: 165 SNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK 203
            NG PK F F  F+    V  A++LLN   + G+EL +K
Sbjct: 37  PNGKPKSFAFVTFKHEVSVPYAIQLLNGIRLFGRELRIK 75

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

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 49/199 (24%), Positives = 80/199 (40%), Gaps = 20/199 (10%)

Query: 330 DSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKER 389
           +++++ +R  IAE + + E  ++      +R E    +R  +    G D       E  R
Sbjct: 257 EAEIEDLRETIAETEREREELAEEVRDLRERLEELEEERDDLLAEAGLDDADAEAVEARR 316

Query: 390 EIDRYEREAERERVRKER-EQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKER 448
           E      E  R+R+ + R   +   EEAE   E      E  E  RE+  + E E E+ R
Sbjct: 317 EELEDRDEELRDRLEECRVAAQAHNEEAESLREDADDLEERAEELREEAAELESELEEAR 376

Query: 449 ERKRKKEILYDEEEDE-DDSRKRW------------RRSVLEEKRRKRIREKEEDLADEV 495
           E    +    +E E+E ++ R+R+                L E  R  +RE+E +L   +
Sbjct: 377 EAVEDRREEIEELEEEIEELRERFGDAPVDLGNAEDFLEELRE-ERDELREREAELEATL 435

Query: 496 REEEEIAVAKRRAEEEQLQ 514
           R   E     R  E E L 
Sbjct: 436 RTARE-----RVEEAEALL 449

Length = 880

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

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
           VYVG I   +  D + S    CG ++      +P  G  +G  F  F++ E   RAL  L
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALA-L 59

Query: 191 NKFNIDGQEL 200
           +  ++ G+ L
Sbjct: 60  DGEDMGGRFL 69

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|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 36/127 (28%), Positives = 69/127 (54%), Gaps = 14/127 (11%)

Query: 382 DLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDW-EYREREREKERQY 440
           ++ +E +R I+R E+  +R    +E      I+E E+E E  L++  E      E   + 
Sbjct: 169 EVIKEIKRRIERLEKFIKRTENIEEL-----IKEKEKELEEVLREINEISSELPELREEL 223

Query: 441 EK-EKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLE-----EKRRKRIREKEEDLADE 494
           EK EKE +   + K+EI  +E E E +S +  +R + E     E+R + ++++ E+L ++
Sbjct: 224 EKLEKEVKELEELKEEI--EELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEK 281

Query: 495 VREEEEI 501
           V+E +E+
Sbjct: 282 VKELKEL 288

Length = 880

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

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 2/75 (2%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
           +YVG ++     + +  +   CG +K           TP GF F E+ + E    A++ L
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 191 NKFNIDGQELMLKVD 205
           N   +D +   ++VD
Sbjct: 61  NGTKLDDRI--IRVD 73

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|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 40.0 bits (93), Expect = 0.003
 Identities = 23/144 (15%), Positives = 60/144 (41%), Gaps = 4/144 (2%)

Query: 380 ERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQ 439
             +LK  +++  ++ E E +    ++E E+ +     + +     ++   + +  E++ +
Sbjct: 736 NEELKLLEQKIKEKEEEEEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKLKVEEEKEE 795

Query: 440 YEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEE 499
             K +E+E     ++     E  +E+           E+ + + + E   +L +E + E+
Sbjct: 796 KLKAQEEELRALEEELKEEAELLEEEQLLI----EQEEKIKEEELEELALELKEEQKLEK 851

Query: 500 EIAVAKRRAEEEQLQQQQRDALKL 523
                  R EEE  +++    L L
Sbjct: 852 LAEEELERLEEEITKEELLQELLL 875

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 40.5 bits (95), Expect = 0.003
 Identities = 39/161 (24%), Positives = 67/161 (41%), Gaps = 14/161 (8%)

Query: 378 DKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAER---EYERCLKDWE-----Y 429
           +   DL    E E+   ++  E +  ++E E  ++IE  E    E E   +  E      
Sbjct: 199 EDIEDLLEALEEELKELKKLEEIQEEQEEEELEQEIEALEERLAELEEEKERLEELKARL 258

Query: 430 REREREKERQYEKEKEKERERKRKKEILYDEEED-EDDSRKRWRRSVLEEKRRKRIREKE 488
            E E  +    +  +E+ RE +R  E L ++ E  E+  R+        E  R  + E E
Sbjct: 259 LEIESLELEALKIREEELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELE 318

Query: 489 EDLADEVREEEEI-----AVAKRRAEEEQLQQQQRDALKLL 524
           E L      EE +      + K  +E E+L +++ +  KLL
Sbjct: 319 ELLEKLKSLEERLEKLEEKLEKLESELEELAEEKNELAKLL 359

Length = 908

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 39.4 bits (92), Expect = 0.003
 Identities = 29/164 (17%), Positives = 66/164 (40%), Gaps = 4/164 (2%)

Query: 366 PDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLK 425
            +R +  +++  + E+    E+ R+ +  +R A  +  ++  +  ++ EE +++ E    
Sbjct: 67  QERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAK- 125

Query: 426 DWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIR 485
               +  E + + + E EK+ + E K++ E     +   +  +K        E   K   
Sbjct: 126 --AKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAKA 183

Query: 486 EKEEDL-ADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNA 528
           E +    A+E + + E A AK  AE     + +  A        
Sbjct: 184 EAKAKAKAEEAKAKAEAAKAKAAAEAAAKAEAEAAAAAAAEAER 227

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 40.4 bits (95), Expect = 0.003
 Identities = 43/205 (20%), Positives = 71/205 (34%), Gaps = 22/205 (10%)

Query: 337 RNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRR-GRDKERDLKREKEREIDRYE 395
             ++  +  D E   +      +R E       R+      R+   +L  E+   I+   
Sbjct: 477 VEELEAELEDLEEEVEEVEERLERAEDLVEAEDRIERLEERREDLEELIAERRETIEEKR 536

Query: 396 REAERERVRKE------REQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERE 449
             AE  R R         E+R    EAE E E   ++      +         E ++  E
Sbjct: 537 ERAEELRERAAELEAEAEEKREAAAEAEEEAEEAREEVAELNSKLA-------ELKERIE 589

Query: 450 RKRKKEILYDEEEDEDD--SRKRWRRSVLEEK---RRKRIREKEE---DLADEVREEEEI 501
              +   L     D +D   R R +R  L E    RR+R+ EK E   +L  E  E    
Sbjct: 590 SLERIRTLLAAIADAEDEIERLREKREALAELNDERRERLAEKRERKRELEAEFDEARIE 649

Query: 502 AVAKRRAEEEQLQQQQRDALKLLSD 526
              + +   E+  +Q  + L  L +
Sbjct: 650 EAREDKERAEEYLEQVEEKLDELRE 674

Length = 880

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 40.0 bits (94), Expect = 0.003
 Identities = 28/138 (20%), Positives = 59/138 (42%), Gaps = 7/138 (5%)

Query: 374 RRGRDKERDLKREKEREIDRYEREAE-RERVRKEREQRRKIEEAEREYERCLKDWEYRER 432
           +     E   ++ +E+  +  ER  E ++ + +  E+ ++++E + + E  +K  E+ E 
Sbjct: 245 KELESLEGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEKAEEYIKLSEFYEE 304

Query: 433 EREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLA 492
             ++ R+ EK   +  E     E    E E E + R         +K+ K + ++ E+L 
Sbjct: 305 YLDELREIEKRLSRLEEEINGIEERIKELE-EKEERLEEL-----KKKLKELEKRLEELE 358

Query: 493 DEVREEEEIAVAKRRAEE 510
           +     EE    K   E 
Sbjct: 359 ERHELYEEAKAKKEELER 376

Length = 880

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

 Score = 36.3 bits (84), Expect = 0.003
 Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 4/70 (5%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
           VY G    +     V  + + CG V+         + T +   F  FE+ E    A+  L
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIETL 57

Query: 191 NKFNIDGQEL 200
           N  ++DG  +
Sbjct: 58  NGASVDGNCI 67

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|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 40.4 bits (94), Expect = 0.003
 Identities = 24/52 (46%), Positives = 38/52 (73%), Gaps = 4/52 (7%)

Query: 402 RVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRK 453
           ++ K+RE+   +E+A+RE E+  K  E RERE+EKE++ E+E+E+E ER  K
Sbjct: 576 KLAKKREE--AVEKAKREAEQ--KAREEREREKEKEKEREREREREAERAAK 623

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|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 40.2 bits (95), Expect = 0.003
 Identities = 24/114 (21%), Positives = 54/114 (47%), Gaps = 12/114 (10%)

Query: 405 KEREQRRKIEEAE---REYERCLKDWEYREREREKERQYEKEKEKERERKRK-KEILYDE 460
            ERE  +K EEAE   +E E+  ++ E      +KE+  E+E +   E +++ ++ + + 
Sbjct: 528 LERELEQKAEEAEALLKEAEKLKEELE-----EKKEKLQEEEDKLLEEAEKEAQQAIKEA 582

Query: 461 EEDEDDSRKRWRRSVLEEK---RRKRIREKEEDLADEVREEEEIAVAKRRAEEE 511
           +++ D+  K  R+         +   + E  + L     ++E+    ++  +EE
Sbjct: 583 KKEADEIIKELRQLQKGGYASVKAHELIEARKRLNKANEKKEKKKKKQKEKQEE 636

Length = 782

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 14/40 (35%), Positives = 25/40 (62%)

Query: 166 NGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD 205
            G  +G G  EF+  E V +AL  +N++ + G++L++K D
Sbjct: 37  EGKSRGCGVVEFKDKESVQKALETMNRYELKGRKLVVKED 76

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|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 39.5 bits (93), Expect = 0.004
 Identities = 32/143 (22%), Positives = 72/143 (50%), Gaps = 3/143 (2%)

Query: 379 KERDLKREKEREID-RYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKE 437
           +E+   + +E+E + R +   E ER++   E+  +  + + E        + +  EREK 
Sbjct: 27  EEKKRIKAEEKEEERRIDEMMEEERLKALAEEEERERKRKEERREGRAVLQEQIEEREKR 86

Query: 438 RQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVRE 497
           RQ E+ +E+ +ER++  EI  +  ++ED++  + +R   ++ R +     EE +  +  E
Sbjct: 87  RQ-EEYEERLQEREQMDEI-IERIQEEDEAEAQEKREKQKKLREEIDEFNEERIERKEEE 144

Query: 498 EEEIAVAKRRAEEEQLQQQQRDA 520
           +E     + +  E Q ++ +R+ 
Sbjct: 145 KEREREEELKILEYQREKAEREE 167

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 39.5 bits (93), Expect = 0.004
 Identities = 36/144 (25%), Positives = 76/144 (52%), Gaps = 7/144 (4%)

Query: 379 KERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKER 438
            E   KREK++++     E   ER+ ++ E++ +  E E +     ++   RE ERE ER
Sbjct: 114 AEAQEKREKQKKLREEIDEFNEERIERKEEEKEREREEELKILEYQREKAEREEEREAER 173

Query: 439 QYEKEKEKERERKRKKEILYDEEEDEDDSRKR--WRRSVLEEKRRKRIREKEEDLADEVR 496
              +E+++E+ER     +   +EE ED+  +    R  + +E+  ++ R+KE++ A E R
Sbjct: 174 ---RERKEEKER-EVARLRAQQEEAEDEREELDELRADLYQEEYERKERQKEKEEA-EKR 228

Query: 497 EEEEIAVAKRRAEEEQLQQQQRDA 520
             ++  + + R E+ + ++++   
Sbjct: 229 RRQKQELQRAREEQIEEKEERLQE 252

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

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

 Score = 39.5 bits (92), Expect = 0.004
 Identities = 24/115 (20%), Positives = 45/115 (39%), Gaps = 7/115 (6%)

Query: 343 DKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKER---DLKREKEREIDRYEREAE 399
           ++         ++S+  R  +    R R   RR R++        R++ R   R  R   
Sbjct: 8   EREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLR 67

Query: 400 RERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKK 454
              VR+ R++ R+   + R  E+  +    R R+R    Q+ K+ +K      K 
Sbjct: 68  YSSVRRSRDRPRRRSRSVRSIEQHRR----RLRDRSPSNQWRKDDKKRSLWDIKP 118

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

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 40.0 bits (94), Expect = 0.004
 Identities = 38/168 (22%), Positives = 62/168 (36%), Gaps = 8/168 (4%)

Query: 376 GRDKERDLKR-EKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWE-YRERE 433
           G   + +    E+ REI+  E + E E   K  E  + + E  +E E   ++ E  R+  
Sbjct: 663 GGSAKTNSSILERRREIEELEEKIE-ELEEKIAELEKALAELRKELEELEEELEQLRKEL 721

Query: 434 REKERQY---EKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEED 490
            E  RQ     K+  +      + E    +   E  +        LEE+  +   E  E 
Sbjct: 722 EELSRQISALRKDLARLEAEVEQLEERIAQLSKEL-TELEAEIEELEERLEEAEEELAEA 780

Query: 491 LADEVREEEEIAVAKRRAEEEQLQQQ-QRDALKLLSDNAVNGSLAEES 537
            A+    E +I   K   +  +      R  L LL++ A N     ES
Sbjct: 781 EAEIEELEAQIEQLKEELKALREALDELRAELTLLNEEAANLRERLES 828

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 39.4 bits (92), Expect = 0.004
 Identities = 19/100 (19%), Positives = 36/100 (36%), Gaps = 6/100 (6%)

Query: 395 EREAERERVRKEREQRRKIEEAEREYER---CLKDW---EYREREREKERQYEKEKEKER 448
           E  AE+    +E+++ +K         R    +  W   E      E ++    EK + +
Sbjct: 285 EHHAEQRAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAENAEIKKTRTAEKNEAK 344

Query: 449 ERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKE 488
            RK++        E E +   R  R+    + R R    +
Sbjct: 345 ARKKEIAQKRRAAEREINREARQERAAAMARARARRAAVK 384

Length = 429

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

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 132 YVGKIAPT-ADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
           +V ++  T  D   +  +    G     + A  P NG P+GF F E+ +AE    A + L
Sbjct: 6   FVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAP-NGQPRGFAFVEYATAEDAEEAQQAL 64

Query: 191 NKFNIDGQEL 200
           N  ++ G  +
Sbjct: 65  NGHSLQGSPI 74

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|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain

 Score = 39.2 bits (92), Expect = 0.004
 Identities = 25/89 (28%), Positives = 48/89 (53%)

Query: 431 EREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEED 490
           E ER K    E E+E  RE+++++E + + +E       +     +E +R K + E+E  
Sbjct: 207 EAERAKAEAAEAEQELLREKQKEEEQMMEAQERSYQEHVKQLIEKMEAEREKLLAEQERM 266

Query: 491 LADEVREEEEIAVAKRRAEEEQLQQQQRD 519
           L  +++E+EE+     + E E LQ++ +D
Sbjct: 267 LEHKLQEQEELLKEGFKTEAESLQKEIQD 295

Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP. Length = 297

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

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 17/78 (21%), Positives = 34/78 (43%), Gaps = 3/78 (3%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL-RALRL 189
           ++VG ++P+     +       GTV   +  +    G  +GF + +  ++E  L +    
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 190 LNKFNIDGQELMLKVDQA 207
           LN     G    LK+++A
Sbjct: 62  LNGTKWKGSV--LKIEEA 77

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	577
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	99.91
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.91
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.85
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.85
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.81
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.81
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.81
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.8
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.78
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.78
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.77
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.76
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.75
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.75
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.74
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.73
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.72
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.71
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.67
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.64
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.63
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.63
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.61
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.6
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.6
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.59
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.57
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.56
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.56
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.55
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.52
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.51
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.5
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.5
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.49
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.48
KOG0122	270	consensus Translation initiation factor 3, subunit	99.47
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.42
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.42
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.39
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.37
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.37
PLN03120	260	nucleic acid binding protein; Provisional	99.37
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.36
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.36
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.35
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.34
PLN03213	759	repressor of silencing 3; Provisional	99.33
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.31
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.3
smart00362	72	RRM_2 RNA recognition motif.	99.29
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.28
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.28
PLN03121	243	nucleic acid binding protein; Provisional	99.28
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.27
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.23
smart00360	71	RRM RNA recognition motif.	99.23
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.23
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.23
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.22
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.21
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.21
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.19
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.17
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.14
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.06
smart00361	70	RRM_1 RNA recognition motif.	99.03
KOG0226	290	consensus RNA-binding proteins [General function p	99.03
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.02
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.01
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.95
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.95
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.93
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.92
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.9
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.87
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.86
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.77
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.72
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.72
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.71
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.65
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.65
KOG0151	877	consensus Predicted splicing regulator, contains R	98.53
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.53
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.5
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.47
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.46
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.45
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	98.42
KOG0226	290	consensus RNA-binding proteins [General function p	98.4
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.35
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	98.34
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.33
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.26
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.25
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	98.15
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.14
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.09
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.97
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	97.89
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.85
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.83
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.82
KOG4210	285	consensus Nuclear localization sequence binding pr	97.79
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.75
KOG0122	270	consensus Translation initiation factor 3, subunit	97.74
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.71
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	97.7
KOG1029	1118	consensus Endocytic adaptor protein intersectin [S	97.69
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.58
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.57
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	97.5
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.5
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	97.47
KOG1029	1118	consensus Endocytic adaptor protein intersectin [S	97.41
KOG3152	278	consensus TBP-binding protein, activator of basal	97.4
KOG4210	285	consensus Nuclear localization sequence binding pr	97.33
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	97.32
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.24
KOG2314	698	consensus Translation initiation factor 3, subunit	97.2
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	97.2
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.16
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.05
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.01
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.89
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	96.87
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.86
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	96.86
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	96.8
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.76
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	96.65
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	96.65
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.65
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.63
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	96.61
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	96.56
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	96.52
PLN03120	260	nucleic acid binding protein; Provisional	96.44
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	96.35
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	96.33
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	96.32
KOG1548	382	consensus Transcription elongation factor TAT-SF1	96.29
PLN03213	759	repressor of silencing 3; Provisional	96.21
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	96.19
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.15
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	96.06
smart00361	70	RRM_1 RNA recognition motif.	95.99
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	95.89
smart00362	72	RRM_2 RNA recognition motif.	95.89
PLN03121	243	nucleic acid binding protein; Provisional	95.84
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	95.76
KOG4207	256	consensus Predicted splicing factor, SR protein su	95.75
smart00360	71	RRM RNA recognition motif.	95.75
COG0724	306	RNA-binding proteins (RRM domain) [General functio	95.6
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	95.57
KOG1923	830	consensus Rac1 GTPase effector FRL [Signal transdu	95.38
KOG1996	378	consensus mRNA splicing factor [RNA processing and	95.17
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	95.08
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	95.0
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	94.71
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	94.57
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.33
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	94.26
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	94.09
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	93.61
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	93.4
KOG1923	830	consensus Rac1 GTPase effector FRL [Signal transdu	93.23
KOG2068	327	consensus MOT2 transcription factor [Transcription	93.2
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	93.17
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	91.66
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	91.1
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	91.08
KOG4672	487	consensus Uncharacterized conserved low complexity	90.82
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	90.75
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	89.62
KOG4246	1194	consensus Predicted DNA-binding protein, contains	89.52
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	89.27
KOG2135	526	consensus Proteins containing the RNA recognition	89.1
KOG2591	684	consensus c-Mpl binding protein, contains La domai	88.68
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	87.67
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	86.94
KOG1925	817	consensus Rac1 GTPase effector FHOS [Signal transd	86.73
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	85.84
KOG4660	549	consensus Protein Mei2, essential for commitment t	85.56
COG5178	2365	PRP8 U5 snRNP spliceosome subunit [RNA processing	85.46
PHA03378	991	EBNA-3B; Provisional	84.88
KOG0533	243	consensus RRM motif-containing protein [RNA proces	84.6
KOG2318	650	consensus Uncharacterized conserved protein [Funct	84.18
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	83.24
KOG0151	877	consensus Predicted splicing regulator, contains R	81.8
PF11600	216	CAF-1_p150: Chromatin assembly factor 1 complex p1	80.67

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=99.91  E-value=1.9e-23  Score=221.69  Aligned_cols=337  Identities=30%  Similarity=0.434  Sum_probs=194.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ++..+||||||...+....++.++..||.|.+|+.+.         |||+.|..+..+..|+..|+-..++|..+.+++.
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            4577899999999999999999999999999998753         9999999999999999999999999999998876


Q ss_pred             hhhHHHHHhhhhhhhhccccccc---cccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHH
Q 008117          206 QATREYLERYVDKKTENTKKLKE---TQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKA  282 (577)
Q Consensus       206 ~~~~~~~~~~~~~k~~~~~~~~~---~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~  282 (577)
                      ..+-...+.+............+   ....+++|++.............               +  .+-++    ....
T Consensus       109 ~q~~~n~~k~~~~~~~~~~~f~p~~srr~e~i~~k~~~l~~~~~~~~~~---------------i--s~s~~----s~~~  167 (668)
T KOG2253|consen  109 EQTIENADKEKSIANKESHKFVPSSSRRQESIQNKPLSLDEQIHKKSLQ---------------I--SSSAA----SRRQ  167 (668)
T ss_pred             hhhhcCccccccchhhhhcccCCchhHHHHHhhccccchhHHHHHHHHh---------------c--cchhh----hhhh
Confidence            33211111111100000000000   11123333333332222211100               0  00000    1112


Q ss_pred             HHHHHHHHhhhHHHHhhcCCCCCCCCCCCCCCCCCCCCccCcccCCCCCccccccccccccccccccccccccCcCCCCC
Q 008117          283 DQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPE  362 (577)
Q Consensus       283 a~~Al~~l~~~i~e~~~~~~~~~p~~~~~~~~~~~~~~e~~~k~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~  362 (577)
                      -..+...+..++......+++.++.+.+..+     ..+....+..+.+..+              .++.....+..   
T Consensus       168 ~~e~d~h~~e~~~~~~~s~~~~~~~~~~~~~-----~~e~~~~s~~~~s~td--------------s~~~~d~~~~~---  225 (668)
T KOG2253|consen  168 IAEADDHCLELEKTETESNSALSKEAESKKS-----PFEDTKDSKRSFSSTD--------------SGSESDSAEVN---  225 (668)
T ss_pred             hHHHHHHHHHHHHhhcccccccCcccccccC-----chhhhchhhhhhcccC--------------ccccchhhhhc---
Confidence            2233344444444444344433322222111     0000011111111111              00000000000   


Q ss_pred             CCCCCcccccc-ccCccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Q 008117          363 TSSPDRSRVHD-RRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYE  441 (577)
Q Consensus       363 ~~~~~r~r~~~-rr~r~r~r~~~r~r~r~~~~~~r~rerer~r~~~~~~~~~~~~er~~~er~r~~e~rer~~e~~r~~~  441 (577)
                            +.++. .+++.+.+.+.|...|.+.+.+.....+..++++.......+.|.+|+.|++.|+.|++.++++++++
T Consensus       226 ------s~~~n~~rd~sr~~~r~R~~~r~Re~~e~~ed~~~~re~r~~~~~~~~~E~Ayq~rl~~we~Rer~~~Ke~eke  299 (668)
T KOG2253|consen  226 ------SSSLNYCRDRSRFDRRSRNDRRIRERLEKNEDSDEYREDRAATIKSVDPEKAYQTRLVFWEIREQTKEKEREKE  299 (668)
T ss_pred             ------ccccccchhhccchhhhHHHHHHHHHhhhccchHHHHHhhhhhhhccChhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                  11111 11111111111111111111111122345566677777888999999999999999999887777766


Q ss_pred             HHHHHHHHH------HHhHHhhhhcccchhhhhhhhhhhHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008117          442 KEKEKERER------KRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQ  515 (577)
Q Consensus       442 ~er~~er~r------~r~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~r~re~e~~~~~r~re~~e~~~~~~~~~~~~~~~  515 (577)
                      +++++++++      ++++++++|||+++++ -+||+++++..|.+++.++.|++.+||.++++|++++|++..++..+.
T Consensus       300 ~~ke~~r~~~~~ke~kr~k~~~ed~DD~rdd-~~y~r~s~l~~r~r~~~re~Ead~~dR~qeqee~~E~Kr~~~~~~~~~  378 (668)
T KOG2253|consen  300 RLKEKSRQYKREKEAKRLKEFLEDYDDERDD-PKYYRGSALQERLRDREREAEADRRDRHQEQEELEEIKRRHSEEEAED  378 (668)
T ss_pred             HHHHHHHHHHHHHHHhhhhhhhhhcchhhhh-HHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHhhhcccc
Confidence            666665543      6788888899999977 599999999999999999999999999999999999999998877766


Q ss_pred             HHHHHH
Q 008117          516 QQRDAL  521 (577)
Q Consensus       516 ~~~~~~  521 (577)
                      ......
T Consensus       379 ~~~e~~  384 (668)
T KOG2253|consen  379 PSAEEE  384 (668)
T ss_pred             cchHHH
Confidence            554443

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.91  E-value=6.3e-23  Score=213.47  Aligned_cols=156  Identities=15%  Similarity=0.240  Sum_probs=130.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+++|+++|+.+|..||.|++|+|+.+..|++++|||||+|.+.++|..||..|||..|.++.|.|.+
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            45689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             chhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccC-CCCCCCCCCCCceEEEEeCCHHHH
Q 008117          205 DQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDN-ETGNKESHDPTNFGVVTEEDRKAD  283 (577)
Q Consensus       205 a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~-~~~~~~~g~~kgfgfV~f~~~e~a  283 (577)
                      +.....              ....++ +||+||+..+++++|++++..++.+... -..+..+|+++|||||+|.+.++|
T Consensus       184 a~p~~~--------------~~~~~~-lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A  248 (346)
T TIGR01659       184 ARPGGE--------------SIKDTN-LYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEA  248 (346)
T ss_pred             cccccc--------------ccccce-eEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHH
Confidence            754211              111233 5999999999999999984422211111 112356899999999999999999


Q ss_pred             HHHHHHHhhhHH
Q 008117          284 QEALEKLTCMVE  295 (577)
Q Consensus       284 ~~Al~~l~~~i~  295 (577)
                      .+||..|++.+-
T Consensus       249 ~~Ai~~lng~~~  260 (346)
T TIGR01659       249 QEAISALNNVIP  260 (346)
T ss_pred             HHHHHHhCCCcc
Confidence            999999998753

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

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

Probab=99.85  E-value=3.4e-21  Score=210.61  Aligned_cols=164  Identities=16%  Similarity=0.249  Sum_probs=128.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++||||||++.+++++|+.+|..||.|.+|.|+.++.+|+++|||||+|.+.++|..||..|||..|+|+.|.|.+.
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            45789999999999999999999999999999999999999999999999999999999999999999999999999864


Q ss_pred             hhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHH
Q 008117          206 QATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQ  284 (577)
Q Consensus       206 ~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~  284 (577)
                      ....... ....   ...........+||+||+..+++++|..++..++....... .+..+|+++|||||.|.+.++|.
T Consensus       185 ~~~p~a~-~~~~---~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~  260 (612)
T TIGR01645       185 SNMPQAQ-PIID---MVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQS  260 (612)
T ss_pred             ccccccc-cccc---cccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHH
Confidence            3321100 0000   00001111223599999999999999988552221111111 12467899999999999999999


Q ss_pred             HHHHHHhhh
Q 008117          285 EALEKLTCM  293 (577)
Q Consensus       285 ~Al~~l~~~  293 (577)
                      +||..||++
T Consensus       261 kAI~amNg~  269 (612)
T TIGR01645       261 EAIASMNLF  269 (612)
T ss_pred             HHHHHhCCC
Confidence            999999976

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.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.85  E-value=9.2e-21  Score=199.72  Aligned_cols=153  Identities=14%  Similarity=0.228  Sum_probs=127.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      +.++|||+|||+.+|+++|+.+|+.||.|.+|+|+.++.+|+++|||||+|.+.++|..||..|||..|.|+.|.|.|+.
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            46899999999999999999999999999999999999999999999999999999999999999999999999999875


Q ss_pred             hhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCc-ccccCCCCCCCCCCCCceEEEEeCCHHHHHH
Q 008117          207 ATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPE-NLKDNETGNKESHDPTNFGVVTEEDRKADQE  285 (577)
Q Consensus       207 ~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~-~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~  285 (577)
                      ....              ..... .+||+||+..+++.+|..++...+ +....-..+..+|.++|||||+|.+.++|..
T Consensus        82 ~~~~--------------~~~~~-~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~  146 (352)
T TIGR01661        82 PSSD--------------SIKGA-NLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADR  146 (352)
T ss_pred             cccc--------------ccccc-eEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHH
Confidence            4311              01112 359999999999999988844221 1110111224567899999999999999999


Q ss_pred             HHHHHhhhH
Q 008117          286 ALEKLTCMV  294 (577)
Q Consensus       286 Al~~l~~~i  294 (577)
                      |+..|++..
T Consensus       147 ai~~l~g~~  155 (352)
T TIGR01661       147 AIKTLNGTT  155 (352)
T ss_pred             HHHHhCCCc
Confidence            999999864

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

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

Probab=99.81  E-value=1.1e-19  Score=203.45  Aligned_cols=152  Identities=18%  Similarity=0.288  Sum_probs=125.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchhhH
Q 008117          130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATR  209 (577)
Q Consensus       130 tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~~~  209 (577)
                      +|||||||+++|+++|..+|+.||.|.+|+|+.+..|++++|||||+|.+.++|.+||..||+..|.|+.|.|.|+....
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~   81 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDP   81 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccc
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999875321


Q ss_pred             HHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHH
Q 008117          210 EYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEK  289 (577)
Q Consensus       210 ~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~  289 (577)
                      .            ......++ +||+||+..+++.+|.+++..++.........+.+|+++|||||.|.+.++|..|+.+
T Consensus        82 ~------------~~~~~~~~-vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~  148 (562)
T TIGR01628        82 S------------LRRSGVGN-IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQK  148 (562)
T ss_pred             c------------ccccCCCc-eEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHH
Confidence            0            01111233 5999999999999999884422211111112246788999999999999999999999


Q ss_pred             HhhhH
Q 008117          290 LTCMV  294 (577)
Q Consensus       290 l~~~i  294 (577)
                      ++++.
T Consensus       149 lng~~  153 (562)
T TIGR01628       149 VNGML  153 (562)
T ss_pred             hcccE
Confidence            98763

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.81  E-value=1.6e-19  Score=183.50  Aligned_cols=148  Identities=22%  Similarity=0.276  Sum_probs=123.5

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CeEEE
Q 008117          123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID-GQELM  201 (577)
Q Consensus       123 ~~~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~-gr~i~  201 (577)
                      +.....+-||||.||.++.+++|.-||.+.|.|-.++|+.++.+|.++|||||+|.+.+.|+.||..||+++|. |+.|.
T Consensus        78 ~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~ig  157 (506)
T KOG0117|consen   78 PPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLG  157 (506)
T ss_pred             CCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeE
Confidence            33456899999999999999999999999999999999999999999999999999999999999999999995 99999


Q ss_pred             EEEchhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCC-CCC-Cccc-ccCCCCCCCCCCCCceEEEEeC
Q 008117          202 LKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEP-TKS-PENL-KDNETGNKESHDPTNFGVVTEE  278 (577)
Q Consensus       202 V~~a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~-~ks-~~~~-k~~~~~~~~~g~~kgfgfV~f~  278 (577)
                      |.++...                     +.+||+|||...++++|.+- .+. -++. -..-.+..+..+++||+||+|.
T Consensus       158 vc~Svan---------------------~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe  216 (506)
T KOG0117|consen  158 VCVSVAN---------------------CRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYE  216 (506)
T ss_pred             EEEeeec---------------------ceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEee
Confidence            9876552                     33699999999998887655 431 1111 0111233557899999999999


Q ss_pred             CHHHHHHHHHHHh
Q 008117          279 DRKADQEALEKLT  291 (577)
Q Consensus       279 ~~e~a~~Al~~l~  291 (577)
                      ++..|..|..+|.
T Consensus       217 ~H~~Aa~aRrKl~  229 (506)
T KOG0117|consen  217 SHRAAAMARRKLM  229 (506)
T ss_pred             cchhHHHHHhhcc
Confidence            9999999988874

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.81  E-value=1e-19  Score=174.34  Aligned_cols=160  Identities=14%  Similarity=0.207  Sum_probs=128.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .....||||.|...++.+.|++.|.+||.|..++|++|..|+++||||||.|.+..+|+.||..|||.-|++|.|+.+|+
T Consensus        60 ~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWA  139 (321)
T KOG0148|consen   60 NQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWA  139 (321)
T ss_pred             ccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccc
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hhhHHHHHhhhhhhhh---cccccccccc-ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHH
Q 008117          206 QATREYLERYVDKKTE---NTKKLKETQD-AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRK  281 (577)
Q Consensus       206 ~~~~~~~~~~~~~k~~---~~~~~~~~~~-~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e  281 (577)
                      .-+.   .....+...   .-...+.+|+ +||+||...+++++++.++...+.+.++     ...+-+||+||.|++++
T Consensus       140 TRKp---~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EV-----RvFk~qGYaFVrF~tkE  211 (321)
T KOG0148|consen  140 TRKP---SEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEV-----RVFKDQGYAFVRFETKE  211 (321)
T ss_pred             ccCc---cccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEE-----EEecccceEEEEecchh
Confidence            6543   111111111   1112334444 7999999999999999885533322211     12345899999999999


Q ss_pred             HHHHHHHHHhhh
Q 008117          282 ADQEALEKLTCM  293 (577)
Q Consensus       282 ~a~~Al~~l~~~  293 (577)
                      +|..||..+|+.
T Consensus       212 aAahAIv~mNnt  223 (321)
T KOG0148|consen  212 AAAHAIVQMNNT  223 (321)
T ss_pred             hHHHHHHHhcCc
Confidence            999999999875

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.80  E-value=3.4e-19  Score=194.47  Aligned_cols=166  Identities=19%  Similarity=0.275  Sum_probs=129.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 008117          124 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  203 (577)
Q Consensus       124 ~~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~  203 (577)
                      .....++|||+|||+.+++.+|..+|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||. |+|..|.|+.|.|.
T Consensus        85 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~  163 (457)
T TIGR01622        85 AERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQ  163 (457)
T ss_pred             cccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEe
Confidence            34567899999999999999999999999999999999999999999999999999999999997 89999999999998


Q ss_pred             EchhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHH
Q 008117          204 VDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKA  282 (577)
Q Consensus       204 ~a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~  282 (577)
                      ++..............   .........+||+||+..+++.+|.+++..++.+.... ..+..+|+++|||||+|.+.++
T Consensus       164 ~~~~~~~~~~~~~~~~---~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~  240 (457)
T TIGR01622       164 SSQAEKNRAAKAATHQ---PGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEE  240 (457)
T ss_pred             ecchhhhhhhhccccc---CCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHH
Confidence            8755332221111000   00011134469999999999999998854222111111 1225668999999999999999


Q ss_pred             HHHHHHHHhhh
Q 008117          283 DQEALEKLTCM  293 (577)
Q Consensus       283 a~~Al~~l~~~  293 (577)
                      |..|+..|+++
T Consensus       241 A~~A~~~l~g~  251 (457)
T TIGR01622       241 AKEALEVMNGF  251 (457)
T ss_pred             HHHHHHhcCCc
Confidence            99999999984

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=99.78  E-value=9.1e-19  Score=177.25  Aligned_cols=161  Identities=16%  Similarity=0.179  Sum_probs=133.2

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce-eC--CeE
Q 008117          123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN-ID--GQE  199 (577)
Q Consensus       123 ~~~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~-i~--gr~  199 (577)
                      .++.....||||.||..+++.+|+.+|.+||.|.+|.|++|+.||.++|||||.|.+..+|..|+.+||... |-  ...
T Consensus        29 ~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~p  108 (510)
T KOG0144|consen   29 NPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHP  108 (510)
T ss_pred             CCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcc
Confidence            345677899999999999999999999999999999999999999999999999999999999999998764 43  357


Q ss_pred             EEEEEchhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCC
Q 008117          200 LMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEED  279 (577)
Q Consensus       200 i~V~~a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~  279 (577)
                      |.|++++..+..+             ....+ +||+-|+...++.++++++..++.+++.....+..+.++|||||.|.+
T Consensus       109 vqvk~Ad~E~er~-------------~~e~K-LFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fst  174 (510)
T KOG0144|consen  109 VQVKYADGERERI-------------VEERK-LFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFST  174 (510)
T ss_pred             eeecccchhhhcc-------------ccchh-hhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEeh
Confidence            8888887753332             11122 499999999999999999554444444444447889999999999999


Q ss_pred             HHHHHHHHHHHhhhHHHH
Q 008117          280 RKADQEALEKLTCMVEER  297 (577)
Q Consensus       280 ~e~a~~Al~~l~~~i~e~  297 (577)
                      ++.|..||+.||+.....
T Consensus       175 ke~A~~Aika~ng~~tme  192 (510)
T KOG0144|consen  175 KEMAVAAIKALNGTQTME  192 (510)
T ss_pred             HHHHHHHHHhhccceeec
Confidence            999999999999875543

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.78  E-value=1.8e-18  Score=189.23  Aligned_cols=143  Identities=21%  Similarity=0.264  Sum_probs=117.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEEEEc
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID-GQELMLKVD  205 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~-gr~i~V~~a  205 (577)
                      ..++|||+|||+++++++|..+|+.||.|..|+|+.+ .+|.++|||||+|.+.++|..||..||+..|. |+.|.|.++
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            4689999999999999999999999999999999999 79999999999999999999999999999985 787777543


Q ss_pred             hhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCC-CCC-Ccccc-cCCCCCCCCCCCCceEEEEeCCHHH
Q 008117          206 QATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEP-TKS-PENLK-DNETGNKESHDPTNFGVVTEEDRKA  282 (577)
Q Consensus       206 ~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~-~ks-~~~~k-~~~~~~~~~g~~kgfgfV~f~~~e~  282 (577)
                      ..                     ...+||+||+..+++++|.+. .+. ..+.. .........++++|||||+|.++++
T Consensus       136 ~~---------------------~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~ed  194 (578)
T TIGR01648       136 VD---------------------NCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRA  194 (578)
T ss_pred             cc---------------------CceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHH
Confidence            21                     123599999999999988776 331 11111 1111223457889999999999999


Q ss_pred             HHHHHHHHh
Q 008117          283 DQEALEKLT  291 (577)
Q Consensus       283 a~~Al~~l~  291 (577)
                      |..|+.+|+
T Consensus       195 Aa~AirkL~  203 (578)
T TIGR01648       195 AAMARRKLM  203 (578)
T ss_pred             HHHHHHHhh
Confidence            999998875

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=99.77  E-value=2.2e-18  Score=163.96  Aligned_cols=154  Identities=14%  Similarity=0.224  Sum_probs=130.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      +...++|.|--||.++|.++|+.||...|.|.+|++++|+.+|.+.|||||.|.++.+|.+||..|||..|..+.|+|.|
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            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCC-CCcccccCCCCCCCCCCCCceEEEEeCCHHHH
Q 008117          205 DQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTK-SPENLKDNETGNKESHDPTNFGVVTEEDRKAD  283 (577)
Q Consensus       205 a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~k-s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a  283 (577)
                      +......+              +..| +||..||.+++..+++.++. ...+...--.++..+|.++|.|||.|+.+.+|
T Consensus       118 ARPSs~~I--------------k~aN-LYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EA  182 (360)
T KOG0145|consen  118 ARPSSDSI--------------KDAN-LYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEA  182 (360)
T ss_pred             ccCChhhh--------------cccc-eEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHH
Confidence            98753322              2234 49999999999999998844 11111111113377899999999999999999


Q ss_pred             HHHHHHHhhh
Q 008117          284 QEALEKLTCM  293 (577)
Q Consensus       284 ~~Al~~l~~~  293 (577)
                      +.||..||+-
T Consensus       183 e~AIk~lNG~  192 (360)
T KOG0145|consen  183 EEAIKGLNGQ  192 (360)
T ss_pred             HHHHHhccCC
Confidence            9999998875

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.76  E-value=2.8e-18  Score=180.81  Aligned_cols=167  Identities=13%  Similarity=0.141  Sum_probs=124.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG--QELMLKV  204 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~g--r~i~V~~  204 (577)
                      ..++|||+|||..+++++|..+|..||.|..+.++.+..+|.++|||||+|.+.++|..||..|||..+.|  ..|.|.|
T Consensus        88 ~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~  167 (352)
T TIGR01661        88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKF  167 (352)
T ss_pred             ccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            35689999999999999999999999999999999988889999999999999999999999999999987  6788888


Q ss_pred             chhhHH-----HHH---hhhhh--hh-------------------------------------------------hc---
Q 008117          205 DQATRE-----YLE---RYVDK--KT-------------------------------------------------EN---  222 (577)
Q Consensus       205 a~~~~~-----~~~---~~~~~--k~-------------------------------------------------~~---  222 (577)
                      +.....     ...   .+...  ..                                                 ..   
T Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (352)
T TIGR01661       168 ANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPP  247 (352)
T ss_pred             CCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCc
Confidence            743220     000   00000  00                                                 00   


Q ss_pred             ----------cc-----cccccccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHH
Q 008117          223 ----------TK-----KLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEA  286 (577)
Q Consensus       223 ----------~~-----~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~A  286 (577)
                                ..     .......+||+||+..+++++|.+++..++.+..... .+..+|.++|||||.|.+.++|..|
T Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~A  327 (352)
T TIGR01661       248 ATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMA  327 (352)
T ss_pred             cccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHH
Confidence                      00     0011113699999999999999998442221111111 1255899999999999999999999


Q ss_pred             HHHHhhh
Q 008117          287 LEKLTCM  293 (577)
Q Consensus       287 l~~l~~~  293 (577)
                      |..|++.
T Consensus       328 i~~lnG~  334 (352)
T TIGR01661       328 ILSLNGY  334 (352)
T ss_pred             HHHhCCC
Confidence            9999875

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

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.75  E-value=3.5e-18  Score=155.25  Aligned_cols=156  Identities=15%  Similarity=0.271  Sum_probs=126.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ....|||||||+..+++..|.++|-.+|+|+.++|..++.+..++|||||+|.+.++|.-||..||...|.|++|+|+.+
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            35789999999999999999999999999999999999999999999999999999999999999999999999999765


Q ss_pred             hhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCC-CCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHH
Q 008117          206 QATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEP-TKSPENLKDNET-GNKESHDPTNFGVVTEEDRKAD  283 (577)
Q Consensus       206 ~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~-~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a  283 (577)
                      .....             ......+ .||+||...+++..+-.+ +....+...... -...+|.++|||||.|.+.+.+
T Consensus        87 s~~~~-------------nl~vgan-lfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeas  152 (203)
T KOG0131|consen   87 SAHQK-------------NLDVGAN-LFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEAS  152 (203)
T ss_pred             ccccc-------------ccccccc-ccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHH
Confidence            42110             0111133 499999999988887666 332222221111 1256799999999999999999


Q ss_pred             HHHHHHHhhhHH
Q 008117          284 QEALEKLTCMVE  295 (577)
Q Consensus       284 ~~Al~~l~~~i~  295 (577)
                      ..|+..+|+-+.
T Consensus       153 d~ai~s~ngq~l  164 (203)
T KOG0131|consen  153 DAAIGSMNGQYL  164 (203)
T ss_pred             HHHHHHhccchh
Confidence            999999887654

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

Probab=99.75  E-value=7.1e-18  Score=188.75  Aligned_cols=166  Identities=19%  Similarity=0.254  Sum_probs=129.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC----CeEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID----GQELM  201 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~----gr~i~  201 (577)
                      ...++|||+||+.++|+++|+.+|+.||.|.++.|+.+ .+|.++|||||.|.+.++|..|+..|||..|.    |..|.
T Consensus       176 ~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~-~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~  254 (562)
T TIGR01628       176 KKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKD-GSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLY  254 (562)
T ss_pred             cCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEEC-CCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeE
Confidence            44678999999999999999999999999999999988 47999999999999999999999999999999    99999


Q ss_pred             EEEchhhHHHHHhhhh----hhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEe
Q 008117          202 LKVDQATREYLERYVD----KKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTE  277 (577)
Q Consensus       202 V~~a~~~~~~~~~~~~----~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f  277 (577)
                      |.++............    ............+ +||+||+..+++++|++++..++.+.......+.+|.++|||||.|
T Consensus       255 v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~-l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f  333 (562)
T TIGR01628       255 VGRAQKRAEREAELRRKFEELQQERKMKAQGVN-LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCF  333 (562)
T ss_pred             eecccChhhhHHHHHhhHHhhhhhhhcccCCCE-EEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEe
Confidence            9887654332111111    1111111222333 5999999999999999985422222211122246799999999999


Q ss_pred             CCHHHHHHHHHHHhhh
Q 008117          278 EDRKADQEALEKLTCM  293 (577)
Q Consensus       278 ~~~e~a~~Al~~l~~~  293 (577)
                      .+.++|.+|+..|++.
T Consensus       334 ~~~~~A~~A~~~~~g~  349 (562)
T TIGR01628       334 SNPEEANRAVTEMHGR  349 (562)
T ss_pred             CCHHHHHHHHHHhcCC
Confidence            9999999999998864

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.74  E-value=1.3e-17  Score=184.44  Aligned_cols=165  Identities=18%  Similarity=0.161  Sum_probs=114.4

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHHhhc------------CceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 008117          123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVC------------GTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL  190 (577)
Q Consensus       123 ~~~~~~~tlfVgnLp~~~te~~L~~~F~~~------------G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~L  190 (577)
                      ......++|||||||+.+|+++|..||..|            +.|..+.+      +..+|||||+|.+.++|..||. |
T Consensus       170 ~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~-l  242 (509)
T TIGR01642       170 QATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMA-L  242 (509)
T ss_pred             cCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhc-C
Confidence            345667999999999999999999999975            23333333      4557999999999999999995 9


Q ss_pred             CCceeCCeEEEEEEchhhHHHHH----hhhhhhhhc----------cccccccccccccCCCcccchhhhcCCCCCCccc
Q 008117          191 NKFNIDGQELMLKVDQATREYLE----RYVDKKTEN----------TKKLKETQDAGAGKEDESVQSVEKNEPTKSPENL  256 (577)
Q Consensus       191 ng~~i~gr~i~V~~a~~~~~~~~----~~~~~k~~~----------~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~  256 (577)
                      ||+.|.|+.|.|...........    .........          .......+.+||+||+..+++++|.+++..++..
T Consensus       243 ~g~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i  322 (509)
T TIGR01642       243 DSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDL  322 (509)
T ss_pred             CCeEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            99999999999964322110000    000000000          0011122346999999999999998885522211


Q ss_pred             ccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhH
Q 008117          257 KDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCMV  294 (577)
Q Consensus       257 k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i  294 (577)
                      ..... .+..+|.++|||||+|.+.++|..||..|+++.
T Consensus       323 ~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~  361 (509)
T TIGR01642       323 KAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKD  361 (509)
T ss_pred             eEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCE
Confidence            11111 124679999999999999999999999998763

Members of this subfamily are found in plants, metazoa and fungi.

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=99.73  E-value=1.2e-15  Score=158.63  Aligned_cols=83  Identities=11%  Similarity=0.249  Sum_probs=77.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||++|+..+...+|+.||++||+|+..+||++..+...+|||||++.+..+|.+||..||.+.|+|+.|.|.-
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999975


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus       482 aKN  484 (940)
T KOG4661|consen  482 AKN  484 (940)
T ss_pred             ccc
Confidence            543

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

Probab=99.72  E-value=1.1e-16  Score=175.47  Aligned_cols=163  Identities=17%  Similarity=0.145  Sum_probs=120.3

Q ss_pred             CCCCceEEEcCCCC-CCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 008117          125 EKPQTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  203 (577)
Q Consensus       125 ~~~~~tlfVgnLp~-~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~  203 (577)
                      ..+.++|||+||++ .+|+++|..+|+.||.|..|+|+.++     +|||||+|.+.++|..||..|||..|.|+.|.|.
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~  346 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVC  346 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEE
Confidence            34678999999998 69999999999999999999998863     5899999999999999999999999999999999


Q ss_pred             EchhhHHHHHh-------------hhhhhh-----hccc----cccccccccccCCCcccchhhhcCCCCCCcc--cccC
Q 008117          204 VDQATREYLER-------------YVDKKT-----ENTK----KLKETQDAGAGKEDESVQSVEKNEPTKSPEN--LKDN  259 (577)
Q Consensus       204 ~a~~~~~~~~~-------------~~~~k~-----~~~~----~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~--~k~~  259 (577)
                      ++.........             +.....     ....    .......+||+||+..+++++|++++...+.  ....
T Consensus       347 ~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~i  426 (481)
T TIGR01649       347 PSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKF  426 (481)
T ss_pred             EcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEE
Confidence            87553211110             000000     0000    0123445799999999999999998542221  1111


Q ss_pred             CCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          260 ETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       260 ~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ......++ .+|||||+|.+.++|..||..|++.
T Consensus       427 k~~~~~~~-~~~~gfVeF~~~e~A~~Al~~ln~~  459 (481)
T TIGR01649       427 KFFPKDNE-RSKMGLLEWESVEDAVEALIALNHH  459 (481)
T ss_pred             EEecCCCC-cceeEEEEcCCHHHHHHHHHHhcCC
Confidence            11112222 5789999999999999999999875

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=99.71  E-value=9.9e-17  Score=177.48  Aligned_cols=166  Identities=15%  Similarity=0.190  Sum_probs=118.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|..+|..||.|..|.|+.+..+|.++|||||+|.+..+|..||..|||..|+|+.|.|.++
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            34689999999999999999999999999999999999899999999999999999999999999999999999999987


Q ss_pred             hhhHHHHH--hh---------hhhhhh-c-cccccccccccccCCCccc---c-------hhhhcCCC-C-----CCccc
Q 008117          206 QATREYLE--RY---------VDKKTE-N-TKKLKETQDAGAGKEDESV---Q-------SVEKNEPT-K-----SPENL  256 (577)
Q Consensus       206 ~~~~~~~~--~~---------~~~k~~-~-~~~~~~~~~~~v~nl~~~~---~-------~~~l~e~~-k-----s~~~~  256 (577)
                      ........  ..         ...... . ......+.++++.|+....   +       .++|.+++ +     ++.+.
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            53211100  00         000000 0 0012245556777764321   1       12333332 2     22222


Q ss_pred             ccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          257 KDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       257 k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +..  .+..++...||+||.|.+.++|.+|+..||+.
T Consensus       453 ~~~--~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr  487 (509)
T TIGR01642       453 RPN--GDRNSTPGVGKVFLEYADVRSAEKAMEGMNGR  487 (509)
T ss_pred             ccC--cCCCcCCCcceEEEEECCHHHHHHHHHHcCCC
Confidence            211  12345677899999999999999999999975

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.67  E-value=3.7e-17  Score=162.02  Aligned_cols=155  Identities=17%  Similarity=0.268  Sum_probs=126.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..|.||||.|.+.+.++.|+..|..||+|+++.+..|+.|++++||+||+|.-++.|..|++.|||..++|+.|+|..-.
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999997433


Q ss_pred             hh---HHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCC------CCcccccCCCCCCCCCCCCceEEEEe
Q 008117          207 AT---REYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTK------SPENLKDNETGNKESHDPTNFGVVTE  277 (577)
Q Consensus       207 ~~---~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~k------s~~~~k~~~~~~~~~g~~kgfgfV~f  277 (577)
                      ..   +..++...+.      ..++.. .||..++..+++.++.-.+.      ++.+.+.     ...+.+|||||++|
T Consensus       192 NmpQAQpiID~vqee------Ak~fnR-iYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~-----pt~~~HkGyGfiEy  259 (544)
T KOG0124|consen  192 NMPQAQPIIDMVQEE------AKKFNR-IYVASVHPDLSETDIKSVFEAFGEIVKCQLARA-----PTGRGHKGYGFIEY  259 (544)
T ss_pred             CCcccchHHHHHHHH------HHhhhe-EEeeecCCCccHHHHHHHHHhhcceeeEEeecc-----CCCCCccceeeEEe
Confidence            21   2233333221      123344 49999999999998765422      4445542     55678999999999


Q ss_pred             CCHHHHHHHHHHHhhh
Q 008117          278 EDRKADQEALEKLTCM  293 (577)
Q Consensus       278 ~~~e~a~~Al~~l~~~  293 (577)
                      .+..+-..|+..||-+
T Consensus       260 ~n~qs~~eAiasMNlF  275 (544)
T KOG0124|consen  260 NNLQSQSEAIASMNLF  275 (544)
T ss_pred             ccccchHHHhhhcchh
Confidence            9999999999888754

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.64  E-value=3.3e-16  Score=162.75  Aligned_cols=166  Identities=16%  Similarity=0.174  Sum_probs=128.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      +.||||++||+.++.++|..+|+.+|+|..|.+++++.++.++|||||+|+-.+++.+||..+++..|+|+.|.|.++..
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~   84 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKK   84 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccc
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999998865


Q ss_pred             hHHHHH--hh----hhhhhhc-----cccccccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEE
Q 008117          208 TREYLE--RY----VDKKTEN-----TKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVT  276 (577)
Q Consensus       208 ~~~~~~--~~----~~~k~~~-----~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~  276 (577)
                      ....-.  ..    ..+..+.     .+.....--+.|.|||..+...+|..++..++...+.....+..|+.-|||||.
T Consensus        85 R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~  164 (678)
T KOG0127|consen   85 RARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQ  164 (678)
T ss_pred             cccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEE
Confidence            432210  00    0000000     111111222589999999999999887442332222222336678888999999


Q ss_pred             eCCHHHHHHHHHHHhhh
Q 008117          277 EEDRKADQEALEKLTCM  293 (577)
Q Consensus       277 f~~~e~a~~Al~~l~~~  293 (577)
                      |....+|..||+.+|+.
T Consensus       165 fk~~~dA~~Al~~~N~~  181 (678)
T KOG0127|consen  165 FKEKKDAEKALEFFNGN  181 (678)
T ss_pred             EeeHHHHHHHHHhccCc
Confidence            99999999999999875

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

Probab=99.63  E-value=1.9e-15  Score=138.36  Aligned_cols=82  Identities=18%  Similarity=0.329  Sum_probs=78.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|..||.|..|.|+.++.|++++|||||+|.+.++|..||..||+..|+|+.|+|.|+
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            45789999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       112 ~~  113 (144)
T PLN03134        112 ND  113 (144)
T ss_pred             Cc
Confidence            54

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

Probab=99.63  E-value=1.3e-15  Score=166.90  Aligned_cols=156  Identities=13%  Similarity=0.020  Sum_probs=114.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCceeCCeEEEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL--NKFNIDGQELMLKV  204 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~L--ng~~i~gr~i~V~~  204 (577)
                      ++++|||+|||+.+++++|..+|+.||.|.+|.|+.+      ++||||+|.+.++|..||..|  ++..|+|+.|.|.|
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            4689999999999999999999999999999999854      489999999999999999864  78999999999999


Q ss_pred             chhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHH
Q 008117          205 DQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQ  284 (577)
Q Consensus       205 a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~  284 (577)
                      +.........  . .............+||+||+..+++++|.+++..++.+...... ..  ..+++|||+|.+.++|.
T Consensus        75 s~~~~~~~~~--~-~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~-~~--~~~~~afVef~~~~~A~  148 (481)
T TIGR01649        75 STSQEIKRDG--N-SDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTF-TK--NNVFQALVEFESVNSAQ  148 (481)
T ss_pred             cCCcccccCC--C-CcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEE-ec--CCceEEEEEECCHHHHH
Confidence            8653210000  0 00000001111125999999999999999884422211100000 11  12479999999999999


Q ss_pred             HHHHHHhhhH
Q 008117          285 EALEKLTCMV  294 (577)
Q Consensus       285 ~Al~~l~~~i  294 (577)
                      +|+..||+..
T Consensus       149 ~A~~~Lng~~  158 (481)
T TIGR01649       149 HAKAALNGAD  158 (481)
T ss_pred             HHHHHhcCCc
Confidence            9999999864

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).

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.61  E-value=1.3e-15  Score=159.61  Aligned_cols=134  Identities=20%  Similarity=0.300  Sum_probs=117.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchhh
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQAT  208 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~~  208 (577)
                      ..||||   +++|+..|..+|+.+|+|++++|+.+. |  +.|||||.|.++.+|.+||..||...|.|+.|+|.|++..
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            468999   899999999999999999999999996 5  9999999999999999999999999999999999988653


Q ss_pred             HHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCC------CCcccccCCCCCCCCCCCCceEEEEeCCHHH
Q 008117          209 REYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTK------SPENLKDNETGNKESHDPTNFGVVTEEDRKA  282 (577)
Q Consensus       209 ~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~k------s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~  282 (577)
                      ..+                    +||+||+..++...|..++.      |+.+..      +.+| ++|| ||.|++.++
T Consensus        76 ~~~--------------------~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~------~~~g-~kg~-FV~f~~e~~  127 (369)
T KOG0123|consen   76 PSL--------------------VFIKNLDESIDNKSLYDTFSEFGNILSCKVAT------DENG-SKGY-FVQFESEES  127 (369)
T ss_pred             Cce--------------------eeecCCCcccCcHHHHHHHHhhcCeeEEEEEE------cCCC-ceee-EEEeCCHHH
Confidence            222                    59999999999999887733      666655      4445 9999 999999999


Q ss_pred             HHHHHHHHhhhHHH
Q 008117          283 DQEALEKLTCMVEE  296 (577)
Q Consensus       283 a~~Al~~l~~~i~e  296 (577)
                      |.+|+..+|+++..
T Consensus       128 a~~ai~~~ng~ll~  141 (369)
T KOG0123|consen  128 AKKAIEKLNGMLLN  141 (369)
T ss_pred             HHHHHHHhcCcccC
Confidence            99999999998664

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.60  E-value=1.9e-15  Score=146.45  Aligned_cols=133  Identities=16%  Similarity=0.260  Sum_probs=110.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchhh
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQAT  208 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~~  208 (577)
                      ..|||||||..+++.+|+.||.+||+|..|.|+.+        ||||..++...|..||..|||+.|+|..|.|.-+++.
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            46999999999999999999999999999999987        9999999999999999999999999999999755442


Q ss_pred             HHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHH
Q 008117          209 REYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALE  288 (577)
Q Consensus       209 ~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~  288 (577)
                                      .+..++ ++|+||....+..+++.++...+-.-       +....++|+||.|+-.++|..|+.
T Consensus        75 ----------------sk~stk-l~vgNis~tctn~ElRa~fe~ygpvi-------ecdivkdy~fvh~d~~eda~~air  130 (346)
T KOG0109|consen   75 ----------------SKASTK-LHVGNISPTCTNQELRAKFEKYGPVI-------ECDIVKDYAFVHFDRAEDAVEAIR  130 (346)
T ss_pred             ----------------CCCccc-cccCCCCccccCHHHhhhhcccCCce-------eeeeecceeEEEEeeccchHHHHh
Confidence                            222334 49999999999999998844222111       112346799999999999999998


Q ss_pred             HHhhh
Q 008117          289 KLTCM  293 (577)
Q Consensus       289 ~l~~~  293 (577)
                      .|++.
T Consensus       131 ~l~~~  135 (346)
T KOG0109|consen  131 GLDNT  135 (346)
T ss_pred             ccccc
Confidence            88765

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.60  E-value=6.8e-15  Score=160.66  Aligned_cols=79  Identities=27%  Similarity=0.496  Sum_probs=76.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      .++|||+|||+.+|+++|..+|..||.|..|.|+.+..+|.++|||||+|.+.++|..||..|||..|.|+.|.|.|+.
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            6899999999999999999999999999999999999899999999999999999999999999999999999999964

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.

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.59  E-value=5.9e-15  Score=153.58  Aligned_cols=162  Identities=17%  Similarity=0.205  Sum_probs=124.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+-..|.|.|||+.|...+|+.+|+.||.|..|.|+... .|+.+|||||.|....+|..||..|||..|+|++|-|.||
T Consensus       115 ~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWA  193 (678)
T KOG0127|consen  115 LPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWA  193 (678)
T ss_pred             CccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeee
Confidence            346789999999999999999999999999999999775 5666699999999999999999999999999999999998


Q ss_pred             hhhHHHHHhh-------hh-----h------------------------------------------------------h
Q 008117          206 QATREYLERY-------VD-----K------------------------------------------------------K  219 (577)
Q Consensus       206 ~~~~~~~~~~-------~~-----~------------------------------------------------------k  219 (577)
                      .....|-+..       ..     .                                                      .
T Consensus       194 V~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~  273 (678)
T KOG0127|consen  194 VDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGK  273 (678)
T ss_pred             cccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhcccccccccccccccccccc
Confidence            7655543311       00     0                                                      0


Q ss_pred             hhccc---------cccccccccccCCCcccchhhhcCC-CC--CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHH
Q 008117          220 TENTK---------KLKETQDAGAGKEDESVQSVEKNEP-TK--SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEAL  287 (577)
Q Consensus       220 ~~~~~---------~~~~~~~~~v~nl~~~~~~~~l~e~-~k--s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al  287 (577)
                      ....+         ...+..++||.||++.+++++|.+. ++  .+.+...+  ..+.+|.++|.|||.|.+..++..+|
T Consensus       274 ~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV--~~k~T~~skGtAFv~Fkt~~~~~~ci  351 (678)
T KOG0127|consen  274 KESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIV--KDKDTGHSKGTAFVKFKTQIAAQNCI  351 (678)
T ss_pred             CcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEE--eccCCCCcccceEEEeccHHHHHHHH
Confidence            00000         0111234699999999999998877 33  33322222  23789999999999999999999987


Q ss_pred             HHH
Q 008117          288 EKL  290 (577)
Q Consensus       288 ~~l  290 (577)
                      ...
T Consensus       352 ~~A  354 (678)
T KOG0127|consen  352 EAA  354 (678)
T ss_pred             Hhc
Confidence            743

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.57  E-value=6.4e-15  Score=161.44  Aligned_cols=150  Identities=15%  Similarity=0.170  Sum_probs=113.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCc-eEEEEEee-cCCCCCcceEEEEEeCCHHHHHHHHHHhCC--ceeCCeEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGT-VKSWKRAQ-YPSNGTPKGFGFCEFESAEGVLRALRLLNK--FNIDGQELML  202 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~-v~~~~i~~-~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng--~~i~gr~i~V  202 (577)
                      ..++|||+|||.++++++|.++|..|+. |+.+.++. ....++++|||||+|.+..+|..|+..|+.  ..|.|+.|.|
T Consensus       137 ~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~V  216 (578)
T TIGR01648       137 DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAV  216 (578)
T ss_pred             cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEE
Confidence            4689999999999999999999999873 44444332 234678899999999999999999988763  4688999999


Q ss_pred             EEchhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCC--cccccCCCCCCCCCCCCceEEEEeCCH
Q 008117          203 KVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSP--ENLKDNETGNKESHDPTNFGVVTEEDR  280 (577)
Q Consensus       203 ~~a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~--~~~k~~~~~~~~~g~~kgfgfV~f~~~  280 (577)
                      .|+......-          .......+++||+||+..+++++|.+++..+  +.+..       ....++||||+|.+.
T Consensus       217 dwA~p~~~~d----------~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~r-------V~~~rgfAFVeF~s~  279 (578)
T TIGR01648       217 DWAEPEEEVD----------EDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVER-------VKKIRDYAFVHFEDR  279 (578)
T ss_pred             Eeeccccccc----------ccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEE-------EEeecCeEEEEeCCH
Confidence            9986542110          0111123446999999999999999885533  32211       123478999999999


Q ss_pred             HHHHHHHHHHhhh
Q 008117          281 KADQEALEKLTCM  293 (577)
Q Consensus       281 e~a~~Al~~l~~~  293 (577)
                      ++|.+|+..||+.
T Consensus       280 e~A~kAi~~lnG~  292 (578)
T TIGR01648       280 EDAVKAMDELNGK  292 (578)
T ss_pred             HHHHHHHHHhCCC
Confidence            9999999999874

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.

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.56  E-value=6.8e-15  Score=140.82  Aligned_cols=87  Identities=16%  Similarity=0.280  Sum_probs=80.3

Q ss_pred             CCCCCCCCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe
Q 008117          119 PTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQ  198 (577)
Q Consensus       119 ~~~~~~~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr  198 (577)
                      +...-..+.+|+|||-.||...++.+|..+|-.||.|++.+|..|+.|+.+||||||.|.++.+|..||.+|||+.|+-+
T Consensus       276 ~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMK  355 (371)
T KOG0146|consen  276 PQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMK  355 (371)
T ss_pred             hhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhh
Confidence            33344467799999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEEc
Q 008117          199 ELMLKVD  205 (577)
Q Consensus       199 ~i~V~~a  205 (577)
                      +|+|.+.
T Consensus       356 RLKVQLK  362 (371)
T KOG0146|consen  356 RLKVQLK  362 (371)
T ss_pred             hhhhhhc
Confidence            9998654

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.56  E-value=1.5e-14  Score=151.71  Aligned_cols=150  Identities=21%  Similarity=0.289  Sum_probs=123.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchhhHH
Q 008117          131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATRE  210 (577)
Q Consensus       131 lfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~~~~  210 (577)
                      |||.||++.++...|..+|+.||.|++|++.++. .| ++|| ||.|.+.++|.+||..|||..+.|+.|.|........
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhh
Confidence            9999999999999999999999999999999984 55 9999 9999999999999999999999999999987655432


Q ss_pred             HHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCC------CCcccccCCCCCCCCCCCCceEEEEeCCHHHHH
Q 008117          211 YLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTK------SPENLKDNETGNKESHDPTNFGVVTEEDRKADQ  284 (577)
Q Consensus       211 ~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~k------s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~  284 (577)
                      ......     . .....+++ +++|+....++..+..+..      +..++.      +..|+++|||||.|++++.|.
T Consensus       156 r~~~~~-----~-~~~~~t~v-~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~------~~~g~~~~~gfv~f~~~e~a~  222 (369)
T KOG0123|consen  156 REAPLG-----E-YKKRFTNV-YVKNLEEDSTDEELKDLFSAYGSITSVAVMR------DSIGKSKGFGFVNFENPEDAK  222 (369)
T ss_pred             hccccc-----c-hhhhhhhh-heeccccccchHHHHHhhcccCcceEEEEee------cCCCCCCCccceeecChhHHH
Confidence            221111     1 22334554 9999998888888888844      333443      677889999999999999999


Q ss_pred             HHHHHHhhhHHH
Q 008117          285 EALEKLTCMVEE  296 (577)
Q Consensus       285 ~Al~~l~~~i~e  296 (577)
                      .|+..|++.+-.
T Consensus       223 ~av~~l~~~~~~  234 (369)
T KOG0123|consen  223 KAVETLNGKIFG  234 (369)
T ss_pred             HHHHhccCCcCC
Confidence            999999887653

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.55  E-value=1e-14  Score=148.86  Aligned_cols=150  Identities=17%  Similarity=0.208  Sum_probs=117.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcC-ceEEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCeEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCG-TVKSWKRAQYP-SNGTPKGFGFCEFESAEGVLRALRLLN--KFNIDGQELM  201 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G-~v~~~~i~~~~-~tg~~kg~gFV~f~~~~~A~~Al~~Ln--g~~i~gr~i~  201 (577)
                      ...+.|||||||.+.+.++|.+.|.+.+ .|+.|.|...+ ...+.+|||||+|.++..|..|-+.|-  .+.|.|..|.
T Consensus       162 van~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~t  241 (506)
T KOG0117|consen  162 VANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAIT  241 (506)
T ss_pred             eecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcce
Confidence            3578999999999999999999999998 57777766554 467889999999999999999987763  3567899999


Q ss_pred             EEEchhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCc-ccccCCCCCCCCCCCCceEEEEeCCH
Q 008117          202 LKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPE-NLKDNETGNKESHDPTNFGVVTEEDR  280 (577)
Q Consensus       202 V~~a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~-~~k~~~~~~~~~g~~kgfgfV~f~~~  280 (577)
                      |.||.....--..          .....+++||.||..++|++.|++++..++ +.+.        -+.+.||||.|.++
T Consensus       242 VdWAep~~e~ded----------~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRV--------kk~rDYaFVHf~eR  303 (506)
T KOG0117|consen  242 VDWAEPEEEPDED----------TMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERV--------KKPRDYAFVHFAER  303 (506)
T ss_pred             eeccCcccCCChh----------hhhheeeeeeeccchhhhHHHHHHHHHhccceEEe--------ecccceeEEeecch
Confidence            9999875222111          122234579999999999999998855222 2221        13466999999999


Q ss_pred             HHHHHHHHHHhhh
Q 008117          281 KADQEALEKLTCM  293 (577)
Q Consensus       281 e~a~~Al~~l~~~  293 (577)
                      ++|.+|+..+|+.
T Consensus       304 ~davkAm~~~ngk  316 (506)
T KOG0117|consen  304 EDAVKAMKETNGK  316 (506)
T ss_pred             HHHHHHHHHhcCc
Confidence            9999999999876

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.52  E-value=2.7e-14  Score=153.38  Aligned_cols=157  Identities=22%  Similarity=0.236  Sum_probs=120.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCC---CCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSN---GTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~t---g~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ++|||.||++.+|...|..+|..+|.|.++.|...+..   -.+.|||||+|.+.++|..|+..|+|+.|+|+.|.|.++
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            44999999999999999999999999999988765422   235599999999999999999999999999999999999


Q ss_pred             hhhHH-HHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCCCCC-CCCCCCceEEEEeCCHHHH
Q 008117          206 QATRE-YLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNK-ESHDPTNFGVVTEEDRKAD  283 (577)
Q Consensus       206 ~~~~~-~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~-~~g~~kgfgfV~f~~~e~a  283 (577)
                      ..... .+.      +........++| .|.||+..++..+++.|+.+.+-.+.+....+ ..+-++|||||+|-++..|
T Consensus       596 ~~k~~~~~g------K~~~~kk~~tKI-lVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea  668 (725)
T KOG0110|consen  596 ENKPASTVG------KKKSKKKKGTKI-LVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREA  668 (725)
T ss_pred             cCccccccc------ccccccccccee-eeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHH
Confidence            82111 111      111122234565 99999999999999999553322222222112 4466899999999999999


Q ss_pred             HHHHHHHhh
Q 008117          284 QEALEKLTC  292 (577)
Q Consensus       284 ~~Al~~l~~  292 (577)
                      ..|+..|.+
T Consensus       669 ~nA~~al~S  677 (725)
T KOG0110|consen  669 KNAFDALGS  677 (725)
T ss_pred             HHHHHhhcc
Confidence            999988863

>PF00076 RRM_1: RNA recognition motif

Probab=99.51  E-value=8.6e-14  Score=110.63  Aligned_cols=70  Identities=33%  Similarity=0.571  Sum_probs=67.5

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 008117          131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  201 (577)
Q Consensus       131 lfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~  201 (577)
                      |||+|||.++|+.+|+.+|+.||.|..+.+..+ .++.+++||||+|.+.++|..|+..|||..|+|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999998 6899999999999999999999999999999999985

(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 ....

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.50  E-value=2.4e-14  Score=150.05  Aligned_cols=168  Identities=15%  Similarity=0.197  Sum_probs=133.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 008117          124 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  203 (577)
Q Consensus       124 ~~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~  203 (577)
                      .....+|||+..|+..++.-+|..||+.+|+|..|.++.+..++.++|.|||+|.+.+++..||. |.|..+.|.+|.|.
T Consensus       175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq  253 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQ  253 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEec
Confidence            35568999999999999999999999999999999999999999999999999999999999996 89999999999999


Q ss_pred             EchhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHH
Q 008117          204 VDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKA  282 (577)
Q Consensus       204 ~a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~  282 (577)
                      ...+.+.........-. ......+..-+||+||+..+++..++.++...+.+..+. ..+..+|.++||||++|.+.+.
T Consensus       254 ~sEaeknr~a~~s~a~~-~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~  332 (549)
T KOG0147|consen  254 LSEAEKNRAANASPALQ-GKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKED  332 (549)
T ss_pred             ccHHHHHHHHhcccccc-ccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHH
Confidence            88776655322222111 001111112159999999999999998855222111111 1224599999999999999999


Q ss_pred             HHHHHHHHhhh
Q 008117          283 DQEALEKLTCM  293 (577)
Q Consensus       283 a~~Al~~l~~~  293 (577)
                      |..|++.||++
T Consensus       333 ar~a~e~lngf  343 (549)
T KOG0147|consen  333 ARKALEQLNGF  343 (549)
T ss_pred             HHHHHHHhccc
Confidence            99999999995

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.50  E-value=4.5e-14  Score=121.37  Aligned_cols=83  Identities=22%  Similarity=0.391  Sum_probs=79.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ..++|||||||++.++++.|.+||++||.|..|.|-.|+.+..+.|||||+|.+.++|..|+..|+|+.|+.+.|.|.|.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus       114 ~GF  116 (153)
T KOG0121|consen  114 AGF  116 (153)
T ss_pred             ccc
Confidence            653

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.49  E-value=1.1e-13  Score=134.89  Aligned_cols=83  Identities=18%  Similarity=0.406  Sum_probs=79.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ..+.+||||+-|++.+++..|+..|..||.|..|.||.+..||+++|||||+|.+..+...|....+|..|+|+.|.|.+
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            45789999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      ...
T Consensus       178 ERg  180 (335)
T KOG0113|consen  178 ERG  180 (335)
T ss_pred             ccc
Confidence            644

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.48  E-value=4.3e-13  Score=132.28  Aligned_cols=82  Identities=18%  Similarity=0.229  Sum_probs=76.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....+.|+|+|||+...+-||+.+|.+||.|.+|.|+.+  .-.+||||||+|.++++|.+|-..|||..|.||+|.|+.
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~  170 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNN  170 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEec
Confidence            445789999999999999999999999999999999997  578899999999999999999999999999999999998


Q ss_pred             chhh
Q 008117          205 DQAT  208 (577)
Q Consensus       205 a~~~  208 (577)
                      +...
T Consensus       171 ATar  174 (376)
T KOG0125|consen  171 ATAR  174 (376)
T ss_pred             cchh
Confidence            7665

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.47  E-value=6.1e-13  Score=126.57  Aligned_cols=82  Identities=23%  Similarity=0.340  Sum_probs=79.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ....+|-|.||+.++++.+|.+||.+||.|..|.|+.|+.||.++|||||.|.+.++|.+||..|||+-++...|.|.|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      .+
T Consensus       267 kP  268 (270)
T KOG0122|consen  267 KP  268 (270)
T ss_pred             CC
Confidence            65

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.42  E-value=8.3e-13  Score=131.10  Aligned_cols=85  Identities=19%  Similarity=0.342  Sum_probs=81.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      .++-..|||..|++.+|+++|..||+.||+|.+|.|+.+..||.+..||||+|.+.+++.+|...|+++.|+.+.|+|.|
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chhhH
Q 008117          205 DQATR  209 (577)
Q Consensus       205 a~~~~  209 (577)
                      +++..
T Consensus       316 SQSVs  320 (479)
T KOG0415|consen  316 SQSVS  320 (479)
T ss_pred             hhhhh
Confidence            98863

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.42  E-value=2.9e-13  Score=128.40  Aligned_cols=81  Identities=23%  Similarity=0.345  Sum_probs=74.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      +...+.||||||++.++.+.|+.+|..||.|+...|+.|+.||+++|||||+|.+.++|.+|+.. ..-.|+||+..|++
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            45578999999999999999999999999999999999999999999999999999999999985 56789999998886


Q ss_pred             ch
Q 008117          205 DQ  206 (577)
Q Consensus       205 a~  206 (577)
                      +-
T Consensus        88 A~   89 (247)
T KOG0149|consen   88 AS   89 (247)
T ss_pred             hh
Confidence            63

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.39  E-value=2e-12  Score=103.21  Aligned_cols=70  Identities=33%  Similarity=0.575  Sum_probs=65.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 008117          131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  201 (577)
Q Consensus       131 lfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~  201 (577)
                      |||+|||+++++++|..+|+.||.|..+.+..++. |.++++|||+|.+.++|..|+..++|..|+|+.|.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999876 99999999999999999999999999999999874

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 ....

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.37  E-value=8.2e-13  Score=122.50  Aligned_cols=82  Identities=20%  Similarity=0.278  Sum_probs=78.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|-|-||.+.++.++|..+|.+||.|..|.|..|+.|+.++|||||-|.+..+|+.|+.+|+|.+|+|+.|.|.+|
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            45789999999999999999999999999999999999999999999999999999999999999999999999999877


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        91 ry   92 (256)
T KOG4207|consen   91 RY   92 (256)
T ss_pred             hc
Confidence            55

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

Probab=99.37  E-value=1.9e-12  Score=142.37  Aligned_cols=82  Identities=24%  Similarity=0.428  Sum_probs=78.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+||++.+++++|+.+|+.||.|.+|+|+.++.+|.++|||||+|.+.++|..||..|||+.|+|+.|+|.++
T Consensus       202 ~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kA  281 (612)
T TIGR01645       202 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  281 (612)
T ss_pred             cccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEec
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       282 i~  283 (612)
T TIGR01645       282 VT  283 (612)
T ss_pred             CC
Confidence            64

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.

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.37  E-value=2.7e-12  Score=126.01  Aligned_cols=76  Identities=14%  Similarity=0.189  Sum_probs=70.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      .++|||+||++.+|+.+|+.||+.||.|..|.|+.+.   .++|||||+|.+.++|..||. |||..|.|+.|.|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~---~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN---ERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC---CCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            5799999999999999999999999999999998874   356899999999999999996 999999999999998764

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.36  E-value=2.8e-12  Score=133.93  Aligned_cols=81  Identities=23%  Similarity=0.393  Sum_probs=75.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG--QELMLKV  204 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~g--r~i~V~~  204 (577)
                      ..++|||+|||+.+|+++|+.+|++||.|..|.|+.++.+|+++|||||+|.+.++|..||..||++.|.|  +.|.|.|
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            46789999999999999999999999999999999999999999999999999999999999999999876  6888888


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus       272 a~~  274 (346)
T TIGR01659       272 AEE  274 (346)
T ss_pred             CCc
Confidence            765

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).

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.36  E-value=6.5e-12  Score=120.14  Aligned_cols=81  Identities=20%  Similarity=0.315  Sum_probs=77.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .....|||-||.+++.+.-|.++|..||.|..|+|++|..|.+++|||||.+.+.++|..||..|||+.++++.|.|.|.
T Consensus       276 ~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFK  355 (360)
T KOG0145|consen  276 GGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFK  355 (360)
T ss_pred             CCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEe
Confidence            34788999999999999999999999999999999999999999999999999999999999999999999999999875


Q ss_pred             h
Q 008117          206 Q  206 (577)
Q Consensus       206 ~  206 (577)
                      .
T Consensus       356 t  356 (360)
T KOG0145|consen  356 T  356 (360)
T ss_pred             c
Confidence            4

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.35  E-value=2.1e-12  Score=117.21  Aligned_cols=76  Identities=29%  Similarity=0.455  Sum_probs=70.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..+.||||||+..++..+|..+|..||.|.+|-|..+     +.|||||+|.++.+|..|+..|+|..|.|..|.|.++.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            3789999999999999999999999999999877664     46999999999999999999999999999999998775


Q ss_pred             h
Q 008117          207 A  207 (577)
Q Consensus       207 ~  207 (577)
                      .
T Consensus        84 G   84 (195)
T KOG0107|consen   84 G   84 (195)
T ss_pred             C
Confidence            5

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.34  E-value=1.4e-13  Score=125.21  Aligned_cols=81  Identities=21%  Similarity=0.329  Sum_probs=76.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ...+.-|||||||+.+|+.+|..+|+.||.|+.|.+++|+.||+++||||+-|.+..+...|+..|||+.|.|+.|+|..
T Consensus        32 YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDH  111 (219)
T KOG0126|consen   32 YKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDH  111 (219)
T ss_pred             cccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeee
Confidence            35677899999999999999999999999999999999999999999999999999999999999999999999999974


Q ss_pred             c
Q 008117          205 D  205 (577)
Q Consensus       205 a  205 (577)
                      .
T Consensus       112 v  112 (219)
T KOG0126|consen  112 V  112 (219)
T ss_pred             c
Confidence            3

>PLN03213 repressor of silencing 3; Provisional

Probab=99.33  E-value=3.9e-12  Score=131.09  Aligned_cols=85  Identities=20%  Similarity=0.381  Sum_probs=74.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCH--HHHHHHHHHhCCceeCCeEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESA--EGVLRALRLLNKFNIDGQELMLK  203 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~--~~A~~Al~~Lng~~i~gr~i~V~  203 (577)
                      ....+||||||++.+|+++|..+|..||.|..|.|++  .+|  +|||||+|.+.  .++.+||..|||..|.|+.|+|+
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            4568999999999999999999999999999999994  477  89999999987  78999999999999999999998


Q ss_pred             EchhhHHHHHhhh
Q 008117          204 VDQATREYLERYV  216 (577)
Q Consensus       204 ~a~~~~~~~~~~~  216 (577)
                      .|..  .|+....
T Consensus        84 KAKP--~YLeRLk   94 (759)
T PLN03213         84 KAKE--HYLARLK   94 (759)
T ss_pred             eccH--HHHHHHH
Confidence            7754  3444433

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.31  E-value=1.2e-11  Score=118.83  Aligned_cols=81  Identities=21%  Similarity=0.356  Sum_probs=72.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC---CeEEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID---GQELMLK  203 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~---gr~i~V~  203 (577)
                      ..+.||||-|...-++++++.+|..||.|.+|.+...+ .|.+|||+||.|.+..+|..||..|||..-.   ...|+|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            57899999999999999999999999999999999884 8999999999999999999999999997543   3578898


Q ss_pred             Echhh
Q 008117          204 VDQAT  208 (577)
Q Consensus       204 ~a~~~  208 (577)
                      |++..
T Consensus        97 ~ADTd  101 (371)
T KOG0146|consen   97 FADTD  101 (371)
T ss_pred             eccch
Confidence            76554

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.30  E-value=1.2e-12  Score=132.96  Aligned_cols=154  Identities=18%  Similarity=0.226  Sum_probs=120.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..+.||||+|++.++++.|+..|..||.|..|.|+.++.++.++||+||+|.+...+..+|.. .-+.|+|+.|.+.-+.
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            578999999999999999999999999999999999999999999999999999999888874 6778999999987665


Q ss_pred             hhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCc-ccccCCCCCCCCCCCCceEEEEeCCHHHHHH
Q 008117          207 ATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPE-NLKDNETGNKESHDPTNFGVVTEEDRKADQE  285 (577)
Q Consensus       207 ~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~-~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~  285 (577)
                      +........         ....+...||+.|+..+++.++++.+...+ +.....-.+..+.+++|||||.|.+.++..+
T Consensus        84 ~r~~~~~~~---------~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdk  154 (311)
T KOG4205|consen   84 SREDQTKVG---------RHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDK  154 (311)
T ss_pred             Ccccccccc---------cccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccce
Confidence            532111110         011233459999999999999998844222 2111122347788999999999999998888


Q ss_pred             HHHHH
Q 008117          286 ALEKL  290 (577)
Q Consensus       286 Al~~l  290 (577)
                      ++...
T Consensus       155 v~~~~  159 (311)
T KOG4205|consen  155 VTLQK  159 (311)
T ss_pred             ecccc
Confidence            77543

>smart00362 RRM_2 RNA recognition motif

Probab=99.29  E-value=1.9e-11  Score=96.41  Aligned_cols=71  Identities=30%  Similarity=0.539  Sum_probs=67.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 008117          130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  202 (577)
Q Consensus       130 tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V  202 (577)
                      +|||+|||..++..+|..+|..||.|..+.+..+.  +.++|||||+|.+..+|..|+..|+|..|.|+.|.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            58999999999999999999999999999998875  788999999999999999999999999999999987

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.28  E-value=1.5e-11  Score=112.26  Aligned_cols=154  Identities=16%  Similarity=0.191  Sum_probs=109.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||||||.++.+.+|..||.+||.|..|.+...   ..+.+||||+|+++.+|..||..-+|+.++|..|.|.|+
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            45789999999999999999999999999999987543   345689999999999999999999999999999999998


Q ss_pred             hhhHHHHHh---hhhhhhhc--------cccccccccccccCCCcccchhhhcCCCC----CCcccccCCCCCCCCCCCC
Q 008117          206 QATREYLER---YVDKKTEN--------TKKLKETQDAGAGKEDESVQSVEKNEPTK----SPENLKDNETGNKESHDPT  270 (577)
Q Consensus       206 ~~~~~~~~~---~~~~k~~~--------~~~~~~~~~~~v~nl~~~~~~~~l~e~~k----s~~~~k~~~~~~~~~g~~k  270 (577)
                      .....-...   +...-.--        .-..-....+.|..|+.+.+=.+|+....    .+. ...         .--
T Consensus        81 rggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCf-adv---------~rD  150 (241)
T KOG0105|consen   81 RGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCF-ADV---------QRD  150 (241)
T ss_pred             cCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeee-eee---------ecc
Confidence            764311100   00000000        00000111246788898888777766521    222 111         112


Q ss_pred             ceEEEEeCCHHHHHHHHHHHhh
Q 008117          271 NFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       271 gfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      |+|+|.|-..++..-|+.+|..
T Consensus       151 g~GvV~~~r~eDMkYAvr~ld~  172 (241)
T KOG0105|consen  151 GVGVVEYLRKEDMKYAVRKLDD  172 (241)
T ss_pred             cceeeeeeehhhHHHHHHhhcc
Confidence            5899999999999999887754

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.28  E-value=6.3e-12  Score=109.10  Aligned_cols=82  Identities=17%  Similarity=0.205  Sum_probs=78.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .....|||.++...+|+++|...|..||.|+.+.+..|..||..+||++|+|.+...|+.||..|||..|.|+.|.|.|+
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            35789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      -.
T Consensus       150 Fv  151 (170)
T KOG0130|consen  150 FV  151 (170)
T ss_pred             Ee
Confidence            43

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.28  E-value=1.6e-11  Score=118.64  Aligned_cols=76  Identities=17%  Similarity=0.195  Sum_probs=69.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ...+|||+||++.+|+.+|+.||+.||.|..|.|+.+   +...|||||+|.+..+|..||. |||..|.++.|.|.-..
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D---~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS---GEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC---CCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            4689999999999999999999999999999999987   4556899999999999999996 89999999999996543

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.27  E-value=7.9e-12  Score=132.33  Aligned_cols=82  Identities=33%  Similarity=0.594  Sum_probs=79.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchhh
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQAT  208 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~~  208 (577)
                      +.|||||||+.++++.|..+|+..|.|.+++++.|+.||+++|||||+|.+.+.|..|+..|||..+.|++|+|.|+...
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            89999999999999999999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             HH
Q 008117          209 RE  210 (577)
Q Consensus       209 ~~  210 (577)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            44

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.23  E-value=4.4e-12  Score=118.58  Aligned_cols=84  Identities=21%  Similarity=0.395  Sum_probs=80.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++||||+|...|++.-|...|-.||.|..+.++.|-.+++++|||||+|...++|..||..||+.+|.|+.|+|+++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hhhH
Q 008117          206 QATR  209 (577)
Q Consensus       206 ~~~~  209 (577)
                      .+.+
T Consensus        88 kP~k   91 (298)
T KOG0111|consen   88 KPEK   91 (298)
T ss_pred             CCcc
Confidence            7654

>smart00360 RRM RNA recognition motif

Probab=99.23  E-value=4.9e-11  Score=93.64  Aligned_cols=70  Identities=31%  Similarity=0.539  Sum_probs=66.9

Q ss_pred             EcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 008117          133 VGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  202 (577)
Q Consensus       133 VgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V  202 (577)
                      |+|||..++.++|+.+|..||.|..+.+..++.++.++|||||+|.+.++|..|+..|++..|+|+.|.|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEe
Confidence            6899999999999999999999999999998778999999999999999999999999999999999887

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.23  E-value=4.5e-11  Score=113.43  Aligned_cols=152  Identities=13%  Similarity=0.142  Sum_probs=116.3

Q ss_pred             CceEEEcCCCCCCCHHHHHH----HHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 008117          128 QTKVYVGKIAPTADSDFVLS----VLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  203 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~----~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~  203 (577)
                      ..||||.||+..+..++|+.    ||+.||.|+.|.+..   |.+.+|-|||.|.+...|..|+..|+|+.|.|+.++|.
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriq   85 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQ   85 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhhee
Confidence            44999999999999998887    999999999987753   78899999999999999999999999999999999999


Q ss_pred             EchhhHHHHHhhh---h---hh--hhc---------------------------cccccccccccccCCCcccchhhhcC
Q 008117          204 VDQATREYLERYV---D---KK--TEN---------------------------TKKLKETQDAGAGKEDESVQSVEKNE  248 (577)
Q Consensus       204 ~a~~~~~~~~~~~---~---~k--~~~---------------------------~~~~~~~~~~~v~nl~~~~~~~~l~e  248 (577)
                      +|......+....   .   ++  .+.                           .....+.++.|+.||+..++.+.+..
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            9988776665521   0   00  000                           01134456689999999998887766


Q ss_pred             CCC------CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          249 PTK------SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       249 ~~k------s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      ++.      .+..+.          .-.+.+||+|.+...+..|...+.+
T Consensus       166 lf~qf~g~keir~i~----------~~~~iAfve~~~d~~a~~a~~~lq~  205 (221)
T KOG4206|consen  166 LFEQFPGFKEIRLIP----------PRSGIAFVEFLSDRQASAAQQALQG  205 (221)
T ss_pred             HHhhCcccceeEecc----------CCCceeEEecchhhhhHHHhhhhcc
Confidence            632      111221          1357999999998887777666554

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.23  E-value=3.1e-11  Score=116.43  Aligned_cols=78  Identities=24%  Similarity=0.394  Sum_probs=73.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      .+..++||||||+..+|+++|+..|+.||.|..|+|..+      +||+||.|.+.++|..||..+|+..|+|..+++.|
T Consensus       161 sp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsW  234 (321)
T KOG0148|consen  161 SPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSW  234 (321)
T ss_pred             CCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEec
Confidence            456899999999999999999999999999999999988      49999999999999999999999999999999998


Q ss_pred             chhh
Q 008117          205 DQAT  208 (577)
Q Consensus       205 a~~~  208 (577)
                      .+..
T Consensus       235 GKe~  238 (321)
T KOG0148|consen  235 GKEG  238 (321)
T ss_pred             cccC
Confidence            7553

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.22  E-value=9.9e-11  Score=97.27  Aligned_cols=84  Identities=15%  Similarity=0.280  Sum_probs=75.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .-.+.|||.|||+.+|.+++..||.+||.|..++|-.   +...+|.|||.|++..+|.+|+..|+|+.+.++.|.|-+-
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~---~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGN---TKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecC---ccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            3478899999999999999999999999999999844   4566899999999999999999999999999999999988


Q ss_pred             hhhHHHH
Q 008117          206 QATREYL  212 (577)
Q Consensus       206 ~~~~~~~  212 (577)
                      +....+.
T Consensus        93 q~~~~~~   99 (124)
T KOG0114|consen   93 QPEDAFK   99 (124)
T ss_pred             CHHHHHH
Confidence            7765544

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.21  E-value=1.4e-10  Score=118.19  Aligned_cols=165  Identities=16%  Similarity=0.211  Sum_probs=118.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHh-hcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLK-VCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~-~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ...+.+||.|||+++.+.+|+.||. +.|.|.+|.+..| .+|+++|||.|+|.+++.+++|++.||.+.+.|+.|+|+-
T Consensus        42 ~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKE  120 (608)
T KOG4212|consen   42 ARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKE  120 (608)
T ss_pred             cccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEec
Confidence            3456799999999999999999996 6889999999999 6999999999999999999999999999999999999984


Q ss_pred             chhhHHH-------------HH--------------------------------------------hhhh----------
Q 008117          205 DQATREY-------------LE--------------------------------------------RYVD----------  217 (577)
Q Consensus       205 a~~~~~~-------------~~--------------------------------------------~~~~----------  217 (577)
                      ....+..             +.                                            .|..          
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            3321100             00                                            0000          


Q ss_pred             -hhhhcccc--ccccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHh
Q 008117          218 -KKTENTKK--LKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLT  291 (577)
Q Consensus       218 -~k~~~~~~--~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~  291 (577)
                       .-...+..  ....+-.||.||...+....|.+.++-.+.+.-.+..-++.|.++||+.+.|.++-.|.+||.++.
T Consensus       201 ~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~  277 (608)
T KOG4212|consen  201 ASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLD  277 (608)
T ss_pred             hhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhc
Confidence             00000000  111122378888888877777766542222222222335667899999999999999999998887

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.21  E-value=1.2e-10  Score=118.90  Aligned_cols=83  Identities=18%  Similarity=0.302  Sum_probs=78.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      .+.+.+|||++||....+.+|...|..||.|++.++..|+.||-++|||||.|++..+|..||..|||..|++++|+|.+
T Consensus       421 GpeGanlfiyhlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQl  500 (510)
T KOG0144|consen  421 GPEGANLFIYHLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQL  500 (510)
T ss_pred             CCCccceeeeeCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEe
Confidence            45678899999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      ...
T Consensus       501 k~~  503 (510)
T KOG0144|consen  501 KRD  503 (510)
T ss_pred             eec
Confidence            543

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.19  E-value=7.1e-11  Score=118.18  Aligned_cols=79  Identities=27%  Similarity=0.462  Sum_probs=76.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..+|||||||..+|+++|..+|..||.|..+.+..++.+|.++|||||.|.+.++|..|+..|+|..|.|+.|.|.++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            6999999999999999999999999999999999998899999999999999999999999999999999999999864

>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=99.17  E-value=2.4e-10  Score=90.52  Aligned_cols=74  Identities=27%  Similarity=0.486  Sum_probs=68.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       130 tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      +|||+|||..++.++|..+|..||.|..+.+..++.+ .+.|+|||.|.+.++|..|+..|++..++|+.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            5899999999999999999999999999999987543 7789999999999999999999999999999999853

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).

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.14  E-value=3.9e-10  Score=106.00  Aligned_cols=83  Identities=14%  Similarity=0.207  Sum_probs=69.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeec-CCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC---CeEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQY-PSNGTPKGFGFCEFESAEGVLRALRLLNKFNID---GQELM  201 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~-~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~---gr~i~  201 (577)
                      ...+||||++||.++..-+|..||..|-....+.+..- +...-++-+|||+|.+..+|..|+..|||+.|+   +..|+
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            34799999999999999999999999988877766442 222224579999999999999999999999996   88899


Q ss_pred             EEEchhh
Q 008117          202 LKVDQAT  208 (577)
Q Consensus       202 V~~a~~~  208 (577)
                      |.++++.
T Consensus       112 iElAKSN  118 (284)
T KOG1457|consen  112 IELAKSN  118 (284)
T ss_pred             eeehhcC
Confidence            9877653

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.06  E-value=2.8e-10  Score=113.65  Aligned_cols=101  Identities=28%  Similarity=0.472  Sum_probs=90.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCC-------CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEE
Q 008117          104 GVRPIMPPVVRPVPLPTVTPA-------EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCE  176 (577)
Q Consensus       104 g~~p~~pp~~~p~~~~~~~~~-------~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~  176 (577)
                      |.+.+  .+++|+++|+..+.       ......|||..+.++.++++|+.+|..||.|++|.+..++.++.++|||||+
T Consensus       181 GGRNi--KVgrPsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiE  258 (544)
T KOG0124|consen  181 GGRNI--KVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIE  258 (544)
T ss_pred             cCccc--cccCCCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEE
Confidence            33555  67788888877654       4567899999999999999999999999999999999999999999999999


Q ss_pred             eCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          177 FESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       177 f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      |.+..+...||..||-+.|+|+.|+|.-+.
T Consensus       259 y~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  259 YNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             eccccchHHHhhhcchhhcccceEeccccc
Confidence            999999999999999999999999997543

>smart00361 RRM_1 RNA recognition motif

Probab=99.03  E-value=1.1e-09  Score=87.49  Aligned_cols=61  Identities=20%  Similarity=0.169  Sum_probs=55.1

Q ss_pred             HHHHHHHHh----hcCceEEEE-EeecCCC--CCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 008117          142 SDFVLSVLK----VCGTVKSWK-RAQYPSN--GTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  202 (577)
Q Consensus       142 e~~L~~~F~----~~G~v~~~~-i~~~~~t--g~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V  202 (577)
                      +++|..+|.    .||.|.++. |+.++.+  |.++|||||+|.+.++|..|+..|||..|.|+.|.+
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            467888888    999999995 7776666  999999999999999999999999999999999986

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=99.03  E-value=2.5e-09  Score=102.70  Aligned_cols=89  Identities=18%  Similarity=0.387  Sum_probs=80.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ......||+|.|...++++.|-..|.+|-.....++++++.||+++|||||.|.++.++..|+..|||..++.+.|.+.-
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRk  266 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRK  266 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhh
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             chhhHHHHH
Q 008117          205 DQATREYLE  213 (577)
Q Consensus       205 a~~~~~~~~  213 (577)
                      +.+....++
T Consensus       267 S~wkeRn~d  275 (290)
T KOG0226|consen  267 SEWKERNLD  275 (290)
T ss_pred             hhHHhhhhH
Confidence            555543333

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.02  E-value=3.1e-10  Score=119.46  Aligned_cols=77  Identities=26%  Similarity=0.517  Sum_probs=73.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ...||||||.+++++++|+.+|..||.|..|.+..+..||.++|||||+|.+.++|..|+..|||++|-|+.|+|.+
T Consensus       278 ~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~  354 (549)
T KOG0147|consen  278 MRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSV  354 (549)
T ss_pred             hhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEE
Confidence            34499999999999999999999999999999999988999999999999999999999999999999999999863

>PF13893 RRM_5: RNA recognition motif

Probab=99.01  E-value=1.6e-09  Score=82.49  Aligned_cols=56  Identities=29%  Similarity=0.452  Sum_probs=50.6

Q ss_pred             HHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          145 VLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       145 L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      |..+|++||.|..+.+....     .++|||+|.+.++|..|+..|||..|+|+.|.|.|+
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            67899999999999987652     589999999999999999999999999999999885

(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 ....

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.95  E-value=6.2e-09  Score=108.51  Aligned_cols=163  Identities=17%  Similarity=0.183  Sum_probs=118.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ...-|-+.+||+++|+++|..||+.|+ |..+.+.+  .+|++.|-|||+|.+.+++..|++ ++...++.+.|.|-.+.
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~   84 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR--RNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAG   84 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec--cCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccC
Confidence            456677889999999999999999998 56655444  589999999999999999999999 49999999999997664


Q ss_pred             hhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCccccc-CCCCCCCCCCCCceEEEEeCCHHHHHH
Q 008117          207 ATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKD-NETGNKESHDPTNFGVVTEEDRKADQE  285 (577)
Q Consensus       207 ~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~-~~~~~~~~g~~kgfgfV~f~~~e~a~~  285 (577)
                      ....  + |.-+.. -........++-...||..+++.+|.+|+.-..+..+ +-......+++.|-+||.|++.+.|++
T Consensus        85 ~~e~--d-~~~~~~-g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~  160 (510)
T KOG4211|consen   85 GAEA--D-WVMRPG-GPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEI  160 (510)
T ss_pred             Cccc--c-ccccCC-CCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHH
Confidence            4321  1 111110 0011112223455679999999999999441111111 112235667899999999999999999


Q ss_pred             HHHHHhhhHHHH
Q 008117          286 ALEKLTCMVEER  297 (577)
Q Consensus       286 Al~~l~~~i~e~  297 (577)
                      ||.+.+..|..+
T Consensus       161 Al~rhre~iGhR  172 (510)
T KOG4211|consen  161 ALGRHRENIGHR  172 (510)
T ss_pred             HHHHHHHhhccc
Confidence            999998887655

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.95  E-value=7.3e-10  Score=106.25  Aligned_cols=151  Identities=19%  Similarity=0.226  Sum_probs=106.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchhh
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQAT  208 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~~  208 (577)
                      ..||||+||+.+.+.+|..||..||.|..|.+..        ||+||+|.+..+|..||.-||+..|.|-.+.|.++...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            4689999999999999999999999999988743        69999999999999999999999999999999888754


Q ss_pred             HHHHHhhhhh-----hhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHH
Q 008117          209 REYLERYVDK-----KTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKAD  283 (577)
Q Consensus       209 ~~~~~~~~~~-----k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a  283 (577)
                      +.....-...     ..............++.++...+...++.....-++....     ..  -..+|+||.|.+..++
T Consensus        74 ~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~-----~~--~~~~~~~v~Fs~~~da  146 (216)
T KOG0106|consen   74 RRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTY-----VD--ARRNFAFVEFSEQEDA  146 (216)
T ss_pred             ccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCch-----hh--hhccccceeehhhhhh
Confidence            3222110000     0000001111222566777777766666555221111110     00  1578999999999999


Q ss_pred             HHHHHHHhhhH
Q 008117          284 QEALEKLTCMV  294 (577)
Q Consensus       284 ~~Al~~l~~~i  294 (577)
                      ..|+..|++.-
T Consensus       147 ~ra~~~l~~~~  157 (216)
T KOG0106|consen  147 KRALEKLDGKK  157 (216)
T ss_pred             hhcchhccchh
Confidence            99999887753

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=98.93  E-value=8.4e-10  Score=107.66  Aligned_cols=76  Identities=24%  Similarity=0.432  Sum_probs=72.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      .+..++||||||.+.|+..+|+..|.+||+|..|.|+.+        |+||.|.-.++|..||+.||+.+|.|++++|.+
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~  146 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQL  146 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeeee
Confidence            557899999999999999999999999999999999886        999999999999999999999999999999998


Q ss_pred             chhh
Q 008117          205 DQAT  208 (577)
Q Consensus       205 a~~~  208 (577)
                      +.+.
T Consensus       147 stsr  150 (346)
T KOG0109|consen  147 STSR  150 (346)
T ss_pred             eccc
Confidence            8764

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=98.92  E-value=1.4e-09  Score=99.58  Aligned_cols=81  Identities=23%  Similarity=0.417  Sum_probs=75.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEE-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSW-KRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~-~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.+||||||.+.+.+..|..+|+.||.+.+. +|++++.||.++|||||.|.+.+.+.+||..+||..++.++|.|.++
T Consensus        95 vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya  174 (203)
T KOG0131|consen   95 VGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYA  174 (203)
T ss_pred             ccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEE
Confidence            45899999999999999999999999987664 78889999999999999999999999999999999999999999877


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       175 ~k  176 (203)
T KOG0131|consen  175 FK  176 (203)
T ss_pred             Ee
Confidence            54

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.90  E-value=6.8e-09  Score=97.17  Aligned_cols=85  Identities=25%  Similarity=0.330  Sum_probs=77.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhhc-CceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 008117          124 AEKPQTKVYVGKIAPTADSDFVLSVLKVC-GTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  202 (577)
Q Consensus       124 ~~~~~~tlfVgnLp~~~te~~L~~~F~~~-G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V  202 (577)
                      .......+||..||..+.+.++..+|..| |.|..+++.+++.||.++|||||+|.+.+.|..|-..||++.|.|+.|.|
T Consensus        45 ~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c  124 (214)
T KOG4208|consen   45 EQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLEC  124 (214)
T ss_pred             ccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeee
Confidence            34557789999999999999999999999 67778888899999999999999999999999999999999999999999


Q ss_pred             EEchhh
Q 008117          203 KVDQAT  208 (577)
Q Consensus       203 ~~a~~~  208 (577)
                      .|-...
T Consensus       125 ~vmppe  130 (214)
T KOG4208|consen  125 HVMPPE  130 (214)
T ss_pred             EEeCch
Confidence            876554

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.87  E-value=1.4e-08  Score=101.55  Aligned_cols=86  Identities=24%  Similarity=0.374  Sum_probs=76.0

Q ss_pred             CCCCCCCCCceEEEcCCCCCCCHHHHHHHHhhcCceE--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 008117          120 TVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVK--------SWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN  191 (577)
Q Consensus       120 ~~~~~~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~--------~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Ln  191 (577)
                      ...+.....+.|||+|||.++|.+++..+|++||.|.        .|++..+. .|+.+|=|.|.|...+++..||..|+
T Consensus       126 ~~~~~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilD  204 (382)
T KOG1548|consen  126 WFNPEPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILD  204 (382)
T ss_pred             ccCcccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhC
Confidence            3344455678899999999999999999999999886        47888884 69999999999999999999999999


Q ss_pred             CceeCCeEEEEEEch
Q 008117          192 KFNIDGQELMLKVDQ  206 (577)
Q Consensus       192 g~~i~gr~i~V~~a~  206 (577)
                      +..|.|+.|+|..|+
T Consensus       205 e~~~rg~~~rVerAk  219 (382)
T KOG1548|consen  205 EDELRGKKLRVERAK  219 (382)
T ss_pred             cccccCcEEEEehhh
Confidence            999999999998654

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.86  E-value=8.2e-09  Score=110.22  Aligned_cols=167  Identities=20%  Similarity=0.214  Sum_probs=114.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      .-....+|||+||..+++..+.+++..||.+..+.++.+..+|.++||||++|.++.-...|+..|||..++++.|+|..
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~  365 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQR  365 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeeh
Confidence            34578899999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             chhhHHHHHhhhh--h-------hhhccccccccccccccCCC---cccchhhhcCC--------CC-----CCcccccC
Q 008117          205 DQATREYLERYVD--K-------KTENTKKLKETQDAGAGKED---ESVQSVEKNEP--------TK-----SPENLKDN  259 (577)
Q Consensus       205 a~~~~~~~~~~~~--~-------k~~~~~~~~~~~~~~v~nl~---~~~~~~~l~e~--------~k-----s~~~~k~~  259 (577)
                      +-........+..  .       ..........+.++...|+-   .-..+.++.++        ++     ++.+.+..
T Consensus       366 A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~  445 (500)
T KOG0120|consen  366 AIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPY  445 (500)
T ss_pred             hhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCC
Confidence            6544333322222  0       00001122233332222220   11122222222        11     22233321


Q ss_pred             CCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          260 ETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       260 ~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                        .+......-|-=||+|.+.+++..|+..|++.
T Consensus       446 --~~~~~~~G~GkVFVefas~ed~qrA~~~L~Gr  477 (500)
T KOG0120|consen  446 --PDENPVPGTGKVFVEFADTEDSQRAMEELTGR  477 (500)
T ss_pred             --CCCCcCCCcccEEEEecChHHHHHHHHHccCc
Confidence              12333344566799999999999999999874

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.77  E-value=5.1e-09  Score=98.42  Aligned_cols=76  Identities=14%  Similarity=0.154  Sum_probs=70.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ..+||||+|+...|+++.|.++|-..|+|..|.|..+. .+..+ ||||.|.+..++.-|+..|||..+.+..|.|.+
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~   83 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTL   83 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhccc
Confidence            47899999999999999999999999999999998874 56666 999999999999999999999999999998864

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.72  E-value=4.4e-09  Score=106.31  Aligned_cols=79  Identities=14%  Similarity=0.156  Sum_probs=60.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecC---CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE-E
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP---SNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML-K  203 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~---~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V-~  203 (577)
                      ...|.|.||.+.+|.+++..||...|.|..+.|+.+.   ........|||.|.+...+..|-. |..+.|-++.|.| -
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            3489999999999999999999999999999887643   222335689999999999988887 5555555555544 4


Q ss_pred             Echh
Q 008117          204 VDQA  207 (577)
Q Consensus       204 ~a~~  207 (577)
                      +...
T Consensus        86 ~~~~   89 (479)
T KOG4676|consen   86 YGDE   89 (479)
T ss_pred             cCCC
Confidence            4433

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.72  E-value=3.3e-08  Score=99.00  Aligned_cols=79  Identities=22%  Similarity=0.355  Sum_probs=71.0

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH-HhCCceeCCeEEE
Q 008117          123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR-LLNKFNIDGQELM  201 (577)
Q Consensus       123 ~~~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~-~Lng~~i~gr~i~  201 (577)
                      |.+....+||||+|...+++.+|+.+|.+||.|.++.++..      ++||||+|.+..+|+.|.. .+|...|+|++|.
T Consensus       223 PeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~  296 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLK  296 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEE
Confidence            44667899999999999999999999999999999999876      3799999999999998874 5688889999999


Q ss_pred             EEEchh
Q 008117          202 LKVDQA  207 (577)
Q Consensus       202 V~~a~~  207 (577)
                      |.|+..
T Consensus       297 i~Wg~~  302 (377)
T KOG0153|consen  297 IKWGRP  302 (377)
T ss_pred             EEeCCC
Confidence            999877

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.71  E-value=2.5e-08  Score=108.71  Aligned_cols=74  Identities=14%  Similarity=0.254  Sum_probs=70.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      ++|||||+|+.++++.+|..+|..||.|.+|.++..      +|||||.+....+|.+|+..|+.+.|.++.|+|.|+..
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            689999999999999999999999999999998765      58999999999999999999999999999999999865

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.65  E-value=2.4e-08  Score=108.14  Aligned_cols=86  Identities=24%  Similarity=0.374  Sum_probs=78.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....+.|+|.|||+..+-.+++.||..||.|.+|.|+.-...+.++|||||+|-++.+|.+|+.+|.++.|.|+.|++.|
T Consensus       610 kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEw  689 (725)
T KOG0110|consen  610 KKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEW  689 (725)
T ss_pred             ccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheeh
Confidence            44578999999999999999999999999999999987656677899999999999999999999999999999999999


Q ss_pred             chhhHH
Q 008117          205 DQATRE  210 (577)
Q Consensus       205 a~~~~~  210 (577)
                      +..-..
T Consensus       690 A~~d~~  695 (725)
T KOG0110|consen  690 AKSDNT  695 (725)
T ss_pred             hccchH
Confidence            876543

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.65  E-value=3.4e-07  Score=93.41  Aligned_cols=155  Identities=15%  Similarity=0.159  Sum_probs=109.2

Q ss_pred             CceEEEcCCCC-CCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          128 QTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       128 ~~tlfVgnLp~-~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ...|.|.||.. .+|.+-|..+|+-||.|..|+|..++     +.-|.|.|.+...|.-|+..|+|+.|.|+.|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk-----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK-----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC-----CcceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            68899999975 79999999999999999999999874     2579999999999999999999999999999999887


Q ss_pred             hhHHHHHhhh-----------h-----hhhhcccc----ccccccccccCCCcccchhhhcCCCC-CCcccccCCCCCCC
Q 008117          207 ATREYLERYV-----------D-----KKTENTKK----LKETQDAGAGKEDESVQSVEKNEPTK-SPENLKDNETGNKE  265 (577)
Q Consensus       207 ~~~~~~~~~~-----------~-----~k~~~~~~----~~~~~~~~v~nl~~~~~~~~l~e~~k-s~~~~k~~~~~~~~  265 (577)
                      .....+....           .     .++...++    ..+....-..|++.+++++++..++. ..+.++.+    +-
T Consensus       372 H~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkaf----kf  447 (492)
T KOG1190|consen  372 HTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAF----KF  447 (492)
T ss_pred             CccccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEee----ee
Confidence            6533322211           1     11111111    11111223578999999999988843 11111111    11


Q ss_pred             CCCCCceEEEEeCCHHHHHHHHHHHh
Q 008117          266 SHDPTNFGVVTEEDRKADQEALEKLT  291 (577)
Q Consensus       266 ~g~~kgfgfV~f~~~e~a~~Al~~l~  291 (577)
                      -++.+-++.+.+++.+.|..|+-.++
T Consensus       448 f~kd~kmal~q~~sveeA~~ali~~h  473 (492)
T KOG1190|consen  448 FQKDRKMALPQLESVEEAIQALIDLH  473 (492)
T ss_pred             cCCCcceeecccCChhHhhhhccccc
Confidence            23345588899999988888766553

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.53  E-value=2.4e-07  Score=100.21  Aligned_cols=85  Identities=25%  Similarity=0.368  Sum_probs=75.4

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecC---CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 008117          123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP---SNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQE  199 (577)
Q Consensus       123 ~~~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~---~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~  199 (577)
                      ..++..++||||||++.+++.+|...|..||+|.+++|+...   ..-....||||.|-+..+|.+|+..|+|..|.+..
T Consensus       169 dgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e  248 (877)
T KOG0151|consen  169 DGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYE  248 (877)
T ss_pred             CCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeee
Confidence            345678999999999999999999999999999999998764   22345679999999999999999999999999999


Q ss_pred             EEEEEchh
Q 008117          200 LMLKVDQA  207 (577)
Q Consensus       200 i~V~~a~~  207 (577)
                      |++.|+.+
T Consensus       249 ~K~gWgk~  256 (877)
T KOG0151|consen  249 MKLGWGKA  256 (877)
T ss_pred             eeeccccc
Confidence            99999854

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=98.53  E-value=1.9e-07  Score=95.71  Aligned_cols=75  Identities=20%  Similarity=0.287  Sum_probs=68.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....|+|||.|||+++|+..|+.-|..||.|.++.|+.   .|+++|  .|.|.++++|+.|+..|||..|.|+.|.|.+
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTY  607 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeee
Confidence            45678999999999999999999999999999999854   577776  8999999999999999999999999999975

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.50  E-value=3.4e-08  Score=99.96  Aligned_cols=66  Identities=14%  Similarity=-0.026  Sum_probs=55.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  196 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~  196 (577)
                      ...+||+|++|+..+-..++-.+|..+|.|.+..+.    .|....||.|+|....+...|+.. +|..+.
T Consensus       149 eirRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~a----sk~~s~~c~~sf~~qts~~halr~-~gre~k  214 (479)
T KOG4676|consen  149 EIRRTREVQSLISAAILPESGESFERKGEVSYAHTA----SKSRSSSCSHSFRKQTSSKHALRS-HGRERK  214 (479)
T ss_pred             HHHhhhhhhcchhhhcchhhhhhhhhcchhhhhhhh----ccCCCcchhhhHhhhhhHHHHHHh-cchhhh
Confidence            345899999999999999999999999999988773    445556888999999999999984 777664

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.47  E-value=5.4e-07  Score=95.36  Aligned_cols=77  Identities=26%  Similarity=0.405  Sum_probs=66.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ...+|||.|||++++..+|.++|..||.|+...|..-.-.++..|||||+|.+..++..||.+ +-..|+|++|.|.-
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Vee  363 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEE  363 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEe
Confidence            345699999999999999999999999999888766432345559999999999999999997 78999999999953

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.46  E-value=5.6e-07  Score=88.40  Aligned_cols=82  Identities=18%  Similarity=0.214  Sum_probs=74.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|+|.||++.|++.+|++||..||.+..+.|.+++ .|.+.|+|-|.|...++|..|+..|||+.++|+.|.+.+
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            4456889999999999999999999999999999998885 899999999999999999999999999999999999875


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      ...
T Consensus       159 i~~  161 (243)
T KOG0533|consen  159 ISS  161 (243)
T ss_pred             ecC
Confidence            543

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.45  E-value=2.5e-07  Score=91.05  Aligned_cols=80  Identities=25%  Similarity=0.387  Sum_probs=75.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ......+||||+.+.+|...+...|..||.|..+.|..+..+|.++||+||+|.+...+..||. |||..|.|+.|.|.+
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            4567899999999999999999999999999999999999999999999999999999999999 899999999999864


Q ss_pred             c
Q 008117          205 D  205 (577)
Q Consensus       205 a  205 (577)
                      -
T Consensus       177 ~  177 (231)
T KOG4209|consen  177 K  177 (231)
T ss_pred             e
Confidence            3

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=98.42  E-value=7.9e-07  Score=97.11  Aligned_cols=8  Identities=13%  Similarity=0.264  Sum_probs=4.0

Q ss_pred             CCceEEEc
Q 008117          127 PQTKVYVG  134 (577)
Q Consensus       127 ~~~tlfVg  134 (577)
                      +....||+
T Consensus       640 s~~cFWvk  647 (1102)
T KOG1924|consen  640 SENCFWVK  647 (1102)
T ss_pred             Cccceeee
Confidence            34455664

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.40  E-value=9.4e-07  Score=85.22  Aligned_cols=154  Identities=14%  Similarity=0.116  Sum_probs=101.5

Q ss_pred             CceEEEcCCCCCCCHHH-H--HHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          128 QTKVYVGKIAPTADSDF-V--LSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~-L--~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ...+|++++-..+..+- |  -..|+.|-.+...+++.+ ..+...+++|+.|........+...-++..|+-..|++.-
T Consensus        96 vf~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~-~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~  174 (290)
T KOG0226|consen   96 VFRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRD-RPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAA  174 (290)
T ss_pred             cccccccccccccCCCCCCcchhhhccchhhhhhhhhhc-CCCccCcccccCcchhhhhhhhccccccccccCcceeecc
Confidence            44556666655555543 2  567787877777777777 4677889999999988887777776677777766655432


Q ss_pred             chhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCC-CC--CCcccccCCCCCCCCCCCCceEEEEeCCHH
Q 008117          205 DQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEP-TK--SPENLKDNETGNKESHDPTNFGVVTEEDRK  281 (577)
Q Consensus       205 a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~-~k--s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e  281 (577)
                      +..       |........ ...... +|++.|...++++.+... .+  +.-..+...+  +-+|+++|||||.|.+..
T Consensus       175 gts-------wedPsl~ew-~~~DfR-IfcgdlgNevnd~vl~raf~Kfpsf~~akviRd--kRTgKSkgygfVSf~~pa  243 (290)
T KOG0226|consen  175 GTS-------WEDPSLAEW-DEDDFR-IFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRD--KRTGKSKGYGFVSFRDPA  243 (290)
T ss_pred             ccc-------cCCcccccC-ccccce-eecccccccccHHHHHHHHHhccchhhcccccc--ccccccccceeeeecCHH
Confidence            211       111111111 111122 488999888888877554 22  3333333333  789999999999999999


Q ss_pred             HHHHHHHHHhhh
Q 008117          282 ADQEALEKLTCM  293 (577)
Q Consensus       282 ~a~~Al~~l~~~  293 (577)
                      ++..|+..|++.
T Consensus       244 d~~rAmrem~gk  255 (290)
T KOG0226|consen  244 DYVRAMREMNGK  255 (290)
T ss_pred             HHHHHHHhhccc
Confidence            999998888765

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.35  E-value=7.5e-07  Score=95.45  Aligned_cols=165  Identities=18%  Similarity=0.196  Sum_probs=114.3

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHHhhc-----------C-ceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 008117          122 TPAEKPQTKVYVGKIAPTADSDFVLSVLKVC-----------G-TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL  189 (577)
Q Consensus       122 ~~~~~~~~tlfVgnLp~~~te~~L~~~F~~~-----------G-~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~  189 (577)
                      .........+||+++++.++++.+..+|..-           | .|+.|.+-..      +.|+|++|.+...|..|+. 
T Consensus       169 ~~~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~------~nfa~ie~~s~~~at~~~~-  241 (500)
T KOG0120|consen  169 SQATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLE------KNFAFIEFRSISEATEAMA-  241 (500)
T ss_pred             cchhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeeccc------ccceeEEecCCCchhhhhc-
Confidence            3345567899999999999999999999753           3 3666666444      5799999999999999998 


Q ss_pred             hCCceeCCeEEEEEEchhh---HHHHHhhh-----hhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCC
Q 008117          190 LNKFNIDGQELMLKVDQAT---REYLERYV-----DKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNET  261 (577)
Q Consensus       190 Lng~~i~gr~i~V~~a~~~---~~~~~~~~-----~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~  261 (577)
                      +++..+.|..+++.--...   ...+....     .............+-.||++|+..+++..+.++..+++..+..+.
T Consensus       242 ~~~~~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~l  321 (500)
T KOG0120|consen  242 LDGIIFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRL  321 (500)
T ss_pred             ccchhhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhhee
Confidence            7999999998887522111   11111110     000000111111222499999999999999888554443333332


Q ss_pred             -CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          262 -GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       262 -~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                       .+..+|.++||+|++|.+.-....|+..||++
T Consensus       322 v~d~~~g~skg~af~ey~dpsvtd~A~agLnGm  354 (500)
T KOG0120|consen  322 VKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGM  354 (500)
T ss_pred             ecccccccccceeeeeeeCCcchhhhhcccchh
Confidence             23555899999999999999999999999987

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=98.34  E-value=4e-07  Score=96.74  Aligned_cols=78  Identities=13%  Similarity=0.177  Sum_probs=64.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhh-cCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee---CCeE
Q 008117          124 AEKPQTKVYVGKIAPTADSDFVLSVLKV-CGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI---DGQE  199 (577)
Q Consensus       124 ~~~~~~tlfVgnLp~~~te~~L~~~F~~-~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i---~gr~  199 (577)
                      ....+..|||.||-.-+|.-.|+.|+.. +|.|..+  +.|    +.+..|||.|.+.++|...+.+|||+.|   +++.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~--WmD----kIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF--WMD----KIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHH--HHH----HhhcceeEecccHHHHHHHHHHHhccccCCCCCce
Confidence            3456789999999999999999999995 5555555  444    3467999999999999999999999988   5778


Q ss_pred             EEEEEchh
Q 008117          200 LMLKVDQA  207 (577)
Q Consensus       200 i~V~~a~~  207 (577)
                      |.|.|+..
T Consensus       514 L~adf~~~  521 (718)
T KOG2416|consen  514 LIADFVRA  521 (718)
T ss_pred             eEeeecch
Confidence            88877654

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.33  E-value=6e-07  Score=91.63  Aligned_cols=81  Identities=20%  Similarity=0.372  Sum_probs=75.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ....||||+||.++++.+|+..|.+||.|..+.++.|..+..++|||||.|.+.+++..++. ...+.|+|+.+.|+.|.
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~  174 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAI  174 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeecc
Confidence            46789999999999999999999999999999999999999999999999999999999988 58999999999998877


Q ss_pred             hh
Q 008117          207 AT  208 (577)
Q Consensus       207 ~~  208 (577)
                      ..
T Consensus       175 pk  176 (311)
T KOG4205|consen  175 PK  176 (311)
T ss_pred             ch
Confidence            65

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.26  E-value=1.4e-07  Score=104.31  Aligned_cols=135  Identities=11%  Similarity=0.109  Sum_probs=109.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..+++||+||++.+.+.+|...|..+|.+..+.+......+..+|+|||.|..+..+.+||....+..+ |+.       
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~-gK~-------  737 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFF-GKI-------  737 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhh-hhh-------
Confidence            357899999999999999999999999998888877778999999999999999999999986444433 211       


Q ss_pred             hhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHH
Q 008117          207 ATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEA  286 (577)
Q Consensus       207 ~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~A  286 (577)
                                              .++|.|.+...+.+.++.+....+.......+....|+.+|.+||.|.+..++..+
T Consensus       738 ------------------------~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~  793 (881)
T KOG0128|consen  738 ------------------------SVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRK  793 (881)
T ss_pred             ------------------------hhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhh
Confidence                                    13888999999999999885534433344455678899999999999999999888


Q ss_pred             HHHHhhh
Q 008117          287 LEKLTCM  293 (577)
Q Consensus       287 l~~l~~~  293 (577)
                      +.+...+
T Consensus       794 ~~s~d~~  800 (881)
T KOG0128|consen  794 VASVDVA  800 (881)
T ss_pred             cccchhh
Confidence            7766554

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.25  E-value=9.9e-07  Score=93.70  Aligned_cols=72  Identities=22%  Similarity=0.399  Sum_probs=65.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  201 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~  201 (577)
                      .....+|||-|||..|++++|+.+|+.||.|..+..     |-...|.+||+|.+..+|..|++.|++..|.|+.|.
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            456789999999999999999999999999999765     445679999999999999999999999999999887

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=98.15  E-value=1.7e-05  Score=86.96  Aligned_cols=11  Identities=0%  Similarity=-0.136  Sum_probs=4.6

Q ss_pred             ccccccccccc
Q 008117           34 ECSLALFKVIC   44 (577)
Q Consensus        34 ~~~~~~~~~~~   44 (577)
                      .+.+++||+..
T Consensus       524 ~~~iP~PP~~p  534 (1102)
T KOG1924|consen  524 DGGIPPPPPLP  534 (1102)
T ss_pred             CCCCCCCCCCC
Confidence            34444444443

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.14  E-value=0.00012  Score=74.26  Aligned_cols=160  Identities=19%  Similarity=0.180  Sum_probs=109.2

Q ss_pred             CCCCceEEEcCCCCC-CCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 008117          125 EKPQTKVYVGKIAPT-ADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  203 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~-~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~  203 (577)
                      ..+++.+.|.+|... ++.+.|..+|..||.|..|+++.-+     .|.|.|++.+....++|+..||+..+.|.+|.|.
T Consensus       284 ~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~  358 (494)
T KOG1456|consen  284 GAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVC  358 (494)
T ss_pred             CCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEEe
Confidence            456789999999874 5667899999999999999998764     3789999999999999999999999999999998


Q ss_pred             EchhhHH-----H--------HHhhhhhhh-------hccc--cccccccccccCCCcccchhhhcCCC--CCC--cccc
Q 008117          204 VDQATRE-----Y--------LERYVDKKT-------ENTK--KLKETQDAGAGKEDESVQSVEKNEPT--KSP--ENLK  257 (577)
Q Consensus       204 ~a~~~~~-----~--------~~~~~~~k~-------~~~~--~~~~~~~~~v~nl~~~~~~~~l~e~~--ks~--~~~k  257 (577)
                      +++..-.     |        +..|...+.       ...+  ...+++++-.-|.+..++++.|-.+.  +.+  ...+
T Consensus       359 ~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svk  438 (494)
T KOG1456|consen  359 VSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVK  438 (494)
T ss_pred             eccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcceEE
Confidence            7654211     1        111111110       0011  12334444455778888888887772  211  1111


Q ss_pred             cCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          258 DNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       258 ~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+..   .+-+ ..-|.++|++..+|..||.++|..
T Consensus       439 vFp~---kser-SssGllEfe~~s~Aveal~~~NH~  470 (494)
T KOG1456|consen  439 VFPL---KSER-SSSGLLEFENKSDAVEALMKLNHY  470 (494)
T ss_pred             eecc---cccc-cccceeeeehHHHHHHHHHHhccc
Confidence            1111   1111 236789999999999999988765

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.09  E-value=2.8e-05  Score=65.80  Aligned_cols=77  Identities=16%  Similarity=0.221  Sum_probs=67.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhh--cCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC----CeEEEE
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKV--CGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID----GQELML  202 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~--~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~----gr~i~V  202 (577)
                      +||.|.|||...|..+|..++..  .|....+.++.|..++-..|||||.|.++..|..-...++|..+.    .+.+.|
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            68999999999999999998875  367777888888888999999999999999999999999999885    556677


Q ss_pred             EEc
Q 008117          203 KVD  205 (577)
Q Consensus       203 ~~a  205 (577)
                      .+|
T Consensus        82 ~yA   84 (97)
T PF04059_consen   82 SYA   84 (97)
T ss_pred             ehh
Confidence            666

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.97  E-value=0.00035  Score=74.16  Aligned_cols=161  Identities=18%  Similarity=0.215  Sum_probs=98.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceE-EEEEeecC-CCCCcce---EEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVK-SWKRAQYP-SNGTPKG---FGFCEFESAEGVLRALRLLNKFNIDGQEL  200 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~-~~~i~~~~-~tg~~kg---~gFV~f~~~~~A~~Al~~Lng~~i~gr~i  200 (577)
                      .-.+.||||+||++++++.|...|..||.+. .|-..... .--.++|   |.|+.|.+..++...|.++.-   +...+
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            4478999999999999999999999999753 44321111 1112456   999999999988777655422   22222


Q ss_pred             EEEEchhh--H--HHHHhhhhh----hhhccccccccccccccCCCcccchhhhcCCCC--CCcccccCCCCCCCCCCCC
Q 008117          201 MLKVDQAT--R--EYLERYVDK----KTENTKKLKETQDAGAGKEDESVQSVEKNEPTK--SPENLKDNETGNKESHDPT  270 (577)
Q Consensus       201 ~V~~a~~~--~--~~~~~~~~~----k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~k--s~~~~k~~~~~~~~~g~~k  270 (577)
                      .++++-.+  .  ..+-+|.-.    .........++.++|||.|+--++..+|..+..  ..++.=.+-|.+.+-.-.+
T Consensus       334 yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPk  413 (520)
T KOG0129|consen  334 YFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPK  413 (520)
T ss_pred             EEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCC
Confidence            22211110  0  011111110    000122345566679999999999988876622  1122222333444666789


Q ss_pred             ceEEEEeCCHHHHHHHHHH
Q 008117          271 NFGVVTEEDRKADQEALEK  289 (577)
Q Consensus       271 gfgfV~f~~~e~a~~Al~~  289 (577)
                      |-|=|+|.+..+-.+||.+
T Consensus       414 GaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  414 GAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CcceeeecccHHHHHHHhh
Confidence            9999999999998888764

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=97.89  E-value=0.0003  Score=74.88  Aligned_cols=59  Identities=15%  Similarity=0.145  Sum_probs=42.0

Q ss_pred             ccccCCCcccchhhhcCC-CC--CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          232 AGAGKEDESVQSVEKNEP-TK--SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~-~k--s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      +||..|...+-..+|..| ++  .++-.+  -..|..+.-.++||||++.+...|.++|..|+-
T Consensus       408 lWVSGLSstTRAtDLKnlFSKyGKVvGAK--VVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHr  469 (940)
T KOG4661|consen  408 LWVSGLSSTTRATDLKNLFSKYGKVVGAK--VVTNARSPGARCYGFVTMSTSAEATKCIEHLHR  469 (940)
T ss_pred             eeeeccccchhhhHHHHHHHHhcceecee--eeecCCCCCcceeEEEEecchHHHHHHHHHhhh
Confidence            488888888888888877 44  111111  112344555789999999999999999988764

>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=97.85  E-value=5.6e-05  Score=61.18  Aligned_cols=71  Identities=20%  Similarity=0.310  Sum_probs=49.0

Q ss_pred             ceEEEcCCCCCCCHHH----HHHHHhhcC-ceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 008117          129 TKVYVGKIAPTADSDF----VLSVLKVCG-TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  203 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~----L~~~F~~~G-~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~  203 (577)
                      ..|||.|||.+.....    |+.|+..|| .|.+|.          .+.|+|-|.+.+.|.+|..-|+|-.+.|..|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            5699999999988875    567777888 566652          2689999999999999999999999999999998


Q ss_pred             EchhhH
Q 008117          204 VDQATR  209 (577)
Q Consensus       204 ~a~~~~  209 (577)
                      |....+
T Consensus        73 ~~~~~r   78 (90)
T PF11608_consen   73 FSPKNR   78 (90)
T ss_dssp             SS--S-
T ss_pred             EcCCcc
Confidence            875543

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.83  E-value=4.4e-05  Score=77.59  Aligned_cols=83  Identities=14%  Similarity=0.235  Sum_probs=74.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceE--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVK--------SWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  196 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~--------~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~  196 (577)
                      .....+|||-+|+..++..+|..+|.+||.|.        .+.|.+++.|+.+|+-|.|+|.++..|+.||.-+++..|.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            34567899999999999999999999999885        4667788899999999999999999999999999999999


Q ss_pred             CeEEEEEEchh
Q 008117          197 GQELMLKVDQA  207 (577)
Q Consensus       197 gr~i~V~~a~~  207 (577)
                      |..|+|.++..
T Consensus       143 gn~ikvs~a~~  153 (351)
T KOG1995|consen  143 GNTIKVSLAER  153 (351)
T ss_pred             CCCchhhhhhh
Confidence            99988865543

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=97.82  E-value=7.2e-05  Score=71.09  Aligned_cols=66  Identities=15%  Similarity=0.226  Sum_probs=56.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI  195 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i  195 (577)
                      ..+.||||.||.++||+++|+.+|+.|.....++|-.    ....+.+||+|.+.+.|..|+..|.|..|
T Consensus       208 ~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~----~~g~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  208 RACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA----RGGMPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec----CCCcceEeecHHHHHHHHHHHHHhhccee
Confidence            4468999999999999999999999998777666632    23346899999999999999999999877

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.79  E-value=2e-05  Score=80.18  Aligned_cols=158  Identities=15%  Similarity=0.073  Sum_probs=113.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC-ceeCCeEEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNK-FNIDGQELMLKV  204 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng-~~i~gr~i~V~~  204 (577)
                      ...+++|||++...+.+.++..+|..+|.+..+.+........+++|++|.|...+.+..||.. .+ +.+.+..+...+
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~-s~~~~~~~~~~~~dl  164 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEE-SGSKVLDGNKGEKDL  164 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHh-hhccccccccccCcc
Confidence            4578999999999999999999999999888887777667889999999999999999999985 55 466666666554


Q ss_pred             chhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCC-CCcccccCCCCCCCCCCCCceEEEEeCCHHHH
Q 008117          205 DQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTK-SPENLKDNETGNKESHDPTNFGVVTEEDRKAD  283 (577)
Q Consensus       205 a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~k-s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a  283 (577)
                      .....    .+...+...........+.+|++++..++.++|...+. ...+....-.....+|.++|||||.|.....+
T Consensus       165 ~~~~~----~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~  240 (285)
T KOG4210|consen  165 NTRRG----LRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSK  240 (285)
T ss_pred             ccccc----ccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhH
Confidence            44432    11111111111222233345999999999999985533 22222222224478899999999999998887


Q ss_pred             HHHHH
Q 008117          284 QEALE  288 (577)
Q Consensus       284 ~~Al~  288 (577)
                      ..++.
T Consensus       241 ~~~~~  245 (285)
T KOG4210|consen  241 KLALN  245 (285)
T ss_pred             HHHhh
Confidence            77654

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.75  E-value=0.00037  Score=75.92  Aligned_cols=76  Identities=17%  Similarity=0.188  Sum_probs=66.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceE-EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVK-SWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~-~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ++.|-|.|+|++++-++|..||..|-.+- +|.+-++ ..|.+.|-|.|.|++.++|.+|...|++..|..+.|.|.+
T Consensus       867 p~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  867 PRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CeEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            45888999999999999999999998664 4444444 7899999999999999999999999999999999988753

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=97.74  E-value=1.7e-05  Score=76.35  Aligned_cols=65  Identities=17%  Similarity=0.119  Sum_probs=50.4

Q ss_pred             cccccccCCCcccchhhhcCCCC-CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTK-SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~k-s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+.+-|.||+..+++.+|.+|+. ...+.+.---.++.+|.+||||||+|.++++|.+||..|++.
T Consensus       189 ~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~  254 (270)
T KOG0122|consen  189 EATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGY  254 (270)
T ss_pred             cceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCc
Confidence            34468899999999999999954 111221111124899999999999999999999999999985

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.71  E-value=0.00028  Score=76.80  Aligned_cols=158  Identities=7%  Similarity=-0.174  Sum_probs=97.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      .+-+-+.+++++....+++.||...- |..+.|..+...+.-.|-++|.|....++..|+.. |...+-.+.|.|.-.-.
T Consensus       311 ~~y~~~~gm~fn~~~nd~rkfF~g~~-~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~r-n~~~~~~R~~q~~P~g~  388 (944)
T KOG4307|consen  311 KYYNNYKGMEFNNDFNDGRKFFPGRN-AQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTR-NPSDDVNRPFQTGPPGN  388 (944)
T ss_pred             hheeeecccccccccchhhhhcCccc-ccccchhhhhcCCCcCCceEEEecCcchHHHHHhc-CchhhhhcceeecCCCc
Confidence            34444568999999999999986532 44555555544444478999999999999999874 66666667766641111


Q ss_pred             h--------HHHHHh---------hhh----hhhhccc---cccccccccccCCCcccchhhhcCCCC-CCcccccCCCC
Q 008117          208 T--------REYLER---------YVD----KKTENTK---KLKETQDAGAGKEDESVQSVEKNEPTK-SPENLKDNETG  262 (577)
Q Consensus       208 ~--------~~~~~~---------~~~----~k~~~~~---~~~~~~~~~v~nl~~~~~~~~l~e~~k-s~~~~k~~~~~  262 (577)
                      .        ......         ...    +..--.+   --.-++++||..|+..++...+-.+++ +..+.+.....
T Consensus       389 ~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt  468 (944)
T KOG4307|consen  389 LGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELT  468 (944)
T ss_pred             cccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEec
Confidence            0        000000         000    0000000   112355689999999999887766643 32222223334


Q ss_pred             CCCCCCCCceEEEEeCCHHHHHHHH
Q 008117          263 NKESHDPTNFGVVTEEDRKADQEAL  287 (577)
Q Consensus       263 ~~~~g~~kgfgfV~f~~~e~a~~Al  287 (577)
                      .--+++..+.|||.|...+++..|+
T Consensus       469 ~~P~~~~~~~afv~F~~~~a~~~a~  493 (944)
T KOG4307|consen  469 RLPTDLLRPAAFVAFIHPTAPLTAS  493 (944)
T ss_pred             cCCcccccchhhheeccccccchhh
Confidence            4677888999999999866655543

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

Probab=97.70  E-value=2.3e-05  Score=71.89  Aligned_cols=62  Identities=15%  Similarity=0.148  Sum_probs=47.9

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++..++.+.... ..+..+++++|||||+|.+.++|..|+..|++.
T Consensus        37 lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~   99 (144)
T PLN03134         37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGK   99 (144)
T ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCC
Confidence            59999999999999999855222111111 123568999999999999999999999988764

>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]

Probab=97.69  E-value=0.024  Score=62.98  Aligned_cols=12  Identities=33%  Similarity=0.659  Sum_probs=4.6

Q ss_pred             hHHHHhhcCCCC
Q 008117          293 MVEERLKTNPLP  304 (577)
Q Consensus       293 ~i~e~~~~~~~~  304 (577)
                      +++....-.++|
T Consensus       257 liema~sGq~lP  268 (1118)
T KOG1029|consen  257 LIEMAKSGQPLP  268 (1118)
T ss_pred             HHHHHhcCCCCC
Confidence            333333333433

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=97.58  E-value=9e-05  Score=75.43  Aligned_cols=165  Identities=15%  Similarity=0.069  Sum_probs=109.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhc----CceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVC----GTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  203 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~----G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~  203 (577)
                      .-.|-+.+||+++++.++..||..-    |.+..+-+++.+ .|++.|-|||.|...++|..||.. |...|+-+.|.|-
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElF  238 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELF  238 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHH
Confidence            4457778999999999999999632    345566666653 799999999999999999999986 7777777776653


Q ss_pred             Echhh--HHHHHhhhhhhhhc--------------cccccccccccccCCCcccchhhhcCCCC----CCcccccCCCCC
Q 008117          204 VDQAT--REYLERYVDKKTEN--------------TKKLKETQDAGAGKEDESVQSVEKNEPTK----SPENLKDNETGN  263 (577)
Q Consensus       204 ~a~~~--~~~~~~~~~~k~~~--------------~~~~~~~~~~~v~nl~~~~~~~~l~e~~k----s~~~~k~~~~~~  263 (577)
                      -+.+.  +..+..+...-.-.              ......+.++-...|+.+++.+++..|.+    ++..- -+.-+.
T Consensus       239 RSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~-gVHmv~  317 (508)
T KOG1365|consen  239 RSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQ-GVHMVL  317 (508)
T ss_pred             HHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccc-eeEEEE
Confidence            22221  22222222110000              00122244455667899999888877744    11110 011123


Q ss_pred             CCCCCCCceEEEEeCCHHHHHHHHHHHhhhHH
Q 008117          264 KESHDPTNFGVVTEEDRKADQEALEKLTCMVE  295 (577)
Q Consensus       264 ~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i~  295 (577)
                      +..|...|-+||.|.+.+.|..|..+.+..+.
T Consensus       318 N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~m  349 (508)
T KOG1365|consen  318 NGQGRPSGEAFIQMRNAERARAAAQKCHKKLM  349 (508)
T ss_pred             cCCCCcChhhhhhhhhhHHHHHHHHHHHHhhc
Confidence            56788999999999999999998887776543

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.57  E-value=0.0021  Score=64.86  Aligned_cols=32  Identities=6%  Similarity=-0.107  Sum_probs=23.9

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCceEEEEEee
Q 008117          131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQ  162 (577)
Q Consensus       131 lfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~  162 (577)
                      +.|+--.+.+++.++..++..--.|.+..|.+
T Consensus       348 r~~~p~~~plSeAEFEdiM~RNraiSSSAIsr  379 (498)
T KOG4849|consen  348 RHVNPQMFPLSEAEFEDIMTRNRAISSSAISR  379 (498)
T ss_pred             ccCCCCCccchHHHHHHHHhhcchhhHHHHHH
Confidence            55666666789999999999888777765543

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=97.50  E-value=2.4e-05  Score=75.13  Aligned_cols=72  Identities=15%  Similarity=0.059  Sum_probs=54.7

Q ss_pred             ccccccccccCCCcccchhhhcCCCC-CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhHHHHh
Q 008117          226 LKETQDAGAGKEDESVQSVEKNEPTK-SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERL  298 (577)
Q Consensus       226 ~~~~~~~~v~nl~~~~~~~~l~e~~k-s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i~e~~  298 (577)
                      ..+|+| ||++|+-.+..+.|+..+. ...+....-..++.+|++||||||+|.+.++|..|+.-.|-+|+-+.
T Consensus        10 T~~TKi-fVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~   82 (247)
T KOG0149|consen   10 TTFTKI-FVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRK   82 (247)
T ss_pred             ceEEEE-EEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccc
Confidence            345665 9999999999998887744 21222222224489999999999999999999999998888887663

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.50  E-value=0.00017  Score=72.57  Aligned_cols=88  Identities=22%  Similarity=0.305  Sum_probs=73.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcC--ceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCG--TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  203 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G--~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~  203 (577)
                      .....+|||||-|.+|+++|.+.+...|  .|..++++.++.+|.++|||+|..-+..++...+..|-...|+|+.-.|-
T Consensus        78 Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   78 GRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             CceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            4467899999999999999999998888  67788889999999999999999999999999999999999999865553


Q ss_pred             -EchhhHHHHH
Q 008117          204 -VDQATREYLE  213 (577)
Q Consensus       204 -~a~~~~~~~~  213 (577)
                       +.+..+..++
T Consensus       158 ~~NK~~~ak~E  168 (498)
T KOG4849|consen  158 SYNKTNQAKLE  168 (498)
T ss_pred             ccchhhHHHHH
Confidence             4444433333

>PF00076 RRM_1: RNA recognition motif

Probab=97.47  E-value=2.8e-05  Score=61.11  Aligned_cols=62  Identities=16%  Similarity=0.130  Sum_probs=46.2

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|..++...+......-..+.++.++|||||.|.+.++|..|+..+++.
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~   62 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGK   62 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCC
Confidence            38999999999999998833222111111111367889999999999999999999998874

(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 ....

>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]

Probab=97.41  E-value=0.11  Score=58.12  Aligned_cols=26  Identities=15%  Similarity=0.134  Sum_probs=11.4

Q ss_pred             HHHHHHHHHHHhhhHHHHhhcCCCCC
Q 008117          280 RKADQEALEKLTCMVEERLKTNPLPP  305 (577)
Q Consensus       280 ~e~a~~Al~~l~~~i~e~~~~~~~~~  305 (577)
                      .+.-.-|+..|.-...-......+|+
T Consensus       248 ~dEfilam~liema~sGq~lP~tlP~  273 (1118)
T KOG1029|consen  248 ADEFILAMHLIEMAKSGQPLPKTLPP  273 (1118)
T ss_pred             HHHHHHHHHHHHHHhcCCCCCCCCCh
Confidence            33444455544444444444444444

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.40  E-value=0.0001  Score=71.52  Aligned_cols=73  Identities=26%  Similarity=0.287  Sum_probs=63.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCC--------CCcceE----EEEEeCCHHHHHHHHHHhCCce
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSN--------GTPKGF----GFCEFESAEGVLRALRLLNKFN  194 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~t--------g~~kg~----gFV~f~~~~~A~~Al~~Lng~~  194 (577)
                      ....||+++||+.+...-|++||+.||.|-.|.+.....+        |....+    |.|+|.+...|..+...||+..
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            4578999999999999999999999999999988766544        333332    7899999999999999999999


Q ss_pred             eCCeE
Q 008117          195 IDGQE  199 (577)
Q Consensus       195 i~gr~  199 (577)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99875

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.33  E-value=0.00011  Score=74.96  Aligned_cols=80  Identities=23%  Similarity=0.388  Sum_probs=72.1

Q ss_pred             CCceEE-EcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          127 PQTKVY-VGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       127 ~~~tlf-VgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      +..++| |++|++.++.++|..+|..||.|..+++..+..+|.++|||||.|.....+..++.. ....|.|+.+.|...
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  261 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEED  261 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccC
Confidence            344555 999999999999999999999999999999999999999999999999999999886 888999999998765


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       262 ~~  263 (285)
T KOG4210|consen  262 EP  263 (285)
T ss_pred             CC
Confidence            44

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=97.32  E-value=0.0011  Score=63.52  Aligned_cols=78  Identities=17%  Similarity=0.300  Sum_probs=68.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEE
Q 008117          124 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID-GQELML  202 (577)
Q Consensus       124 ~~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~-gr~i~V  202 (577)
                      ..++..+||+.|||..++.+.|..+|..|+....++++...     .+.|||+|.+...|..|...|.|..|. ...+.|
T Consensus       142 ~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i  216 (221)
T KOG4206|consen  142 MAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQI  216 (221)
T ss_pred             CCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEe
Confidence            35678899999999999999999999999999999987653     479999999999999999999999987 777777


Q ss_pred             EEch
Q 008117          203 KVDQ  206 (577)
Q Consensus       203 ~~a~  206 (577)
                      .++.
T Consensus       217 ~~a~  220 (221)
T KOG4206|consen  217 TFAK  220 (221)
T ss_pred             cccC
Confidence            6653

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.24  E-value=0.00061  Score=72.37  Aligned_cols=64  Identities=20%  Similarity=0.362  Sum_probs=60.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHh-hcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLK-VCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL  189 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~-~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~  189 (577)
                      .+.+|||||+||.-++..+|..||. -||.|..+.|-+|+.-+.++|-|-|+|.+..+..+||.+
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            4579999999999999999999999 799999999999988999999999999999999999974

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.20  E-value=0.0012  Score=70.53  Aligned_cols=78  Identities=18%  Similarity=0.286  Sum_probs=63.9

Q ss_pred             CCCceEEEcCCCCCCCH------HHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-Ce
Q 008117          126 KPQTKVYVGKIAPTADS------DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID-GQ  198 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te------~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~-gr  198 (577)
                      .-...|+|-|+|..-..      .-|..+|+++|+|+.+.++.+. .|+++||.|++|.+..+|..|+..|||+.|+ .+
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e-~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknH  134 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDE-EGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNH  134 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCc-cCCeeeEEEEEecChhhHHHHHHhcccceecccc
Confidence            34577899999854332      2567899999999999998885 4559999999999999999999999999986 56


Q ss_pred             EEEEEE
Q 008117          199 ELMLKV  204 (577)
Q Consensus       199 ~i~V~~  204 (577)
                      .+.|..
T Consensus       135 tf~v~~  140 (698)
T KOG2314|consen  135 TFFVRL  140 (698)
T ss_pred             eEEeeh
Confidence            777763

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=97.20  E-value=0.00061  Score=67.58  Aligned_cols=79  Identities=6%  Similarity=0.041  Sum_probs=54.0

Q ss_pred             HHhhhhhhhhccccccccccccccCCCcccchhhhcCCCC---CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHH
Q 008117          212 LERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTK---SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALE  288 (577)
Q Consensus       212 ~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~k---s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~  288 (577)
                      +..|............. .++||+-|+..++++.|+..+.   .|..+..+  .++.+|+++|||||+|++..+...|-.
T Consensus        85 l~~wdP~~dp~a~gDPy-~TLFv~RLnydT~EskLrreF~~YG~IkrirlV--~d~vTgkskGYAFIeye~erdm~~AYK  161 (335)
T KOG0113|consen   85 LKLWDPNNDPNAIGDPY-KTLFVARLNYDTSESKLRREFEKYGPIKRIRLV--RDKVTGKSKGYAFIEYEHERDMKAAYK  161 (335)
T ss_pred             HHhcCCCCCCcccCCcc-ceeeeeeccccccHHHHHHHHHhcCcceeEEEe--eecccCCccceEEEEeccHHHHHHHHH
Confidence            34444444433334333 3359999999999999876633   23222222  237899999999999999999999988


Q ss_pred             HHhhh
Q 008117          289 KLTCM  293 (577)
Q Consensus       289 ~l~~~  293 (577)
                      ...++
T Consensus       162 ~adG~  166 (335)
T KOG0113|consen  162 DADGI  166 (335)
T ss_pred             hccCc
Confidence            77765

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=97.16  E-value=0.00029  Score=68.05  Aligned_cols=70  Identities=19%  Similarity=0.330  Sum_probs=62.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  202 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V  202 (577)
                      ....+.|+|-||+..+...+|..+|..+|.+....+        ..+++||.|....+|..||..|+|..|.|+.|.|
T Consensus        96 ~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen   96 SRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             ccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeee
Confidence            456788999999999999999999999999844433        2369999999999999999999999999999998

>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=97.05  E-value=0.001  Score=57.45  Aligned_cols=83  Identities=19%  Similarity=0.333  Sum_probs=49.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC-----CceeCCeEEEEE
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN-----KFNIDGQELMLK  203 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Ln-----g~~i~gr~i~V~  203 (577)
                      +.|+|.+++..++-++|+.+|+.||.|..|.+...      -..|||-|.+.+.|..|+..+.     +..|.+..+.+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            57899999999999999999999999999988553      2489999999999999997663     346666666665


Q ss_pred             Ec--hhhHHHHHhhhh
Q 008117          204 VD--QATREYLERYVD  217 (577)
Q Consensus       204 ~a--~~~~~~~~~~~~  217 (577)
                      +-  ..-..|+.....
T Consensus        76 vLeGeeE~~Yw~ki~e   91 (105)
T PF08777_consen   76 VLEGEEEEEYWKKIIE   91 (105)
T ss_dssp             ---HHHHHHHHHHHHH
T ss_pred             ECCCHHHHHHHHHHHH
Confidence            42  334455555444

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.01  E-value=0.0016  Score=65.46  Aligned_cols=80  Identities=16%  Similarity=0.225  Sum_probs=61.6

Q ss_pred             CceEEEcCCCCCCCHHH----H--HHHHhhcCceEEEEEeecCCC-CCcce-E-EEEEeCCHHHHHHHHHHhCCceeCCe
Q 008117          128 QTKVYVGKIAPTADSDF----V--LSVLKVCGTVKSWKRAQYPSN-GTPKG-F-GFCEFESAEGVLRALRLLNKFNIDGQ  198 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~----L--~~~F~~~G~v~~~~i~~~~~t-g~~kg-~-gFV~f~~~~~A~~Al~~Lng~~i~gr  198 (577)
                      ..-+||-+|++.+..++    |  .++|.+||.|..+.|-....+ ....+ + .||+|.+.++|.+||..++|..++|+
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            45689999999887776    2  479999999998876543211 11122 3 39999999999999999999999999


Q ss_pred             EEEEEEchh
Q 008117          199 ELMLKVDQA  207 (577)
Q Consensus       199 ~i~V~~a~~  207 (577)
                      .|+..+...
T Consensus       194 ~lkatYGTT  202 (480)
T COG5175         194 VLKATYGTT  202 (480)
T ss_pred             eEeeecCch
Confidence            999876643

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.89  E-value=0.00035  Score=78.32  Aligned_cols=145  Identities=11%  Similarity=0.060  Sum_probs=103.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ..+.|||+|||...+++.+|+..|..+|.|..|.|-+.+ -+....||||.|.+...+-.|+..+.+..|..-.+.+.+.
T Consensus       370 ~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  370 RATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            457899999999999999999999999999999886653 3455579999999999999999989998887666666544


Q ss_pred             hhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHH
Q 008117          206 QATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQE  285 (577)
Q Consensus       206 ~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~  285 (577)
                      +.                 ....++-.+++.|........+...+.-++.++..   +-..|  .-|++|.|++...+..
T Consensus       449 ~~-----------------kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~I---dy~hg--q~yayi~yes~~~aq~  506 (975)
T KOG0112|consen  449 QP-----------------KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRII---DYRHG--QPYAYIQYESPPAAQA  506 (975)
T ss_pred             cc-----------------ccccceeeccCCCCCCChHHHHHHHhhccCcceee---ecccC--CcceeeecccCccchh
Confidence            32                 11122234777777666665554333311211110   01122  3499999999999999


Q ss_pred             HHHHHhhh
Q 008117          286 ALEKLTCM  293 (577)
Q Consensus       286 Al~~l~~~  293 (577)
                      |+..+.+.
T Consensus       507 a~~~~rga  514 (975)
T KOG0112|consen  507 ATHDMRGA  514 (975)
T ss_pred             hHHHHhcC
Confidence            98877654

>PF14259 RRM_6: RNA recognition motif (a

Probab=96.87  E-value=0.0006  Score=53.86  Aligned_cols=59  Identities=12%  Similarity=0.033  Sum_probs=41.7

Q ss_pred             cccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHh
Q 008117          233 GAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLT  291 (577)
Q Consensus       233 ~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~  291 (577)
                      +|+|||..++..+|.+++...+......-.....|..+|+|||+|.+.++|..|+..++
T Consensus         2 ~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~   60 (70)
T PF14259_consen    2 YISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLN   60 (70)
T ss_dssp             EEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             EEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCC
Confidence            78999999999999988552221111111112237889999999999999999999876

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 ....

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.86  E-value=0.001  Score=69.09  Aligned_cols=81  Identities=23%  Similarity=0.365  Sum_probs=64.5

Q ss_pred             CCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeec---C--CCCCc--------ceEEEEEeCCHH
Q 008117          115 PVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQY---P--SNGTP--------KGFGFCEFESAE  181 (577)
Q Consensus       115 p~~~~~~~~~~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~---~--~tg~~--------kg~gFV~f~~~~  181 (577)
                      -.++|......-+.++|.+.|||.+-.-+-|..||+.||.|..|+|+..   +  ..|.+        +-||||+|...+
T Consensus       218 isPlp~~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~  297 (484)
T KOG1855|consen  218 ISPLPEFDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVE  297 (484)
T ss_pred             cCCCCCccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhH
Confidence            3444555555668999999999999999999999999999999999876   3  22222        457999999999


Q ss_pred             HHHHHHHHhCCcee
Q 008117          182 GVLRALRLLNKFNI  195 (577)
Q Consensus       182 ~A~~Al~~Lng~~i  195 (577)
                      .|.+|...|+....
T Consensus       298 ~A~KA~e~~~~e~~  311 (484)
T KOG1855|consen  298 AARKARELLNPEQN  311 (484)
T ss_pred             HHHHHHHhhchhhh
Confidence            99999998765443

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=96.86  E-value=0.00049  Score=69.10  Aligned_cols=66  Identities=18%  Similarity=0.106  Sum_probs=46.5

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhHHH
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEE  296 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i~e  296 (577)
                      +.++|.||++.+-+-+|...+..++.+-+++...++ --|||||||+|++.++|++|..+||+-+.+
T Consensus        97 kRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE-RGSKGFGFVTmen~~dadRARa~LHgt~VE  162 (376)
T KOG0125|consen   97 KRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE-RGSKGFGFVTMENPADADRARAELHGTVVE  162 (376)
T ss_pred             ceeEeecCCccccCccHHHHHHhhCceeeEEEEecc-CCCCccceEEecChhhHHHHHHHhhcceee
Confidence            346999999999999988773311111111111122 347999999999999999999999986443

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=96.80  E-value=0.003  Score=66.86  Aligned_cols=75  Identities=19%  Similarity=0.172  Sum_probs=63.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKS-WKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  203 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~-~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~  203 (577)
                      ....|-+.+||+.||+.+|.+||+..-.|.. +.++.+ .-+++.|-|||.|++.+.|+.||.. |...|+.+-|.|-
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d-~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF  177 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMD-QRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVF  177 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeecc-CCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEee
Confidence            4667889999999999999999998765544 444555 4678899999999999999999985 8888998998885

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=96.76  E-value=0.0077  Score=61.73  Aligned_cols=169  Identities=14%  Similarity=0.051  Sum_probs=110.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ....|-..+||+..++.+|-.||....-......+.....|.-.|++.|.|.+.+.-..|+.. |...++++.|.|.-+.
T Consensus        59 ~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkR-hkhh~g~ryievYka~  137 (508)
T KOG1365|consen   59 DNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKR-HKHHMGTRYIEVYKAT  137 (508)
T ss_pred             cceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHh-hhhhccCCceeeeccC
Confidence            344556679999999999999998654332222222224677779999999999999999985 8888899999985433


Q ss_pred             hhHHHHHhhhhhhhhcccc-ccc-cccccccCCCcccchhhhcCCCC---CCcccccCCC-CCCCCCCCCceEEEEeCCH
Q 008117          207 ATREYLERYVDKKTENTKK-LKE-TQDAGAGKEDESVQSVEKNEPTK---SPENLKDNET-GNKESHDPTNFGVVTEEDR  280 (577)
Q Consensus       207 ~~~~~~~~~~~~k~~~~~~-~~~-~~~~~v~nl~~~~~~~~l~e~~k---s~~~~k~~~~-~~~~~g~~kgfgfV~f~~~  280 (577)
                      .. .++.-..-...+...- .+. .-++-...|+...++.++.+|+.   -+....++-. +...+|+..|-+||.|...
T Consensus       138 ge-~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~e  216 (508)
T KOG1365|consen  138 GE-EFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACE  216 (508)
T ss_pred             ch-hheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCH
Confidence            21 1110000011111110 111 12245568999999999998853   2221221111 3355789999999999999


Q ss_pred             HHHHHHHHHHhhhHHHH
Q 008117          281 KADQEALEKLTCMVEER  297 (577)
Q Consensus       281 e~a~~Al~~l~~~i~e~  297 (577)
                      ++|..||.+-.+.|..+
T Consensus       217 e~aq~aL~khrq~iGqR  233 (508)
T KOG1365|consen  217 EDAQFALRKHRQNIGQR  233 (508)
T ss_pred             HHHHHHHHHHHHHHhHH
Confidence            99999999988887655

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=96.65  E-value=0.0062  Score=62.25  Aligned_cols=143  Identities=15%  Similarity=0.110  Sum_probs=98.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH--hCCceeCCeEEEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL--LNKFNIDGQELMLKV  204 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~--Lng~~i~gr~i~V~~  204 (577)
                      ++..|+|.+|-..+++.+|.+.++.||.|..+.++..      +.-+.|+|.+.+.|..|+..  -+...|.|+.-.+++
T Consensus        30 ~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~------~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~Ny  103 (494)
T KOG1456|consen   30 PSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPH------KRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNY  103 (494)
T ss_pred             CCceEEEeccccccchhHHHHHHhcCCceEEEEeccc------cceeeeeeccccchhhheehhccCcccccCchhhccc
Confidence            4567999999999999999999999999999987655      35899999999999999852  255667788777766


Q ss_pred             chhhHHHHHhhhhhhhhcccccccccc--ccccCCCcccchhhhcCCCC------CCcccccCCCCCCCCCCCCceEEEE
Q 008117          205 DQATREYLERYVDKKTENTKKLKETQD--AGAGKEDESVQSVEKNEPTK------SPENLKDNETGNKESHDPTNFGVVT  276 (577)
Q Consensus       205 a~~~~~~~~~~~~~k~~~~~~~~~~~~--~~v~nl~~~~~~~~l~e~~k------s~~~~k~~~~~~~~~g~~kgfgfV~  276 (577)
                      +.+..  +..    ..  ........+  .-|-|-...++-+.|-.+.-      -+++.+       .+|   -.+.|+
T Consensus       104 Stsq~--i~R----~g--~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfk-------kng---VQAmVE  165 (494)
T KOG1456|consen  104 STSQC--IER----PG--DESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFK-------KNG---VQAMVE  165 (494)
T ss_pred             chhhh--hcc----CC--CCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEe-------ccc---eeeEEe
Confidence            64321  100    00  111222223  23445556666666666632      122222       122   368999


Q ss_pred             eCCHHHHHHHHHHHhhh
Q 008117          277 EEDRKADQEALEKLTCM  293 (577)
Q Consensus       277 f~~~e~a~~Al~~l~~~  293 (577)
                      |++.+.|.+|...||+.
T Consensus       166 Fdsv~~AqrAk~alNGA  182 (494)
T KOG1456|consen  166 FDSVEVAQRAKAALNGA  182 (494)
T ss_pred             echhHHHHHHHhhcccc
Confidence            99999999999999975

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=96.65  E-value=0.0038  Score=64.50  Aligned_cols=78  Identities=14%  Similarity=0.213  Sum_probs=66.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe-EEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQ-ELMLKV  204 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr-~i~V~~  204 (577)
                      +++.+|+.+|||.++++++|+.+|..-|..+.....    -++.+.++++.+.+.+.|..|+..||.+.+++. .|+|.|
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkf----f~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSF  487 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKF----FQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSF  487 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeee----cCCCcceeecccCChhHhhhhccccccccCCCCceEEEEe
Confidence            567899999999999999999999999876554432    234567999999999999999999999999855 899998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      ++.
T Consensus       488 Sks  490 (492)
T KOG1190|consen  488 SKS  490 (492)
T ss_pred             ecc
Confidence            865

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.65  E-value=0.0083  Score=54.29  Aligned_cols=71  Identities=21%  Similarity=0.314  Sum_probs=53.0

Q ss_pred             CCCceEEEcCCC-----C-CCCH---HHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 008117          126 KPQTKVYVGKIA-----P-TADS---DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  196 (577)
Q Consensus       126 ~~~~tlfVgnLp-----~-~~te---~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~  196 (577)
                      ++..||.|.-+.     . .+.+   .+|...|..||.|.-++++-+        .-+|+|.+-.+|.+|+. |+|..|+
T Consensus        25 PpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v~   95 (146)
T PF08952_consen   25 PPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQVN   95 (146)
T ss_dssp             -TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEET
T ss_pred             CCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEEC
Confidence            345677776555     1 2332   277788999999998888654        68999999999999999 7999999


Q ss_pred             CeEEEEEEc
Q 008117          197 GQELMLKVD  205 (577)
Q Consensus       197 gr~i~V~~a  205 (577)
                      |+.|.|.+-
T Consensus        96 g~~l~i~LK  104 (146)
T PF08952_consen   96 GRTLKIRLK  104 (146)
T ss_dssp             TEEEEEEE-
T ss_pred             CEEEEEEeC
Confidence            999999754

; PDB: 1UFW_A 2DNR_A.

>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=96.63  E-value=0.0098  Score=50.73  Aligned_cols=78  Identities=19%  Similarity=0.141  Sum_probs=52.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecC-------CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe-E
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP-------SNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQ-E  199 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~-------~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr-~  199 (577)
                      .+.|.|-+.|+. .-..|...|++||.|+...-+...       .......|-.|.|.++.+|.+||.. ||..|+|. .
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcCcEE
Confidence            456888888887 556788899999999877511110       0012236999999999999999995 99999885 5


Q ss_pred             EEEEEchh
Q 008117          200 LMLKVDQA  207 (577)
Q Consensus       200 i~V~~a~~  207 (577)
                      +-|.++..
T Consensus        84 vGV~~~~~   91 (100)
T PF05172_consen   84 VGVKPCDP   91 (100)
T ss_dssp             EEEEE-HH
T ss_pred             EEEEEcHH
Confidence            55766644

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.

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=96.61  E-value=0.0022  Score=60.72  Aligned_cols=64  Identities=11%  Similarity=0.033  Sum_probs=45.6

Q ss_pred             cccccCCCcccchhhhcCCCC-CCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhH
Q 008117          231 DAGAGKEDESVQSVEKNEPTK-SPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCMV  294 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~k-s~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i  294 (577)
                      +.++..++.-+.+.++..++. ..+....... -|..||.|||||||+|++.+.|.-|-+.||+.|
T Consensus        51 ~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYL  116 (214)
T KOG4208|consen   51 VVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYL  116 (214)
T ss_pred             ceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhh
Confidence            346666777676666655533 2222222222 568999999999999999999999999999864

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.56  E-value=0.00026  Score=65.36  Aligned_cols=63  Identities=13%  Similarity=0.044  Sum_probs=47.6

Q ss_pred             cccccCCCcccchhhhcCCCCCCc-ccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPE-NLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~-~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      -.||++|+..+++.++.-++...+ ++...-.-++.||+|+||+|+.|++..+..-|+.-||++
T Consensus        37 ~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGi  100 (219)
T KOG0126|consen   37 YIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGI  100 (219)
T ss_pred             EEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCc
Confidence            369999999999999877644111 111111123899999999999999999999998888886

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=96.52  E-value=0.003  Score=63.97  Aligned_cols=65  Identities=11%  Similarity=0.078  Sum_probs=53.4

Q ss_pred             cccccccccccCCCcccchhhhcCCCC------CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhH
Q 008117          225 KLKETQDAGAGKEDESVQSVEKNEPTK------SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMV  294 (577)
Q Consensus       225 ~~~~~~~~~v~nl~~~~~~~~l~e~~k------s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i  294 (577)
                      .+.+.|++||-.|.+.+++++|.-++.      ++.+++   +  ..+|.+-.|+||+|++.++.++|.-+|.+.|
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIR---D--~ktgdsLqyaFiEFen~escE~AyFKMdNvL  305 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIR---D--RKTGDSLQYAFIEFENKESCEQAYFKMDNVL  305 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEe---c--ccccchhheeeeeecchhhHHHHHhhhccee
Confidence            466788999999999999999987743      444443   2  6789999999999999999999999987653

>PLN03120 nucleic acid binding protein; Provisional

Probab=96.44  E-value=0.0016  Score=64.63  Aligned_cols=59  Identities=14%  Similarity=0.112  Sum_probs=42.0

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      .+||+||+..+++.+|.+++..++.+.....  ...+..+|||||+|.+.+++..||. |++
T Consensus         6 tVfVgNLs~~tTE~dLrefFS~~G~I~~V~I--~~d~~~~GfAFVtF~d~eaAe~All-LnG   64 (260)
T PLN03120          6 TVKVSNVSLKATERDIKEFFSFSGDIEYVEM--QSENERSQIAYVTFKDPQGAETALL-LSG   64 (260)
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeEEEEE--eecCCCCCEEEEEeCcHHHHHHHHH-hcC
Confidence            3599999999999999999553332221111  1112357999999999999999996 544

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=96.35  E-value=0.012  Score=54.76  Aligned_cols=65  Identities=18%  Similarity=0.258  Sum_probs=58.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  196 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~  196 (577)
                      ..+...|.|.+||++.++.+|+.++...|.|....+..|       |+|.|+|...++..-||..|+...+.
T Consensus       112 rrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  112 RRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             cccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhcccccc
Confidence            345688999999999999999999999999999999888       69999999999999999999876653

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=96.33  E-value=0.0014  Score=60.38  Aligned_cols=59  Identities=17%  Similarity=0.159  Sum_probs=43.1

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhH
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMV  294 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i  294 (577)
                      +||+||...+++.+|+.++...+.+..++.  .  -..-|||||+|++..+|+.|+..|++..
T Consensus        13 VYVGnL~~~a~k~eLE~~F~~yG~lrsvWv--A--rnPPGfAFVEFed~RDA~DAvr~LDG~~   71 (195)
T KOG0107|consen   13 VYVGNLGSRATKRELERAFSKYGPLRSVWV--A--RNPPGFAFVEFEDPRDAEDAVRYLDGKD   71 (195)
T ss_pred             EEeccCCCCcchHHHHHHHHhcCcceeEEE--e--ecCCCceEEeccCcccHHHHHhhcCCcc
Confidence            499999999999999877442221111111  0  1457899999999999999999998753

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=96.32  E-value=0.0028  Score=67.95  Aligned_cols=61  Identities=13%  Similarity=0.107  Sum_probs=49.2

Q ss_pred             cccccCCCcccchhhhcCCCC---CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTK---SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~k---s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..||+|++..++++.|..++.   .+...+..  .+..+|+++|||||+|.+.+.+..|+..||+.
T Consensus        20 ~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v--~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~   83 (435)
T KOG0108|consen   20 SVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLV--YDRETGKPKGFGFCEFTDEETAERAIRNLNGA   83 (435)
T ss_pred             ceEecCCCCcccHHHHHHHHhccCccceeeec--ccccCCCcCceeeEecCchhhHHHHHHhcCCc
Confidence            359999999999999988833   22222222  23789999999999999999999999999965

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=96.29  E-value=0.012  Score=59.91  Aligned_cols=78  Identities=13%  Similarity=0.190  Sum_probs=62.0

Q ss_pred             CCCceEEEcCCCC----CCCH-------HHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 008117          126 KPQTKVYVGKIAP----TADS-------DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN  194 (577)
Q Consensus       126 ~~~~tlfVgnLp~----~~te-------~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~  194 (577)
                      ...++|.|.||=.    ..+.       ++|..-+.+||.|.+|.|.-    ..+.|.+-|.|.+.+.|..||..|+|..
T Consensus       263 r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d----~hPdGvvtV~f~n~eeA~~ciq~m~GR~  338 (382)
T KOG1548|consen  263 RADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYD----RHPDGVVTVSFRNNEEADQCIQTMDGRW  338 (382)
T ss_pred             cCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEec----cCCCceeEEEeCChHHHHHHHHHhcCee
Confidence            3468899988732    3332       35566688999999998753    3567999999999999999999999999


Q ss_pred             eCCeEEEEEEchh
Q 008117          195 IDGQELMLKVDQA  207 (577)
Q Consensus       195 i~gr~i~V~~a~~  207 (577)
                      |+|+.|...+...
T Consensus       339 fdgRql~A~i~DG  351 (382)
T KOG1548|consen  339 FDGRQLTASIWDG  351 (382)
T ss_pred             ecceEEEEEEeCC
Confidence            9999999875544

>PLN03213 repressor of silencing 3; Provisional

Probab=96.21  E-value=0.0023  Score=67.34  Aligned_cols=59  Identities=10%  Similarity=0.001  Sum_probs=44.3

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCH--HHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDR--KADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~--e~a~~Al~~l~~~  293 (577)
                      +|||||...+++++|..++..++.+...... ..+|  +|||||+|...  .++.+||..|++.
T Consensus        13 IYVGNLSydVTEDDLravFSeFGsVkdVEIp-RETG--RGFAFVEMssdddaEeeKAISaLNGA   73 (759)
T PLN03213         13 LHVGGLGESVGRDDLLKIFSPMGTVDAVEFV-RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGC   73 (759)
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe-cccC--CceEEEEecCCcHHHHHHHHHHhcCC
Confidence            5999999999999999885533333222222 3456  99999999987  6789999988764

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.19  E-value=0.0039  Score=52.58  Aligned_cols=63  Identities=11%  Similarity=0.016  Sum_probs=48.6

Q ss_pred             cccccccccCCCcccchhhhcCCCC---CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhH
Q 008117          227 KETQDAGAGKEDESVQSVEKNEPTK---SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMV  294 (577)
Q Consensus       227 ~~~~~~~v~nl~~~~~~~~l~e~~k---s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i  294 (577)
                      ..+.++||.|||..++.++.-++++   .+.-.+.+.     +...+|-|||.|++..+|.+|++.|++..
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~-----~k~TrGTAFVVYedi~dAk~A~dhlsg~n   81 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGN-----TKETRGTAFVVYEDIFDAKKACDHLSGYN   81 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecC-----ccCcCceEEEEehHhhhHHHHHHHhcccc
Confidence            3466789999999999999888844   233333322     23458999999999999999999998763

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.15  E-value=0.012  Score=44.03  Aligned_cols=52  Identities=13%  Similarity=0.252  Sum_probs=41.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHH
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRAL  187 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al  187 (577)
                      +.|-|.+.++...+.-| .+|..||.|..+.+..      ...+.||.|.+..+|.+||
T Consensus         2 ~wI~V~Gf~~~~~~~vl-~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEEVL-EHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHHHH-HHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            56788898877665544 5888999999988752      2359999999999999985

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=96.06  E-value=0.0036  Score=55.21  Aligned_cols=65  Identities=12%  Similarity=0.051  Sum_probs=49.8

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .-|+||.+++..++++++..++...+-++.... .+-.+|-.|||+.|+|++.+.|..|+..+|+.
T Consensus        72 GwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~  137 (170)
T KOG0130|consen   72 GWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGA  137 (170)
T ss_pred             eEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccch
Confidence            345689999999999998877553332222222 34678999999999999999999999999964

>smart00361 RRM_1 RNA recognition motif

Probab=95.99  E-value=0.0085  Score=47.59  Aligned_cols=27  Identities=15%  Similarity=0.051  Sum_probs=25.3

Q ss_pred             CCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          267 HDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       267 g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +.++|||||.|.+.++|..|+..|++.
T Consensus        34 ~~~rG~~fV~f~~~~dA~~A~~~l~g~   60 (70)
T smart00361       34 NHKRGNVYITFERSEDAARAIVDLNGR   60 (70)
T ss_pred             CCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            889999999999999999999998874

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=95.89  E-value=0.0045  Score=58.90  Aligned_cols=62  Identities=15%  Similarity=0.154  Sum_probs=46.5

Q ss_pred             cccccccCCCcccchhhhcCCCC---CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTK---SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~k---s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      .+++||+.|...+++..|...+-   .+....-.  .+-.+.+++|||||+|+..++|..||.-||+
T Consensus        10 KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiP--lDyesqkHRgFgFVefe~aEDAaaAiDNMne   74 (298)
T KOG0111|consen   10 KRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIP--LDYESQKHRGFGFVEFEEAEDAAAAIDNMNE   74 (298)
T ss_pred             ceeEEeccchHHHHHHHHHhccccccchhhcccc--cchhcccccceeEEEeeccchhHHHhhcCch
Confidence            34579999999999998876522   22222211  3368899999999999999999999887765

>smart00362 RRM_2 RNA recognition motif

Probab=95.89  E-value=0.0061  Score=47.03  Aligned_cols=60  Identities=15%  Similarity=0.129  Sum_probs=41.5

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      .+|.||+..++..++..++...+......-.... +.++|+|||+|.+...|..|+..+++
T Consensus         2 v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-~~~~~~~~v~f~~~~~a~~a~~~~~~   61 (72)
T smart00362        2 LFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT-GKSKGFAFVEFESEEDAEKAIEALNG   61 (72)
T ss_pred             EEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-CCCCceEEEEeCCHHHHHHHHHHhCC
Confidence            3788999999998888773321111111111112 67889999999999999999987775

>PLN03121 nucleic acid binding protein; Provisional

Probab=95.84  E-value=0.0048  Score=60.40  Aligned_cols=65  Identities=12%  Similarity=-0.019  Sum_probs=45.5

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhHHHH
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEER  297 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i~e~  297 (577)
                      .+||+||+..+++.+|++|+..++.+.....  ...+..++||||+|.+.+++..|+..-...|...
T Consensus         7 TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I--~~D~et~gfAfVtF~d~~aaetAllLnGa~l~d~   71 (243)
T PLN03121          7 TAEVTNLSPKATEKDVYDFFSHCGAIEHVEI--IRSGEYACTAYVTFKDAYALETAVLLSGATIVDQ   71 (243)
T ss_pred             EEEEecCCCCCCHHHHHHHHHhcCCeEEEEE--ecCCCcceEEEEEECCHHHHHHHHhcCCCeeCCc
Confidence            3599999999999999999553332222222  1124567899999999999999985444445444

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=95.76  E-value=0.0061  Score=53.41  Aligned_cols=65  Identities=14%  Similarity=0.054  Sum_probs=49.6

Q ss_pred             cccccccCCCcccchhhhcCC-CCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEP-TKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~-~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..++++.+-+| ++...+.+...-.+..+-.+=||+||+|-+.++|+.|+.=|++.
T Consensus        36 S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~Alryisgt  101 (153)
T KOG0121|consen   36 SCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGT  101 (153)
T ss_pred             cceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccC
Confidence            344699999999999999999 44222333333344566667899999999999999999988775

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=95.75  E-value=0.0047  Score=58.41  Aligned_cols=65  Identities=9%  Similarity=0.060  Sum_probs=48.3

Q ss_pred             ccccCCCcccchhhhcCCCC-CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhHHH
Q 008117          232 AGAGKEDESVQSVEKNEPTK-SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEE  296 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~k-s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i~e  296 (577)
                      +.|.||..-++.++|..++. -..++...--.+.-++.++|||||.|.+..+|+.|++.|.+.+.+
T Consensus        16 LkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ld   81 (256)
T KOG4207|consen   16 LKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLD   81 (256)
T ss_pred             EEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeec
Confidence            46789999999999987744 111111111133678899999999999999999999999887554

>smart00360 RRM RNA recognition motif

Probab=95.75  E-value=0.0068  Score=46.53  Aligned_cols=59  Identities=20%  Similarity=0.228  Sum_probs=39.6

Q ss_pred             ccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          234 AGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       234 v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      |+||+..++..++..++...+......- ....++.++|||||.|.+.++|..|+..+++
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~   60 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNG   60 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCC
Confidence            4677888888888777331111110000 1133688899999999999999999887763

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=95.60  E-value=0.007  Score=60.01  Aligned_cols=63  Identities=17%  Similarity=0.173  Sum_probs=48.0

Q ss_pred             ccccccCCCcccchhhhcCCCCCCccc-ccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENL-KDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~-k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      ..+||+||+..+++++|..+++..+.. ......+..+|.++|||||.|.+.+++..|+..+++
T Consensus       116 ~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~  179 (306)
T COG0724         116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNG  179 (306)
T ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCC
Confidence            446999999999999999885522211 111112237899999999999999999999999983

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=95.57  E-value=0.0047  Score=69.30  Aligned_cols=79  Identities=14%  Similarity=0.167  Sum_probs=70.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      ...|||.|+|+..|.++|+.+|.++|.+.++.+++.+ .|+++|.+||.|.+..++..++...++..+.-..+.|.++..
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            5679999999999999999999999999999988884 899999999999999999999988887777777777765544

>KOG1923 consensus Rac1 GTPase effector FRL [Signal transduction mechanisms; Cytoskeleton]

Probab=95.38  E-value=0.056  Score=60.42  Aligned_cols=11  Identities=36%  Similarity=0.286  Sum_probs=4.6

Q ss_pred             HHhhhHHHHhh
Q 008117          289 KLTCMVEERLK  299 (577)
Q Consensus       289 ~l~~~i~e~~~  299 (577)
                      ++..+++..+.
T Consensus       562 ~lr~VleiILA  572 (830)
T KOG1923|consen  562 KLRPVLEIILA  572 (830)
T ss_pred             HHHHHHHHHHH
Confidence            33444444443

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=95.17  E-value=0.058  Score=53.70  Aligned_cols=63  Identities=22%  Similarity=0.133  Sum_probs=50.4

Q ss_pred             HHHHHHHhhcCceEEEEEeecCCCCCc-ceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          143 DFVLSVLKVCGTVKSWKRAQYPSNGTP-KGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       143 ~~L~~~F~~~G~v~~~~i~~~~~tg~~-kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      +++..-+.+||.|..|.|.-.+.-... .---||+|...++|.+|+..|||..|+|+.+...|.
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFY  364 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheec
Confidence            366788889999999988776422222 234799999999999999999999999999887654

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=95.08  E-value=0.023  Score=59.02  Aligned_cols=73  Identities=16%  Similarity=0.271  Sum_probs=57.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc-eeCCeEEEEEEch
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKS-WKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKF-NIDGQELMLKVDQ  206 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~-~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~-~i~gr~i~V~~a~  206 (577)
                      ..||+|||.+.++..+|..+|...-...+ -.++.       .||+||.+.+...|.+|+..|+|. .+.|+++.|..+.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k-------~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv   74 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK-------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee-------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence            46899999999999999999985421111 12222       289999999999999999999986 5789999997665


Q ss_pred             hh
Q 008117          207 AT  208 (577)
Q Consensus       207 ~~  208 (577)
                      ..
T Consensus        75 ~k   76 (584)
T KOG2193|consen   75 PK   76 (584)
T ss_pred             hH
Confidence            43

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=95.00  E-value=0.05  Score=61.69  Aligned_cols=79  Identities=14%  Similarity=0.286  Sum_probs=68.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEE
Q 008117          124 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG--QELM  201 (577)
Q Consensus       124 ~~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~g--r~i~  201 (577)
                      .....+.+|||+|..++....|...|..||.|..|.+-.    |  ..|+||.|.+...++.|+..|-|..|+|  +.|.
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h----g--q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~r  524 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH----G--QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLR  524 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc----C--CcceeeecccCccchhhHHHHhcCcCCCCCcccc
Confidence            345678999999999999999999999999998876532    2  3599999999999999999999999985  6799


Q ss_pred             EEEchhh
Q 008117          202 LKVDQAT  208 (577)
Q Consensus       202 V~~a~~~  208 (577)
                      |.|+...
T Consensus       525 vdla~~~  531 (975)
T KOG0112|consen  525 VDLASPP  531 (975)
T ss_pred             cccccCC
Confidence            9887653

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=94.71  E-value=0.034  Score=54.43  Aligned_cols=62  Identities=19%  Similarity=0.304  Sum_probs=56.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN  191 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Ln  191 (577)
                      ..|||.||+..++.+.|..-|+.||.|....++.| ..+++.+-++|.|...-.|..|+..++
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhc
Confidence            78999999999999999999999999988777766 578999999999999999999998773

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=94.57  E-value=0.039  Score=59.74  Aligned_cols=63  Identities=8%  Similarity=-0.044  Sum_probs=49.1

Q ss_pred             ccccccccccCCCcccchhhhcCC-CCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          226 LKETQDAGAGKEDESVQSVEKNEP-TKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       226 ~~~~~~~~v~nl~~~~~~~~l~e~-~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ....|+++|.||---+|..+|.+| +..++++.+.     ...+.|.-+||.|.+.+.|...+..||++
T Consensus       441 ~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-----WmDkIKShCyV~yss~eEA~atr~AlhnV  504 (718)
T KOG2416|consen  441 KEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-----WMDKIKSHCYVSYSSVEEAAATREALHNV  504 (718)
T ss_pred             CCccceEeeecccccchHHHHHHHHhhccCchHHH-----HHHHhhcceeEecccHHHHHHHHHHHhcc
Confidence            456788899999999999999988 4444444322     33456778999999999999999999876

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.33  E-value=0.17  Score=45.36  Aligned_cols=75  Identities=17%  Similarity=0.237  Sum_probs=57.2

Q ss_pred             CCCCceEEEcCCCCCCCH----HHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 008117          125 EKPQTKVYVGKIAPTADS----DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL  200 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te----~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i  200 (577)
                      +++..||.|.=|..++..    ..+...++.||+|.+|.+.     |+  .-|.|.|.+..+|..|+.+++. ...|..+
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----Gr--qsavVvF~d~~SAC~Av~Af~s-~~pgtm~  154 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----GR--QSAVVVFKDITSACKAVSAFQS-RAPGTMF  154 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----CC--ceEEEEehhhHHHHHHHHhhcC-CCCCceE
Confidence            556788888866655543    3566677899999999763     32  4799999999999999999876 5667888


Q ss_pred             EEEEchh
Q 008117          201 MLKVDQA  207 (577)
Q Consensus       201 ~V~~a~~  207 (577)
                      .+.|.+.
T Consensus       155 qCsWqqr  161 (166)
T PF15023_consen  155 QCSWQQR  161 (166)
T ss_pred             Eeecccc
Confidence            8877543

>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=94.26  E-value=0.033  Score=43.03  Aligned_cols=61  Identities=18%  Similarity=0.156  Sum_probs=41.2

Q ss_pred             cccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          233 GAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       233 ~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +|.+|+..++..++..++...+......-.....+..+|+|||.|.+.++|..|+..+++.
T Consensus         3 ~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~   63 (74)
T cd00590           3 FVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGK   63 (74)
T ss_pred             EEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCC
Confidence            7888999998888877733111111000111222366899999999999999999888765

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).

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=94.09  E-value=0.027  Score=55.18  Aligned_cols=63  Identities=19%  Similarity=0.217  Sum_probs=51.3

Q ss_pred             HHHHHHh-hcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          144 FVLSVLK-VCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       144 ~L~~~F~-~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      +|...|. +||.|..+.|..+ ..-...|-.||.|...++|.+|+..||+-.|.|++|...+..-
T Consensus        84 d~f~E~~~kygEiee~~Vc~N-l~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDN-LGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhcc-cchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            3444444 9999999977665 3445578899999999999999999999999999999876543

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=93.61  E-value=2.5  Score=42.73  Aligned_cols=62  Identities=24%  Similarity=0.275  Sum_probs=47.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 008117          130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQE  199 (577)
Q Consensus       130 tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~  199 (577)
                      =|-|-++++.-. ..|..+|.+||.|+.....      ..-.|-+|-|.+..+|.+||.. ||..|+|..
T Consensus       199 WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALsk-ng~ii~g~v  260 (350)
T KOG4285|consen  199 WVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALSK-NGTIIDGDV  260 (350)
T ss_pred             eEEEeccCccch-hHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhhh-cCeeeccce
Confidence            344556776533 5677899999999887543      2235999999999999999995 999998754

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=93.40  E-value=0.38  Score=37.20  Aligned_cols=55  Identities=15%  Similarity=0.039  Sum_probs=45.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhc---CceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVC---GTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL  190 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~---G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~L  190 (577)
                      ...|+|.|+. .++..+|+.+|..|   .....+.++-|.       -|-|.|.+...|.+||.+|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            4579999986 68889999999998   235678888773       5779999999999999764

>KOG1923 consensus Rac1 GTPase effector FRL [Signal transduction mechanisms; Cytoskeleton]

Probab=93.23  E-value=0.43  Score=53.62  Aligned_cols=7  Identities=29%  Similarity=0.819  Sum_probs=2.7

Q ss_pred             ccccccc
Q 008117            9 VGRLQIL   15 (577)
Q Consensus         9 ~~~~~~~   15 (577)
                      +|-++..
T Consensus       244 i~emq~~  250 (830)
T KOG1923|consen  244 IGEMQLA  250 (830)
T ss_pred             ccccccc
Confidence            3334433

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=93.20  E-value=0.033  Score=56.76  Aligned_cols=78  Identities=21%  Similarity=0.293  Sum_probs=60.4

Q ss_pred             CceEEEcCCCCCCCHHHHH---HHHhhcCceEEEEEeecCC----CCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 008117          128 QTKVYVGKIAPTADSDFVL---SVLKVCGTVKSWKRAQYPS----NGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL  200 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~---~~F~~~G~v~~~~i~~~~~----tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i  200 (577)
                      ..-+||-+|+..+-.+.+.   ..|..||.|..+.+..++.    .|.+ +-+||+|...++|..||...+|+.++|+.|
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~-~s~yITy~~~eda~rci~~v~g~~~dg~~l  155 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGT-CSVYITYEEEEDADRCIDDVDGFVDDGRAL  155 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCC-CcccccccchHhhhhHHHHhhhHHhhhhhh
Confidence            3568888999877666543   6889999999998877652    2222 338999999999999999999999999987


Q ss_pred             EEEEch
Q 008117          201 MLKVDQ  206 (577)
Q Consensus       201 ~V~~a~  206 (577)
                      +..+..
T Consensus       156 ka~~gt  161 (327)
T KOG2068|consen  156 KASLGT  161 (327)
T ss_pred             HHhhCC
Confidence            665443

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=93.17  E-value=0.31  Score=55.21  Aligned_cols=76  Identities=18%  Similarity=0.150  Sum_probs=63.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee--CCeEEEEEEc
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI--DGQELMLKVD  205 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i--~gr~i~V~~a  205 (577)
                      ....++.|.+-+.+-..|..+|+.||.|.+....++      ...+.|+|.+.+.|..|+.+|+|..+  .|-+.+|.++
T Consensus       298 qp~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~------~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~a  371 (1007)
T KOG4574|consen  298 QPKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRD------LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFA  371 (1007)
T ss_pred             cchhhhhcccccchHHHHHHHHHhhcchhhheeccc------ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEec
Confidence            345667777888899999999999999998876665      25899999999999999999999876  4888899888


Q ss_pred             hhhH
Q 008117          206 QATR  209 (577)
Q Consensus       206 ~~~~  209 (577)
                      ....
T Consensus       372 k~~~  375 (1007)
T KOG4574|consen  372 KTLP  375 (1007)
T ss_pred             cccc
Confidence            6643

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=91.66  E-value=0.55  Score=38.38  Aligned_cols=56  Identities=7%  Similarity=0.071  Sum_probs=41.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNK  192 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng  192 (577)
                      ....||+ .|..+...+|.++|+.||.|. |..+.+       .-|||.....+.|..++..+..
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d-------TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND-------TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT-------TEEEEEECCCHHHHHHHHHHTT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC-------CcEEEEeecHHHHHHHHHHhcc
Confidence            3445555 999999999999999999864 444555       3799999999999999988763

; 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.

>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=91.10  E-value=0.5  Score=45.03  Aligned_cols=62  Identities=19%  Similarity=0.151  Sum_probs=45.9

Q ss_pred             CHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCeEEEEEEchhh
Q 008117          141 DSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN--KFNIDGQELMLKVDQAT  208 (577)
Q Consensus       141 te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Ln--g~~i~gr~i~V~~a~~~  208 (577)
                      ....|+.+|..|+.+..+.+...      .+=..|.|.+.+.|..|...|+  +..|.|..|+|.|+...
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            34789999999999998876543      2457899999999999999999  99999999999888443

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.

>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=91.08  E-value=2.2  Score=37.14  Aligned_cols=67  Identities=12%  Similarity=0.035  Sum_probs=48.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcC-ceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCG-TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  196 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G-~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~  196 (577)
                      ...+.+...|+.++.++|..+.+.+- .|..++|+.+.  ...+..+.+.|.+..+|..-...+||..++
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            34444455555666667766666655 56677888762  235566889999999999999999999885

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG4672 consensus Uncharacterized conserved low complexity protein [Function unknown]

Probab=90.82  E-value=1.2  Score=46.64  Aligned_cols=10  Identities=0%  Similarity=0.242  Sum_probs=4.5

Q ss_pred             HHHHHHHhhh
Q 008117          284 QEALEKLTCM  293 (577)
Q Consensus       284 ~~Al~~l~~~  293 (577)
                      ...|+.|.++
T Consensus       477 ~~FMkEM~gL  486 (487)
T KOG4672|consen  477 NAFMKEMDGL  486 (487)
T ss_pred             HHHHHHHhcc
Confidence            4444444443

>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=90.75  E-value=0.31  Score=46.25  Aligned_cols=81  Identities=11%  Similarity=0.110  Sum_probs=50.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhh-cCceEEEEEe---ecCCCC--CcceEEEEEeCCHHHHHHHHHHhCCceeC---C
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKV-CGTVKSWKRA---QYPSNG--TPKGFGFCEFESAEGVLRALRLLNKFNID---G  197 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~-~G~v~~~~i~---~~~~tg--~~kg~gFV~f~~~~~A~~Al~~Lng~~i~---g  197 (577)
                      ....|.|.+||+++|++++...++. ++.-..|..+   ....+.  ..-+-|||.|.+.+++...+..++|+.|.   |
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            4568999999999999999997776 6655222222   221111  12356999999999999999999998873   2


Q ss_pred             --eEEEEEEchh
Q 008117          198 --QELMLKVDQA  207 (577)
Q Consensus       198 --r~i~V~~a~~  207 (577)
                        ....|.+|-.
T Consensus        86 ~~~~~~VE~Apy   97 (176)
T PF03467_consen   86 NEYPAVVEFAPY   97 (176)
T ss_dssp             -EEEEEEEE-SS
T ss_pred             CCcceeEEEcch
Confidence              2445555544

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.

>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=89.62  E-value=1.7  Score=34.81  Aligned_cols=67  Identities=12%  Similarity=0.168  Sum_probs=39.1

Q ss_pred             eEEEc-CCCCCCCHHHHHHHHhhcCc-----eEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 008117          130 KVYVG-KIAPTADSDFVLSVLKVCGT-----VKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  203 (577)
Q Consensus       130 tlfVg-nLp~~~te~~L~~~F~~~G~-----v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~  203 (577)
                      +|||. +--..++..+|..+|...+.     |-.+.|..+        |+||+.... .|..++..|++..+.|+.|.|.
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve   72 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPEE-VAEKVLEALNGKKIKGKKVRVE   72 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-TT--HHHHHHHHTT--SSS----EE
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECHH-HHHHHHHHhcCCCCCCeeEEEE
Confidence            45553 23347888889988887654     446666543        999998765 6788999999999999999997


Q ss_pred             Ec
Q 008117          204 VD  205 (577)
Q Consensus       204 ~a  205 (577)
                      .|
T Consensus        73 ~A   74 (74)
T PF03880_consen   73 RA   74 (74)
T ss_dssp             E-
T ss_pred             EC
Confidence            54

; PDB: 2G0C_A 3MOJ_B.

>KOG4246 consensus Predicted DNA-binding protein, contains SAP domain [General function prediction only]

Probab=89.52  E-value=1.2  Score=50.46  Aligned_cols=9  Identities=11%  Similarity=0.508  Sum_probs=4.6

Q ss_pred             CceEEEcCC
Q 008117          128 QTKVYVGKI  136 (577)
Q Consensus       128 ~~tlfVgnL  136 (577)
                      ...+|+|++
T Consensus       145 ~qR~f~gvv  153 (1194)
T KOG4246|consen  145 PQRRFAGVV  153 (1194)
T ss_pred             cceeeehhh
Confidence            445566533

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=89.27  E-value=6.5  Score=43.89  Aligned_cols=11  Identities=55%  Similarity=0.673  Sum_probs=5.0

Q ss_pred             HHHHHHHHhHh
Q 008117          480 RRKRIREKEED  490 (577)
Q Consensus       480 ~~~r~re~e~~  490 (577)
                      .++|.++.++-
T Consensus       354 ~~dR~qeqee~  364 (668)
T KOG2253|consen  354 RRDRHQEQEEL  364 (668)
T ss_pred             hhHHHHHHHHH
Confidence            34455544433

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=89.10  E-value=0.22  Score=52.84  Aligned_cols=73  Identities=7%  Similarity=-0.018  Sum_probs=58.8

Q ss_pred             CceEEEcCCCCCCC-HHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          128 QTKVYVGKIAPTAD-SDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       128 ~~tlfVgnLp~~~t-e~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      .+.|-+..+++... -++|...|.+||.|..|.|-..      --.|.|+|.+..+|-.|.. .++..|+++.|+|.|-.
T Consensus       372 hs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whn  444 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHN  444 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhc-cccceecCceeEEEEec
Confidence            45555566666554 4699999999999999987543      3479999999999988887 59999999999998865


Q ss_pred             h
Q 008117          207 A  207 (577)
Q Consensus       207 ~  207 (577)
                      .
T Consensus       445 p  445 (526)
T KOG2135|consen  445 P  445 (526)
T ss_pred             C
Confidence            5

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=88.68  E-value=4.9  Score=43.85  Aligned_cols=70  Identities=23%  Similarity=0.290  Sum_probs=56.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhh--cCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCeEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKV--CGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN--KFNIDGQELML  202 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~--~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Ln--g~~i~gr~i~V  202 (577)
                      ..|.|.+.-||.++..++++.||..  |-++.+|.+..+.       -=||+|.+..+|+.|...|.  -..|.|+.|..
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            4578889999999999999999985  8899999887662       35899999999999998773  34567777664


Q ss_pred             E
Q 008117          203 K  203 (577)
Q Consensus       203 ~  203 (577)
                      .
T Consensus       247 R  247 (684)
T KOG2591|consen  247 R  247 (684)
T ss_pred             h
Confidence            3

>PF13893 RRM_5: RNA recognition motif

Probab=87.67  E-value=0.74  Score=34.37  Aligned_cols=24  Identities=25%  Similarity=0.297  Sum_probs=22.0

Q ss_pred             CceEEEEeCCHHHHHHHHHHHhhh
Q 008117          270 TNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       270 kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ++++||+|.+.++|..|+..|++.
T Consensus        21 ~~~a~V~f~~~~~A~~a~~~l~~~   44 (56)
T PF13893_consen   21 RGFAFVEFASVEDAQKAIEQLNGR   44 (56)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTS
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCC
Confidence            589999999999999999998864

(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 ....

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=86.94  E-value=0.3  Score=52.35  Aligned_cols=64  Identities=19%  Similarity=0.097  Sum_probs=45.1

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhHH
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCMVE  295 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i~  295 (577)
                      +||+||+..++..+|+++++..+.++...- +..-.+++.+||||+|.+..++..||.+--..|.
T Consensus       291 i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig  355 (419)
T KOG0116|consen  291 IFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIG  355 (419)
T ss_pred             eEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccC
Confidence            499999999999999999774443332221 1122355559999999999999998876533333

>KOG1925 consensus Rac1 GTPase effector FHOS [Signal transduction mechanisms; Cytoskeleton]

Probab=86.73  E-value=1.9  Score=46.28  Aligned_cols=28  Identities=11%  Similarity=0.208  Sum_probs=18.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhh
Q 008117          124 AEKPQTKVYVGKIAPTADSDFVLSVLKV  151 (577)
Q Consensus       124 ~~~~~~tlfVgnLp~~~te~~L~~~F~~  151 (577)
                      ...+..++|-.-=+-.+...-|..+|..
T Consensus       302 ~~r~~~t~W~s~D~~~~D~~r~~~LFEs  329 (817)
T KOG1925|consen  302 ASRPCATLWASLDPVSVDTARLEHLFES  329 (817)
T ss_pred             cccccchhhhccCcceecHHHHHHHHHH
Confidence            3455666776544556777889999973

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=85.84  E-value=2.8  Score=44.64  Aligned_cols=69  Identities=10%  Similarity=0.104  Sum_probs=59.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcC-ceEEEEEeecCCCCCcceE-EEEEeCCHHHHHHHHHHhCCceeCC
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCG-TVKSWKRAQYPSNGTPKGF-GFCEFESAEGVLRALRLLNKFNIDG  197 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G-~v~~~~i~~~~~tg~~kg~-gFV~f~~~~~A~~Al~~Lng~~i~g  197 (577)
                      .+++.|+|-.+|..+|-.+|..|+..|- .|..++|+++   |.+..| .+|.|.+..+|......+||..|+.
T Consensus        72 ~~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd---~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   72 SSSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRD---GMPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CCCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeec---CCCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            3488999999999999999999998765 6889999985   455445 6899999999999999999998863

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=85.56  E-value=1.3  Score=48.20  Aligned_cols=54  Identities=17%  Similarity=0.164  Sum_probs=39.7

Q ss_pred             cCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC----CeEEEEEEc
Q 008117          152 CGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID----GQELMLKVD  205 (577)
Q Consensus       152 ~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~----gr~i~V~~a  205 (577)
                      .|.-..+.++.|=.+....|||||.|.+++++..+.+++||+.+.    .+.+.+.||
T Consensus       413 ~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYA  470 (549)
T KOG4660|consen  413 KGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYA  470 (549)
T ss_pred             cCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehh
Confidence            454455556666555566799999999999999999999998763    344455554

>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]

Probab=85.46  E-value=0.68  Score=54.01  Aligned_cols=37  Identities=8%  Similarity=0.069  Sum_probs=25.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeec
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQY  163 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~  163 (577)
                      ...+++|--+-..+..+.|+.+.+.|+...++....|
T Consensus        71 kak~~~v~t~ka~~PpeHLrki~~~~sdm~s~~~~~D  107 (2365)
T COG5178          71 KAKTLHVLTLKAPIPPEHLRKIQSPCSDMPSVLTKVD  107 (2365)
T ss_pred             hhhheeeeccCCCCCHHHHHhhhCccccchhhhhhhh
Confidence            3566777777777777888888887776655544333

>PHA03378 EBNA-3B; Provisional

Probab=84.88  E-value=8.2  Score=43.20  Aligned_cols=12  Identities=8%  Similarity=0.194  Sum_probs=6.8

Q ss_pred             CCCHHHHHHHHh
Q 008117          139 TADSDFVLSVLK  150 (577)
Q Consensus       139 ~~te~~L~~~F~  150 (577)
                      .-+...|+.|+.
T Consensus       819 gp~k~ilrqllt  830 (991)
T PHA03378        819 GPTKQILRQLLT  830 (991)
T ss_pred             CcHHHHHHHHhh
Confidence            345556666663

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=84.60  E-value=0.61  Score=46.29  Aligned_cols=62  Identities=11%  Similarity=0.019  Sum_probs=48.9

Q ss_pred             ccccCCCcccchhhhcCCCCCC-cccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhH
Q 008117          232 AGAGKEDESVQSVEKNEPTKSP-ENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMV  294 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~-~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i  294 (577)
                      ++|.||+..+++.+|.+|+..+ .+.+ .-.-.+..|.+.|.|-|.|...++|..|+..++++.
T Consensus        86 v~v~NL~~~V~~~Dl~eLF~~~~~~~r-~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~  148 (243)
T KOG0533|consen   86 VNVSNLPYGVIDADLKELFAEFGELKR-VAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVA  148 (243)
T ss_pred             eeeecCCcCcchHHHHHHHHHhccceE-EeeccCCCCCCCccceeeecchHhHHHHHHHhcCcc
Confidence            4899999999999999995522 2211 112237789999999999999999999999999853

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.18  E-value=4.5  Score=44.41  Aligned_cols=80  Identities=13%  Similarity=0.136  Sum_probs=60.5

Q ss_pred             CCCCceEEEcCCCC-CCCHHHHHHHHhhc----CceEEEEEeecC----------CCCC---------------------
Q 008117          125 EKPQTKVYVGKIAP-TADSDFVLSVLKVC----GTVKSWKRAQYP----------SNGT---------------------  168 (577)
Q Consensus       125 ~~~~~tlfVgnLp~-~~te~~L~~~F~~~----G~v~~~~i~~~~----------~tg~---------------------  168 (577)
                      ...+++|-|.||.| .+...+|.-+|+.|    |.|.+|.|...-          ..|.                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            45678999999998 57778999999876    589999876421          1222                     


Q ss_pred             ---------------c-ceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 008117          169 ---------------P-KGFGFCEFESAEGVLRALRLLNKFNIDG--QELMLKV  204 (577)
Q Consensus       169 ---------------~-kg~gFV~f~~~~~A~~Al~~Lng~~i~g--r~i~V~~  204 (577)
                                     . .-||.|+|.++..|...+..++|+.|..  ..|-+.|
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRF  304 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRF  304 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeee
Confidence                           1 1368999999999999999999999964  4444443

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=83.24  E-value=0.99  Score=44.71  Aligned_cols=61  Identities=18%  Similarity=0.086  Sum_probs=45.1

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccc-cCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLK-DNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k-~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      ..|++|+....+...+...+.+++... ..-..+...|.+|||+||+|.+.+.+..|+. |++
T Consensus       103 sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~g  164 (231)
T KOG4209|consen  103 SVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDG  164 (231)
T ss_pred             eEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCC
Confidence            359999999988888665566554332 1222346777899999999999999999988 544

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=81.80  E-value=0.88  Score=50.74  Aligned_cols=68  Identities=19%  Similarity=0.118  Sum_probs=48.5

Q ss_pred             ccccccccccCCCcccchhhhcCCCC------CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhHHH
Q 008117          226 LKETQDAGAGKEDESVQSVEKNEPTK------SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEE  296 (577)
Q Consensus       226 ~~~~~~~~v~nl~~~~~~~~l~e~~k------s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i~e  296 (577)
                      ...||+ |++||+..+++..|...++      ++.++-.-  +....-.-..||||.|.++.+++.|+..|++++-.
T Consensus       172 P~TTNl-yv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpR--tEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~  245 (877)
T KOG0151|consen  172 PQTTNL-YVGNLNPSVDENFLLRTFGRFGPLASVKIMWPR--TEEEKRRERNCGFVAFMNRADAERALKELQGIIVM  245 (877)
T ss_pred             Ccccce-eeecCCccccHHHHHHHhcccCcccceeeeccc--chhhhccccccceeeehhhhhHHHHHHHhcceeee
Confidence            445665 9999999999998765532      33332211  11333455779999999999999999999997653

>PF11600 CAF-1_p150: Chromatin assembly factor 1 complex p150 subunit, N-terminal; InterPro: IPR021644 P150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesised and acetylated histones H3/H4 into chromatin during DNA replication and repair []

Probab=80.67  E-value=59  Score=31.77  Aligned_cols=11  Identities=45%  Similarity=0.516  Sum_probs=5.2

Q ss_pred             HHHHHHHHHHH
Q 008117          501 IAVAKRRAEEE  511 (577)
Q Consensus       501 ~~~~~~~~~~~  511 (577)
                      .++.+++.+|.
T Consensus       162 keeekr~~eE~  172 (216)
T PF11600_consen  162 KEEEKRKKEEE  172 (216)
T ss_pred             HHHHHHhhHHH
Confidence            44444555544

P150 is the HP1 interaction site of CAF-1 and lies within the N-terminal region of the protein [].

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	577
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		1e-05
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-05
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		2e-05
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		8e-05

>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 = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
           V+VG I   A  + +  +    G V S++       G PKG+GFCE++  E  L A+R L
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 191 NKFNIDGQELMLKVDQATRE 210
           N     G+   L+VD A  E
Sbjct: 71  NGREFSGR--ALRVDNAASE 88

>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 = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 39/71 (54%)
Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
           ++YV  +      D + SV +  G +KS   A+ P+ G  KG+GF E+E A+    A+  
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
Query: 190 LNKFNIDGQEL 200
           +N F++ GQ L
Sbjct: 187 MNLFDLGGQYL 197

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 39/71 (54%)
Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
           ++YV  +      D + SV +  G +KS   A+ P+ G  KG+GF E+E A+    A+  
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Query: 190 LNKFNIDGQEL 200
           +N F++ GQ L
Sbjct: 172 MNLFDLGGQYL 182

>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 = 45.4 bits (106), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 38/71 (53%)
Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
           ++YV  +      D + SV +  G +KS   A+ P+ G  KG+GF E+E A+    A+  
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170
Query: 190 LNKFNIDGQEL 200
            N F++ GQ L
Sbjct: 171 XNLFDLGGQYL 181

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	577
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	9e-14
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-13
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	9e-08
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-12
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-06
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	7e-12
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-11
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-10
2ycu_A	995	Non muscle myosin 2C, alpha-actinin; motor protein	6e-11
2ycu_A	995	Non muscle myosin 2C, alpha-actinin; motor protein	1e-05
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	7e-11
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-11
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	9e-11
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-10
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-08
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-10
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-10
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-10
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	5e-10
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	5e-10
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	5e-10
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	6e-09
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	5e-07
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	1e-09
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-09
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-09
2zuo_A	861	MVP, major vault protein; repeat domains, protein-	2e-09
2zuo_A	861	MVP, major vault protein; repeat domains, protein-	7e-07
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-09
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-05
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-09
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-09
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-07
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-09
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-09
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-09
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	7e-09
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	4e-08
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	4e-08
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	5e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	7e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	7e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	5e-04
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-09
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-05
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-04
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-09
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-09
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	3e-09
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	1e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	4e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	7e-07
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	4e-04
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-09
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-08
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-05
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-09
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-07
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	5e-09
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	7e-09
2div_A	99	TRNA selenocysteine associated protein; structural	7e-09
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	9e-09
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	9e-09
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-08
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-08
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-08
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-08
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-08
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	2e-08
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	2e-04
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-08
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-08
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-08
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-08
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-08
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-08
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	4e-08
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-08
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	5e-08
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	5e-08
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	6e-08
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	7e-08
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-05
1x4e_A	85	RNA binding motif, single-stranded interacting pro	7e-08
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	8e-08
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	8e-08
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	9e-08
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-07
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-07
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	7e-05
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-07
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-07
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-07
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-07
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-07
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-07
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-07
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-07
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-07
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	3e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-07
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	4e-07
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-07
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	5e-07
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	5e-07
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	6e-07
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	7e-07
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	8e-07
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	9e-07
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	9e-07
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	9e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-04
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-06
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-06
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-06
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-06
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-06
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-06
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-06
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-06
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-06
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	4e-06
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-06
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-06
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-04
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-06
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-06
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	6e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	6e-06
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	7e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	7e-06
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-05
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-05
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-05
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-05
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-05
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-05
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-05
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-05
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-05
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-05
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	5e-05
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	5e-05
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	5e-05
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	5e-05
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	6e-05
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	7e-05
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-04
2dis_A	109	Unnamed protein product; structural genomics, RRM	8e-05
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	9e-05
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-04
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-04
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-04
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-04
1w1w_A	430	Structural maintenance of chromosome 1; cohesin, c	3e-04
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	3e-04
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	3e-04
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	5e-04
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-04
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-04
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	5e-04
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	7e-04
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	7e-04
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	8e-04

>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 = 66.2 bits (162), Expect = 9e-14
 Identities = 17/94 (18%), Positives = 29/94 (30%), Gaps = 10/94 (10%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPS--------NGTPKGFGF 174
            +      ++V  +      + V    K  G +K+ K+   P          G  KG   
Sbjct: 8   HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 67

Query: 175 CEFESAEGVLRALRLLNKFNIDGQELMLKVDQAT 208
             F+       A+   +     G    +KV  AT
Sbjct: 68  VSFDDPPSAKAAIDWFDGKEFSGNP--IKVSFAT 99

>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 = 68.5 bits (168), Expect = 1e-13
 Identities = 27/115 (23%), Positives = 48/115 (41%), Gaps = 4/115 (3%)

Query: 94  VARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCG 153
           + RP            P V  P  + TV P      K+++G +    + D V  +L   G
Sbjct: 82  IRRPHDYQPLPGMSENPSVYVPGVVSTVVP--DSAHKLFIGGLPNYLNDDQVKELLTSFG 139

Query: 154 TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQAT 208
            +K++   +  + G  KG+ FCE+       +A+  LN   +  +   L V +A+
Sbjct: 140 PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK--KLLVQRAS 192

>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 = 51.6 bits (124), Expect = 9e-08
 Identities = 28/177 (15%), Positives = 53/177 (29%), Gaps = 22/177 (12%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQY-----PSNGTPKGFGFCEFESAEGVL 184
           ++YVG I      + ++        +    +A             K F F EF S +   
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 185 RALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGK-------- 236
           +A+   +     GQ L ++     +       +        +       A K        
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124

Query: 237 --EDESVQSV-EKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKL 290
              D+ V+ +     P K+   +KD+ TG         +      D     +A+  L
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGL-----SKGYAFCEYVDINVTDQAIAGL 176

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 63.4 bits (155), Expect = 6e-12
 Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 2/82 (2%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
              K+++G +    + D V  +L   G +K++   +  + G  KG+ FCE+       +A
Sbjct: 93  GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 152

Query: 187 LRLLNKFNIDGQELMLKVDQAT 208
           +  LN   +  ++  L V +A+
Sbjct: 153 IAGLNGMQLGDKK--LLVQRAS 172

>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 = 46.1 bits (110), Expect = 5e-06
 Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 6/79 (7%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQY-----PSNGTPKGFGFCEFESAEGVL 184
           ++YVG I      + ++        +    +A             K F F EF S +   
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 185 RALRLLNKFNIDGQELMLK 203
           +A+   +     GQ L ++
Sbjct: 66  QAMA-FDGIIFQGQSLKIR 83

>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 = 60.7 bits (148), Expect = 7e-12
 Identities = 21/89 (23%), Positives = 35/89 (39%), Gaps = 8/89 (8%)

Query: 123 PAEKPQ-TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPS--NGTPKGFGFCEFES 179
           PA++     V+VG +      + +  +    G +             G PK FGF  F+ 
Sbjct: 10  PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTK---VTICKDREGKPKSFGFVCFKH 66

Query: 180 AEGVLRALRLLNKFNIDGQELMLKVDQAT 208
            E V  A+ LLN   + G+   + V   +
Sbjct: 67  PESVSYAIALLNGIRLYGRP--INVSGPS 93

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 60.9 bits (148), Expect = 1e-11
 Identities = 18/93 (19%), Positives = 29/93 (31%), Gaps = 10/93 (10%)

Query: 125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPS--------NGTPKGFGFCE 176
                 ++V  +      + V    K  G +K+ K+   P          G  KG     
Sbjct: 4   NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63

Query: 177 FESAEGVLRALRLLNKFNIDGQELMLKVDQATR 209
           F+       A+   +     G    +KV  ATR
Sbjct: 64  FDDPPSAKAAIDWFDGKEFSGNP--IKVSFATR 94

>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 = 59.2 bits (144), Expect = 3e-11
 Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 2/82 (2%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
           P   VY+G I      + +L +    G V + K    P  G  KG+ F EF   E    A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 187 LRLLNKFNIDGQELMLKVDQAT 208
           +R LN + +  +   LK   ++
Sbjct: 61  VRNLNGYQLGSRF--LKCGYSS 80

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 61.6 bits (150), Expect = 5e-11
 Identities = 23/114 (20%), Positives = 42/114 (36%), Gaps = 6/114 (5%)

Query: 117 PLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCE 176
                  A    ++VYVG I      D +       G +KS   +        KGF F E
Sbjct: 17  SAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 76

Query: 177 FESAEGVLRALRLLNKFNIDGQELMLKVDQAT----REYLERYVDKKTENTKKL 226
           +E  E    AL  +N   + G+   +KV + +     + +   + ++     ++
Sbjct: 77  YEVPEAAQLALEQMNSVMLGGRN--IKVGRPSNIGQAQPIIDQLAEEARAFNRI 128

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 59.6 bits (145), Expect = 2e-10
 Identities = 26/96 (27%), Positives = 46/96 (47%), Gaps = 2/96 (2%)

Query: 114 RPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFG 173
               +  +    +   ++YV  +      D + SV +  G +KS   A+ P+ G  KG+G
Sbjct: 111 AQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYG 170

Query: 174 FCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATR 209
           F E+E A+    A+  +N F++ GQ   L+V +A  
Sbjct: 171 FIEYEKAQSSQDAVSSMNLFDLGGQ--YLRVGKAVT 204

>2ycu_A Non muscle myosin 2C, alpha-actinin; motor protein; HET: AOV; 2.25A {Homo sapiens} PDB: 1br1_A* 1br4_A* 1br2_A* Length = 995

 Score = 64.3 bits (157), Expect = 6e-11
 Identities = 19/156 (12%), Positives = 47/156 (30%), Gaps = 7/156 (4%)

Query: 377 RDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREK 436
                  + +          +   E +R E ++++KI    ++Y R LK  E     +  
Sbjct: 840 PAGLTPNEIDSTWSALEKAEQEHAEALRIELKRQKKIAVLLQKYNRILKKLENWATTKSV 899

Query: 437 ERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSV------LEEKRRKRIREKEED 490
                +  +     + K + L   + +      +    +      L E     + E  E 
Sbjct: 900 YLGSNETGDSITAVQAKLKNLEAFDGECQSLEGQSNSDLLSILAQLTELNYNGVPELTER 959

Query: 491 LADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSD 526
                 ++     +     +  L  +  + L+ + D
Sbjct: 960 KDTFFAQQWTGVKSSAETYKNTLLAEL-ERLQKIED 994

>2ycu_A Non muscle myosin 2C, alpha-actinin; motor protein; HET: AOV; 2.25A {Homo sapiens} PDB: 1br1_A* 1br4_A* 1br2_A* Length = 995

 Score = 47.7 bits (114), Expect = 1e-05
 Identities = 17/147 (11%), Positives = 51/147 (34%), Gaps = 2/147 (1%)

Query: 378 DKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRERERE-- 435
           ++ER  ++ K   + R     +    ++   + R   ++    +  +   +  ++  +  
Sbjct: 751 EEERASEQTKSDYLKRANELVQWINDKQASLESRDFGDSIESVQSFMNAHKEYKKTEKPP 810

Query: 436 KERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEV 495
           K ++  + +      + K  ++  E                     K  +E  E L  E+
Sbjct: 811 KGQEVSELEAIYNSLQTKLRLIKREPFVAPAGLTPNEIDSTWSALEKAEQEHAEALRIEL 870

Query: 496 REEEEIAVAKRRAEEEQLQQQQRDALK 522
           + +++IAV  ++      + +     K
Sbjct: 871 KRQKKIAVLLQKYNRILKKLENWATTK 897

>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 = 58.6 bits (142), Expect = 7e-11
 Identities = 24/100 (24%), Positives = 36/100 (36%), Gaps = 11/100 (11%)

Query: 119 PTVTPAEKPQ-TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPS--------NGTP 169
            +  P E    + +YV  +  +   D +    K CG VK  KR   P          G P
Sbjct: 5   SSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKP 64

Query: 170 KGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATR 209
           KG     +E       A+   +  +  G +  LKV  A +
Sbjct: 65  KGDATVSYEDPPTAKAAVEWFDGKDFQGSK--LKVSLARK 102

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 57.7 bits (140), Expect = 9e-11
 Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 7/93 (7%)

Query: 109 MPPVVRPVPLPTVTPAEKPQ-TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNG 167
           +PP V P  +  +  +  P+ T  Y+G I   A    ++ + +  G +  +K        
Sbjct: 7   LPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKH------Y 60

Query: 168 TPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL 200
             KG  F ++++ E     +  L  F   G+ L
Sbjct: 61  PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNL 93

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 58.2 bits (141), Expect = 9e-11
 Identities = 14/91 (15%), Positives = 36/91 (39%)

Query: 125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 184
           + P  +V   ++       F+  + +  G V+  +   +P      G     F S  G  
Sbjct: 3   QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAK 62

Query: 185 RALRLLNKFNIDGQELMLKVDQATREYLERY 215
             ++ L+  ++ G  +  ++D   ++ ++ Y
Sbjct: 63  ETVKNLHLTSVMGNIIHAQLDIKGQQRMKYY 93

>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 = 58.7 bits (143), Expect = 2e-10
 Identities = 16/81 (19%), Positives = 33/81 (40%), Gaps = 2/81 (2%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
           T + V  +        + ++ +  G + + +  +    G   G+ F +F S     RA++
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63

Query: 189 LLNKFNIDGQELMLKVDQATR 209
           +LN   +  +   LKV  A  
Sbjct: 64  VLNGITVRNK--RLKVSYARP 82

>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 = 52.2 bits (126), Expect = 4e-08
 Identities = 18/81 (22%), Positives = 30/81 (37%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
             T +YV  +  T   D + ++    G++      +    G P+G  F  +   E    A
Sbjct: 88  KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 147

Query: 187 LRLLNKFNIDGQELMLKVDQA 207
           +  LN    +G    L V  A
Sbjct: 148 ISALNNVIPEGGSQPLSVRLA 168

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 56.4 bits (137), Expect = 2e-10
 Identities = 22/86 (25%), Positives = 33/86 (38%), Gaps = 9/86 (10%)

Query: 125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 184
           E     +YVG +   A ++ + +    CG+V          +G PKGF + EF   E V 
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 185 RALRLLNKFNIDGQELM---LKVDQA 207
            +L L      D        +KV   
Sbjct: 63  TSLAL------DESLFRGRQIKVIPK 82

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 17/86 (19%), Positives = 35/86 (40%), Gaps = 3/86 (3%)

Query: 122 TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 181
                 + K+++  +  +   + +  + K  GTVK   R      G PKG  + E+E+  
Sbjct: 11  YSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKD-LRLVTNRAGKPKGLAYVEYENES 69

Query: 182 GVLRALRLLNKFNIDGQELMLKVDQA 207
              +A+  ++   I      +KV  +
Sbjct: 70  QASQAVMKMDGMTIKENI--IKVAIS 93

>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 = 56.2 bits (136), Expect = 3e-10
 Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 2/90 (2%)

Query: 119 PTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFE 178
              +  +   T + V  +  T   D +L        +      +Y   G P G     FE
Sbjct: 6   SGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFE 65

Query: 179 SAEGVLRALRLLNKFNIDGQELMLKVDQAT 208
           S +    A+  LN   I  ++  +K+   +
Sbjct: 66  SRDEATAAVIDLNDRPIGSRK--VKLSGPS 93

>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 = 56.2 bits (136), Expect = 5e-10
 Identities = 19/97 (19%), Positives = 37/97 (38%), Gaps = 9/97 (9%)

Query: 117 PLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCE 176
           P+  ++P E+    V+  ++A       +       G V+  +     ++   KG  + E
Sbjct: 14  PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 73

Query: 177 FESAEGVLRALRLLNKFNIDGQELM---LKVDQATRE 210
           F   + V  A+ L       GQ L+   + V  +  E
Sbjct: 74  FCEIQSVPLAIGL------TGQRLLGVPIIVQASQAE 104

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 55.7 bits (135), Expect = 5e-10
 Identities = 17/93 (18%), Positives = 34/93 (36%), Gaps = 10/93 (10%)

Query: 119 PTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFE 178
           P           +++G + P      +   +                 GT + FG+ +FE
Sbjct: 8   PVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFE 66

Query: 179 SAEGVLRALRLLNKFNIDGQELM---LKVDQAT 208
           SAE + +AL L       G ++    +K+++  
Sbjct: 67  SAEDLEKALEL------TGLKVFGNEIKLEKPK 93

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 58.2 bits (140), Expect = 5e-10
 Identities = 16/74 (21%), Positives = 38/74 (51%), Gaps = 3/74 (4%)

Query: 395 EREAERERVRKEREQRRK-IEEAEREYERCLKDWEYREREREKE--RQYEKEKEKERERK 451
               E E +RK RE++RK ++E +   +   ++W  + ++  +E  ++  ++ EK +   
Sbjct: 79  RLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINN 138

Query: 452 RKKEILYDEEEDED 465
           R  +  + ++ D D
Sbjct: 139 RIADKAFYQQPDAD 152

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 55.2 bits (132), Expect = 6e-09
 Identities = 19/104 (18%), Positives = 41/104 (39%), Gaps = 24/104 (23%)

Query: 398 AERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEIL 457
           A+ +R+ +E E  RK              W    RE +++R  E +      +  ++E  
Sbjct: 75  AQADRLTQEPESIRK--------------W----REEQRKRLQELD---AASKVMEQEWR 113

Query: 458 YDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEI 501
              ++D ++  +R    V  EK +   R  ++    +  + + I
Sbjct: 114 EKAKKDLEEWNQRQSEQV--EKNKINNRIADKAFYQQ-PDADII 154

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 49.4 bits (117), Expect = 5e-07
 Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 28/85 (32%)

Query: 458 YDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAK------------ 505
            D    E +S ++WR     E++RKR++E +   A +V E+E    AK            
Sbjct: 77  ADRLTQEPESIRKWR-----EEQRKRLQELDA--ASKVMEQEWREKAKKDLEEWNQRQSE 129

Query: 506 ---------RRAEEEQLQQQQRDAL 521
                    R A++   QQ   D +
Sbjct: 130 QVEKNKINNRIADKAFYQQPDADII 154

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010

 Score = 60.4 bits (147), Expect = 1e-09
 Identities = 15/160 (9%), Positives = 47/160 (29%), Gaps = 4/160 (2%)

Query: 368  RSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQR-RKIEEAEREYERCLKD 426
             + +           L++ ++   +    E +R++      Q+  +I +    +      
Sbjct: 848  PAGLTPNEIDSTWSALEKAEQEHAEALRIELKRQKKIAVLLQKYNRILKKLENWATTKSV 907

Query: 427  WEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIRE 486
            +       +     + + +       + + L  +   +  S       +      +    
Sbjct: 908  YLGSNETGDSITAVQAKLKNLEAFDGECQSLEGQSNSDLLSILAQLTELNYNGVPELTER 967

Query: 487  KEEDLADEVREEEEIAVAKR---RAEEEQLQQQQRDALKL 523
            K+   A +    +  A   +    AE E+LQ+ +      
Sbjct: 968  KDTFFAQQWTGVKSSAETYKNTLLAELERLQKIEDLHHHH 1007

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 54.1 bits (131), Expect = 2e-09
 Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 2/85 (2%)

Query: 122 TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 181
           +       +++V  +        +      CG V          NG  KG G  +FES E
Sbjct: 2   SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFESPE 59

Query: 182 GVLRALRLLNKFNIDGQELMLKVDQ 206
              RA R++N   + G+E+ +++D+
Sbjct: 60  VAERACRMMNGMKLSGREIDVRIDR 84

>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 = 54.6 bits (132), Expect = 2e-09
 Identities = 22/90 (24%), Positives = 38/90 (42%), Gaps = 2/90 (2%)

Query: 119 PTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFE 178
             +        ++YVG +      D +  + +  G ++S +       G  KG+GF  F 
Sbjct: 17  NNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS 76

Query: 179 SAEGVLRALRLLNKFNIDGQELMLKVDQAT 208
            +E   +AL  LN F + G+   +KV   T
Sbjct: 77  DSECAKKALEQLNGFELAGRP--MKVGHVT 104

>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex, cytoplasm, ribonucleoprotein, structural protein; 3.50A {Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A Length = 861

 Score = 59.8 bits (144), Expect = 2e-09
 Identities = 31/191 (16%), Positives = 64/191 (33%), Gaps = 3/191 (1%)

Query: 345 LDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVR 404
           +D  T    + S     E ++  +        +  E++ +   ER+    + EAE+ R  
Sbjct: 646 VDQRTRDALQRSVQLAIEITTNSQEAAAKHEAQRLEQEARGRLERQKILDQSEAEKARKE 705

Query: 405 KEREQ--RRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEE 462
               +     +E             E    E E      K K +    + + E+   ++ 
Sbjct: 706 LLELEAMSMAVESTGNAKAEAESRAEAARIEGEGSVLQAKLKAQALAIETEAELERVKKV 765

Query: 463 DEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAE-EEQLQQQQRDAL 521
            E +      +  LE  + +++   E     E+ E       +  A    ++Q +   +L
Sbjct: 766 REMELIYARAQLELEVSKAQQLANVEAKKFKEMTEALGPGTIRDLAVAGPEMQVKLLQSL 825

Query: 522 KLLSDNAVNGS 532
            L S    +GS
Sbjct: 826 GLKSTLITDGS 836

>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex, cytoplasm, ribonucleoprotein, structural protein; 3.50A {Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A Length = 861

 Score = 51.4 bits (122), Expect = 7e-07
 Identities = 25/143 (17%), Positives = 51/143 (35%), Gaps = 11/143 (7%)

Query: 390 EIDRYEREAERERVRKEREQRRKI-EEAEREYERCLKDWEYREREREKERQYEKEK---E 445
            +D    E   +R R   ++  ++  E     +      E +  E+E   + E++K   +
Sbjct: 637 SVDVQSVEPVDQRTRDALQRSVQLAIEITTNSQEAAAKHEAQRLEQEARGRLERQKILDQ 696

Query: 446 KERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDL-------ADEVREE 498
            E E+ RK+ +  +      +S    +          RI  +   L       A  +  E
Sbjct: 697 SEAEKARKELLELEAMSMAVESTGNAKAEAESRAEAARIEGEGSVLQAKLKAQALAIETE 756

Query: 499 EEIAVAKRRAEEEQLQQQQRDAL 521
            E+   K+  E E +  + +  L
Sbjct: 757 AELERVKKVREMELIYARAQLEL 779

>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 = 53.8 bits (130), Expect = 2e-09
 Identities = 14/85 (16%), Positives = 28/85 (32%), Gaps = 2/85 (2%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
                ++ VYV  +  +  ++ +  +    G V      +       KG  F  F   + 
Sbjct: 11  GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDS 70

Query: 183 VLRALRLLNKFNIDGQELMLKVDQA 207
                R +N   + G+   +K   A
Sbjct: 71  AQNCTRAINNKQLFGRV--IKASIA 93

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 56.4 bits (136), Expect = 2e-09
 Identities = 21/130 (16%), Positives = 39/130 (30%), Gaps = 1/130 (0%)

Query: 81  PPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTA 140
            PR   P        RP     P   P                  +   K+ V  +    
Sbjct: 41  GPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGV 100

Query: 141 DSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL 200
               +  +    GT+K      Y  +G   G     FE     L+A++      +DG+ +
Sbjct: 101 SDADIQELFAEFGTLKKAA-VDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPM 159

Query: 201 MLKVDQATRE 210
            +++  +  +
Sbjct: 160 DIQLVASQID 169

>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 = 58.1 bits (141), Expect = 2e-09
 Identities = 22/114 (19%), Positives = 40/114 (35%), Gaps = 13/114 (11%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
             +++    P+     +  +L+    V    R       T + F + +  S E     + 
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177

Query: 189 LLNKFNIDGQELMLKV----------DQATREYLERYV---DKKTENTKKLKET 229
            LN   I+G  L+ KV          D AT E  E  +     +  +   L+E+
Sbjct: 178 KLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRES 231

>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 = 51.5 bits (124), Expect = 2e-07
 Identities = 22/131 (16%), Positives = 45/131 (34%), Gaps = 7/131 (5%)

Query: 119 PTVTPAEKPQ-TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEF 177
                    + T V V  +  + + + V    K CG +     A   S      F   EF
Sbjct: 31  ANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVAD--SLKKNFRFARIEF 88

Query: 178 ESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKET-QDAGAGK 236
              +G L A+   +K  +   E+++        ++  +    T+  + +++  QD     
Sbjct: 89  ARYDGALAAITKTHKV-VGQNEIIVSHLTECTLWMTNFPPSYTQ--RNIRDLLQDINVVA 145

Query: 237 EDESVQSVEKN 247
               + S+  N
Sbjct: 146 LSIRLPSLRFN 156

>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 = 45.0 bits (107), Expect = 3e-05
 Identities = 15/107 (14%), Positives = 41/107 (38%), Gaps = 6/107 (5%)

Query: 106 RPIMPPVVRPVPLPTVTPAEKPQ-TKVYVGKIAPTADSDFVLSVL-KVCGTVKSWKRAQ- 162
             ++  V  P+     T +   +  ++ +  ++     + +L    +  G+++       
Sbjct: 187 YTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAG 246

Query: 163 YPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATR 209
              +       F  FE+ +   RAL+ +N+  +  +E  + V  A +
Sbjct: 247 QKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNRE--ISVSLADK 290

>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 = 53.8 bits (130), Expect = 2e-09
 Identities = 13/90 (14%), Positives = 30/90 (33%), Gaps = 7/90 (7%)

Query: 119 PTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFE 178
           P  +   +    +    ++     D +  V +    ++   +     +G  KG  + EF+
Sbjct: 7   PCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFK 61

Query: 179 SAEGVLRALRLLNKFNIDGQELMLKVDQAT 208
           S     + L       IDG+   + +    
Sbjct: 62  SEADAEKNLEEKQGAEIDGRS--VSLYYTG 89

>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 = 56.0 bits (136), Expect = 2e-09
 Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 2/80 (2%)

Query: 128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRAL 187
           +T + V  +      +   S+    G ++S K  +    G   G+GF  +   +   +A+
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 188 RLLNKFNIDGQELMLKVDQA 207
             LN   +  +   +KV  A
Sbjct: 62  NTLNGLRLQTK--TIKVSYA 79

>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 = 49.5 bits (119), Expect = 3e-07
 Identities = 15/83 (18%), Positives = 27/83 (32%)

Query: 125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 184
                 +YV  +  T     +  +    G + + +       G  +G GF  F+      
Sbjct: 85  SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 144

Query: 185 RALRLLNKFNIDGQELMLKVDQA 207
            A++ LN     G    + V  A
Sbjct: 145 EAIKGLNGQKPSGATEPITVKFA 167

>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 = 53.8 bits (130), Expect = 2e-09
 Identities = 27/91 (29%), Positives = 42/91 (46%), Gaps = 3/91 (3%)

Query: 124 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 183
            ++    V+VG I   A  + +  +    G V S++       G PKG+GFCE++  E  
Sbjct: 4   VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63

Query: 184 LRALRLLNKFNIDGQELMLKVDQATREYLER 214
           L A+R LN     G+   L+VD A      +
Sbjct: 64  LSAMRNLNGREFSGRA--LRVDNA-ASEKNK 91

>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 = 53.8 bits (130), Expect = 2e-09
 Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 6/86 (6%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
                   + +  ++ +A  + +  V +    +K  +      NG  KG+ F EF S E 
Sbjct: 10  TWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQ----NGKSKGYAFIEFASFED 65

Query: 183 VLRALRLLNKFNIDGQELMLKVDQAT 208
              AL   NK  I+G+   ++++   
Sbjct: 66  AKEALNSCNKREIEGRA--IRLELQG 89

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 59.1 bits (143), Expect = 3e-09
 Identities = 24/153 (15%), Positives = 66/153 (43%), Gaps = 9/153 (5%)

Query: 374  RRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRERE 433
                 +++  +  +E+ + + + +AE E   +  E R ++   ++E E  L +       
Sbjct: 879  ELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHE------M 932

Query: 434  REKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLAD 493
              +  + E+  ++ +  K+K +    + E++ +  +  R+ +  EK       K + + D
Sbjct: 933  EARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTA--DGKIKKMED 990

Query: 494  EVREEEEIAVAKRRAEEEQLQQQQRDALKLLSD 526
            ++   E+    K   E + L+++  D    L++
Sbjct: 991  DILIMED-QNNKLTKERKLLEERVSDLTTNLAE 1022

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 57.9 bits (140), Expect = 7e-09
 Identities = 27/147 (18%), Positives = 60/147 (40%), Gaps = 8/147 (5%)

Query: 383 LKREKEREIDRYEREAER-ERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYE 441
           +       +  +       +  R+E E + K EE +R  ER  K     +   +K  Q  
Sbjct: 832 MNVXHWPWMXLFFXIXPLLKVTRQEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLC 891

Query: 442 KEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEI 501
           +EK   +E+ + +  LY E E       R R +  +++  + + E E  + +E    +++
Sbjct: 892 EEKNLLQEKLQAETELYAEAE-----EMRVRLAAKKQELEEILHEMEARIEEEEERSQQL 946

Query: 502 AVAKRRAEEE--QLQQQQRDALKLLSD 526
              K++ +++   L++Q  +       
Sbjct: 947 QAEKKKMQQQMLDLEEQLEEEEAARQK 973

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 55.2 bits (133), Expect = 4e-08
 Identities = 36/207 (17%), Positives = 80/207 (38%), Gaps = 12/207 (5%)

Query: 370  RVHDRRGRDKERDLKREKEREIDRYEREAE-RERVRKEREQRRKIEEAEREYERCLKDWE 428
            +       + E    R   ++ +  E   E   R+ +E E+ ++++  +++ ++ + D E
Sbjct: 902  QAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLE 961

Query: 429  YREREREKERQ-YEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREK 487
             +  E E  RQ  + EK     + +K E      ED+++            K RK + E+
Sbjct: 962  EQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKL---------TKERKLLEER 1012

Query: 488  EEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEE-SAVESKGMDV 546
              DL   + EEEE A    + + +         ++L  +      L +    +E +  D+
Sbjct: 1013 VSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDL 1072

Query: 547  EHDYHDDSIRENHMEIRLHKMVMGMNQ 573
                 +   +   ++ +L K    +  
Sbjct: 1073 HEQIAELQAQIAELKAQLAKKEEELQA 1099

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 55.2 bits (133), Expect = 4e-08
 Identities = 28/197 (14%), Positives = 88/197 (44%), Gaps = 13/197 (6%)

Query: 374  RRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRERE 433
            +  R +E    +++E +  +  ++     +++  ++  ++ E +   +  L+       E
Sbjct: 851  KVTRQEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAE 910

Query: 434  REKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRK---RIREKEED 490
             E+ R     K++E E       L++ E   ++  +R ++  L+ +++K   ++ + EE 
Sbjct: 911  AEEMRVRLAAKKQELEEI-----LHEMEARIEEEEERSQQ--LQAEKKKMQQQMLDLEEQ 963

Query: 491  LADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEHDY 550
            L +E    +++ + K    + ++++ + D L +  ++  N    E   +E +  D+  + 
Sbjct: 964  LEEEEAARQKLQLEK-VTADGKIKKMEDDILIM--EDQNNKLTKERKLLEERVSDLTTNL 1020

Query: 551  HDDSIRENHMEIRLHKM 567
             ++  +  ++    +K 
Sbjct: 1021 AEEEEKAKNLTKLKNKH 1037

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 48.7 bits (116), Expect = 5e-06
 Identities = 29/151 (19%), Positives = 65/151 (43%), Gaps = 11/151 (7%)

Query: 378  DKERDLKREKEREIDRYEREAE--RERVRKEREQRRKIEEAEREYERCLKDWEYRERERE 435
             +E +  +   +  +++E        R++KE + R+++E+ +R+ E    D    E+  E
Sbjct: 1021 AEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSD--LHEQIAE 1078

Query: 436  KERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEV 495
             + Q  + K +  +++ + +      EDE   +    + + E +    I + +EDL    
Sbjct: 1079 LQAQIAELKAQLAKKEEELQAALARLEDETSQKNNALKKIRELE--SHISDLQEDL---- 1132

Query: 496  REEEEIAVAKRRAEEEQLQQQQRDALKLLSD 526
             E E+ A  K   ++  L ++       L D
Sbjct: 1133 -ESEKAARNKAEKQKRDLSEELEALKTELED 1162

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 48.3 bits (115), Expect = 7e-06
 Identities = 41/201 (20%), Positives = 77/201 (38%), Gaps = 37/201 (18%)

Query: 377  RDKERDLKREKEREIDRYER--EAERERVRKEREQRRKIEEAEREYERCLKDWEYRERER 434
            R +    K+E E  +   E   E E ER ++ + +++K+++   + E  L++ E   ++ 
Sbjct: 915  RVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKL 974

Query: 435  EKERQYEKEKEK----------ERERKRKKEILYDEEEDED-------DSRKRWRRSVLE 477
            + E+     K K          ++  K  KE    EE   D       +  K    + L+
Sbjct: 975  QLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLK 1034

Query: 478  EKRRKRIREKEEDLADEVREEEEIAVAKRRAEEE----------------QLQQQQRDAL 521
             K    I E E  L  E +  +E+   KR+ E E                +L+ Q     
Sbjct: 1035 NKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKE 1094

Query: 522  KLLSDNAVNGSLAEESAVESK 542
            + L   A    L +E++ ++ 
Sbjct: 1095 EEL--QAALARLEDETSQKNN 1113

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 48.3 bits (115), Expect = 7e-06
 Identities = 28/191 (14%), Positives = 72/191 (37%), Gaps = 19/191 (9%)

Query: 374  RRGRDKERDLKREKEREIDRYER--EAERERVRKEREQRRKIEEAEREYERCLKDWEYRE 431
                 + +  K++ ++++   E   E E    +K + ++   +   ++ E  +   E + 
Sbjct: 940  EERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQN 999

Query: 432  REREKER------------QYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEK 479
             +  KER               +E+EK +   + K        + +   K+  +S  E +
Sbjct: 1000 NKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELE 1059

Query: 480  RRKRIREKE-EDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESA 538
            + KR  E E  DL +++ E +     +    + QL +++ +    L+      S    + 
Sbjct: 1060 KIKRKLEGESSDLHEQIAELQA----QIAELKAQLAKKEEELQAALARLEDETSQKNNAL 1115

Query: 539  VESKGMDVEHD 549
             + + ++    
Sbjct: 1116 KKIRELESHIS 1126

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 43.7 bits (103), Expect = 2e-04
 Identities = 23/161 (14%), Positives = 65/161 (40%), Gaps = 25/161 (15%)

Query: 377  RDKERDLKREK---EREIDRYEREAERERVRKE--REQRRKIEEAEREYERCLKD----- 426
             +K ++L + K   E  I   E   ++E   ++   + +RK+E    +    + +     
Sbjct: 1024 EEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQI 1083

Query: 427  WEYREREREKERQYEKEKEKERERKRKKEIL----------YDEEEDEDDSRKRWRRSVL 476
             E + +  +KE + +    +  +   +K               + +++ +S K  R    
Sbjct: 1084 AELKAQLAKKEEELQAALARLEDETSQKNNALKKIRELESHISDLQEDLESEKAARNKAE 1143

Query: 477  EEKRR-----KRIREKEEDLADEVREEEEIAVAKRRAEEEQ 512
            ++KR      + ++ + ED  D    ++E+  +  + ++++
Sbjct: 1144 KQKRDLSEELEALKTELEDTLDTTATQQELRGSDYKDDDDK 1184

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 42.1 bits (99), Expect = 5e-04
 Identities = 21/129 (16%), Positives = 54/129 (41%), Gaps = 9/129 (6%)

Query: 400 RERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYD 459
           R  +         +        +  +  E  + + E+ ++ ++ ++K     ++ E  + 
Sbjct: 829 RSFMNVXHWPWMXLFFXIXPLLKVTRQEEEMQAKDEELQRTKERQQKAEAELKELEQKHT 888

Query: 460 EEEDEDDSRKRWRRSVLE-----EKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQ 514
           +  +E +  +   ++  E     E+ R R+  K+++L + + E E     +   EEE+ Q
Sbjct: 889 QLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEA----RIEEEEERSQ 944

Query: 515 QQQRDALKL 523
           Q Q +  K+
Sbjct: 945 QLQAEKKKM 953

>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 = 58.3 bits (140), Expect = 3e-09
 Identities = 42/337 (12%), Positives = 91/337 (27%), Gaps = 7/337 (2%)

Query: 117 PLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCE 176
           P             ++V ++        +    +V G +K         +G P+G+ F E
Sbjct: 91  PHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIE 150

Query: 177 FESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGK 236
           +E    +  A +  +   IDG+ +++ V++       R            +   D     
Sbjct: 151 YEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRH 210

Query: 237 EDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEE 296
                 S     P  SP   +D +   +      +     E +R+  +            
Sbjct: 211 SGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSR-------SRDRR 263

Query: 297 RLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKAS 356
           R   +       ++               +R  +                 +    ++A 
Sbjct: 264 RRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAG 323

Query: 357 DHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEA 416
           D    +    +          +K RD  RE+ R               ++R++  K  E 
Sbjct: 324 DAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGER 383

Query: 417 EREYERCLKDWEYREREREKERQYEKEKEKERERKRK 453
             E  R         ++   E      ++   E +  
Sbjct: 384 GSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGG 420

>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 = 48.3 bits (114), Expect = 4e-06
 Identities = 25/157 (15%), Positives = 52/157 (33%), Gaps = 1/157 (0%)

Query: 343 DKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERER 402
            +       + +    +R +    DR R   R      R+ +R++E      +     E 
Sbjct: 263 RRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEA 322

Query: 403 VRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEE 462
                +     E      +   +    R+RER +  + E+E+ ++R+R R ++    +  
Sbjct: 323 GDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDR-EHKRG 381

Query: 463 DEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEE 499
           +    R R         +   +     D  D   E E
Sbjct: 382 ERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESE 418

>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 = 45.2 bits (106), Expect = 4e-05
 Identities = 23/159 (14%), Positives = 51/159 (32%)

Query: 351 SDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQR 410
                S        S +RS+  DR  + +    +    RE +R E          E  + 
Sbjct: 263 RRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEA 322

Query: 411 RKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKR 470
                 +        D      E+ ++R  E+ +    ER+R+++   D + D +  R  
Sbjct: 323 GDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGE 382

Query: 471 WRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAE 509
                  ++ R     ++  L     +  ++ +     +
Sbjct: 383 RGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGD 421

>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 = 43.3 bits (101), Expect = 1e-04
 Identities = 41/208 (19%), Positives = 67/208 (32%), Gaps = 6/208 (2%)

Query: 312 ADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRV 371
           ADG  I    +      G +        +                 H   + +S    R 
Sbjct: 164 ADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERP 223

Query: 372 HDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRE 431
                  ++RD  RE+ER     ER+ ERER R     RR+   +  + ER       R 
Sbjct: 224 GPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEER------RRS 277

Query: 432 REREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDL 491
           RER K++  ++++   R R+R +     +EE           S   +         E   
Sbjct: 278 RERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGP 337

Query: 492 ADEVREEEEIAVAKRRAEEEQLQQQQRD 519
                 EE+     R        +++R 
Sbjct: 338 DGPDGPEEKGRDRDRERRRSHRSERERR 365

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 53.5 bits (129), Expect = 3e-09
 Identities = 17/94 (18%), Positives = 31/94 (32%), Gaps = 2/94 (2%)

Query: 117 PLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCE 176
                +  +   T + V  +  T   D +L        +      +Y   G P G     
Sbjct: 4   GSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 177 FESAEGVLRALRLLNKFNIDGQELMLKVDQATRE 210
           FES +    A+  LN   I  ++  +K+   +  
Sbjct: 64  FESRDEATAAVIDLNDRPIGSRK--VKLVLGSGP 95

>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 = 54.4 bits (131), Expect = 3e-09
 Identities = 25/111 (22%), Positives = 44/111 (39%), Gaps = 2/111 (1%)

Query: 97  PPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVK 156
            P      ++ +     + +P   + P       + V  I  T D   +  + +  G ++
Sbjct: 11  DPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIE 70

Query: 157 SWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA 207
           S K          +G+GF +F+S     +A+  LN FNI  +   LKV  A
Sbjct: 71  SVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKR--LKVALA 119

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 59.0 bits (143), Expect = 3e-09
 Identities = 23/159 (14%), Positives = 60/159 (37%), Gaps = 16/159 (10%)

Query: 378  DKERDLKREKEREIDRYER--EAERERVRKEREQRRKIEEAEREYERCLKDWE--YRERE 433
            ++ + L    E +I + +R  + + +  +   E+   +E         L+      R  E
Sbjct: 917  ERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSE 976

Query: 434  REKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLE--------EKRRKRIR 485
             E +    +    + E  + ++ L+  + ++    +   +   E        +++   ++
Sbjct: 977  EEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLK 1036

Query: 486  EKEEDL----ADEVREEEEIAVAKRRAEEEQLQQQQRDA 520
             ++E+L     D+ +E  E    K   E +QL+    D 
Sbjct: 1037 TEKEELNRRIHDQAKEITETMEKKLVEETKQLELDLNDE 1075

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 57.0 bits (138), Expect = 1e-08
 Identities = 35/199 (17%), Positives = 73/199 (36%), Gaps = 9/199 (4%)

Query: 375  RGRDKERDLKREKEREIDRYEREAERERVRKEREQRR-KIEEAEREYERCLKDWEYRERE 433
            RG        R  +  +     +    R+  +RE ++ KIE    E  + L      +  
Sbjct: 875  RGWLARVHYHRTLKAIV---YLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIM 931

Query: 434  REKERQYEKEKEKER--ERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRR--KRIREKEE 489
            + + +  E+ KE +   E+    EI Y  E ++  S     R   EE +    R+   +E
Sbjct: 932  QLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQE 991

Query: 490  DLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSL-AEESAVESKGMDVEH 548
            ++A   +E  +    K+  EE   + +      +      N  L  E+  +  +  D   
Sbjct: 992  EIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAK 1051

Query: 549  DYHDDSIRENHMEIRLHKM 567
            +  +   ++   E +  ++
Sbjct: 1052 EITETMEKKLVEETKQLEL 1070

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 55.5 bits (134), Expect = 4e-08
 Identities = 32/195 (16%), Positives = 69/195 (35%), Gaps = 12/195 (6%)

Query: 369  SRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWE 428
            + +     R+K + + RE +  I +        R        + I   +  Y R +   E
Sbjct: 847  ALLRGYLVRNKYQMMLREHKSIIIQKHVRGWLAR-VHYHRTLKAIVYLQCCYRRMMAKRE 905

Query: 429  YREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKE 488
             ++ + E  R  E+ K+     + K   L  + ++++   K      L EK         
Sbjct: 906  LKKLKIE-ARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKS-----LLEKMNNLEITY- 958

Query: 489  EDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEH 548
                +++R + E    + R  EE+ +      L L  + A       ++  E K ++   
Sbjct: 959  STETEKLRSDVE----RLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWA 1014

Query: 549  DYHDDSIRENHMEIR 563
            D +     +   E++
Sbjct: 1015 DKYKHETEQLVSELK 1029

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 51.3 bits (123), Expect = 7e-07
 Identities = 22/207 (10%), Positives = 63/207 (30%), Gaps = 17/207 (8%)

Query: 374  RRGRDKERDLKREKEREIDRYEREAERERVRKE-REQRRKIEEAEREYERCLKDWEYRER 432
            R  + +       + R     ++      VRK  +  R      +      L   +Y+  
Sbjct: 802  RGHQARCYATFLRRTRAAIIIQKFQRMYVVRKRYQCMRDATIALQALLRGYLVRNKYQMM 861

Query: 433  EREK-----ERQYEKEKEKERERKRKKEILYDEEEDEDD-SRKRWRRSVLEEKRRKRIRE 486
             RE      ++       +    +  K I+Y +       +++  ++  +E +  +R ++
Sbjct: 862  LREHKSIIIQKHVRGWLARVHYHRTLKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKK 921

Query: 487  KEEDLADEVRE--------EEEIA--VAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEE 536
                L +++ +         +E    + K    E     +       +    ++   A+ 
Sbjct: 922  LHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKN 981

Query: 537  SAVESKGMDVEHDYHDDSIRENHMEIR 563
            +      +  E       + +   E +
Sbjct: 982  ATNRVLSLQEEIAKLRKELHQTQTEKK 1008

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 42.4 bits (100), Expect = 4e-04
 Identities = 20/115 (17%), Positives = 46/115 (40%), Gaps = 2/115 (1%)

Query: 368  RSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDW 427
            RS V   R  ++E      +   +   E    R+ + + + +++ IEE   +Y+   +  
Sbjct: 966  RSDVERLRMSEEEAKNATNRVLSLQE-EIAKLRKELHQTQTEKKTIEEWADKYKHETEQL 1024

Query: 428  EYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRK 482
                +E+    + EKE E  R    + + + +  E +     +     L ++R +
Sbjct: 1025 VSELKEQNTLLKTEKE-ELNRRIHDQAKEITETMEKKLVEETKQLELDLNDERLR 1078

>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 = 57.3 bits (139), Expect = 3e-09
 Identities = 20/89 (22%), Positives = 34/89 (38%), Gaps = 4/89 (4%)

Query: 122 TPAEKPQTKVYVGKIAPTA-DSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESA 180
           TPA      + V ++ P   D D +   L    +     +     +G  KGF   E+E+A
Sbjct: 178 TPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTF-CQLACGQDGQLKGFAVLEYETA 236

Query: 181 EGVLRALRLLNKFNIDGQELMLKVDQATR 209
           E    A +  +  ++ G    L+V     
Sbjct: 237 EMAEEAQQQADGLSLGGS--HLRVSFCAP 263

>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 = 55.4 bits (134), Expect = 1e-08
 Identities = 14/84 (16%), Positives = 28/84 (33%), Gaps = 2/84 (2%)

Query: 126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 185
                + V  + P+        +++  G+++          G  KG+GF E+   +   R
Sbjct: 93  PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152

Query: 186 ALRLLNKFNIDGQELMLKVDQATR 209
           A   L    +  +   L V     
Sbjct: 153 AKSDLLGKPLGPRT--LYVHWTDA 174

>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 = 45.4 bits (108), Expect = 2e-05
 Identities = 14/101 (13%), Positives = 29/101 (28%), Gaps = 9/101 (8%)

Query: 109 MPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGT 168
           + P      L       + + K+ +  +     +  V  +L     +K            
Sbjct: 3   LDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCF------VDK 55

Query: 169 PKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATR 209
            KG  F    + E    A+   ++  +  +E  L V     
Sbjct: 56  YKGTAFVTLLNGEQAEAAINAFHQSRLRERE--LSVQLQPT 94

>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 = 54.8 bits (133), Expect = 5e-09
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 3/79 (3%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
           +YVG +      D +    +V G + +  +     N     + F E+  +     AL+ L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIAN-IKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 191 NKFNIDGQELMLKVDQATR 209
           N   I+     +K++ A +
Sbjct: 62  NGKQIENNI--VKINWAFQ 78

>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 = 50.2 bits (121), Expect = 2e-07
 Identities = 17/86 (19%), Positives = 35/86 (40%), Gaps = 8/86 (9%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
               ++VG +    D + + +  K   +  S         G+ +G+GF  F S +    A
Sbjct: 86  DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 145

Query: 187 LRLLNKFNIDGQELM---LKVDQATR 209
           +  +      GQ+L    L+++ A +
Sbjct: 146 MDSMQ-----GQDLNGRPLRINWAAK 166

>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 = 52.6 bits (127), Expect = 5e-09
 Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 2/85 (2%)

Query: 124 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 183
                + +YVG +      D +  + +  G + +    +    G  KG+GF  F  +E  
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 184 LRALRLLNKFNIDGQELMLKVDQAT 208
            RAL  LN F + G+   ++V   T
Sbjct: 61  RRALEQLNGFELAGRP--MRVGHVT 83

>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 = 52.6 bits (127), Expect = 7e-09
 Identities = 18/89 (20%), Positives = 36/89 (40%), Gaps = 5/89 (5%)

Query: 124 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWK---RAQYPSNGTPKGFGFCEFESA 180
                + +++  +  +   + +  V    G +KS     +          GFGF E++  
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 181 EGVLRALRLLNKFNIDGQELMLKVDQATR 209
           E   +AL+ L    +DG +  L+V  + R
Sbjct: 61  EQAQKALKQLQGHTVDGHK--LEVRISER 87

>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 = 52.3 bits (126), Expect = 7e-09
 Identities = 21/91 (23%), Positives = 36/91 (39%), Gaps = 3/91 (3%)

Query: 122 TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCG-TVKSWKRAQYPSNGTPKGFGFCEFESA 180
           + +      +++G + P  D +F+       G TV S K  +    G P G+ F EF   
Sbjct: 3   SGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADL 62

Query: 181 EGVLRALRLLNKFNIDGQEL--MLKVDQATR 209
               + L  +N   + G       K++ AT 
Sbjct: 63  ATAEKCLHKINGKPLPGATPAKRFKLNYATY 93

>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 = 51.8 bits (125), Expect = 9e-09
 Identities = 20/88 (22%), Positives = 33/88 (37%), Gaps = 8/88 (9%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
                +  +YVG +A   D   + +     G +   +          +GF F EFE AE 
Sbjct: 2   SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61

Query: 183 VLRALRLLNKFNIDGQELM---LKVDQA 207
              A+  +N       EL    ++V+ A
Sbjct: 62  AAAAIDNMN-----ESELFGRTIRVNLA 84

>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 = 52.3 bits (126), Expect = 9e-09
 Identities = 17/89 (19%), Positives = 34/89 (38%), Gaps = 1/89 (1%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
             +    K+++G+I    D   +  + +  G +      +    G  KG  F  +   E 
Sbjct: 8   MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERES 67

Query: 183 VLRALRLLN-KFNIDGQELMLKVDQATRE 210
            L+A   L+ +  + G    ++V  A  E
Sbjct: 68  ALKAQSALHEQKTLPGMNRPIQVKPADSE 96

>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 = 53.8 bits (130), Expect = 1e-08
 Identities = 12/86 (13%), Positives = 27/86 (31%), Gaps = 7/86 (8%)

Query: 124 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 183
             +    +    ++     D +  V +    ++         +G  KG  + EF+S    
Sbjct: 95  KVRAARTLLAKNLSFNITEDELKEVFEDALEIRL-----VSQDGKSKGIAYIEFKSEADA 149

Query: 184 LRALRLLNKFNIDGQELMLKVDQATR 209
            + L       IDG+   + +     
Sbjct: 150 EKNLEEKQGAEIDGRS--VSLYYTGE 173

>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 = 53.0 bits (128), Expect = 3e-08
 Identities = 17/86 (19%), Positives = 33/86 (38%), Gaps = 4/86 (4%)

Query: 125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 184
                 +++G + P      +   +                 GT + FG+ +FESAE + 
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLE 68

Query: 185 RALRLLNKFNIDGQELMLKVDQATRE 210
           +AL  L    + G E  +K+++    
Sbjct: 69  KALE-LTGLKVFGNE--IKLEKPKGR 91

>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 = 51.9 bits (125), Expect = 1e-08
 Identities = 18/84 (21%), Positives = 37/84 (44%), Gaps = 2/84 (2%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
               VYVG +        +  +    G V +    +    G  +G+GF EF S E    A
Sbjct: 14  QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 73

Query: 187 LRLLNKFNIDGQELMLKVDQATRE 210
           +++++   + G+   ++V++A+  
Sbjct: 74  IKIMDMIKLYGKP--IRVNKASAH 95

>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 = 53.3 bits (128), Expect = 1e-08
 Identities = 17/84 (20%), Positives = 31/84 (36%), Gaps = 2/84 (2%)

Query: 126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 185
           K    +YVG ++     + +  +    G +K           T  GF F E+ S      
Sbjct: 37  KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96

Query: 186 ALRLLNKFNIDGQELMLKVDQATR 209
           A+R +N   +D +   ++ D    
Sbjct: 97  AMRYINGTRLDDRI--IRTDWDAG 118

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 52.9 bits (127), Expect = 1e-08
 Identities = 20/94 (21%), Positives = 34/94 (36%), Gaps = 8/94 (8%)

Query: 117 PLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCE 176
                  +   +  +YVG +A   D   + +     G +   +          +GF F E
Sbjct: 52  GSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 111

Query: 177 FESAEGVLRALRLLNKFNIDGQELM---LKVDQA 207
           FE AE    A+  +N       EL    ++V+ A
Sbjct: 112 FELAEDAAAAIDNMN-----ESELFGRTIRVNLA 140

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 56.5 bits (135), Expect = 2e-08
 Identities = 26/150 (17%), Positives = 68/150 (45%), Gaps = 7/150 (4%)

Query: 377 RDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLK-DWEYRERERE 435
           +     L  +K +++ +   E  R+ ++ E   +  ++  E   +  L+ D    E+E+E
Sbjct: 429 KPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKE 488

Query: 436 KERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSV------LEEKRRKRIREKEE 489
            E +  K +  +   K   E+    E+  +   + ++  +      +E  R + ++E+E 
Sbjct: 489 IEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQER 548

Query: 490 DLADEVREEEEIAVAKRRAEEEQLQQQQRD 519
            LA +++E+E++     + E   ++ + +D
Sbjct: 549 TLALKLQEQEQLLKEGFQKESRIMKNEIQD 578

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 43.4 bits (101), Expect = 2e-04
 Identities = 22/126 (17%), Positives = 51/126 (40%), Gaps = 6/126 (4%)

Query: 375 RGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRERER 434
           + ++   D   + ++ +   E+E E ERV+ E  Q       E + +      +     +
Sbjct: 466 KSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQ 525

Query: 435 EKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADE 494
           E  +Q  ++ E +R +  K      E+E     + + +  +L+E  +K  R  + ++ D 
Sbjct: 526 EHLKQLTEKMENDRVQLLK------EQERTLALKLQEQEQLLKEGFQKESRIMKNEIQDL 579

Query: 495 VREEEE 500
             +   
Sbjct: 580 QTKMRR 585

>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 = 50.6 bits (122), Expect = 2e-08
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 9/83 (10%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSN----GTPKGFGFCEFESAEGVL 184
           TKV++G++      D ++ +    G +K       P         KG+ + EFE+ +   
Sbjct: 5   TKVHIGRLTRNVTKDHIMEIFSTYGKIKM---IDMPVERMHPHLSKGYAYVEFENPDEAE 61

Query: 185 RALRLLNKFNIDGQELMLKVDQA 207
           +AL+ ++   IDGQE  +     
Sbjct: 62  KALKHMDGGQIDGQE--ITATAV 82

>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 = 51.2 bits (123), Expect = 2e-08
 Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 4/87 (4%)

Query: 126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 185
                V++  ++  ++ + +  VL+  G +K  +   +P     KG  F +F + E   +
Sbjct: 13  TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72

Query: 186 ALRLLNKFN-IDGQELM---LKVDQAT 208
            L   +      G +L    LKVD A 
Sbjct: 73  CLAAASLEAEGGGLKLDGRQLKVDLAV 99

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 52.6 bits (126), Expect = 3e-08
 Identities = 29/117 (24%), Positives = 47/117 (40%), Gaps = 4/117 (3%)

Query: 95  ARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGT 154
           +  P P +       P    P  L T +     +  VYVG  +       ++ V++  G 
Sbjct: 22  SMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGV 81

Query: 155 --VKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATR 209
             V   K A+  +NG  KG+      S   V + L LL    ++G++  + V  ATR
Sbjct: 82  YDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEK--VDVRPATR 136

>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 = 51.6 bits (124), Expect = 3e-08
 Identities = 21/106 (19%), Positives = 36/106 (33%), Gaps = 9/106 (8%)

Query: 105 VRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP 164
           +         P PL      E  +  VYVG +   + +  + +    CG++         
Sbjct: 13  MTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDK 72

Query: 165 SNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM---LKVDQA 207
            +G PKG+ + EF     V  A+ +      D        +KV   
Sbjct: 73  FSGHPKGYAYIEFAERNSVDAAVAM------DETVFRGRTIKVLPK 112

>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 = 50.7 bits (122), Expect = 3e-08
 Identities = 16/85 (18%), Positives = 33/85 (38%), Gaps = 6/85 (7%)

Query: 126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 185
            P T+++VG + P      +       G++++              F + ++ES +    
Sbjct: 15  NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQA 68

Query: 186 ALRLLNKFNIDGQELMLKVDQATRE 210
           A   +  F + G +  L+VD A   
Sbjct: 69  ACAKMRGFPLGGPDRRLRVDFAKSG 93

>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 = 50.2 bits (121), Expect = 3e-08
 Identities = 15/81 (18%), Positives = 36/81 (44%), Gaps = 2/81 (2%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
             ++VG +    D + + +  K   +  S         G+ +G+GF  F S +    A+ 
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 189 LLNKFNIDGQELMLKVDQATR 209
            +   +++G+   L+++ A +
Sbjct: 62  SMQGQDLNGRP--LRINWAAK 80

>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 = 50.7 bits (122), Expect = 4e-08
 Identities = 19/87 (21%), Positives = 39/87 (44%), Gaps = 2/87 (2%)

Query: 122 TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 181
           +     + K++VG ++   +   +  V    G +      +       +GFGF  FE+ +
Sbjct: 6   SGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENID 65

Query: 182 GVLRALRLLNKFNIDGQELMLKVDQAT 208
               A+  +N  ++DG+   ++VDQA 
Sbjct: 66  DAKDAMMAMNGKSVDGR--QIRVDQAG 90

>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 = 50.8 bits (122), Expect = 4e-08
 Identities = 18/112 (16%), Positives = 41/112 (36%), Gaps = 3/112 (2%)

Query: 126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 185
           +    +Y+  +     ++ +  +    G ++     +  +    +G  +  +E       
Sbjct: 6   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKN 62

Query: 186 ALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKE 237
           A+  L+ FN+  + L++    A R + +    KK E  K LKE         
Sbjct: 63  AVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPP 114

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 50.0 bits (120), Expect = 5e-08
 Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 8/89 (8%)

Query: 125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGT--VKSWKRAQYPSNGTPKGFGFCEFESAEG 182
                 + +  IAP    D +++ L    +  V + +  +       +GF F +  SA  
Sbjct: 6   HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMD 65

Query: 183 VLRALRLLNK----FNIDGQELMLKVDQA 207
             + L++L        IDG+   + VD A
Sbjct: 66  ASQLLQILQSLHPPLKIDGKT--IGVDFA 92

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 50.4 bits (121), Expect = 5e-08
 Identities = 21/118 (17%), Positives = 37/118 (31%), Gaps = 12/118 (10%)

Query: 100 PGIPGVRPIMPPVVRPV---------PLPTVTPAEKPQ-TKVYVGKIAPTADSDFVLSVL 149
            G+P           P+                 E P+   +++  +        + S  
Sbjct: 2   AGLPQFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTF 61

Query: 150 KVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA 207
              G V S K          K FGF  F++ +    A++ +N F +  +   LKV   
Sbjct: 62  LPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKR--LKVQLK 117

>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 = 50.4 bits (121), Expect = 6e-08
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

Query: 125 EKPQ-TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 183
           E P+   +++  +        +L +    G V S K          K FGF  +++    
Sbjct: 21  EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 80

Query: 184 LRALRLLNKFNIDGQELMLKVDQATRE 210
             A++ +N F I  +   LKV     +
Sbjct: 81  QAAIQSMNGFQIGMKR--LKVQLKRSK 105

>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 = 52.3 bits (126), Expect = 7e-08
 Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 4/95 (4%)

Query: 117 PLPTVTPA--EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGF 174
           PL ++ P+    P   +YVG + P      +       G + S +  +        G+ +
Sbjct: 2   PLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAY 61

Query: 175 CEFESAEGVLRALRLLNKFNIDGQELMLKVDQATR 209
             F+      RAL  +N   I G+   +++  + R
Sbjct: 62  VNFQQPADAERALDTMNFDVIKGKP--VRIMWSQR 94

>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 = 44.6 bits (106), Expect = 3e-05
 Identities = 15/83 (18%), Positives = 33/83 (39%), Gaps = 4/83 (4%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
               +++  +  + D+  +       G + S K          KG+GF  FE+ E   RA
Sbjct: 102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERA 159

Query: 187 LRLLNKFNIDGQELMLKVDQATR 209
           +  +N   ++ ++  + V +   
Sbjct: 160 IEKMNGMLLNDRK--VFVGRFKS 180

>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 = 49.1 bits (118), Expect = 7e-08
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 2/79 (2%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
           + +Y+  + P      ++ + +  G + S K     +    KG+GF +F+S     +A+ 
Sbjct: 6   SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65

Query: 189 LLNKFNIDGQELMLKVDQA 207
            L    +  Q  M K    
Sbjct: 66  ALKASGVQAQ--MAKQSGP 82

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 49.6 bits (119), Expect = 8e-08
 Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 2/83 (2%)

Query: 126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 185
                ++V  +   A  + +       G +K+         G  KG+   E+E+ +    
Sbjct: 21  VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 80

Query: 186 ALRLLNKFNIDGQELMLKVDQAT 208
           A+  LN  ++ GQ   + VD   
Sbjct: 81  AMEGLNGQDLMGQP--ISVDWCF 101

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 52.4 bits (125), Expect = 8e-08
 Identities = 23/125 (18%), Positives = 37/125 (29%), Gaps = 9/125 (7%)

Query: 92  PSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQ-----TKVYVGKIAPTADSDFVL 146
           PS      P        +PP V         P            +Y+G +      + + 
Sbjct: 27  PSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLT 86

Query: 147 SVLKVCGT--VKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV 204
             +   G   +   K  +  +NG  KGF      S     + + LL K  + GQ     V
Sbjct: 87  EAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQN--PVV 144

Query: 205 DQATR 209
               +
Sbjct: 145 TPVNK 149

>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 = 49.5 bits (118), Expect = 9e-08
 Identities = 19/87 (21%), Positives = 33/87 (37%), Gaps = 8/87 (9%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGT------VKSWKRAQYPSNGTPKGFGFCEFESAEGVL 184
           V+V  ++       VL   +  G       V       Y  +  P    +  +  +E  L
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 185 RALRLLNKFNIDGQELMLKVDQATREY 211
           RA++ +N   +DG+   LK    T +Y
Sbjct: 78  RAIQCVNNVVVDGR--TLKASLGTTKY 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 = 49.6 bits (119), Expect = 1e-07
 Identities = 18/86 (20%), Positives = 32/86 (37%), Gaps = 5/86 (5%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
           PA     ++YVG + P   +  +  V    G ++        +      F F EFE    
Sbjct: 17  PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDID---LKNRRGGPPFAFVEFEDPRD 73

Query: 183 VLRALRLLNKFNIDGQELMLKVDQAT 208
              A+   + ++ DG    L+V+   
Sbjct: 74  AEDAVYGRDGYDYDGYR--LRVEFPR 97

>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 = 51.1 bits (123), Expect = 1e-07
 Identities = 19/95 (20%), Positives = 35/95 (36%), Gaps = 3/95 (3%)

Query: 128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTP--KGFGFCEFESAEGVLR 185
             K++VG++  T     +  + +  G V      +  S   P  KG  F  F + +  L 
Sbjct: 3   AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62

Query: 186 ALRLLNKFNIDGQELM-LKVDQATREYLERYVDKK 219
           A   L+   +       +++  A  E      D+K
Sbjct: 63  AQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRK 97

>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 = 42.6 bits (101), Expect = 7e-05
 Identities = 10/63 (15%), Positives = 26/63 (41%), Gaps = 1/63 (1%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
            K+++G I+     + +  +    G ++   R     +G  +G  F  F +      A++
Sbjct: 96  RKLFIGMISKKCTENDIRVMFSSFGQIEE-CRILRGPDGLSRGCAFVTFTTRAMAQTAIK 154

Query: 189 LLN 191
            ++
Sbjct: 155 AMH 157

>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 = 49.7 bits (119), Expect = 1e-07
 Identities = 14/92 (15%), Positives = 32/92 (34%), Gaps = 1/92 (1%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
              +   K+ V  +        +  +    GT+K      Y  +G   G     FE    
Sbjct: 30  EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAA-VDYDRSGRSLGTADVHFERRAD 88

Query: 183 VLRALRLLNKFNIDGQELMLKVDQATREYLER 214
            L+A++      +DG+ + +++  +  +    
Sbjct: 89  ALKAMKQYKGVPLDGRPMDIQLVASQIDLEHH 120

>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 = 48.7 bits (117), Expect = 1e-07
 Identities = 14/87 (16%), Positives = 28/87 (32%), Gaps = 2/87 (2%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
               P   + V  ++       +  V    G +          +   +GF F  FE+ + 
Sbjct: 10  ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 69

Query: 183 VLRALRLLNKFNIDGQELMLKVDQATR 209
              A    N   +DG+   ++V   + 
Sbjct: 70  AKEAKERANGMELDGRR--IRVSGPSS 94

>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 = 49.2 bits (118), Expect = 1e-07
 Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 3/80 (3%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
            K+ V  +        +  +    GT+K      Y  +G   G     FE     L+A++
Sbjct: 30  GKLLVSNLDFGVSDADIQELFAEFGTLKKAA-VHYDRSGRSLGTADVHFERKADALKAMK 88

Query: 189 LLNKFNIDGQELMLKVDQAT 208
             N   +DG+   + +   T
Sbjct: 89  QYNGVPLDGRP--MNIQLVT 106

>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 = 48.8 bits (117), Expect = 2e-07
 Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 2/85 (2%)

Query: 124 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 183
               +  +YVG +A   D   + +     G +   +          +GF F EFE AE  
Sbjct: 8   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67

Query: 184 LRALRLLNKFNIDGQELMLKVDQAT 208
             A+  +N+  + G+   ++V+ A 
Sbjct: 68  AAAIDNMNESELFGRT--IRVNLAK 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 = 48.4 bits (116), Expect = 2e-07
 Identities = 19/87 (21%), Positives = 30/87 (34%), Gaps = 2/87 (2%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
           P       + V  +      D +  V +  G V      + P    P+GF F  F     
Sbjct: 8   PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRD 67

Query: 183 VLRALRLLNKFNIDGQELMLKVDQATR 209
              A   ++   +DG+E  L+V  A  
Sbjct: 68  AQDAEAAMDGAELDGRE--LRVQVARY 92

>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 = 48.8 bits (117), Expect = 2e-07
 Identities = 15/85 (17%), Positives = 34/85 (40%), Gaps = 1/85 (1%)

Query: 122 TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 181
             A +  + V+V  +        +  V  + G V          +G  +G G   FE + 
Sbjct: 9   LQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRAD-ILEDKDGKSRGIGTVTFEQSI 67

Query: 182 GVLRALRLLNKFNIDGQELMLKVDQ 206
             ++A+ + N   +  + + +K+D+
Sbjct: 68  EAVQAISMFNGQLLFDRPMHVKMDE 92

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 23/98 (23%), Positives = 37/98 (37%), Gaps = 15/98 (15%)

Query: 114 RPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFG 173
               LPT     +P    YVG +        + ++ K    ++S +  +       KGF 
Sbjct: 6   SGKELPT-----EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFC 59

Query: 174 FCEFESAEGVLRALRLLNKFNIDGQELM---LKVDQAT 208
           + EF+  + +  AL        DG  L    L+VD A 
Sbjct: 60  YVEFDEVDSLKEALTY------DGALLGDRSLRVDIAE 91

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 16/86 (18%), Positives = 32/86 (37%), Gaps = 2/86 (2%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
                  +++V  ++ T+  + +  +    G +             PKGF F  F   E 
Sbjct: 3   SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62

Query: 183 VLRALRLLNKFNIDGQELMLKVDQAT 208
            ++A   ++     G+  ML V  +T
Sbjct: 63  AVKAYAEVDGQVFQGR--MLHVLPST 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 = 48.0 bits (115), Expect = 2e-07
 Identities = 20/88 (22%), Positives = 33/88 (37%), Gaps = 12/88 (13%)

Query: 125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKS----WKRAQYPSNGTPKGFGFCEFESA 180
           +     +YVG ++       +L +    G  KS     +        +   + F EF   
Sbjct: 12  DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT------SNDPYCFVEFYEH 65

Query: 181 EGVLRALRLLNKFNIDGQELMLKVDQAT 208
                AL  +N   I G+E  +KV+ AT
Sbjct: 66  RDAAAALAAMNGRKILGKE--VKVNWAT 91

>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 = 48.5 bits (116), Expect = 3e-07
 Identities = 16/83 (19%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
               V+VG ++P   ++ + +     G +   +  +  + G  KG+GF  F +      A
Sbjct: 14  NHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 73

Query: 187 LRLLNKFNIDGQELMLKVDQATR 209
           ++ +    + G++  ++ + ATR
Sbjct: 74  IQQMGGQWLGGRQ--IRTNWATR 94

>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 = 48.0 bits (115), Expect = 3e-07
 Identities = 19/102 (18%), Positives = 34/102 (33%), Gaps = 14/102 (13%)

Query: 110 PPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTP 169
                   LP       P    ++G +      + +    +           +  +    
Sbjct: 2   SSGSSGSRLPK-----SPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERL 56

Query: 170 KGFGFCEFESAEGVLRALRLLNKFNIDGQELM---LKVDQAT 208
           KGFG+ EFE  + +L AL L      + + L    ++VD A 
Sbjct: 57  KGFGYAEFEDLDSLLSALSL------NEESLGNKRIRVDVAD 92

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 47.5 bits (113), Expect = 4e-07
 Identities = 15/90 (16%), Positives = 27/90 (30%), Gaps = 11/90 (12%)

Query: 114 RPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTV---KSWKRAQYPSNGTPK 170
              P             VYVG +   A    +   L+  G+V    +W+         P+
Sbjct: 5   SSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQG--------PR 56

Query: 171 GFGFCEFESAEGVLRALRLLNKFNIDGQEL 200
              F  +  +    +A+  L    +    L
Sbjct: 57  RRAFLHYPDSAAAQQAVSCLQGLRLGTDTL 86

>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 = 47.2 bits (113), Expect = 4e-07
 Identities = 14/83 (16%), Positives = 34/83 (40%), Gaps = 9/83 (10%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
              K+Y+G ++P   +D +  +        + +           G+ F ++      +RA
Sbjct: 7   GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV------LLKSGYAFVDYPDQNWAIRA 60

Query: 187 LRLLN-KFNIDGQELMLKVDQAT 208
           +  L+ K  + G+   ++VD + 
Sbjct: 61  IETLSGKVELHGKI--MEVDYSV 81

>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 = 47.6 bits (114), Expect = 5e-07
 Identities = 15/81 (18%), Positives = 33/81 (40%), Gaps = 4/81 (4%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
             +++  +  + D+  +       G + S K          KG+GF  FE+ E   RA+ 
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIE 63

Query: 189 LLNKFNIDGQELMLKVDQATR 209
            +N   ++ ++  + V +   
Sbjct: 64  KMNGMLLNDRK--VFVGRFKS 82

>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 = 47.3 bits (113), Expect = 5e-07
 Identities = 13/91 (14%), Positives = 37/91 (40%), Gaps = 10/91 (10%)

Query: 119 PTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFE 178
            + +        ++V  +A T   + +       G ++  K+         K + F  F+
Sbjct: 2   SSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK--------LKDYAFIHFD 53

Query: 179 SAEGVLRALRLLNKFNIDGQELMLKVDQATR 209
             +G ++A+  +N  +++G+   +++  A  
Sbjct: 54  ERDGAVKAMEEMNGKDLEGEN--IEIVFAKP 82

>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 = 46.9 bits (112), Expect = 6e-07
 Identities = 18/88 (20%), Positives = 38/88 (43%), Gaps = 6/88 (6%)

Query: 122 TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSN-GTPKGFGFCEFESA 180
           + ++    +++V  I        +  +    G +      +   N    KGFGF  FE++
Sbjct: 9   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILD---VEIIFNERGSKGFGFVTFENS 65

Query: 181 EGVLRALRLLNKFNIDGQELMLKVDQAT 208
               RA   L+   ++G++  ++V+ AT
Sbjct: 66  ADADRAREKLHGTVVEGRK--IEVNNAT 91

>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 = 46.9 bits (112), Expect = 7e-07
 Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 2/79 (2%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
            ++V  I   A  D +       G +K+         G  KG+   E+E+ +  L A   
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 190 LNKFNIDGQELMLKVDQAT 208
           LN   I GQ   ++VD   
Sbjct: 88  LNGAEIMGQT--IQVDWCF 104

>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 = 46.8 bits (112), Expect = 8e-07
 Identities = 18/82 (21%), Positives = 33/82 (40%), Gaps = 2/82 (2%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
               + V  ++       +  + +  G++     A+  + G  KGF F  F   E   RA
Sbjct: 14  DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73

Query: 187 LRLLNKFNIDGQELMLKVDQAT 208
           +  ++ F  D   L+L V+ A 
Sbjct: 74  IAGVSGFGYDH--LILNVEWAK 93

>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 = 46.4 bits (111), Expect = 9e-07
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 9/87 (10%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKR-AQYPSNGTPKGFGFCEFESAEGVLR 185
             + +++G + P  D   +       G +    +  + P  G  KG+ F  F S +    
Sbjct: 4   GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63

Query: 186 ALRLLNKFNIDGQELM---LKVDQATR 209
           A+  +N     GQ L    + V  A +
Sbjct: 64  AIEAMN-----GQYLCNRPITVSYAFK 85

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 46.6 bits (111), Expect = 9e-07
 Identities = 15/84 (17%), Positives = 29/84 (34%), Gaps = 3/84 (3%)

Query: 132 YVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN 191
            +           + S+    G V + +     + G  KGF F E  S     + ++  +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 192 KFNIDGQELMLKVDQATREYLERY 215
              +D +   L +       +ERY
Sbjct: 76  GKRLDLKH-RLFLYTMKD--VERY 96

>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 = 46.5 bits (111), Expect = 9e-07
 Identities = 18/89 (20%), Positives = 40/89 (44%), Gaps = 4/89 (4%)

Query: 122 TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQ-YPSNGTPKGFGFCEFESA 180
            P ++  +K+ V  I   A+   +  +    G +K+ +  +     G  +GFGF +F + 
Sbjct: 9   VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 68

Query: 181 EGVLRALR-LLNKFNIDGQELMLKVDQAT 208
           +   +A   L +  ++ G+   L ++ A 
Sbjct: 69  QDAKKAFNALCHSTHLYGRR--LVLEWAD 95

>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 = 49.1 bits (116), Expect = 2e-06
 Identities = 24/146 (16%), Positives = 41/146 (28%), Gaps = 6/146 (4%)

Query: 64  GLPRYPAPYPSMVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTP 123
           G+P        M      P    P G++P     P    PG  P    +   +P      
Sbjct: 143 GMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLS 202

Query: 124 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 183
              P   +++  +    +   +  +       K  +              F EF++    
Sbjct: 203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP-----GRHDIAFVEFDNEVQA 257

Query: 184 LRALRLLNKFNIDGQELMLKVDQATR 209
             A   L  F I     M K+  A +
Sbjct: 258 GAARDALQGFKITQNNAM-KISFAKK 282

>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 = 41.4 bits (96), Expect = 5e-04
 Identities = 14/93 (15%), Positives = 29/93 (31%), Gaps = 9/93 (9%)

Query: 122 TPAEKPQTKVYVGKIAPTADSDFVLSVL----KVCGTVKSWKRAQYPSNGTPKGFGFCEF 177
            P  +P   +Y+  +      D +   L       G +          +   +G  F  F
Sbjct: 3   VPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIF 59

Query: 178 ESAEGVLRALRLLNKFNIDGQELMLKVDQATRE 210
           +       ALR +  F    +   +++  A  +
Sbjct: 60  KEVSSATNALRSMQGFPFYDKP--MRIQYAKTD 90

>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 = 45.2 bits (108), Expect = 2e-06
 Identities = 16/83 (19%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
               V+VG ++P   +  + +     G +   +  +  + G  KG+GF  F +      A
Sbjct: 5   SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64

Query: 187 LRLLNKFNIDGQELMLKVDQATR 209
           ++ +    + G++  ++ + ATR
Sbjct: 65  IQQMGGQWLGGRQ--IRTNWATR 85

>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 = 45.3 bits (108), Expect = 2e-06
 Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 4/83 (4%)

Query: 128 QTKVYVGKIAPTADSDFVLSVLKVCGT--VKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 185
           +  +Y+G +      + +   +   G   +   K  +  +NG  KGF      S     +
Sbjct: 1   RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60

Query: 186 ALRLLNKFNIDGQELMLKVDQAT 208
            + LL K  + GQ     V  + 
Sbjct: 61  LMDLLPKRELHGQN--PVVTPSN 81

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 45.9 bits (109), Expect = 2e-06
 Identities = 19/104 (18%), Positives = 41/104 (39%), Gaps = 15/104 (14%)

Query: 121 VTPAEKPQTKVYVGKIAPTADSD-------FVLSVLKVCGTVKSWKRAQYP-SNGTPKGF 172
              A+   + + V  + P    D        +  +    G + +     YP  +G  KG+
Sbjct: 8   PQEADGIDSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITN---DFYPEEDGKTKGY 63

Query: 173 GFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYV 216
            F E+ S    + A++  + + +D Q    +V+  T    ++Y+
Sbjct: 64  IFLEYASPAHAVDAVKNADGYKLDKQH-TFRVNLFTD--FDKYM 104

>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 = 45.3 bits (108), Expect = 2e-06
 Identities = 23/108 (21%), Positives = 41/108 (37%), Gaps = 16/108 (14%)

Query: 105 VRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP 164
           +R           LP       P    ++G +      + +    +    + + +  + P
Sbjct: 1   MRGSHHHHHHRSRLPK-----SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREP 54

Query: 165 SN-GTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM---LKVDQAT 208
           SN    KGFG+ EFE  + +L AL L      + + L    ++VD A 
Sbjct: 55  SNPERLKGFGYAEFEDLDSLLSALSL------NEESLGNRRIRVDVAD 96

>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 = 45.4 bits (108), Expect = 2e-06
 Identities = 18/87 (20%), Positives = 32/87 (36%), Gaps = 2/87 (2%)

Query: 125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 184
                K++VG +      + VL + +  G +          +G+ KG  F +F S     
Sbjct: 12  GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDE-CTVLRGPDGSSKGCAFVKFSSHTEAQ 70

Query: 185 RALRLLN-KFNIDGQELMLKVDQATRE 210
            A+  L+    + G    L V  A  +
Sbjct: 71  AAIHALHGSQTMPGASSSLVVKFADTD 97

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 46.3 bits (110), Expect = 2e-06
 Identities = 22/141 (15%), Positives = 38/141 (26%), Gaps = 17/141 (12%)

Query: 69  PAPYPSMVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQ 128
            + +         PR      +             G  P               P  +  
Sbjct: 3   SSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPP---------------PDVEGM 47

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
           T + V  +      D +  V +  G V      +       +GF F  F        A+ 
Sbjct: 48  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107

Query: 189 LLNKFNIDGQELMLKVDQATR 209
            ++   +DG+E  L+V  A  
Sbjct: 108 AMDGAVLDGRE--LRVQMARY 126

>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 = 45.4 bits (108), Expect = 3e-06
 Identities = 18/98 (18%), Positives = 40/98 (40%), Gaps = 2/98 (2%)

Query: 113 VRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGF 172
           +R +P+ +     +P   +Y+  ++P      ++S+       K          G  +G 
Sbjct: 10  IRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQ 69

Query: 173 GFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATRE 210
            F  F + E   +AL L+N + + G+   L ++    +
Sbjct: 70  AFITFPNKEIAWQALHLVNGYKLYGKI--LVIEFGKNK 105

>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 = 45.9 bits (109), Expect = 3e-06
 Identities = 17/115 (14%), Positives = 33/115 (28%), Gaps = 2/115 (1%)

Query: 96  RPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTV 155
             P             + R            P   + V  ++       +  V    G +
Sbjct: 14  LVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPI 73

Query: 156 KSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATRE 210
                     +   +GF F  FE+ +    A    N   +DG+   ++VD +  +
Sbjct: 74  ADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR--IRVDFSITK 126

>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 = 44.9 bits (107), Expect = 3e-06
 Identities = 16/83 (19%), Positives = 32/83 (38%), Gaps = 8/83 (9%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
            +++++VG + P    + +  + +  G                KGFGF   E+      A
Sbjct: 14  QRSRLFVGNLPPDITEEEMRKLFEKYGKAGE---VFIH---KDKGFGFIRLETRTLAEIA 67

Query: 187 LRLLNKFNIDGQELMLKVDQATR 209
              L+   + G++  L+V  A  
Sbjct: 68  KVELDNMPLRGKQ--LRVRFACH 88

>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 = 47.0 bits (111), Expect = 3e-06
 Identities = 15/133 (11%), Positives = 30/133 (22%), Gaps = 15/133 (11%)

Query: 87  PVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTK-----------VYVGK 135
            + V  S     +PG            +            P+             ++   
Sbjct: 71  KMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFN 130

Query: 136 IAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI 195
                  +    +    G  +      +         G  E++S    L  L  LN + +
Sbjct: 131 APLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQM 190

Query: 196 DGQ----ELMLKV 204
                     LK+
Sbjct: 191 KNPNGPYPYTLKL 203

>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 = 45.4 bits (108), Expect = 4e-06
 Identities = 17/86 (19%), Positives = 36/86 (41%), Gaps = 7/86 (8%)

Query: 126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGT--PKGFGFCEFESAEGV 183
               K+++G +    +   + +V    G +          + T   +GF F  FE+    
Sbjct: 5   DHPGKLFIGGLNRETNEKMLKAVFGKHGPISE---VLLIKDRTSKSRGFAFITFENPADA 61

Query: 184 LRALRLLNKFNIDGQELMLKVDQATR 209
             A + +N  ++ G+   +KV+QA +
Sbjct: 62  KNAAKDMNGKSLHGKA--IKVEQAKK 85

>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 = 44.9 bits (107), Expect = 4e-06
 Identities = 21/78 (26%), Positives = 32/78 (41%), Gaps = 1/78 (1%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
             E+  T +Y+  +  + D   + ++LK  G V S  R    S+GT +G GF   ES E 
Sbjct: 20  QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVIS-TRILRDSSGTSRGVGFARMESTEK 78

Query: 183 VLRALRLLNKFNIDGQEL 200
               +   N   I     
Sbjct: 79  CEAVIGHFNGKFIKTPPG 96

>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 = 47.3 bits (112), Expect = 4e-06
 Identities = 26/209 (12%), Positives = 57/209 (27%), Gaps = 27/209 (12%)

Query: 79  AFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAP 138
           +         G++P  +      IPG+                       + + V  + P
Sbjct: 3   SSHHHHHHSSGLVPRGSHMGRIAIPGLAGA------------------GNSVLLVSNLNP 44

Query: 139 -TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG 197
                  +  +  V G V+  K          K     +         A+  LN   + G
Sbjct: 45  ERVTPQSLFILFGVYGDVQRVKILF-----NKKENALVQMADGNQAQLAMSHLNGHKLHG 99

Query: 198 QELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSP--EN 255
           + + + + +     L R   +    TK    +      K   S        P+ +    N
Sbjct: 100 KPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKK-PGSKNFQNIFPPSATLHLSN 158

Query: 256 LKDNETGNKESHDPTNFGVVTEEDRKADQ 284
           +  + +        ++ G V +  +   +
Sbjct: 159 IPPSVSEEDLKVLFSSNGGVVKGFKFFQK 187

>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 = 40.4 bits (94), Expect = 8e-04
 Identities = 11/78 (14%), Positives = 27/78 (34%), Gaps = 5/78 (6%)

Query: 124 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 183
              P   +++  I P+   + +  +    G V    +         +     +  S E  
Sbjct: 147 IFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEA 202

Query: 184 LRALRLLNKFNI-DGQEL 200
           ++AL  L+  ++ +   L
Sbjct: 203 VQALIDLHNHDLGENHHL 220

>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 = 44.5 bits (106), Expect = 4e-06
 Identities = 15/80 (18%), Positives = 30/80 (37%), Gaps = 10/80 (12%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
            K+++G +   A    + S+ +  G V              K +GF   E       A+R
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQYGKVLECD--------IIKNYGFVHIEDKTAAEDAIR 60

Query: 189 LLNKFNIDGQELMLKVDQAT 208
            L+ + + G    + V+ + 
Sbjct: 61  NLHHYKLHGVN--INVEASK 78

>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 = 45.1 bits (107), Expect = 4e-06
 Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 2/83 (2%)

Query: 126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 185
                ++V  +   A  + +       G +K+         G  KG+   E+E+ +    
Sbjct: 20  VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 79

Query: 186 ALRLLNKFNIDGQELMLKVDQAT 208
           A+  LN  ++ GQ   + VD   
Sbjct: 80  AMEGLNGQDLMGQP--ISVDWCF 100

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 44.1 bits (105), Expect = 6e-06
 Identities = 23/81 (28%), Positives = 35/81 (43%), Gaps = 5/81 (6%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
             V+VG I    D   + S     G+VK  K     + G  KG+GF  F +   V + + 
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT-GVSKGYGFVSFYNDVDVQKIVE 68

Query: 189 LLNKFNIDGQELMLKVDQATR 209
             ++ N  G+   LK+  A R
Sbjct: 69  --SQINFHGK--KLKLGPAIR 85

>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 = 44.8 bits (106), Expect = 6e-06
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 3/97 (3%)

Query: 122 TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 181
               +    VY+  +   A++  V+   K    V+      Y  NG   G GF EF +  
Sbjct: 19  RSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEA 78

Query: 182 GVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDK 218
               AL   +K  +  +   ++V   T++ +   +D 
Sbjct: 79  DYKAALC-RHKQYMGNRF--IQVHPITKKGMLEKIDM 112

>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 = 43.7 bits (104), Expect = 7e-06
 Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 3/78 (3%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
            +YVG +  +A S+ V  +    G V + K         PKGFGF E +       A+  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESV-SEAIAK 61

Query: 190 LNKFNIDGQELMLKVDQA 207
           L+  +  G+   ++V +A
Sbjct: 62  LDNTDFMGRT--IRVTEA 77

>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 = 44.5 bits (105), Expect = 7e-06
 Identities = 15/97 (15%), Positives = 34/97 (35%), Gaps = 3/97 (3%)

Query: 119 PTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFE 178
            + +        V +  +      + ++        V +         G   G  F +F 
Sbjct: 33  GSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFA 92

Query: 179 SAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERY 215
           S E   +AL   +K  I  +   ++V ++++E +  Y
Sbjct: 93  SQELAEKALG-KHKERIGHRY--IEVFKSSQEEVRSY 126

>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 = 43.0 bits (102), Expect = 1e-05
 Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 10/86 (11%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
            + K  TK++VG I+PT  +  + +  +  G V              K + F   E AE 
Sbjct: 5   SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAED 56

Query: 183 VLRALRLLNKFNIDGQELMLKVDQAT 208
            + A+R L+     G+   + V  +T
Sbjct: 57  AVEAIRGLDNTEFQGKR--MHVQLST 80

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 43.5 bits (103), Expect = 1e-05
 Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 6/88 (6%)

Query: 122 TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSN-GTPKGFGFCEFESA 180
           T  +    +++V  I        +  +    G +      +   N    KGFGF  FE++
Sbjct: 23  TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILD---VEIIFNERGSKGFGFVTFENS 79

Query: 181 EGVLRALRLLNKFNIDGQELMLKVDQAT 208
               RA   L+   ++G++  ++V+ AT
Sbjct: 80  ADADRAREKLHGTVVEGRK--IEVNNAT 105

>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 = 44.8 bits (107), Expect = 1e-05
 Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 3/86 (3%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
             +    K++VG I P              GT+   +       G  +GFGF  ++SA+ 
Sbjct: 82  DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141

Query: 183 VLRALRLLNKFNIDGQELMLKVDQAT 208
           V R        +   +   +++ +A 
Sbjct: 142 VDRVC-QNKFIDFKDR--KIEIKRAE 164

>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 = 43.4 bits (103), Expect = 1e-05
 Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 5/82 (6%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
           P   ++V  ++     +   ++ +        +       G+ KGFGF +F S E    A
Sbjct: 14  PSKTLFVKGLSEDTTEE---TLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAA 70

Query: 187 LRLLNKFNIDGQELMLKVDQAT 208
              +    IDG +  + +D A 
Sbjct: 71  KEAMEDGEIDGNK--VTLDWAK 90

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 20/90 (22%), Positives = 34/90 (37%), Gaps = 5/90 (5%)

Query: 121 VTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESA 180
             P  +   K+ +  I P    + + S+L   G V+S ++    S           + S 
Sbjct: 8   SVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSK 64

Query: 181 EGVLRALRLLNKFNIDGQELMLKVDQATRE 210
           +   +AL  LN F ++     LKV     E
Sbjct: 65  DQARQALDKLNGFQLENF--TLKVAYIPDE 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 = 43.4 bits (103), Expect = 1e-05
 Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 4/81 (4%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
             +YV  +    D + +       GT+ S K       G  KGFGF  F S E   +A+ 
Sbjct: 16  VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATKAVT 73

Query: 189 LLNKFNIDGQELMLKVDQATR 209
            +N   +  +   L V  A R
Sbjct: 74  EMNGRIVATKP--LYVALAQR 92

>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 = 42.8 bits (101), Expect = 2e-05
 Identities = 16/76 (21%), Positives = 24/76 (31%), Gaps = 6/76 (7%)

Query: 130 KVYVGKIAPTADSD-----FVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 184
           ++YVG I      +     F   +     T               K F F EF S +   
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 185 RALRLLNKFNIDGQEL 200
           +A+   +     GQ L
Sbjct: 68  QAMA-FDGIIFQGQSL 82

>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 = 43.2 bits (102), Expect = 2e-05
 Identities = 15/87 (17%), Positives = 34/87 (39%), Gaps = 3/87 (3%)

Query: 124 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 183
               +   ++  I  +     VL  L+     ++       +NG   G    +F++ +  
Sbjct: 11  VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 70

Query: 184 LRALRLLNKFNIDGQELMLKVDQATRE 210
            ++ R L++  ++G+E    V   T E
Sbjct: 71  RKSER-LHRKKLNGRE--AFVHVVTLE 94

>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 = 44.6 bits (106), Expect = 2e-05
 Identities = 15/99 (15%), Positives = 35/99 (35%), Gaps = 1/99 (1%)

Query: 106 RPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPS 165
           R + P             A     K++VG I    +   +    +  G ++  +      
Sbjct: 82  RVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRG 141

Query: 166 NGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV 204
           +G  +GF F  F+  + V + + +     ++G    ++ 
Sbjct: 142 SGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRK 179

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 46.4 bits (109), Expect = 2e-05
 Identities = 66/480 (13%), Positives = 133/480 (27%), Gaps = 148/480 (30%)

Query: 72  YPSMVRP-AFPPRPPGPVGVLPSVARPPVPGIPGVRPIMP-PVVRPVPLPTVTPA---EK 126
           Y  ++ P     R P  +  +    R  +      +      V R  P   +  A    +
Sbjct: 91  YKFLMSPIKTEQRQPSMMTRMYIEQRDRLYN--DNQVFAKYNVSRLQPYLKLRQALLELR 148

Query: 127 PQTKVYV------GKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNG----TPKGFGFCE 176
           P   V +      GK           + +       S+K                   C 
Sbjct: 149 PAKNVLIDGVLGSGK-----------TWV-ALDVCLSYKVQCKMDFKIFWLN---LKNCN 193

Query: 177 FESAEGVLRAL-RLLNKFNIDGQEL-------MLKVDQATREYLERYV------------ 216
             S E VL  L +LL + + +            L++    +  L R +            
Sbjct: 194 --SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSI-QAELRRLLKSKPYENCLLVL 250

Query: 217 ----DKKTENT-----KKLKETQDAG----AGKEDESVQSVEKNEPTKSPENLKD---NE 260
               + K  N      K L  T+             +  S++ +  T +P+ +K      
Sbjct: 251 LNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKY 310

Query: 261 TGNKE--------SHDPTNFGVVTEEDRKA-------DQEALEKLTCMVEERLKTNPLPP 305
              +         + +P    ++ E  R              +KLT ++E  L  N L P
Sbjct: 311 LDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSL--NVLEP 368

Query: 306 PPPQTTADGSGI--SNSELPAK------ARDGDSDVDMIRNDIAEDKLDDETTSDTKASD 357
              +   D   +   ++ +P             SDV ++ N + +  L ++   ++  S 
Sbjct: 369 AEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISI 428

Query: 358 HD---RPETSSPDRSRVHDR--------RGRDKERDLKREKE------------REIDRY 394
                  +    +   +H          +  D + DL                 + I+  
Sbjct: 429 PSIYLELKVKLENEYALHRSIVDHYNIPKTFDSD-DLIPPYLDQYFYSHIGHHLKNIEHP 487

Query: 395 EREAE-----------RERVRKE-----------------REQRRKIEEAEREYERCLKD 426
           ER               +++R +                 +  +  I + + +YER +  
Sbjct: 488 ERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNA 547

>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 = 43.3 bits (101), Expect = 2e-04
 Identities = 57/451 (12%), Positives = 124/451 (27%), Gaps = 93/451 (20%)

Query: 176 EFESAEGVLRALRLLNKFNIDGQELMLKVDQATREY--LERYVDKKTENTKKLKET---Q 230
           + +  + + +++  L+K  ID   +++  D  +         + K+ E  +K  E     
Sbjct: 34  DCKDVQDMPKSI--LSKEEID--HIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRI 89

Query: 231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKL 290
           +          +  + +  T+     +D    + +     N  V   +     ++AL +L
Sbjct: 90  NYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYN--VSRLQPYLKLRQALLEL 147

Query: 291 TCMVEERLKTNPLPPPPPQTTADG-SGISNSELPAKA-RDGDSD---------VDMIRND 339
                          P      DG  G   + +                    +++   +
Sbjct: 148 R--------------PAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCN 193

Query: 340 IAEDKLDDETT--SDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYER- 396
             E  L+           +   R + SS  + R+H    + + R L + K      YE  
Sbjct: 194 SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHS--IQAELRRLLKSK-----PYENC 246

Query: 397 -----EAERERVRKEREQRRKI------------EEAEREYERCLKDWEYREREREKERQ 439
                  +  +         KI              A       L          E +  
Sbjct: 247 LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL 306

Query: 440 YEK--EKEKERERKRKKEI------LYDEEEDEDDSR-KRWRRSVLEEKRRKRIREKEED 490
             K  +   +   +           +  E   +  +    W+  V  +K    I      
Sbjct: 307 LLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKH-VNCDKLTTIIESSLNV 365

Query: 491 L-ADEVREE-EEIAV----AKRRAE------EEQLQQQQRDALKLLSDNAVNGSLAEESA 538
           L   E R+  + ++V    A            + ++      +  L       SL E+  
Sbjct: 366 LEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKL----HKYSLVEKQP 421

Query: 539 VESKGMDVE-HDYHDDSIRENHMEIRLHKMV 568
            ES    +     + +   +   E  LH+ +
Sbjct: 422 KEST---ISIPSIYLELKVKLENEYALHRSI 449

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 20/103 (19%), Positives = 35/103 (33%), Gaps = 9/103 (8%)

Query: 125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 184
           +     VY+      A  D +   L+  G V + +  +   +   KG  F  F+S E   
Sbjct: 8   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAK 66

Query: 185 RALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLK 227
           + +           +L++            Y  KK E  K+ K
Sbjct: 67  KFVE-TPGQKYKETDLLILFKDD-------YFAKKNEERKQNK 101

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 16/72 (22%), Positives = 27/72 (37%), Gaps = 8/72 (11%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
           T+++V           +  +    G +K  K           GF F EFE AE   +A+ 
Sbjct: 32  TRLFVRPFPLDVQESELNEIFGPFGPMKEVK--------ILNGFAFVEFEEAESAAKAIE 83

Query: 189 LLNKFNIDGQEL 200
            ++  +   Q L
Sbjct: 84  EVHGKSFANQPL 95

>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 = 42.3 bits (100), Expect = 3e-05
 Identities = 17/91 (18%), Positives = 28/91 (30%), Gaps = 8/91 (8%)

Query: 119 PTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFE 178
             V  +      VY G IA       +       G +      +       KG+ F  F 
Sbjct: 16  DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIME---IRVFPE---KGYSFVRFS 69

Query: 179 SAEGVLRALRLLNKFNIDGQELMLKVDQATR 209
           + E    A+  +N   I+G   ++K      
Sbjct: 70  THESAAHAIVSVNGTTIEGH--VVKCYWGKE 98

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 41.2 bits (97), Expect = 5e-05
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 16/82 (19%)

Query: 118 LPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP-SNGTPKGFGFCE 176
           +P V P    + K            + +  +    G + +     YP  +G  KG+ F E
Sbjct: 9   VPQVGPDRLEKLK------------NVIHKIFSKFGKITN---DFYPEEDGKTKGYIFLE 53

Query: 177 FESAEGVLRALRLLNKFNIDGQ 198
           + S    + A++  + + +D Q
Sbjct: 54  YASPAHAVDAVKNADGYKLDKQ 75

>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 = 41.5 bits (98), Expect = 5e-05
 Identities = 12/81 (14%), Positives = 27/81 (33%), Gaps = 8/81 (9%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
             +YV  +  +   + +             +          + + F  F + E  + A++
Sbjct: 16  KILYVRNLMLSTSEEMIEKEFNNIKPGAVER------VKKIRDYAFVHFSNREDAVEAMK 69

Query: 189 LLNKFNIDGQELMLKVDQATR 209
            LN   +DG    ++V  A  
Sbjct: 70  ALNGKVLDGSP--IEVTLAKP 88

>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 = 41.0 bits (97), Expect = 5e-05
 Identities = 16/81 (19%), Positives = 31/81 (38%), Gaps = 10/81 (12%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
            K++VG ++    S  + S+ +  G V              K + F   E       A+ 
Sbjct: 10  WKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIA 61

Query: 189 LLNKFNIDGQELMLKVDQATR 209
            LN   + G+   + V+ +T+
Sbjct: 62  QLNGKEVKGKR--INVELSTK 80

>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 = 42.9 bits (101), Expect = 5e-05
 Identities = 17/87 (19%), Positives = 30/87 (34%), Gaps = 2/87 (2%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
              +  T + V  +      D +  V +  G V      +       +GF F  F     
Sbjct: 65  MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 124

Query: 183 VLRALRLLNKFNIDGQELMLKVDQATR 209
              A+  ++   +DG+E  L+V  A  
Sbjct: 125 AEDAMDAMDGAVLDGRE--LRVQMARY 149

>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 = 42.9 bits (101), Expect = 6e-05
 Identities = 20/85 (23%), Positives = 32/85 (37%), Gaps = 2/85 (2%)

Query: 126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 185
                ++V  I   A  D +       G +K+         G  KG+   E+E+ +  L 
Sbjct: 70  VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 129

Query: 186 ALRLLNKFNIDGQELMLKVDQATRE 210
           A   LN   I GQ   ++VD    +
Sbjct: 130 AKEALNGAEIMGQ--TIQVDWCFVK 152

>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 = 43.5 bits (103), Expect = 7e-05
 Identities = 14/81 (17%), Positives = 28/81 (34%), Gaps = 8/81 (9%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
            +++VG +      +    + +  G            +   +GFGF   ES      A  
Sbjct: 23  CRLFVGNLPTDITEEDFKRLFERYGEPSE---VFINRD---RGFGFIRLESRTLAEIAKA 76

Query: 189 LLNKFNIDGQELMLKVDQATR 209
            L+   +  +   L++  AT 
Sbjct: 77  ELDGTILKSRP--LRIRFATH 95

>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 = 41.6 bits (98), Expect = 4e-04
 Identities = 15/77 (19%), Positives = 25/77 (32%), Gaps = 5/77 (6%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
               + V  ++P   ++ +       G V+          G   G GF EF +     +A
Sbjct: 95  HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVV-VDDRGRATGKGFVEFAAKPPARKA 153

Query: 187 LRLLNKFNIDGQELMLK 203
           L        DG  L+  
Sbjct: 154 LERCG----DGAFLLTT 166

>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 = 41.3 bits (97), Expect = 8e-05
 Identities = 19/88 (21%), Positives = 30/88 (34%), Gaps = 6/88 (6%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGT----VKSWKRAQYPSNGTPKGFGFCEFESAEG 182
              ++++G I      + +L  +         V  +  A        +GF F E+ES   
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADK--MKNRGFAFVEYESHRA 64

Query: 183 VLRALRLLNKFNIDGQELMLKVDQATRE 210
              A R L    I      + VD A  E
Sbjct: 65  AAMARRKLMPGRIQLWGHQIAVDWAEPE 92

>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 = 40.9 bits (96), Expect = 9e-05
 Identities = 14/92 (15%), Positives = 32/92 (34%), Gaps = 3/92 (3%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
           P       V +  +      + ++        V +         G   G  F +F S E 
Sbjct: 10  PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEI 69

Query: 183 VLRALRLLNKFNIDGQELMLKVDQATREYLER 214
             +AL+  +K  I  +   +++ +++R  +  
Sbjct: 70  AEKALK-KHKERIGHRY--IEIFKSSRAEVRT 98

>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 = 42.6 bits (100), Expect = 1e-04
 Identities = 10/76 (13%), Positives = 26/76 (34%), Gaps = 4/76 (5%)

Query: 126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 185
            P   +++  I P+   + +  +    G V    +         +     +  S E  ++
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQ 173

Query: 186 ALRLLNKFNIDGQELM 201
           AL  L+  ++     +
Sbjct: 174 ALIDLHNHDLGENHHL 189

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 39.8 bits (93), Expect = 2e-04
 Identities = 12/83 (14%), Positives = 27/83 (32%), Gaps = 3/83 (3%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
                + ++ +  +        +  + +      ++            G G  EF S E 
Sbjct: 23  KLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVN---TRDFDGTGALEFPSEEI 79

Query: 183 VLRALRLLNKFNIDGQELMLKVD 205
           ++ AL  LN     G  + ++ D
Sbjct: 80  LVEALERLNNIEFRGSVITVERD 102

>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 = 39.8 bits (93), Expect = 2e-04
 Identities = 15/88 (17%), Positives = 31/88 (35%), Gaps = 7/88 (7%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
           P+ + + +V V  + P+     +   ++  G V         ++    G G  EF   E 
Sbjct: 10  PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCY-------ADVYRDGTGVVEFVRKED 62

Query: 183 VLRALRLLNKFNIDGQELMLKVDQATRE 210
           +  A+R L+       E      +   +
Sbjct: 63  MTYAVRKLDNTKFRSHEGETAYIRVKVD 90

>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 = 39.2 bits (92), Expect = 3e-04
 Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 7/82 (8%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
             +K  T +YVG +  T     + +     G +++            +   F +F + + 
Sbjct: 7   GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV------QRQQCAFIQFATRQA 60

Query: 183 VLRAL-RLLNKFNIDGQELMLK 203
              A  +  NK  ++G+ L +K
Sbjct: 61  AEVAAEKSFNKLIVNGRRLNVK 82

>1w1w_A Structural maintenance of chromosome 1; cohesin, chromosome segregation, cell adhesion, kleisin, MIT cell cycle; HET: ATG; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.12 Length = 430

 Score = 42.4 bits (100), Expect = 3e-04
 Identities = 22/131 (16%), Positives = 45/131 (34%), Gaps = 7/131 (5%)

Query: 375 RGRDKERDLKRE----KEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYR 430
             +D    L+ E    K +    ++ + E+   +   E  R  EE     +      EY 
Sbjct: 127 SYKDYSIFLENENILIKAKNFLVFQGDVEQIAAQSPVELSRMFEEVSGSIQY---KKEYE 183

Query: 431 EREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEED 490
           E + + E+  +   E  + R+R    L   +    +   +  R    ++   R      +
Sbjct: 184 ELKEKIEKLSKSATESIKNRRRIHGELKTYKSPGLEVLFQGPRGSRYDEAEGRFEVINNE 243

Query: 491 LADEVREEEEI 501
                 EE++I
Sbjct: 244 TEQLKAEEKKI 254

>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 = 40.2 bits (94), Expect = 3e-04
 Identities = 12/88 (13%), Positives = 28/88 (31%), Gaps = 3/88 (3%)

Query: 110 PPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTP 169
             + R       T        V++  +   A  + + +       V+     +   +G  
Sbjct: 28  QQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR--VHIEIGPDGRV 85

Query: 170 KGFGFCEFESAEGVLRALRLLNKFNIDG 197
            G    EF + E  + A+   ++ N+  
Sbjct: 86  TGEADVEFATHEEAVAAMS-KDRANMQH 112

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 427

 Score = 42.4 bits (99), Expect = 3e-04
 Identities = 19/119 (15%), Positives = 52/119 (43%), Gaps = 5/119 (4%)

Query: 401 ERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDE 460
           E  R+ + +    ++ + + +       Y   E ++     + ++KE E ++       E
Sbjct: 296 ELYRRCKLEEMGFKDTDPDSKPFSLQETY---EAKRNEFLGELQKKEEEMRQMFVQRVKE 352

Query: 461 EEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVRE-EEEIAVAKRRAEEEQLQQQQR 518
           +E E    ++       ++ +K  +++++ L D+ +  ++E+   K+R    +L Q Q 
Sbjct: 353 KEAELKEAEK-ELHEKFDRLKKLHQDEKKKLEDKKKSLDDEVNAFKQRKTAAELLQSQG 410

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 427

 Score = 41.7 bits (97), Expect = 5e-04
 Identities = 18/117 (15%), Positives = 44/117 (37%), Gaps = 10/117 (8%)

Query: 352 DTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRR 411
               S     + +   +        + KE ++++   + +    +E E E    E+E   
Sbjct: 311 TDPDSKPFSLQETYEAKRNEFLGELQKKEEEMRQMFVQRV----KEKEAELKEAEKELHE 366

Query: 412 KIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSR 468
           K +  ++ ++   K  E      +K++  + E    ++RK   E+L  +      S+
Sbjct: 367 KFDRLKKLHQDEKKKLE------DKKKSLDDEVNAFKQRKTAAELLQSQGSQAGGSQ 417

>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 = 38.9 bits (91), Expect = 3e-04
 Identities = 11/72 (15%), Positives = 28/72 (38%), Gaps = 7/72 (9%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
           + + V  +   ++   V  +LK           +Y      K   F    + E    A++
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 189 LLNKFNIDGQEL 200
           + ++++  G++L
Sbjct: 59  MFHQYSFRGKDL 70

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 21/78 (26%), Positives = 32/78 (41%), Gaps = 7/78 (8%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
           KVYVG +   A    +       G +++   A       P GF F EFE       A+R 
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIA-----RNPPGFAFVEFEDPRDAEDAVRG 56

Query: 190 LNKFNIDGQELMLKVDQA 207
           L+   I G    ++V+ +
Sbjct: 57  LDGKVICGSR--VRVELS 72

>2qag_C Septin-7; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 418

 Score = 41.7 bits (97), Expect = 5e-04
 Identities = 20/121 (16%), Positives = 50/121 (41%), Gaps = 4/121 (3%)

Query: 368 RSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDW 427
               +       +  L +    +++   RE   +  + E E  +  E   +E  + LKD 
Sbjct: 297 AVTYNGVDNNKNKGQLTKSPLAQMEEERREHVAKMKKMEMEMEQVFEMKVKEKVQKLKDS 356

Query: 428 E--YREREREKERQYEKEKEKERERKRK--KEILYDEEEDEDDSRKRWRRSVLEEKRRKR 483
           E   + R  + ++  E + ++  E++R+   E    E +     ++   R++ + K++ +
Sbjct: 357 EAELQRRHEQMKKNLEAQHKELEEKRRQFEDEKANWEAQQRILEQQNSSRTLEKNKKKGK 416

Query: 484 I 484
           I
Sbjct: 417 I 417

>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 = 39.5 bits (92), Expect = 7e-04
 Identities = 20/81 (24%), Positives = 32/81 (39%), Gaps = 7/81 (8%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
              KVYVG +    +   +       G ++S   A       P GF F EFE       A
Sbjct: 72  LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVA-----RNPPGFAFVEFEDPRDAADA 126

Query: 187 LRLLNKFNIDGQELMLKVDQA 207
           +R L+   + G    ++V+ +
Sbjct: 127 VRELDGRTLCGCR--VRVELS 145

>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H Length = 423

 Score = 41.4 bits (97), Expect = 7e-04
 Identities = 24/161 (14%), Positives = 48/161 (29%), Gaps = 15/161 (9%)

Query: 328 DGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREK 387
           + D D++     + +D LD     +    + +  +   P  S            D  R+ 
Sbjct: 35  EPDPDLEDPDLALEDDLLDLPEEGEGLDLEEEEEDLPIPKISTS----------DPVRQY 84

Query: 388 EREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRER-----EREKERQYEK 442
             EI +       E V   R+    +E  ++  E    D +              R    
Sbjct: 85  LHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHI 144

Query: 443 EKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKR 483
              KE    +  E +  + +      KR+     E +  ++
Sbjct: 145 PGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAREGEAARQ 185

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 39.8 bits (92), Expect = 8e-04
 Identities = 21/115 (18%), Positives = 36/115 (31%), Gaps = 13/115 (11%)

Query: 109 MPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGT 168
             P      +      +     VY+      A  D +   L+  G V +  + +   +  
Sbjct: 90  RSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNI-QMRRTLHKA 148

Query: 169 PKGFGFCEFESAEGVLRALRLLNKFNIDGQEL--MLKVDQATREYLERYVDKKTE 221
            KG  F  F+S E   + +    +      +L  + K D         Y  KK E
Sbjct: 149 FKGSIFVVFDSIESAKKFVETPGQ-KYKETDLLILFKDD---------YFAKKNE 193

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	577
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.89
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.88
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.88
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.87
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.86
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.86
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.86
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.85
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.84
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.84
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.84
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.83
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.82
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.81
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.79
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.79
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.78
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.78
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.78
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.78
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.77
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.77
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.76
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.75
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.74
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.73
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.72
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.71
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.71
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.71
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.71
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.71
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.71
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.7
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.7
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.69
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.69
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.69
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.69
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.69
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.69
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.69
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.69
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.69
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.68
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.68
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.68
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.68
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.68
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.68
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.68
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.68
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.68
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.68
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.68
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.67
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.67
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.67
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.67
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.67
2div_A	99	TRNA selenocysteine associated protein; structural	99.67
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.67
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.67
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.66
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.66
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.66
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.66
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.66
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.66
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.66
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.65
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.65
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.65
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.65
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.65
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.65
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.65
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.65
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.65
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.65
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.64
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.64
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.64
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.64
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.64
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.64
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.64
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.64
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.64
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.64
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.64
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.64
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.64
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.64
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.64
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.64
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.63
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.63
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.63
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.63
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.62
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.62
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.62
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.62
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.62
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.62
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.62
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.62
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.62
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.61
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.61
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.61
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.61
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.61
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.61
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.6
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.6
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.6
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.6
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.6
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.6
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.59
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.59
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.59
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.59
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.59
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.59
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.59
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.59
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.59
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.59
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.59
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.58
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.58
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.58
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.58
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.58
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.57
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.57
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.57
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.57
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.57
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.57
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.57
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.57
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.56
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.55
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.55
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.55
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.54
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.54
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.54
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.54
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.54
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.3
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.54
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.53
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.53
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.53
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.52
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.52
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.51
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.51
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.51
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.51
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.5
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.5
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.5
1x5p_A	97	Negative elongation factor E; structure genomics,	99.49
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.49
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.49
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.49
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.48
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.48
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.47
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.47
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.47
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.46
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.46
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.46
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.46
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.46
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.46
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.45
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.45
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.44
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.44
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.42
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.42
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.41
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.38
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.36
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.36
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.33
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.29
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.28
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.26
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.26
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.25
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.24
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.21
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.12
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.11
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.08
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.02
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	98.95
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.92
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.87
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.71
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.53
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	98.3
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	98.24
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	98.24
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	98.14
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.13
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	98.12
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	98.11
1x4e_A	85	RNA binding motif, single-stranded interacting pro	98.07
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	98.07
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	97.94
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	97.91
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	97.9
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	97.89
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	97.89
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	97.85
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	97.84
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	97.84
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	97.84
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	97.84
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	97.84
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	97.84
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	97.84
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	97.83
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	97.83
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	97.83
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	97.82
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	97.82
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	97.82
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	97.81
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	97.81
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	97.81
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	97.8
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	97.8
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	97.8
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	97.8
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	97.79
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	97.79
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	97.78
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	97.78
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	97.76
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	97.76
1x5o_A	114	RNA binding motif, single-stranded interacting pro	97.75
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	97.75
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	97.75
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	97.75
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	97.74
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	97.74
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	97.74
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	97.73
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	97.73
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	97.73
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	97.73
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	97.73
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	97.72
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	97.71
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	97.71
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	97.71
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	97.71
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	97.71
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	97.71
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	97.69
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	97.69
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	97.69
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	97.69
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	97.69
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	97.68
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	97.67
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	97.67
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	97.66
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	97.65
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	97.65
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	97.65
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	97.65
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	97.64
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	97.64
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	97.64
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	97.63
2div_A	99	TRNA selenocysteine associated protein; structural	97.62
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	97.62
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	97.62
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	97.62
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	97.61
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	97.6
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	97.6
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	97.6
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	97.59
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	97.59
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	97.58
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	97.58
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	97.57
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	97.56
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	97.55
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	97.55
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	97.55
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	97.54
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	97.53
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	97.53
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	97.53
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	97.52
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	97.52
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	96.66
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	97.51
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	97.48
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	97.48
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	97.48
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	97.47
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	97.46
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	97.46
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	97.45
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	97.45
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.44
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	97.44
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	97.44
2dis_A	109	Unnamed protein product; structural genomics, RRM	97.43
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	97.42
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	97.41
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	97.38
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	97.38
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	97.37
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	97.36
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	97.35
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	97.35
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	97.33
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	97.33
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	97.3
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	97.28
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	97.28
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	97.25
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	97.23
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	97.23
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	97.2
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	97.2
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	97.17
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	97.17
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	97.17
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	97.13
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	97.12
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	97.09
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	97.08
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	97.08
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	97.0
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	96.99
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	96.98
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	96.96
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	96.95
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	96.94
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	96.88
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	96.86
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	96.85
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	96.85
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	96.8
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.79
1x5p_A	97	Negative elongation factor E; structure genomics,	96.75
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	96.72
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	96.71
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	96.61
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.61
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	96.57
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	96.57
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	96.55
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	96.46
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.27
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	96.18
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	96.17
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	96.1
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	95.82
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	95.77
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	95.75
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	95.6
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	95.37
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	94.66
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	94.13
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	93.78
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.18
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	91.95
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	91.68
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	86.7
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	80.55

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.89  E-value=1.1e-23  Score=204.96  Aligned_cols=154  Identities=18%  Similarity=0.256  Sum_probs=123.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||||||+++|+++|+.+|+.||.|.+|.|+.++.+|.++|||||+|.+.++|..||..||+..+.|+.|.|.++
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            35689999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             hhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHH
Q 008117          206 QATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQE  285 (577)
Q Consensus       206 ~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~  285 (577)
                      ........            .. ...+||+||+..+++.+|.+++..++........ ...+.++|||||.|.+.++|.+
T Consensus        93 ~~~~~~~~------------~~-~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~-~d~~~~~g~~fV~f~~~~~a~~  158 (213)
T 4f02_A           93 QRDPSLRK------------SG-VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV-CDENGSKGYGFVHFETQEAAER  158 (213)
T ss_dssp             CCCTHHHH------------HC-TTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEE-EETTEEEEEEEEEESSHHHHHH
T ss_pred             cccccccc------------cc-cccceECCcccccHHHHHHHHHhhcCCeEEEEee-ccCCCCceEEEEEeCCHHHHHH
Confidence            65422111            11 1225999999999999999884411111111000 1123479999999999999999


Q ss_pred             HHHHHhhh
Q 008117          286 ALEKLTCM  293 (577)
Q Consensus       286 Al~~l~~~  293 (577)
                      ||..||+.
T Consensus       159 Ai~~lng~  166 (213)
T 4f02_A          159 AIEKMNGM  166 (213)
T ss_dssp             HHHHHTTC
T ss_pred             HHHHhCCC
Confidence            99999874

>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=99.88  E-value=2.2e-22  Score=186.40  Aligned_cols=152  Identities=13%  Similarity=0.192  Sum_probs=126.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      +.++|||+|||+.+|+++|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++.
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            36899999999999999999999999999999999998899999999999999999999999999999999999999886


Q ss_pred             hhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHH
Q 008117          207 ATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQE  285 (577)
Q Consensus       207 ~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~  285 (577)
                      ....               ......+||+||+..+++.+|.+++...+...... ..+..+|.++|||||+|.+.++|..
T Consensus        81 ~~~~---------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~  145 (167)
T 1fxl_A           81 PSSA---------------SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEE  145 (167)
T ss_dssp             CCCG---------------GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHH
T ss_pred             CCcc---------------cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHH
Confidence            5311               11123359999999999999988844221111011 1124578899999999999999999


Q ss_pred             HHHHHhhh
Q 008117          286 ALEKLTCM  293 (577)
Q Consensus       286 Al~~l~~~  293 (577)
                      |+..|++.
T Consensus       146 A~~~l~g~  153 (167)
T 1fxl_A          146 AIKGLNGQ  153 (167)
T ss_dssp             HHHHHTTC
T ss_pred             HHHHhcCC
Confidence            99998875

>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=99.88  E-value=1.8e-22  Score=187.53  Aligned_cols=152  Identities=14%  Similarity=0.230  Sum_probs=127.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      +.++|||+|||+.+++++|+.+|+.||.|..|.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++.
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            46899999999999999999999999999999999998899999999999999999999999999999999999999886


Q ss_pred             hhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHH
Q 008117          207 ATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQE  285 (577)
Q Consensus       207 ~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~  285 (577)
                      ...               .......+||+||+..+++.+|.+++...+....... .+..+|.++|||||.|.+.++|.+
T Consensus        82 ~~~---------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~  146 (168)
T 1b7f_A           82 PGG---------------ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE  146 (168)
T ss_dssp             CCS---------------STTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHH
T ss_pred             CCc---------------ccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHH
Confidence            531               1122334699999999999999988442221111111 124578899999999999999999


Q ss_pred             HHHHHhhh
Q 008117          286 ALEKLTCM  293 (577)
Q Consensus       286 Al~~l~~~  293 (577)
                      |+..|++.
T Consensus       147 A~~~l~g~  154 (168)
T 1b7f_A          147 AISALNNV  154 (168)
T ss_dssp             HHHHHTTC
T ss_pred             HHHHhcCC
Confidence            99998875

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.87  E-value=7.6e-22  Score=182.61  Aligned_cols=151  Identities=15%  Similarity=0.223  Sum_probs=123.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchhh
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQAT  208 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~~  208 (577)
                      ++|||+|||+++|+++|..+|+.||.|.+|.|+.++ +|.++|||||+|.+.++|..|+..|||..|.|+.|.|.++...
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            589999999999999999999999999999999986 6889999999999999999999999999999999999988553


Q ss_pred             HHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHH
Q 008117          209 REYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEAL  287 (577)
Q Consensus       209 ~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al  287 (577)
                      ..             ........+||+||+..+++.+|.+++...+....... .+..+|.++|||||.|.+.++|..|+
T Consensus        80 ~~-------------~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~  146 (166)
T 3md3_A           80 QQ-------------SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM  146 (166)
T ss_dssp             CC-------------CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHH
T ss_pred             CC-------------CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHH
Confidence            11             11223344699999999999999988442221111111 12467899999999999999999999


Q ss_pred             HHHhhh
Q 008117          288 EKLTCM  293 (577)
Q Consensus       288 ~~l~~~  293 (577)
                      ..|++.
T Consensus       147 ~~l~g~  152 (166)
T 3md3_A          147 DSMQGQ  152 (166)
T ss_dssp             HHHTTC
T ss_pred             HHhCCC
Confidence            998864

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.86  E-value=7e-22  Score=191.42  Aligned_cols=163  Identities=15%  Similarity=0.212  Sum_probs=126.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..++|||+|||+++|+++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            46899999999999999999999999999999999998899999999999999999999999999999999999998875


Q ss_pred             hhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHH
Q 008117          207 ATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQE  285 (577)
Q Consensus       207 ~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~  285 (577)
                      ...........    ........+.+||+||+..+++++|.+++..++....... .+..+|.++|||||+|.+.++|..
T Consensus       107 ~~~~~~~~~~~----~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~  182 (216)
T 2qfj_A          107 NIGQAQPIIDQ----LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQD  182 (216)
T ss_dssp             CCGGGHHHHHH----HHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHH
T ss_pred             Cccccchhhhh----hhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHH
Confidence            54221111100    0011223345699999999999999988442221111111 124578999999999999999999


Q ss_pred             HHHHHhhh
Q 008117          286 ALEKLTCM  293 (577)
Q Consensus       286 Al~~l~~~  293 (577)
                      |+..|++.
T Consensus       183 A~~~l~g~  190 (216)
T 2qfj_A          183 AVSSMNLF  190 (216)
T ss_dssp             HHHHHTTC
T ss_pred             HHHHccCC
Confidence            99999874

>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=99.86  E-value=7.6e-22  Score=184.42  Aligned_cols=153  Identities=15%  Similarity=0.152  Sum_probs=122.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCC--CcceEEEEEeCCHHHHHHHHHHhCCceeC---CeEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNG--TPKGFGFCEFESAEGVLRALRLLNKFNID---GQELM  201 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg--~~kg~gFV~f~~~~~A~~Al~~Lng~~i~---gr~i~  201 (577)
                      ..++|||+|||+++|+++|+.+|+.||.|.+|.|+.++.+|  .++|||||+|.+.++|..|+..|||..+.   ++.|.
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            46899999999999999999999999999999999998776  89999999999999999999999998876   67788


Q ss_pred             EEEchhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHH
Q 008117          202 LKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRK  281 (577)
Q Consensus       202 V~~a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e  281 (577)
                      |.++....              ........+||+||+..+++.+|.+++...+.........+.+|.++|||||+|.+.+
T Consensus        82 ~~~~~~~~--------------~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~  147 (175)
T 3nmr_A           82 MKPADSEK--------------NNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRA  147 (175)
T ss_dssp             EEECGGGC--------------CSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHH
T ss_pred             Eccccccc--------------cccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHH
Confidence            77665421              0111233469999999999999998844111111111111346889999999999999


Q ss_pred             HHHHHHHHHhhh
Q 008117          282 ADQEALEKLTCM  293 (577)
Q Consensus       282 ~a~~Al~~l~~~  293 (577)
                      +|.+|+..|++.
T Consensus       148 ~A~~A~~~l~g~  159 (175)
T 3nmr_A          148 MAQTAIKAMHQA  159 (175)
T ss_dssp             HHHHHHHHHTTS
T ss_pred             HHHHHHHHhcCC
Confidence            999999999864

>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=99.86  E-value=1.3e-21  Score=186.64  Aligned_cols=154  Identities=16%  Similarity=0.224  Sum_probs=122.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+++|+++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||.. ++..|+|+.|.|.++
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRA   89 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecc
Confidence            4678999999999999999999999999999999999999999999999999999999999985 999999999999988


Q ss_pred             hhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHH
Q 008117          206 QATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQ  284 (577)
Q Consensus       206 ~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~  284 (577)
                      ........         .........+||+||+..+++.+|.+++..++....... .+..+|.++|||||.|.+.++|.
T Consensus        90 ~~~~~~~~---------~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~  160 (196)
T 1l3k_A           90 VSREDSQR---------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD  160 (196)
T ss_dssp             CC--------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             cCcccccc---------cccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHH
Confidence            65422110         011122344699999999999999988442221111111 12457899999999999999999


Q ss_pred             HHHHH
Q 008117          285 EALEK  289 (577)
Q Consensus       285 ~Al~~  289 (577)
                      +|+..
T Consensus       161 ~A~~~  165 (196)
T 1l3k_A          161 KIVIQ  165 (196)
T ss_dssp             HHHHC
T ss_pred             HHHHh
Confidence            99875

>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=99.85  E-value=3.4e-21  Score=206.66  Aligned_cols=82  Identities=18%  Similarity=0.406  Sum_probs=78.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+.||+.+|..+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||+.|+|+.|.|.|+
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45789999999999999999999999999999999999899999999999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       180 ~~  181 (437)
T 3pgw_S          180 RG  181 (437)
T ss_pred             CC
Confidence            75

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.84  E-value=2.5e-21  Score=179.80  Aligned_cols=145  Identities=22%  Similarity=0.295  Sum_probs=119.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      +.++|||+|||+.+|+++|+.+|+.||.|.+|.|+.++.+|.++|||||+|.+.++|..||.  ++..|+|+.|.|.++.
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            46899999999999999999999999999999999998899999999999999999999998  4689999999999876


Q ss_pred             hhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHH
Q 008117          207 ATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQE  285 (577)
Q Consensus       207 ~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~  285 (577)
                      .....               .....+||+||+..+++.+|.+++...+....... .+..+|.++|||||.|.+.++|.+
T Consensus        80 ~~~~~---------------~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~  144 (167)
T 2cjk_A           80 PRDEQ---------------DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR  144 (167)
T ss_dssp             CHHHH---------------HHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHH
T ss_pred             chhhc---------------cCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHH
Confidence            54211               11223699999999999999988332221111111 224679999999999999999999


Q ss_pred             HHH
Q 008117          286 ALE  288 (577)
Q Consensus       286 Al~  288 (577)
                      |+.
T Consensus       145 A~~  147 (167)
T 2cjk_A          145 VCQ  147 (167)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            987

>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=99.84  E-value=2.4e-21  Score=181.65  Aligned_cols=150  Identities=16%  Similarity=0.229  Sum_probs=123.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+|+++|+.+|..||.|.. .++.+..+|.++|||||+|.+.++|..||. |||..|.|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~   87 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEec
Confidence            356899999999999999999999999998776 334444688999999999999999999995 999999999999998


Q ss_pred             chhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHH
Q 008117          205 DQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQ  284 (577)
Q Consensus       205 a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~  284 (577)
                      +.....             ........+||+||+..+++.+|.+++..++.....    ..+|.++|||||+|.+.++|.
T Consensus        88 ~~~~~~-------------~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~A~  150 (175)
T 1fje_B           88 PKGRDS-------------KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAE  150 (175)
T ss_dssp             CCCSSC-------------STTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHHHH
T ss_pred             CCCccc-------------cccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHHHH
Confidence            865310             111223446999999999999999986644433222    567889999999999999999


Q ss_pred             HHHHHHhhh
Q 008117          285 EALEKLTCM  293 (577)
Q Consensus       285 ~Al~~l~~~  293 (577)
                      +|+..|++.
T Consensus       151 ~A~~~l~g~  159 (175)
T 1fje_B          151 KNLEEKQGA  159 (175)
T ss_dssp             HHHHHHTEE
T ss_pred             HHHHHhCCC
Confidence            999998863

>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=99.84  E-value=3.9e-21  Score=185.88  Aligned_cols=158  Identities=15%  Similarity=0.125  Sum_probs=119.1

Q ss_pred             CCceEEEcCCC-CCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          127 PQTKVYVGKIA-PTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       127 ~~~tlfVgnLp-~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      +.++|||+||| +.+|+++|..+|+.||.|.+|+|+.+     .+|||||+|.+.++|..||..|||..|.|+.|.|.++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            57899999999 89999999999999999999999865     3699999999999999999999999999999999998


Q ss_pred             hhhHHHH-------------Hhhhhhhh--------hc-cccccccccccccCCCcccchhhhcCCCC---CC--ccccc
Q 008117          206 QATREYL-------------ERYVDKKT--------EN-TKKLKETQDAGAGKEDESVQSVEKNEPTK---SP--ENLKD  258 (577)
Q Consensus       206 ~~~~~~~-------------~~~~~~k~--------~~-~~~~~~~~~~~v~nl~~~~~~~~l~e~~k---s~--~~~k~  258 (577)
                      .......             ..+.....        .. .....+...+||+||+..+++++|.+++.   .+  ...+.
T Consensus        78 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~  157 (205)
T 3tyt_A           78 KQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKV  157 (205)
T ss_dssp             SCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEE
T ss_pred             cCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE
Confidence            6432100             00000000        00 00012234579999999999999998844   22  21211


Q ss_pred             CCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          259 NETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       259 ~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .    ...|..+|||||+|.+.++|..||..||+.
T Consensus       158 ~----~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~  188 (205)
T 3tyt_A          158 F----SGKSERSSSGLLEWDSKSDALETLGFLNHY  188 (205)
T ss_dssp             C----SCCSSSSEEEEEECSSHHHHHHHHHHHTTC
T ss_pred             E----cCCCCCceEEEEEeCCHHHHHHHHHHhCCC
Confidence            1    112556799999999999999999999875

>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=99.83  E-value=3.4e-20  Score=187.75  Aligned_cols=155  Identities=14%  Similarity=0.151  Sum_probs=127.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..++|||+|||+.+|+++|..+|+.||.|..+.++.+..+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            35799999999999999999999999999999999998899999999999999999999999999999999999999986


Q ss_pred             hhHHHHHhhhhhhhhccccccccccccccCCCccc-chhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHH
Q 008117          207 ATREYLERYVDKKTENTKKLKETQDAGAGKEDESV-QSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQE  285 (577)
Q Consensus       207 ~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~-~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~  285 (577)
                      ....            .........+||+||+..+ ++++|.+++..++.........+.+|.++|||||.|.+.++|..
T Consensus       174 ~~~~------------~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~  241 (284)
T 3smz_A          174 AGQL------------TPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEE  241 (284)
T ss_dssp             GGGC------------CTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHH
T ss_pred             CCCC------------CcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHH
Confidence            6311            0111233446999999995 88999888553222211111224578999999999999999999


Q ss_pred             HHHHHhhh
Q 008117          286 ALEKLTCM  293 (577)
Q Consensus       286 Al~~l~~~  293 (577)
                      |+..|++.
T Consensus       242 A~~~l~g~  249 (284)
T 3smz_A          242 AQQQADGL  249 (284)
T ss_dssp             HHHHHTTC
T ss_pred             HHHHhCCC
Confidence            99999874

>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=99.82  E-value=2.7e-20  Score=186.60  Aligned_cols=140  Identities=14%  Similarity=0.127  Sum_probs=117.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+++|+++|+.+|+.||.|..|.|..+      +|||||+|.+.++|..||..|||..|.|+.|.|.++
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   93 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA   93 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec
Confidence            45789999999999999999999999999999998644      699999999999999999999999999999999987


Q ss_pred             hhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHH
Q 008117          206 QATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQE  285 (577)
Q Consensus       206 ~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~  285 (577)
                      ..                     ...+||+||+..+++.+|.+++..++.+.......+.+|.++|||||+|.+.++|..
T Consensus        94 ~~---------------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~  152 (261)
T 3sde_A           94 TH---------------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARK  152 (261)
T ss_dssp             CC---------------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHH
T ss_pred             cc---------------------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHH
Confidence            53                     223699999999999999888442221111111113578999999999999999999


Q ss_pred             HHHHHhh
Q 008117          286 ALEKLTC  292 (577)
Q Consensus       286 Al~~l~~  292 (577)
                      |+..|++
T Consensus       153 A~~~l~~  159 (261)
T 3sde_A          153 ALERCGD  159 (261)
T ss_dssp             HHHHHHH
T ss_pred             HHHHhcC
Confidence            9998854

>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=99.81  E-value=8.3e-20  Score=184.72  Aligned_cols=162  Identities=10%  Similarity=0.145  Sum_probs=121.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHH----HHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVL----SVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL  200 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~----~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i  200 (577)
                      ..+.++|||+|||+.+|+++|+    .+|+.||.|..|.|+.   +|.++|||||+|.+.++|..||..|||..|.|+.|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            4568999999999999999976    8999999999999875   78899999999999999999999999999999999


Q ss_pred             EEEEchhhHHHHHhhhh----hhhh-------------------------------------------------------
Q 008117          201 MLKVDQATREYLERYVD----KKTE-------------------------------------------------------  221 (577)
Q Consensus       201 ~V~~a~~~~~~~~~~~~----~k~~-------------------------------------------------------  221 (577)
                      .|.|+............    ....                                                       
T Consensus        83 ~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  162 (282)
T 3pgw_A           83 RIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPP  162 (282)
T ss_pred             EEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCC
Confidence            99998654322111000    0000                                                       


Q ss_pred             -------------------------------------ccccccccccccccCCCcccchhhhcCCCCCCcccccCCCCCC
Q 008117          222 -------------------------------------NTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNK  264 (577)
Q Consensus       222 -------------------------------------~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~  264 (577)
                                                           ..........+||+||+..+++++|.+++..++........  
T Consensus       163 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~--  240 (282)
T 3pgw_A          163 YMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV--  240 (282)
T ss_pred             CCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEe--
Confidence                                                 00011123447999999999999999884422211111110  


Q ss_pred             CCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          265 ESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       265 ~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                       .+ .+|||||+|.+.++|..|+..|++.
T Consensus       241 -~~-~~g~afV~f~~~~~A~~A~~~l~g~  267 (282)
T 3pgw_A          241 -PG-RHDIAFVEFDNEVQAGAARDALQGF  267 (282)
T ss_pred             -cC-CCcEEEEEeCCHHHHHHHHHHcCCc
Confidence             11 1589999999999999999999874

>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=99.79  E-value=1.6e-19  Score=183.60  Aligned_cols=157  Identities=12%  Similarity=0.145  Sum_probs=116.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcC-ceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCG-TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G-~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ..++|||+|||+.+++++|..+|+.|| .|..|.|+.+. .|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  194 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            478999999999999999999999999 99999999886 4889999999999999999999999999999999999998


Q ss_pred             hhhHHHHHhhhhhhhhccccccccccccccCCCcc-cchhhhcCCCCCCcccccCCCCCCC--CCCCCceEEEEeCCHHH
Q 008117          206 QATREYLERYVDKKTENTKKLKETQDAGAGKEDES-VQSVEKNEPTKSPENLKDNETGNKE--SHDPTNFGVVTEEDRKA  282 (577)
Q Consensus       206 ~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~-~~~~~l~e~~ks~~~~k~~~~~~~~--~g~~kgfgfV~f~~~e~  282 (577)
                      .........        .........+||+||+.. +++++|.+++..++.........+.  +|.++|||||.|.+.++
T Consensus       195 ~~~~~~~~~--------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~  266 (292)
T 2ghp_A          195 NPLEKSKRT--------DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDS  266 (292)
T ss_dssp             CCC-----------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHH
T ss_pred             CCCcccccc--------cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHH
Confidence            754321111        011223344699999999 9999998884422211111111122  48999999999999999


Q ss_pred             HHHHHHHHhhh
Q 008117          283 DQEALEKLTCM  293 (577)
Q Consensus       283 a~~Al~~l~~~  293 (577)
                      |..|+ .|++.
T Consensus       267 A~~A~-~l~g~  276 (292)
T 2ghp_A          267 AERAL-QMNRS  276 (292)
T ss_dssp             HHHHG-GGTTE
T ss_pred             HHHHH-HhcCC
Confidence            99999 88874

>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=99.79  E-value=1.7e-19  Score=168.16  Aligned_cols=145  Identities=18%  Similarity=0.236  Sum_probs=114.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhc----C-------ceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVC----G-------TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI  195 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~----G-------~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i  195 (577)
                      +.++|||+|||+.+|+++|+.+|+.|    |       .|..+.+.      .++|||||+|.+.++|..|+ .|||..|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            46899999999999999999999999    6       67777664      44799999999999999999 7999999


Q ss_pred             CCeEEEEEEchhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEE
Q 008117          196 DGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGV  274 (577)
Q Consensus       196 ~gr~i~V~~a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgf  274 (577)
                      +|+.|.|.++....               .......+||+||+..+++.+|.+++...+....... .+..+|.++||||
T Consensus        76 ~g~~i~v~~~~~~~---------------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~af  140 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQ---------------PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAF  140 (172)
T ss_dssp             TTEECEEECCSSCC---------------CCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEE
T ss_pred             cCceeeecCCcccC---------------CCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEE
Confidence            99999998764421               1112344699999999999999888332221111111 1245789999999


Q ss_pred             EEeCCHHHHHHHHHHHhhh
Q 008117          275 VTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       275 V~f~~~e~a~~Al~~l~~~  293 (577)
                      |.|.+.++|.+|+..|++.
T Consensus       141 V~f~~~~~A~~A~~~l~g~  159 (172)
T 2g4b_A          141 CEYVDINVTDQAIAGLNGM  159 (172)
T ss_dssp             EEESSTTHHHHHHHHHTTC
T ss_pred             EEeCCHHHHHHHHHHcCCC
Confidence            9999999999999998863

>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=99.78  E-value=7.6e-19  Score=149.59  Aligned_cols=82  Identities=21%  Similarity=0.323  Sum_probs=78.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ..+++|||+|||+++|+++|+.+|+.||.|.+|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.||
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            34689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      .+
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            64

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.78  E-value=2.6e-19  Score=175.92  Aligned_cols=159  Identities=13%  Similarity=0.110  Sum_probs=118.6

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          126 KPQTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       126 ~~~~tlfVgnLp~-~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      .+.++|||+|||+ .+++++|+.+|+.||.|..|.|+.++     +|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        32 ~~~~~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           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL  106 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            4578999999999 99999999999999999999998874     78999999999999999999999999999999998


Q ss_pred             chhhHHHHHhhhhh-----------h---------hhccccccccccccccCCCcccchhhhcCCCCCCc-ccccCCCCC
Q 008117          205 DQATREYLERYVDK-----------K---------TENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPE-NLKDNETGN  263 (577)
Q Consensus       205 a~~~~~~~~~~~~~-----------k---------~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~-~~k~~~~~~  263 (577)
                      +.............           .         ............+||+||+..+++.+|.+++...+ ........ 
T Consensus       107 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~-  185 (229)
T 2adc_A          107 SKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF-  185 (229)
T ss_dssp             CSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC-
T ss_pred             ecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEE-
Confidence            86431111000000           0         00000112244579999999999999988843222 11111110 


Q ss_pred             CCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          264 KESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       264 ~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                         ...+|||||+|.+.++|.+|+..|++.
T Consensus       186 ---~~~~g~afV~f~~~~~A~~Ai~~l~g~  212 (229)
T 2adc_A          186 ---QKDRKMALIQMGSVEEAVQALIDLHNH  212 (229)
T ss_dssp             ---SSSTTCEEEEESSHHHHHHHHHHHTTC
T ss_pred             ---ECCCcEEEEEECCHHHHHHHHHHHCCC
Confidence               124799999999999999999998874

>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=99.78  E-value=4.7e-19  Score=155.09  Aligned_cols=109  Identities=15%  Similarity=0.247  Sum_probs=74.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..++|||+|||+++|+++|+.+|+.||.|.+|+|+.+.  +.++|||||+|.+.++|..||..|||..|+|+.|.|.++.
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            35789999999999999999999999999999999984  5689999999999999999999999999999999999986


Q ss_pred             hhHHHHHhhhhhhhhccccccccccccccCCCcccchh
Q 008117          207 ATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSV  244 (577)
Q Consensus       207 ~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~  244 (577)
                      .........      .......++ +||+||+..+|++
T Consensus        82 ~~~~~~~~~------~~~~~~~~~-lyv~Nl~~~~T~~  112 (115)
T 4f25_A           82 SRKEREAEL------GARAKEFTN-VYIKNFGPGSTRA  112 (115)
T ss_dssp             CCCC----------------------------------
T ss_pred             Ccccccccc------ccccCCCCc-eEeCCCCCCcccc
Confidence            532111111      111223344 4999999888765

>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=99.78  E-value=7.1e-19  Score=178.76  Aligned_cols=144  Identities=14%  Similarity=0.129  Sum_probs=112.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+|+++|..+|+.||.|..|.|+.+..  .++|||||+|.+.++|..||. |||..|+|+.|.|.+
T Consensus        38 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~~  114 (292)
T 2ghp_A           38 NRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSH  114 (292)
T ss_dssp             ----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC--CCcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEEE
Confidence            45689999999999999999999999999999999999853  257999999999999999996 899999999999987


Q ss_pred             chhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCc-ccccCCCCCCCCCCCCceEEEEeCCHHHH
Q 008117          205 DQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPE-NLKDNETGNKESHDPTNFGVVTEEDRKAD  283 (577)
Q Consensus       205 a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~-~~k~~~~~~~~~g~~kgfgfV~f~~~e~a  283 (577)
                      +.                      ...+||+||+..+++.+|.+++..++ ............|.++|||||.|.+.++|
T Consensus       115 ~~----------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a  172 (292)
T 2ghp_A          115 LT----------------------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDA  172 (292)
T ss_dssp             CC----------------------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHH
T ss_pred             CC----------------------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHH
Confidence            52                      22359999999999999988733222 11111122234478999999999999999


Q ss_pred             HHHHHHHhhh
Q 008117          284 QEALEKLTCM  293 (577)
Q Consensus       284 ~~Al~~l~~~  293 (577)
                      ..|+..|++.
T Consensus       173 ~~A~~~l~g~  182 (292)
T 2ghp_A          173 RYCVEKLNGL  182 (292)
T ss_dssp             HHHHHHHTTC
T ss_pred             HHHHHHhCCC
Confidence            9999988864

>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=99.77  E-value=7e-19  Score=178.10  Aligned_cols=139  Identities=12%  Similarity=0.113  Sum_probs=115.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      +.++|||+|||+++|+++|..+|+.|| |.+|.+      +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~------~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~   93 (284)
T 3smz_A           21 NRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP   93 (284)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE------ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC
Confidence            568999999999999999999999999 999987      4567999999999999999999999999999999998753


Q ss_pred             hhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHH
Q 008117          207 ATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQE  285 (577)
Q Consensus       207 ~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~  285 (577)
                      .                     ...+||+||+..+++.+|.+++..++...... ..+..+|.++|||||.|.+.++|..
T Consensus        94 ~---------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~  152 (284)
T 3smz_A           94 T---------------------DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR  152 (284)
T ss_dssp             C---------------------SCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHH
T ss_pred             C---------------------CCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHH
Confidence            2                     12359999999999999988844222111111 1125678999999999999999999


Q ss_pred             HHHHHhhh
Q 008117          286 ALEKLTCM  293 (577)
Q Consensus       286 Al~~l~~~  293 (577)
                      |+..|++.
T Consensus       153 A~~~l~~~  160 (284)
T 3smz_A          153 AKSDLLGK  160 (284)
T ss_dssp             HHHHHTTC
T ss_pred             HHHHhCCC
Confidence            99998874

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.77  E-value=2.8e-19  Score=170.64  Aligned_cols=160  Identities=16%  Similarity=0.183  Sum_probs=115.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhc----C-------ceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVC----G-------TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI  195 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~----G-------~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i  195 (577)
                      ..++|||+|||+.+|+++|..+|+.|    |       .|..+.+      +.++|||||+|.+.++|..|| .|||..|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            47899999999999999999999999    4       5555554      456799999999999999999 7999999


Q ss_pred             CCeEEEEEEchhhHHHHHhhhhhh-----hhccccccccccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCC
Q 008117          196 DGQELMLKVDQATREYLERYVDKK-----TENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDP  269 (577)
Q Consensus       196 ~gr~i~V~~a~~~~~~~~~~~~~k-----~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~  269 (577)
                      +|+.|.|.++..............     ............+||+||+..+++.+|.+++..++....... .+..+|.+
T Consensus        76 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~  155 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLS  155 (198)
T ss_dssp             TTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSE
T ss_pred             cCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCc
Confidence            999999998755311100000000     000001123344799999999999999888332221111111 12457899


Q ss_pred             CceEEEEeCCHHHHHHHHHHHhhh
Q 008117          270 TNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       270 kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +|||||.|.+.++|..|+..|++.
T Consensus       156 ~g~afV~f~~~~~a~~A~~~l~g~  179 (198)
T 2yh0_A          156 KGYAFCEYVDINVTDQAIAGLNGM  179 (198)
T ss_dssp             EEEEEEEESSSSHHHHHHHHHTTC
T ss_pred             ceEEEEEECCHHHHHHHHHHcCCC
Confidence            999999999999999999998874

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.76  E-value=3.9e-19  Score=170.13  Aligned_cols=157  Identities=13%  Similarity=0.118  Sum_probs=117.0

Q ss_pred             CceEEEcCCCC-CCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          128 QTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       128 ~~tlfVgnLp~-~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      .++|||+|||+ .+++++|..+|+.||.|..|.|+.++     +|||||+|.+.++|..||..|||..|.|+.|.|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            58999999999 99999999999999999999998764     6899999999999999999999999999999999986


Q ss_pred             hhHHHHHhhhhhhh--------------------hccccccccccccccCCCcccchhhhcCCCCCCc-ccccCCCCCCC
Q 008117          207 ATREYLERYVDKKT--------------------ENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPE-NLKDNETGNKE  265 (577)
Q Consensus       207 ~~~~~~~~~~~~k~--------------------~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~-~~k~~~~~~~~  265 (577)
                      ..............                    ...........+||+||+..+++++|.+++...+ ........   
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~---  154 (198)
T 1qm9_A           78 HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF---  154 (198)
T ss_dssp             CCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEES---
T ss_pred             CCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEE---
Confidence            53211100000000                    0000112245579999999999999988733112 11111110   


Q ss_pred             CCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          266 SHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       266 ~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                       ...+|||||.|.+.++|..|+..|++.
T Consensus       155 -~~~~g~afV~f~~~~~A~~A~~~l~g~  181 (198)
T 1qm9_A          155 -QKDRKMALIQMGSVEEAVQALIDLHNH  181 (198)
T ss_dssp             -STTSSCEEEECSSHHHHHHHHHHHTSS
T ss_pred             -eCCCcEEEEEeCCHHHHHHHHHHhcCC
Confidence             123799999999999999999998874

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.75  E-value=8.8e-18  Score=145.82  Aligned_cols=84  Identities=15%  Similarity=0.253  Sum_probs=79.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      +.++|||+|||+.+++++|+.+|++||.|.+|.|+.++.||.++|||||+|.+.++|..||..|||..|+|+.|.|.++.
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            57899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             hhHH
Q 008117          207 ATRE  210 (577)
Q Consensus       207 ~~~~  210 (577)
                      ....
T Consensus        85 ~~~~   88 (110)
T 3s8s_A           85 KGQQ   88 (110)
T ss_dssp             TTHH
T ss_pred             CCcH
Confidence            6543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.74  E-value=2.4e-17  Score=144.65  Aligned_cols=82  Identities=17%  Similarity=0.276  Sum_probs=77.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+++++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|
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            34679999999999999999999999999999999999988999999999999999999999999999999999999988


Q ss_pred             ch
Q 008117          205 DQ  206 (577)
Q Consensus       205 a~  206 (577)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            63

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.73  E-value=1.6e-17  Score=153.35  Aligned_cols=83  Identities=23%  Similarity=0.344  Sum_probs=77.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcC--ceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCG--TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  203 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G--~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~  203 (577)
                      ...++|||||||+++|+++|+.+|+.||  .|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~  132 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR  132 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEE
Confidence            3568999999999999999999999999  99999999999999999999999999999999999999999999999999


Q ss_pred             Echhh
Q 008117          204 VDQAT  208 (577)
Q Consensus       204 ~a~~~  208 (577)
                      ++...
T Consensus       133 ~a~~~  137 (156)
T 3n9u_C          133 PATRQ  137 (156)
T ss_dssp             ECCHH
T ss_pred             EcCCC
Confidence            99764

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.72  E-value=1.1e-17  Score=141.24  Aligned_cols=83  Identities=19%  Similarity=0.370  Sum_probs=77.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCc--eEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc----eeCCe
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGT--VKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKF----NIDGQ  198 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~--v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~----~i~gr  198 (577)
                      .....||||+|||+.+|+++|+.+|+.||.  |..|+|+.|+.||.++|||||+|.+.++|..||..|||.    .|+|+
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            345789999999999999999999999995  679999999999999999999999999999999999996    59999


Q ss_pred             EEEEEEchh
Q 008117          199 ELMLKVDQA  207 (577)
Q Consensus       199 ~i~V~~a~~  207 (577)
                      .|.|.||.+
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

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.71  E-value=3.4e-18  Score=143.23  Aligned_cols=81  Identities=21%  Similarity=0.343  Sum_probs=75.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcC-ceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh-CCceeCCeEEEEEEc
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCG-TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL-NKFNIDGQELMLKVD  205 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G-~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~L-ng~~i~gr~i~V~~a  205 (577)
                      +.+|||+|||+++|+++|+.+|+.|| .|.+|+|+.++.||.++|||||+|.+.++|.+||..| |+..|+|+.|.|.|+
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            46899999999999999999999999 8999999999999999999999999999999999877 567899999999998


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus        81 ~~~   83 (91)
T 2lxi_A           81 DPK   83 (91)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            653

>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=99.71  E-value=5.2e-17  Score=134.18  Aligned_cols=82  Identities=16%  Similarity=0.320  Sum_probs=77.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||..+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.|+
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            35789999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        84 ~~   85 (87)
T 3bs9_A           84 TR   85 (87)
T ss_dssp             C-
T ss_pred             CC
Confidence            65

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.71  E-value=1.2e-17  Score=142.36  Aligned_cols=86  Identities=17%  Similarity=0.217  Sum_probs=80.9

Q ss_pred             CCCceEEEcCCCC------CCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC-e
Q 008117          126 KPQTKVYVGKIAP------TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG-Q  198 (577)
Q Consensus       126 ~~~~tlfVgnLp~------~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~g-r  198 (577)
                      ...++|||+|||+      .+++++|+.+|+.||.|.+|.|+.++.||.++|||||+|.+.++|..||..|||..|+| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            3468999999999      99999999999999999999999999999999999999999999999999999999999 9


Q ss_pred             EEEEEEchhhHHH
Q 008117          199 ELMLKVDQATREY  211 (577)
Q Consensus       199 ~i~V~~a~~~~~~  211 (577)
                      .|.|.++.....+
T Consensus        84 ~l~V~~a~~~~~~   96 (100)
T 3ns6_A           84 RLFLYTMKDVERY   96 (100)
T ss_dssp             BCEEEESHHHHHH
T ss_pred             EEEEEECchhhhh
Confidence            9999999876554

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.71  E-value=5.2e-17  Score=137.87  Aligned_cols=81  Identities=14%  Similarity=0.225  Sum_probs=77.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKS--------WKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG  197 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~--------~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~g  197 (577)
                      .+.++|||+|||+++++++|+.+|+.||.|..        |.|+.++.+|.++|||||+|.+.++|..||..|||..|+|
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            45799999999999999999999999999999        9999998999999999999999999999999999999999


Q ss_pred             eEEEEEEch
Q 008117          198 QELMLKVDQ  206 (577)
Q Consensus       198 r~i~V~~a~  206 (577)
                      +.|.|.++.
T Consensus        91 ~~l~V~~A~   99 (99)
T 2la6_A           91 NPIKVSFAT   99 (99)
T ss_dssp             SBCEEEECC
T ss_pred             cEEEEEecC
Confidence            999999873

>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=99.71  E-value=6e-17  Score=132.58  Aligned_cols=80  Identities=18%  Similarity=0.325  Sum_probs=77.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      +.+|||+|||+.+++++|+.+|+.||.|..|.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++..
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            36899999999999999999999999999999999989999999999999999999999999999999999999999865

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=8.4e-17  Score=135.06  Aligned_cols=81  Identities=15%  Similarity=0.232  Sum_probs=77.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             CCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEec
Confidence            45789999999999999999999999999999999999989999999999999999999999999999999999999987


Q ss_pred             h
Q 008117          206 Q  206 (577)
Q Consensus       206 ~  206 (577)
                      .
T Consensus        94 k   94 (94)
T 2e5h_A           94 I   94 (94)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.71  E-value=5.3e-17  Score=133.56  Aligned_cols=81  Identities=21%  Similarity=0.362  Sum_probs=77.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.|+
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            46799999999999999999999999999999999999889999999999999999999999999999999999999987


Q ss_pred             h
Q 008117          206 Q  206 (577)
Q Consensus       206 ~  206 (577)
                      .
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.70  E-value=6.7e-17  Score=136.39  Aligned_cols=84  Identities=26%  Similarity=0.405  Sum_probs=79.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      +.++|||+|||..+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            46899999999999999999999999999999999998899999999999999999999999999999999999999997


Q ss_pred             hhHH
Q 008117          207 ATRE  210 (577)
Q Consensus       207 ~~~~  210 (577)
                      ....
T Consensus        81 ~~~~   84 (96)
T 2x1f_A           81 NSDI   84 (96)
T ss_dssp             CSSG
T ss_pred             CCCC
Confidence            7543

>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=4.7e-17  Score=141.86  Aligned_cols=82  Identities=17%  Similarity=0.251  Sum_probs=78.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..|| .|||..|+|+.|.|.++
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            45689999999999999999999999999999999999989999999999999999999999 89999999999999998


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus       102 ~~~  104 (114)
T 2cq4_A          102 QAE  104 (114)
T ss_dssp             HHH
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=99.69  E-value=2.7e-16  Score=141.93  Aligned_cols=83  Identities=23%  Similarity=0.332  Sum_probs=79.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||..+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.+
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            45679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus       119 a~~  121 (139)
T 1u6f_A          119 AAS  121 (139)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            865

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1.2e-16  Score=134.19  Aligned_cols=82  Identities=16%  Similarity=0.216  Sum_probs=78.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
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            45789999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        93 ~~   94 (95)
T 2cqc_A           93 SS   94 (95)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>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=99.69  E-value=1.7e-16  Score=138.58  Aligned_cols=82  Identities=17%  Similarity=0.281  Sum_probs=78.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
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            45789999999999999999999999999999999999889999999999999999999999999999999999999987


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       103 ~~  104 (115)
T 2cpz_A          103 RS  104 (115)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.1e-16  Score=135.84  Aligned_cols=82  Identities=23%  Similarity=0.381  Sum_probs=77.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||. ||+..|+|+.|.|.+
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            3467899999999999999999999999999999999999899999999999999999999999 899999999999998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        86 a~~   88 (99)
T 2dgs_A           86 AEP   88 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            865

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=1e-16  Score=134.78  Aligned_cols=82  Identities=23%  Similarity=0.431  Sum_probs=78.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++
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            35789999999999999999999999999999999999889999999999999999999999999999999999999988


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        83 ~~   84 (95)
T 2dnz_A           83 TE   84 (95)
T ss_dssp             SC
T ss_pred             cc
Confidence            65

>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=99.69  E-value=1.2e-16  Score=137.08  Aligned_cols=83  Identities=20%  Similarity=0.398  Sum_probs=79.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++
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            45789999999999999999999999999999999999889999999999999999999999999999999999999988


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus        93 ~~~   95 (105)
T 1x5u_A           93 SAH   95 (105)
T ss_dssp             TTT
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=99.69  E-value=1.1e-16  Score=138.49  Aligned_cols=83  Identities=23%  Similarity=0.432  Sum_probs=78.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ..+.++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.+
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            45679999999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus       103 a~~  105 (108)
T 2jrs_A          103 VTE  105 (108)
T ss_dssp             SCS
T ss_pred             ccc
Confidence            754

>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=99.69  E-value=2.2e-17  Score=137.81  Aligned_cols=80  Identities=19%  Similarity=0.296  Sum_probs=72.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcC--ceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCG--TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G--~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      .+|||+|||+++|+++|+.+|+.||  .|.+|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5799999999999999999999999  99999999999999999999999999999999999999999999999998876


Q ss_pred             hh
Q 008117          207 AT  208 (577)
Q Consensus       207 ~~  208 (577)
                      ..
T Consensus        82 ~~   83 (90)
T 3p5t_L           82 KL   83 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            54

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.69  E-value=2.2e-16  Score=137.74  Aligned_cols=84  Identities=15%  Similarity=0.311  Sum_probs=79.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+++++|+.+|..||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|
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            34689999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             chhh
Q 008117          205 DQAT  208 (577)
Q Consensus       205 a~~~  208 (577)
                      +...
T Consensus        92 a~~~   95 (115)
T 2dgo_A           92 ATRK   95 (115)
T ss_dssp             SSCC
T ss_pred             ccCC
Confidence            8653

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.1e-16  Score=137.49  Aligned_cols=82  Identities=17%  Similarity=0.187  Sum_probs=78.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
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            35789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       101 ~~  102 (106)
T 1p27_B          101 FV  102 (106)
T ss_dssp             EE
T ss_pred             cC
Confidence            65

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=8.4e-17  Score=137.57  Aligned_cols=83  Identities=20%  Similarity=0.326  Sum_probs=79.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ..+.++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.+
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            34579999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        90 a~~   92 (103)
T 2dnm_A           90 ARY   92 (103)
T ss_dssp             CSS
T ss_pred             CCc
Confidence            865

>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=1.7e-16  Score=134.54  Aligned_cols=83  Identities=16%  Similarity=0.255  Sum_probs=79.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45789999999999999999999999999999999999889999999999999999999999999999999999999988


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus        86 ~~~   88 (99)
T 1whw_A           86 TIK   88 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            664

>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=99.68  E-value=1.3e-16  Score=138.03  Aligned_cols=82  Identities=22%  Similarity=0.237  Sum_probs=78.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  103 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  103 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEc
Confidence            45789999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       104 ~~  105 (110)
T 1oo0_B          104 FV  105 (110)
T ss_dssp             EE
T ss_pred             cc
Confidence            65

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.7e-16  Score=135.59  Aligned_cols=83  Identities=18%  Similarity=0.292  Sum_probs=79.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ..+.++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|
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            34579999999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        92 a~~   94 (103)
T 2cq0_A           92 AKP   94 (103)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            865

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.1e-16  Score=136.53  Aligned_cols=83  Identities=20%  Similarity=0.352  Sum_probs=79.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   89 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeC
Confidence            46789999999999999999999999999999999999899999999999999999999999999999999999999998


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus        90 ~~~   92 (102)
T 2cqb_A           90 KPM   92 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.68  E-value=2.3e-16  Score=135.77  Aligned_cols=80  Identities=18%  Similarity=0.241  Sum_probs=76.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+.+|+++|+.+|+.||.|..|.|+.+. +|.++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus        27 ~~~~~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           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV  105 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            457999999999999999999999999999999999997 9999999999999999999999999999999999999987


Q ss_pred             h
Q 008117          206 Q  206 (577)
Q Consensus       206 ~  206 (577)
                      .
T Consensus       106 ~  106 (107)
T 3ulh_A          106 T  106 (107)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.68  E-value=2.5e-16  Score=130.26  Aligned_cols=80  Identities=24%  Similarity=0.380  Sum_probs=75.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||. +++..|+|+.|.|.+
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            3567899999999999999999999999999999999999999999999999999999999997 589999999999987


Q ss_pred             c
Q 008117          205 D  205 (577)
Q Consensus       205 a  205 (577)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=3.2e-16  Score=133.15  Aligned_cols=81  Identities=17%  Similarity=0.361  Sum_probs=77.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|..||.|..|.|+.++ +|.++|||||+|.+.++|..||..|||..|+|+.|.|.++
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   93 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            457899999999999999999999999999999999997 9999999999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        94 ~~   95 (100)
T 2do4_A           94 NS   95 (100)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.1e-16  Score=134.97  Aligned_cols=82  Identities=17%  Similarity=0.370  Sum_probs=78.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEE-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSW-KRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~-~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      .+.++|||+|||+.+|+++|..+|+.||.|..| .|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.+
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            357899999999999999999999999999999 9999988999999999999999999999999999999999999998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        83 a~~   85 (96)
T 1x5t_A           83 AFK   85 (96)
T ss_dssp             SCC
T ss_pred             ecc
Confidence            865

>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=1.7e-16  Score=133.50  Aligned_cols=81  Identities=22%  Similarity=0.431  Sum_probs=76.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+++++|+.+|+.||.|..|.|+.++. |.++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus        14 ~~~~~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           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP   92 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEc
Confidence            4578999999999999999999999999999999999974 999999999999999999999999999999999999987


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        93 ~~   94 (95)
T 2ywk_A           93 SS   94 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.67  E-value=2.3e-16  Score=136.62  Aligned_cols=82  Identities=18%  Similarity=0.359  Sum_probs=78.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC------CceeCCeE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN------KFNIDGQE  199 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Ln------g~~i~gr~  199 (577)
                      .+.++|||+|||+.+|+++|+.+|..||.|..|.|+.++.+|.++|||||+|.+.++|..||..||      |..|+|+.
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            457899999999999999999999999999999999999999999999999999999999999999      99999999


Q ss_pred             EEEEEchh
Q 008117          200 LMLKVDQA  207 (577)
Q Consensus       200 i~V~~a~~  207 (577)
                      |.|.|+..
T Consensus        93 l~v~~a~~  100 (111)
T 1x4h_A           93 LKVDLAVT  100 (111)
T ss_dssp             EEEECCCC
T ss_pred             EEEEECCC
Confidence            99998765

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.6e-16  Score=135.49  Aligned_cols=82  Identities=18%  Similarity=0.361  Sum_probs=78.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+.+++++|+.+|+.||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus        10 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   89 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   89 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45789999999999999999999999999999999999889999999999999999999999999999999999999988


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        90 ~~   91 (102)
T 1x5s_A           90 GK   91 (102)
T ss_dssp             EC
T ss_pred             CC
Confidence            65

>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=3e-16  Score=134.54  Aligned_cols=82  Identities=21%  Similarity=0.355  Sum_probs=77.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC---eEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG---QELML  202 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~g---r~i~V  202 (577)
                      ...++|||+|||+.+++++|+.+|+.||.|..|.|+.++ +|.++|||||+|.+.++|..||..|||..|.|   +.|.|
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            458999999999999999999999999999999999997 89999999999999999999999999999998   99999


Q ss_pred             EEchhh
Q 008117          203 KVDQAT  208 (577)
Q Consensus       203 ~~a~~~  208 (577)
                      .|+...
T Consensus        92 ~~a~~~   97 (105)
T 2dnh_A           92 KFADTD   97 (105)
T ss_dssp             EESCSS
T ss_pred             EECccC
Confidence            998653

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=2.4e-16  Score=135.50  Aligned_cols=84  Identities=20%  Similarity=0.411  Sum_probs=79.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeec-CCCCCcceEEEEEeCCHHHHHHHHHHh-CCceeCCeEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQY-PSNGTPKGFGFCEFESAEGVLRALRLL-NKFNIDGQELML  202 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~-~~tg~~kg~gFV~f~~~~~A~~Al~~L-ng~~i~gr~i~V  202 (577)
                      ....++|||+|||+.+|+++|+.+|+.||.|..|.|+.+ +.+|.++|||||+|.+.++|..||..| ||..|+|+.|.|
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            456799999999999999999999999999999999998 789999999999999999999999999 999999999999


Q ss_pred             EEchhh
Q 008117          203 KVDQAT  208 (577)
Q Consensus       203 ~~a~~~  208 (577)
                      .|+...
T Consensus        92 ~~a~~~   97 (107)
T 2cph_A           92 EWADSE   97 (107)
T ss_dssp             EECCCC
T ss_pred             EeCCCC
Confidence            998653

>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=99.67  E-value=1.8e-16  Score=136.16  Aligned_cols=83  Identities=17%  Similarity=0.281  Sum_probs=78.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee---CCeEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI---DGQELM  201 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i---~gr~i~  201 (577)
                      ....++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|   .|+.|.
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            34679999999999999999999999999999999999999999999999999999999999999999988   899999


Q ss_pred             EEEchh
Q 008117          202 LKVDQA  207 (577)
Q Consensus       202 V~~a~~  207 (577)
                      |.++..
T Consensus        90 v~~a~~   95 (106)
T 2dgp_A           90 VKPADS   95 (106)
T ss_dssp             EEECCC
T ss_pred             EEECCc
Confidence            998865

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=1.8e-16  Score=134.37  Aligned_cols=82  Identities=21%  Similarity=0.368  Sum_probs=78.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceE-EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeE----E
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVK-SWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQE----L  200 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~-~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~----i  200 (577)
                      ...++|||+|||+++++++|+.+|+.||.|. .|.|+.++.+|.++|||||+|.+.++|..||..|||..|.|+.    |
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l   86 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF   86 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeE
Confidence            4579999999999999999999999999999 9999999999999999999999999999999999999999999    9


Q ss_pred             EEEEchh
Q 008117          201 MLKVDQA  207 (577)
Q Consensus       201 ~V~~a~~  207 (577)
                      .|.|+..
T Consensus        87 ~v~~a~~   93 (99)
T 2div_A           87 KLNYATY   93 (99)
T ss_dssp             CEEETTC
T ss_pred             EEeecCC
Confidence            9988764

>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=99.67  E-value=4.7e-17  Score=138.57  Aligned_cols=81  Identities=20%  Similarity=0.423  Sum_probs=74.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP-SNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  203 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~-~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~  203 (577)
                      ....++|||+|||+++++++|+.+|+.|| |..|.|+.++ .+|.++|||||+|.+.++|..|| .|||..|+|+.|.|.
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVD   93 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEE
Confidence            34579999999999999999999999999 9999999987 69999999999999999999999 899999999999999


Q ss_pred             Echh
Q 008117          204 VDQA  207 (577)
Q Consensus       204 ~a~~  207 (577)
                      ++..
T Consensus        94 ~a~~   97 (100)
T 2j76_E           94 VADQ   97 (100)
T ss_dssp             ECCC
T ss_pred             eccC
Confidence            8865

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=1.8e-16  Score=134.19  Aligned_cols=82  Identities=20%  Similarity=0.405  Sum_probs=77.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCC---CCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPS---NGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  202 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~---tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V  202 (577)
                      .+.++|||+|||+.+|+++|+.+|+.||.|..|.|+.++.   |+.++|||||+|.+.++|..||..|||..|+|+.|.|
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            3578999999999999999999999999999999998876   6689999999999999999999999999999999999


Q ss_pred             EEchh
Q 008117          203 KVDQA  207 (577)
Q Consensus       203 ~~a~~  207 (577)
                      .++..
T Consensus        83 ~~a~~   87 (98)
T 2cpf_A           83 RISER   87 (98)
T ss_dssp             ECSSC
T ss_pred             EEccC
Confidence            98765

>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=99.66  E-value=3.1e-16  Score=130.10  Aligned_cols=79  Identities=24%  Similarity=0.417  Sum_probs=76.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      .++|||+|||+.+|+++|+.+|+.||.|..|.++.++.+|.++|||||+|.+.++|..|+ .|||..|+|+.|.|.++..
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            579999999999999999999999999999999999889999999999999999999999 8999999999999998865

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=3e-16  Score=136.46  Aligned_cols=83  Identities=19%  Similarity=0.331  Sum_probs=78.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceE--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVK--------SWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  196 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~--------~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~  196 (577)
                      ....++|||+|||+.+|+++|+.+|+.||.|.        .|.|+.++.+|.++|||||+|.+.++|..||..|||..|+
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            45689999999999999999999999999999        6999999889999999999999999999999999999999


Q ss_pred             CeEEEEEEchh
Q 008117          197 GQELMLKVDQA  207 (577)
Q Consensus       197 gr~i~V~~a~~  207 (577)
                      |+.|.|.++..
T Consensus        92 g~~l~V~~a~~  102 (113)
T 2cpe_A           92 GSKLKVSLARK  102 (113)
T ss_dssp             TEECEEECSSC
T ss_pred             CCEEEEEECCC
Confidence            99999998765

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=1.4e-16  Score=136.54  Aligned_cols=80  Identities=18%  Similarity=0.160  Sum_probs=75.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||||||+.+|+++|+.+|+.||.|.+|.|+.++. |.++|||||+|.+.++|..||. +||..|+|+.|.|.++
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            4568999999999999999999999999999999999976 9999999999999999999999 8999999999999987


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            65

>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=99.66  E-value=2.2e-16  Score=140.12  Aligned_cols=82  Identities=17%  Similarity=0.187  Sum_probs=78.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|..+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
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            45789999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       100 ~~  101 (126)
T 3ex7_B          100 FV  101 (126)
T ss_dssp             EE
T ss_pred             cC
Confidence            65

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.66  E-value=4.3e-16  Score=133.19  Aligned_cols=80  Identities=18%  Similarity=0.321  Sum_probs=76.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+.+++++|+.+|+.|| |..|.|+.++.+|.++|||||+|.+.++|..|| .|||..|+|+.|.|.++
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            4579999999999999999999999997 999999999999999999999999999999999 79999999999999988


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        91 ~~   92 (103)
T 2dng_A           91 EG   92 (103)
T ss_dssp             CC
T ss_pred             cC
Confidence            65

>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=99.66  E-value=2.5e-16  Score=130.26  Aligned_cols=81  Identities=25%  Similarity=0.430  Sum_probs=76.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCC-cceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGT-PKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~-~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ..++|||+|||+++|+++|..+|+.||.|..|.|+.+..++. ++|||||+|.+.++|..|+..|||..|+|+.|.|.++
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            468999999999999999999999999999999999887766 8999999999999999999999999999999999987


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        83 ~~   84 (88)
T 4a8x_A           83 LA   84 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.66  E-value=9.1e-16  Score=131.09  Aligned_cols=82  Identities=21%  Similarity=0.308  Sum_probs=75.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+++++|+.+|+.||.|..|.|+.++  +.++|||||+|.+.++|..||..|||..|.|+.|.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~--~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCC--CSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecC--CCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            4567999999999999999999999999999999999984  34689999999999999999999999999999999999


Q ss_pred             chhh
Q 008117          205 DQAT  208 (577)
Q Consensus       205 a~~~  208 (577)
                      +...
T Consensus        90 a~~~   93 (103)
T 2cqi_A           90 ATTP   93 (103)
T ss_dssp             CCCT
T ss_pred             CCCC
Confidence            8663

>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=99.65  E-value=2.1e-16  Score=141.06  Aligned_cols=82  Identities=16%  Similarity=0.225  Sum_probs=78.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
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            45789999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       124 ~~  125 (129)
T 2kxn_B          124 IT  125 (129)
T ss_dssp             SS
T ss_pred             cC
Confidence            65

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=4.7e-16  Score=132.86  Aligned_cols=81  Identities=25%  Similarity=0.341  Sum_probs=77.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+|+++|+.+|+.||.|..|.|+.+  +|.++|||||+|.+.++|..||..|||..|+|+.|.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            346889999999999999999999999999999999998  899999999999999999999999999999999999999


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        90 a~~   92 (103)
T 2d9p_A           90 AQR   92 (103)
T ss_dssp             CSS
T ss_pred             ecc
Confidence            865

>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=99.65  E-value=5.4e-16  Score=132.81  Aligned_cols=80  Identities=23%  Similarity=0.449  Sum_probs=76.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCC-CCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSN-GTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~t-g~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      .+.++|||+|||+.+++++|+.+|..|| |..|.|+.++.+ |.++|||||+|.+.++|..|| .|||..|+|+.|.|.+
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            4569999999999999999999999999 999999999887 999999999999999999999 8999999999999998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        91 a~~   93 (104)
T 1wi8_A           91 ADQ   93 (104)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            865

>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=99.65  E-value=3e-16  Score=132.79  Aligned_cols=82  Identities=21%  Similarity=0.227  Sum_probs=77.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+++++|+.+|..||.|..+.++.+..+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            45789999999999999999999999999998888888889999999999999999999999999999999999999987


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        93 ~~   94 (98)
T 2cqp_A           93 SG   94 (98)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>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=99.65  E-value=3.4e-16  Score=137.05  Aligned_cols=82  Identities=15%  Similarity=0.319  Sum_probs=77.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+++|+++|..+|+.||.|..|.|+.+. +|.++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            457899999999999999999999999999999999997 9999999999999999999999999999999999999998


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus        84 ~~~   86 (116)
T 2fy1_A           84 KKP   86 (116)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            653

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=8e-16  Score=134.44  Aligned_cols=82  Identities=18%  Similarity=0.290  Sum_probs=77.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+|+++|+.+|..||.|..|.|+.++.++.++|||||+|.+.++|..||..||+ .|.|+.|.|.|
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            45689999999999999999999999999999999999999999999999999999999999999998 89999999999


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        93 a~~   95 (116)
T 2cqd_A           93 AYL   95 (116)
T ss_dssp             STT
T ss_pred             ccc
Confidence            854

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.65  E-value=3.8e-16  Score=135.16  Aligned_cols=82  Identities=21%  Similarity=0.328  Sum_probs=74.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+|+++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..+ +..|+|+.|.|.+
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            456789999999999999999999999999999999999989999999999999999999999975 6999999999998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus       101 a~~  103 (109)
T 2rs2_A          101 AFP  103 (109)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            865

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.65  E-value=5.3e-16  Score=129.58  Aligned_cols=80  Identities=25%  Similarity=0.423  Sum_probs=75.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+.+++++|+.+|+.||.|..|.|+.+  +|.++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45789999999999999999999999999999999884  8999999999999999999999999999999999999988


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        84 ~~   85 (92)
T 2dgv_A           84 RN   85 (92)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>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=99.65  E-value=1.5e-15  Score=129.66  Aligned_cols=81  Identities=19%  Similarity=0.245  Sum_probs=75.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+|+++|+.+|+.||.|..|.|+.+.  +.++|||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~--~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   89 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC--CCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3467999999999999999999999999999999999885  34899999999999999999999999999999999998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        90 a~~   92 (103)
T 2cq3_A           90 ATA   92 (103)
T ss_dssp             CCS
T ss_pred             ccc
Confidence            865

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.65  E-value=1.4e-16  Score=142.64  Aligned_cols=82  Identities=17%  Similarity=0.368  Sum_probs=77.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEE--EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc----eeCCe
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKS--WKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKF----NIDGQ  198 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~--~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~----~i~gr  198 (577)
                      ....++|||+|||+.+|+++|+.+|..||.|..  |.|+.++.+|.++|||||+|.+. +|..||..|||.    .|+|+
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            345789999999999999999999999999977  99999999999999999999999 999999999999    99999


Q ss_pred             EEEEEEchh
Q 008117          199 ELMLKVDQA  207 (577)
Q Consensus       199 ~i~V~~a~~  207 (577)
                      .|.|.++..
T Consensus        99 ~l~V~~a~~  107 (131)
T 2m2b_A           99 TINVEFAKG  107 (131)
T ss_dssp             CCCCEECCC
T ss_pred             EEEEEECCC
Confidence            999998865

>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=99.64  E-value=7.1e-16  Score=143.61  Aligned_cols=83  Identities=22%  Similarity=0.235  Sum_probs=78.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+.+|+.+|..+|+.||.|..|.|+.++.+|.++|||||+|.+..+|..||..|||..|+|+.|.|.|+
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            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus       150 ~~~  152 (165)
T 1rk8_A          150 FVK  152 (165)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            653

>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=99.64  E-value=8e-16  Score=129.88  Aligned_cols=79  Identities=14%  Similarity=0.199  Sum_probs=73.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHH----HHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVL----SVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  201 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~----~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~  201 (577)
                      ...++|||+|||+.+++++|+    .+|+.||.|..|.|+.++.+   +|||||+|.+.++|..||..|||..|+|+.|.
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            357899999999999999999    99999999999999988654   88999999999999999999999999999999


Q ss_pred             EEEchh
Q 008117          202 LKVDQA  207 (577)
Q Consensus       202 V~~a~~  207 (577)
                      |.++..
T Consensus        84 V~~a~~   89 (96)
T 2dgx_A           84 VSLATG   89 (96)
T ss_dssp             EEECCC
T ss_pred             EEEcCC
Confidence            998865

>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=2.9e-16  Score=134.31  Aligned_cols=83  Identities=29%  Similarity=0.536  Sum_probs=79.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++
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            35689999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus        86 ~~~   88 (104)
T 1p1t_A           86 ASE   88 (104)
T ss_dssp             TCT
T ss_pred             CCc
Confidence            764

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=4.2e-16  Score=134.92  Aligned_cols=81  Identities=19%  Similarity=0.243  Sum_probs=75.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||..+|+++|+.+|+.||.|..|.|+.+.  +.++|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  103 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN  103 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3467899999999999999999999999999999999884  45899999999999999999999999999999999998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus       104 a~~  106 (109)
T 2err_A          104 ATA  106 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            865

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=1.1e-15  Score=132.90  Aligned_cols=81  Identities=17%  Similarity=0.293  Sum_probs=76.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+.+++++|+.+|..||.|..|.|+.++ +|.++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus        13 ~~~~~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           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            457899999999999999999999999999999999996 6999999999999999999999999999999999999987


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        92 ~~   93 (114)
T 2do0_A           92 ER   93 (114)
T ss_dssp             SC
T ss_pred             cc
Confidence            54

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=3.8e-16  Score=133.63  Aligned_cols=81  Identities=21%  Similarity=0.359  Sum_probs=77.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhh-cCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce-eCCeEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKV-CGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN-IDGQELMLK  203 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~-~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~-i~gr~i~V~  203 (577)
                      .+.++|||+|||+.+|+++|+.+|+. ||.|..|.|+.++ +|.++|||||+|.+.++|..||..|||.. |+|+.|.|.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            45789999999999999999999999 9999999999998 99999999999999999999999999999 999999998


Q ss_pred             Echh
Q 008117          204 VDQA  207 (577)
Q Consensus       204 ~a~~  207 (577)
                      ++..
T Consensus        86 ~a~~   89 (104)
T 2dhg_A           86 VAIP   89 (104)
T ss_dssp             BCCC
T ss_pred             EccC
Confidence            8754

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.64  E-value=1.9e-16  Score=127.12  Aligned_cols=75  Identities=21%  Similarity=0.313  Sum_probs=72.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       130 tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      +|||+|||+.+++++|+.+|+.||.|..|.++.++.+|.++|||||+|.+.++|..|+. |||..|+|+.|.|.+|
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            59999999999999999999999999999999998899999999999999999999998 8999999999999865

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.64  E-value=7.3e-16  Score=126.28  Aligned_cols=74  Identities=12%  Similarity=0.235  Sum_probs=70.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      .+.-||||||++.+|+++|+.+|..||+|.+|.++.      ++|||||+|.+.++|..|+..||+..|.|+.|.|+++.
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            467899999999999999999999999999999865      57999999999999999999999999999999999984

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.64  E-value=1.1e-15  Score=137.83  Aligned_cols=80  Identities=21%  Similarity=0.360  Sum_probs=76.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.|..+.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.||
T Consensus        61 ~~~~~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           61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            45799999999999999999999999999999999999899999999999999999999999999999999999999875

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.64  E-value=2.3e-16  Score=135.61  Aligned_cols=81  Identities=14%  Similarity=0.259  Sum_probs=74.8

Q ss_pred             CCCceEEEcCCCCCC------CHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe-
Q 008117          126 KPQTKVYVGKIAPTA------DSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQ-  198 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~------te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr-  198 (577)
                      ...++|||+|||+.+      |+++|+.+|+.||.|..|.|+  ..+|.++|||||+|.+.++|..||..|||..|+|+ 
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            457899999999999      789999999999999999988  36899999999999999999999999999999998 


Q ss_pred             EEEEEEchhh
Q 008117          199 ELMLKVDQAT  208 (577)
Q Consensus       199 ~i~V~~a~~~  208 (577)
                      .|.|.++...
T Consensus        91 ~l~V~~a~~~  100 (105)
T 2nlw_A           91 TFRVNLFTDF  100 (105)
T ss_dssp             EEEEECSCCC
T ss_pred             eEEEEEcchH
Confidence            9999987653

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=9.6e-17  Score=132.13  Aligned_cols=80  Identities=18%  Similarity=0.292  Sum_probs=75.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|+|.++
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            45789999999999999999999999999999999999889999999999999999999999999999999999988654

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=1.2e-15  Score=127.30  Aligned_cols=80  Identities=16%  Similarity=0.226  Sum_probs=75.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+|+++|+.+|+.| .|..|.|+.+ .+|.++|||||+|.+.++|..||. |||..|+|+.|.|.+
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            3467899999999999999999999999 9999999999 799999999999999999999999 999999999999998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        84 a~~   86 (91)
T 2dgw_A           84 EKS   86 (91)
T ss_dssp             ESS
T ss_pred             CCc
Confidence            765

>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=3.1e-16  Score=138.73  Aligned_cols=80  Identities=19%  Similarity=0.370  Sum_probs=76.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..++|||+|||+.+|+++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..|| .|||..|+|+.|.|.++.
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            4689999999999999999999999999999999999889999999999999999999999 799999999999999876


Q ss_pred             h
Q 008117          207 A  207 (577)
Q Consensus       207 ~  207 (577)
                      .
T Consensus       114 ~  114 (124)
T 2jwn_A          114 T  114 (124)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.64  E-value=1.8e-15  Score=129.28  Aligned_cols=82  Identities=18%  Similarity=0.245  Sum_probs=76.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+++++|+.+|..||.|..|.|+.++.+|.++|||||+|.+.++|..||.  ++..|+|+.|.|.+
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            4567899999999999999999999999999999999998899999999999999999999998  58899999999998


Q ss_pred             chhh
Q 008117          205 DQAT  208 (577)
Q Consensus       205 a~~~  208 (577)
                      +...
T Consensus        90 a~~~   93 (103)
T 2cqg_A           90 PNSK   93 (103)
T ss_dssp             CCTT
T ss_pred             cCCC
Confidence            8653

>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=99.64  E-value=2.8e-16  Score=132.09  Aligned_cols=80  Identities=21%  Similarity=0.217  Sum_probs=75.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      +.++|||+|||+.+|+++|+.+|..||.|..+.++.+..+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++.
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            46899999999999999999999999999999898888899999999999999999999999999999999999998764

>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=3.8e-15  Score=131.81  Aligned_cols=83  Identities=16%  Similarity=0.221  Sum_probs=78.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+++++|+.+|+.||.|..|.|+.+. +|.++|||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            3467899999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             chhh
Q 008117          205 DQAT  208 (577)
Q Consensus       205 a~~~  208 (577)
                      +...
T Consensus       111 a~~~  114 (124)
T 2kt5_A          111 VASQ  114 (124)
T ss_dssp             ECCT
T ss_pred             eCCC
Confidence            8653

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=7.5e-16  Score=132.10  Aligned_cols=82  Identities=20%  Similarity=0.297  Sum_probs=77.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+++++|+.+|..||.|..|.|+.++.+|.++|||||+|.+.++|..||.. |+..|+|+.|.|.+
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            34679999999999999999999999999999999999999999999999999999999999998 99999999999988


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        92 a~~   94 (105)
T 2dh8_A           92 CTP   94 (105)
T ss_dssp             SCC
T ss_pred             ccC
Confidence            755

>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=99.63  E-value=1.4e-15  Score=140.10  Aligned_cols=82  Identities=21%  Similarity=0.307  Sum_probs=78.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|..+|+.||.|..|.|+.++.++.++|||||+|.+.++|..||..||+..|+|+.|.|.|+
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            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       117 ~~  118 (156)
T 1h2v_Z          117 AG  118 (156)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.63  E-value=9.2e-16  Score=136.41  Aligned_cols=81  Identities=12%  Similarity=0.269  Sum_probs=73.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHH----HHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVL----SVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  201 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~----~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~  201 (577)
                      .+.++|||+|||+.+++++|+    .+|+.||.|..|.+.   .+|.++|||||+|.+.++|..||..|||..|.|+.|.
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~---~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC---CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec---cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            457899999999999999876    799999999998774   3688999999999999999999999999999999999


Q ss_pred             EEEchhhH
Q 008117          202 LKVDQATR  209 (577)
Q Consensus       202 V~~a~~~~  209 (577)
                      |.|+....
T Consensus       104 V~~a~~~~  111 (127)
T 2a3j_A          104 ITFSETPQ  111 (127)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCcc
Confidence            99987653

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.63  E-value=2.7e-16  Score=126.72  Aligned_cols=76  Identities=22%  Similarity=0.359  Sum_probs=73.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ++|||+|||+.+++++|+.+|+.||.|..|.++.++.+|.++|||||+|.+.++|..|+..|+ ..|+|+.|.|.++
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            579999999999999999999999999999999998899999999999999999999999988 9999999999876

>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=3.2e-15  Score=129.12  Aligned_cols=80  Identities=19%  Similarity=0.357  Sum_probs=73.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+|+++|+.+|+.||.|..|.|..   ++.++|||||+|.+.++|..||..||+..|+|+.|.|.|
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34578999999999999999999999999999999955   456899999999999999999999999999999999998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        96 a~~   98 (109)
T 1x4a_A           96 PRS   98 (109)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            865

>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=99.62  E-value=1.6e-15  Score=139.91  Aligned_cols=82  Identities=18%  Similarity=0.281  Sum_probs=78.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
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            45789999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       148 ~~  149 (158)
T 2kn4_A          148 RY  149 (158)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.62  E-value=1.1e-15  Score=134.21  Aligned_cols=82  Identities=18%  Similarity=0.156  Sum_probs=76.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCc---eEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGT---VKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  201 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~---v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~  201 (577)
                      ....++|||+|||+++|+++|+.+|+.||.   |..|.|+.++. |+++|||||+|.+.++|..||. |||..|+|+.|.
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   91 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIE   91 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEE
Confidence            345789999999999999999999999999   89999999975 9999999999999999999999 899999999999


Q ss_pred             EEEchhh
Q 008117          202 LKVDQAT  208 (577)
Q Consensus       202 V~~a~~~  208 (577)
                      |.++...
T Consensus        92 V~~a~~~   98 (118)
T 2db1_A           92 VFKSHRT   98 (118)
T ss_dssp             EEEECHH
T ss_pred             EEECCHH
Confidence            9988654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=9e-16  Score=131.24  Aligned_cols=76  Identities=16%  Similarity=0.187  Sum_probs=69.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCeEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN--KFNIDGQELMLK  203 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Ln--g~~i~gr~i~V~  203 (577)
                      .+.++|||+|||+.+|+++|+.+|+.||.|.+|.|+.+      +|||||+|.+.++|..||..|+  +..|.|+.|.|.
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            35789999999999999999999999999999999875      6999999999999999999886  479999999998


Q ss_pred             Echh
Q 008117          204 VDQA  207 (577)
Q Consensus       204 ~a~~  207 (577)
                      |+..
T Consensus        88 ~A~~   91 (105)
T 1sjq_A           88 FSNH   91 (105)
T ss_dssp             CCSS
T ss_pred             EcCC
Confidence            8755

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=9.7e-16  Score=133.93  Aligned_cols=82  Identities=21%  Similarity=0.331  Sum_probs=77.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|..||.|..|.|+.++.+|.++|||||+|.+.++|..||.. |+..|+|+.|.|.++
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            3468999999999999999999999999999999999999999999999999999999999997 999999999999987


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus       104 ~~~  106 (116)
T 1x4b_A          104 VAR  106 (116)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            653

>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=99.62  E-value=2e-16  Score=131.73  Aligned_cols=79  Identities=25%  Similarity=0.404  Sum_probs=74.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchhh
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQAT  208 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~~  208 (577)
                      ++|||+|||..+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.+ |..|+..|||..|+|+.|.|.++...
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            68999999999999999999999999999999999989999999999999999 99999999999999999999998764

>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=99.62  E-value=1e-15  Score=132.05  Aligned_cols=83  Identities=17%  Similarity=0.270  Sum_probs=77.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCc-eEEEEEe-ecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCeEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGT-VKSWKRA-QYPSNGTPKGFGFCEFESAEGVLRALRLLN--KFNIDGQELM  201 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~-v~~~~i~-~~~~tg~~kg~gFV~f~~~~~A~~Al~~Ln--g~~i~gr~i~  201 (577)
                      .+.++|||+|||+.+|+++|+.+|..||. |..|.|+ .+..+|.++|||||+|.+.++|..||..||  +..|+|+.|.
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            35789999999999999999999999998 9999998 788889999999999999999999999996  5999999999


Q ss_pred             EEEchhh
Q 008117          202 LKVDQAT  208 (577)
Q Consensus       202 V~~a~~~  208 (577)
                      |.|+...
T Consensus        86 V~~a~~~   92 (109)
T 2dis_A           86 VDWAEPE   92 (109)
T ss_dssp             EEESCSS
T ss_pred             EEEcCCC
Confidence            9998653

>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=99.62  E-value=9.3e-16  Score=150.53  Aligned_cols=83  Identities=18%  Similarity=0.268  Sum_probs=78.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcC--ceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCG--TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G--~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ..++|||+||++.+|+++|+.+|+.||  .|..|.|+.++.+|+++|||||+|.+.++|.+||..|||+.|+|+.|.|.+
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            578999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             chhhH
Q 008117          205 DQATR  209 (577)
Q Consensus       205 a~~~~  209 (577)
                      +....
T Consensus       147 a~~~~  151 (229)
T 3q2s_C          147 VNKQF  151 (229)
T ss_dssp             CCHHH
T ss_pred             CCCCc
Confidence            87653

>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=99.62  E-value=1.2e-15  Score=133.01  Aligned_cols=81  Identities=16%  Similarity=0.181  Sum_probs=76.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCce-EEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTV-KSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v-~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.| ..|.|+.++ +|.++|||||+|.+.++|..||.. |+..|+|+.|.|.+
T Consensus        13 ~~~~~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           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHV   90 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEE
Confidence            457899999999999999999999999999 899999997 999999999999999999999996 99999999999999


Q ss_pred             chhh
Q 008117          205 DQAT  208 (577)
Q Consensus       205 a~~~  208 (577)
                      +...
T Consensus        91 a~~~   94 (114)
T 2cpy_A           91 VTLE   94 (114)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8664

>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=4.3e-15  Score=129.29  Aligned_cols=82  Identities=26%  Similarity=0.356  Sum_probs=76.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee--------C
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI--------D  196 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i--------~  196 (577)
                      ....++|||+|||+.+|+++|+.+|..||.|..|.|+.++ +|.++|||||+|.+.++|..||..|||..|        .
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            3467899999999999999999999999999999999997 999999999999999999999999999999        5


Q ss_pred             CeEEEEEEchh
Q 008117          197 GQELMLKVDQA  207 (577)
Q Consensus       197 gr~i~V~~a~~  207 (577)
                      ++.|.|.|+..
T Consensus       101 ~~~l~v~~a~p  111 (114)
T 1x5o_A          101 TEPLLCKFSGP  111 (114)
T ss_dssp             SSCBEEEECCC
T ss_pred             CCceeEEccCC
Confidence            78899988764

>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=99.61  E-value=1e-15  Score=135.53  Aligned_cols=82  Identities=21%  Similarity=0.247  Sum_probs=75.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|..||.|..+.++.+..+|.++|||||+|.+.++|..||. |||..|+|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            456899999999999999999999999999886666666799999999999999999999999 9999999999999998


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus       102 ~~~  104 (124)
T 1wel_A          102 TKK  104 (124)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            664

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.61  E-value=5.1e-16  Score=139.74  Aligned_cols=82  Identities=18%  Similarity=0.281  Sum_probs=78.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
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            45789999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       125 ~~  126 (135)
T 2lea_A          125 RY  126 (135)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.61  E-value=5.3e-16  Score=126.60  Aligned_cols=73  Identities=15%  Similarity=0.324  Sum_probs=68.2

Q ss_pred             CceEEEcCCCCCC------CHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe-EE
Q 008117          128 QTKVYVGKIAPTA------DSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQ-EL  200 (577)
Q Consensus       128 ~~tlfVgnLp~~~------te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr-~i  200 (577)
                      .++|||+|||+.+      |+++|+.+|+.||.|..|.|+  +.+|.++|||||+|.+.++|..||..|||..|+|+ .|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            3689999999999      779999999999999999987  35899999999999999999999999999999999 88


Q ss_pred             EE
Q 008117          201 ML  202 (577)
Q Consensus       201 ~V  202 (577)
                      .|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            76

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.61  E-value=1.3e-15  Score=133.00  Aligned_cols=81  Identities=12%  Similarity=0.162  Sum_probs=73.6

Q ss_pred             ceEEEcCC----CCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCC----HHH----HHHHHH--HhCCce
Q 008117          129 TKVYVGKI----APTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFES----AEG----VLRALR--LLNKFN  194 (577)
Q Consensus       129 ~tlfVgnL----p~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~----~~~----A~~Al~--~Lng~~  194 (577)
                      +.||||||    |+.+++..|+.+|+.||.|.+|.++.|+.||.++|||||+|.+    +.+    |..||.  .|||..
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    9999999999999999999999999999999999999999996    333    788888  789999


Q ss_pred             eCCeEEEEEEchhhH
Q 008117          195 IDGQELMLKVDQATR  209 (577)
Q Consensus       195 i~gr~i~V~~a~~~~  209 (577)
                      |+|+.|+|.+.....
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            999999999987653

>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=99.61  E-value=1.9e-14  Score=145.28  Aligned_cols=77  Identities=12%  Similarity=0.211  Sum_probs=71.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID-GQELMLK  203 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~-gr~i~V~  203 (577)
                      ..+.++|||+|||..+|+++|+.+|+.||.|..|.|+.+.     +|||||+|.+.++|..||..|||..|+ |+.|.|.
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  278 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS  278 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEE
Confidence            4467899999999999999999999999999999998653     589999999999999999999999999 9999999


Q ss_pred             Ech
Q 008117          204 VDQ  206 (577)
Q Consensus       204 ~a~  206 (577)
                      |+.
T Consensus       279 ~ak  281 (282)
T 3pgw_A          279 FAK  281 (282)
T ss_pred             Eec
Confidence            875

>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=99.60  E-value=4e-15  Score=126.83  Aligned_cols=77  Identities=13%  Similarity=0.167  Sum_probs=70.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCceeCCeEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL--NKFNIDGQELML  202 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~L--ng~~i~gr~i~V  202 (577)
                      ..+.++|||+|||+.+|+++|+.+|+.||.|..|.|+.+      +|||||+|.+.++|..||..|  ++..|.|+.|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            346789999999999999999999999999999988764      699999999999999999976  578899999999


Q ss_pred             EEchh
Q 008117          203 KVDQA  207 (577)
Q Consensus       203 ~~a~~  207 (577)
                      .|+..
T Consensus        86 ~~a~~   90 (101)
T 2cq1_A           86 QYSNH   90 (101)
T ss_dssp             EECSC
T ss_pred             EEcCc
Confidence            99865

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.60  E-value=3e-16  Score=133.59  Aligned_cols=80  Identities=21%  Similarity=0.363  Sum_probs=74.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+++|+++|+.+|+.||.|.. .++.+..+|.++|||||+|.+.++|..||. |||..|.|+.|.|.++
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            45789999999999999999999999999988 666777789999999999999999999999 9999999999999987


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        93 ~~   94 (101)
T 1fj7_A           93 KG   94 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>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=99.60  E-value=4.2e-15  Score=125.77  Aligned_cols=75  Identities=16%  Similarity=0.386  Sum_probs=69.9

Q ss_pred             CCCCceEEEcCCCC-CCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 008117          125 EKPQTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  203 (577)
Q Consensus       125 ~~~~~tlfVgnLp~-~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~  203 (577)
                      ..+.++|||+|||+ .+++++|+.+|+.||.|..|.|.        +|||||+|.+.++|..||..|||..|+|+.|.|.
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   90 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34689999999998 99999999999999999999983        6899999999999999999999999999999999


Q ss_pred             Echh
Q 008117          204 VDQA  207 (577)
Q Consensus       204 ~a~~  207 (577)
                      ++..
T Consensus        91 ~a~~   94 (97)
T 2xnq_A           91 VSSS   94 (97)
T ss_dssp             ECCC
T ss_pred             ecCC
Confidence            8764

>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=3.5e-15  Score=130.06  Aligned_cols=81  Identities=14%  Similarity=0.271  Sum_probs=74.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+.+|+++|..+|+.||.|..|.|+.+   +.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            35789999999999999999999999999999999865   566899999999999999999999999999999999998


Q ss_pred             hhhH
Q 008117          206 QATR  209 (577)
Q Consensus       206 ~~~~  209 (577)
                      ....
T Consensus        83 ~~~~   86 (115)
T 3lqv_A           83 NANR   86 (115)
T ss_dssp             CHHH
T ss_pred             cCCh
Confidence            7653

>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=99.60  E-value=2.9e-15  Score=128.36  Aligned_cols=80  Identities=15%  Similarity=0.107  Sum_probs=74.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKS-WKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~-~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ...++|||+|||+.+|+++|+.+|..||.|.. |.|+.+ .+|.++|||||+|.+.++|..||.. |+..|+|+.|.|.+
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFK   90 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEE
Confidence            45789999999999999999999999999987 888888 7999999999999999999999997 99999999999987


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        91 ~~~   93 (104)
T 1wg5_A           91 SSR   93 (104)
T ss_dssp             ECT
T ss_pred             CCH
Confidence            643

>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=99.60  E-value=1.5e-15  Score=131.88  Aligned_cols=83  Identities=18%  Similarity=0.271  Sum_probs=75.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHH---HHHhhcCceEEEEEeecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 008117          126 KPQTKVYVGKIAPTADSDFVL---SVLKVCGTVKSWKRAQYPSNG---TPKGFGFCEFESAEGVLRALRLLNKFNIDGQE  199 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~---~~F~~~G~v~~~~i~~~~~tg---~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~  199 (577)
                      ...++|||+|||+.+++++|.   .+|+.||.|..|.|+.+..++   .++|||||+|.+.++|..||..|||..|+|+.
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            347899999999999999999   999999999999999887644   56699999999999999999999999999999


Q ss_pred             EEEEEchhh
Q 008117          200 LMLKVDQAT  208 (577)
Q Consensus       200 i~V~~a~~~  208 (577)
                      |.|.|+...
T Consensus        93 l~V~~a~~k  101 (111)
T 2cpi_A           93 LKASLGTTK  101 (111)
T ss_dssp             EEEESCCCC
T ss_pred             EEEEecccc
Confidence            999988653

>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=6.3e-15  Score=127.13  Aligned_cols=75  Identities=21%  Similarity=0.285  Sum_probs=71.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC-----eEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG-----QEL  200 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~g-----r~i  200 (577)
                      ...++|||+|||+++|+++|+.+|..||.|..|.|+.+       |||||+|.+.++|..||..|||..|+|     +.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            45789999999999999999999999999999999876       899999999999999999999999999     999


Q ss_pred             EEEEchh
Q 008117          201 MLKVDQA  207 (577)
Q Consensus       201 ~V~~a~~  207 (577)
                      .|.++..
T Consensus        86 ~V~~a~~   92 (108)
T 1x4c_A           86 RVKVDGP   92 (108)
T ss_dssp             EEEESSC
T ss_pred             EEEeCCC
Confidence            9998865

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.59  E-value=3.7e-15  Score=126.17  Aligned_cols=77  Identities=14%  Similarity=0.148  Sum_probs=70.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce--eCCeEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN--IDGQELML  202 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~--i~gr~i~V  202 (577)
                      ..++++|||+|||+.+|+++|..+|+.||.|.+|.++..      +|||||+|.+.++|..||..|+|..  |.|+.|.|
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            346889999999999999999999999999999998753      6899999999999999999999875  78999999


Q ss_pred             EEchh
Q 008117          203 KVDQA  207 (577)
Q Consensus       203 ~~a~~  207 (577)
                      .|+..
T Consensus        92 ~~S~~   96 (100)
T 3r27_A           92 NYSTS   96 (100)
T ss_dssp             EECSC
T ss_pred             Eeccc
Confidence            99865

>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=99.59  E-value=1.6e-15  Score=129.65  Aligned_cols=79  Identities=15%  Similarity=0.135  Sum_probs=72.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|..|| ++.|.|+.++ +|+++|||||+|.+.++|..||. +|+..|+|+.|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            3568999999999999999999999999 4599999997 99999999999999999999995 7999999999999876


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        90 ~~   91 (102)
T 1wez_A           90 ST   91 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.59  E-value=7.5e-16  Score=123.50  Aligned_cols=75  Identities=21%  Similarity=0.345  Sum_probs=71.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       130 tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      +|||+|||+.+|+++|+.+|+.||.|..|.++.++.+|.++|||||+|.+.++|..||. +++..|+|+.|.|.++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            69999999999999999999999999999999998899999999999999999999999 4999999999999875

>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=5.8e-15  Score=121.28  Aligned_cols=76  Identities=21%  Similarity=0.303  Sum_probs=70.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh-CCceeCCeEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL-NKFNIDGQELMLK  203 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~L-ng~~i~gr~i~V~  203 (577)
                      ....++|||+|||..+++++|+.+|+.||.|..|.++.+      +|||||+|.+.++|..|+..| ||..|+|+.|.|.
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~   82 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK   82 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEE
Confidence            345789999999999999999999999999999999864      689999999999999999988 9999999999999


Q ss_pred             Ech
Q 008117          204 VDQ  206 (577)
Q Consensus       204 ~a~  206 (577)
                      |+.
T Consensus        83 ~ak   85 (85)
T 2ytc_A           83 WGR   85 (85)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            873

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.59  E-value=3.6e-15  Score=128.80  Aligned_cols=76  Identities=22%  Similarity=0.327  Sum_probs=71.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+|+++|+.+|+.||.|..|.|+        +|||||+|.+.++|..|+..|||..|+|+.|.|.|
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   99 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY   99 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            4567999999999999999999999999999999987        58999999999999999999999999999999998


Q ss_pred             chhh
Q 008117          205 DQAT  208 (577)
Q Consensus       205 a~~~  208 (577)
                      +...
T Consensus       100 a~~~  103 (108)
T 2jvo_A          100 SKLP  103 (108)
T ss_dssp             CSCC
T ss_pred             ecCC
Confidence            8653

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=5.9e-15  Score=125.52  Aligned_cols=80  Identities=25%  Similarity=0.385  Sum_probs=73.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+|+++|+.+|..||.|   .++.+ .+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            3468999999999999999999999999987   56666 6899999999999999999999999999999999999999


Q ss_pred             chhh
Q 008117          205 DQAT  208 (577)
Q Consensus       205 a~~~  208 (577)
                      +...
T Consensus        88 a~~~   91 (101)
T 2fc9_A           88 QGPR   91 (101)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            8653

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.59  E-value=1.8e-15  Score=128.70  Aligned_cols=75  Identities=27%  Similarity=0.400  Sum_probs=71.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchhh
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQAT  208 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~~  208 (577)
                      ++|||+|||+.+|+++|+.+|+.||.|..|.|+.+     ++|||||+|.+.++|..|+..|||..|+|+.|.|.++...
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            58999999999999999999999999999999876     6799999999999999999999999999999999998764

>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=1.6e-15  Score=127.91  Aligned_cols=80  Identities=14%  Similarity=0.308  Sum_probs=74.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHH----HHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVL----SVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  201 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~----~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~  201 (577)
                      .+.++|||+|||+.+++++|+    .+|+.||.|..|.++.   +|.++|||||+|.+.++|..|+..|||..|+|+.|.
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            457899999999999999999    9999999999998873   578889999999999999999999999999999999


Q ss_pred             EEEchhh
Q 008117          202 LKVDQAT  208 (577)
Q Consensus       202 V~~a~~~  208 (577)
                      |.|+...
T Consensus        83 v~~a~~~   89 (97)
T 1nu4_A           83 IQYAKTD   89 (97)
T ss_dssp             EEECSSC
T ss_pred             EEEccCC
Confidence            9998764

>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=99.59  E-value=1.7e-15  Score=132.03  Aligned_cols=83  Identities=19%  Similarity=0.319  Sum_probs=72.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+.+|+++|+.+|..||.|..|.+..+..+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
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            45789999999999999999999999999943322222237899999999999999999999999999999999999998


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus       103 ~~~  105 (115)
T 2cpx_A          103 KNK  105 (115)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            653

>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=99.59  E-value=2.5e-15  Score=135.19  Aligned_cols=81  Identities=16%  Similarity=0.133  Sum_probs=75.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCc---eEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGT---VKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  202 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~---v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V  202 (577)
                      ...++|||+|||+++|+++|+.+|+.||.   |..|.|+.++. |+++|||||+|.+.++|..||. |||..|+|+.|.|
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V  119 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV  119 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            45789999999999999999999999999   89999999976 9999999999999999999999 9999999999999


Q ss_pred             EEchhh
Q 008117          203 KVDQAT  208 (577)
Q Consensus       203 ~~a~~~  208 (577)
                      .++...
T Consensus       120 ~~a~~~  125 (136)
T 2hgl_A          120 FKSHRT  125 (136)
T ss_dssp             EECCHH
T ss_pred             EECChH
Confidence            987553

>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=99.58  E-value=1.3e-15  Score=131.34  Aligned_cols=82  Identities=13%  Similarity=0.119  Sum_probs=76.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCc---eEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGT---VKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  201 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~---v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~  201 (577)
                      ....++|||+|||+++|+++|+.+|+.||.   |..|.|+.++. |.++|||||+|.+.++|..||. |||..|+|+.|.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            346789999999999999999999999998   89999999976 9999999999999999999999 999999999999


Q ss_pred             EEEchhh
Q 008117          202 LKVDQAT  208 (577)
Q Consensus       202 V~~a~~~  208 (577)
                      |.++...
T Consensus        86 V~~a~~~   92 (107)
T 2lmi_A           86 VYEINNE   92 (107)
T ss_dssp             CEECCHH
T ss_pred             EEECCHH
Confidence            9988653

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=6.6e-15  Score=127.31  Aligned_cols=79  Identities=16%  Similarity=0.108  Sum_probs=73.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ...+|||+|||+.+|+++|+.+|+.| .|..|.|+.++ +|+++|||||+|.+.++|.+|| .||+..|+|+.|.|..+.
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            45899999999999999999999999 89999999996 4999999999999999999999 589999999999998876


Q ss_pred             hh
Q 008117          207 AT  208 (577)
Q Consensus       207 ~~  208 (577)
                      ..
T Consensus        92 ~~   93 (109)
T 2dnn_A           92 ER   93 (109)
T ss_dssp             HH
T ss_pred             cc
Confidence            53

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=7e-15  Score=125.24  Aligned_cols=80  Identities=20%  Similarity=0.356  Sum_probs=73.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ..+.++|||+|||+.+|+++|+.+|+.|+   .|.++.++.+|.++|||||+|.+.++|..||..|||..|.|+.|.|.|
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            34679999999999999999999999874   577888888999999999999999999999999999999999999999


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        89 a~~   91 (102)
T 2fc8_A           89 AKP   91 (102)
T ss_dssp             CCC
T ss_pred             ecC
Confidence            865

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.58  E-value=5.5e-15  Score=128.14  Aligned_cols=77  Identities=16%  Similarity=0.172  Sum_probs=71.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcC-ceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCG-TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G-~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ..++|||+|||+++|+++|+.+|+.|| .|..+.|+.    +.++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            478999999999999999999999999 899998853    357899999999999999999999999999999999988


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       103 ~~  104 (111)
T 2jvr_A          103 DN  104 (111)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=7.7e-15  Score=122.11  Aligned_cols=74  Identities=19%  Similarity=0.399  Sum_probs=69.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+++|+++|+.+|+.||.|..|.|+        +|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus         6 ~~~~~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            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS   77 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECS
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEEC
Confidence            467999999999999999999999999999999987        479999999999999999999999999999999987


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        78 ~~   79 (90)
T 2dnq_A           78 KN   79 (90)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>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=99.57  E-value=3.9e-15  Score=127.01  Aligned_cols=76  Identities=12%  Similarity=0.114  Sum_probs=69.7

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC--ceeCCeEEEE
Q 008117          126 KPQTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNK--FNIDGQELML  202 (577)
Q Consensus       126 ~~~~tlfVgnLp~-~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng--~~i~gr~i~V  202 (577)
                      .+.++|||+|||+ .+|+++|+.+|+.||.|.+|.|+.+      +|||||+|.+.++|..||..||+  ..|.|+.|.|
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   86 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   86 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEE
Confidence            3678999999999 9999999999999999999999875      48999999999999999998886  4699999999


Q ss_pred             EEchh
Q 008117          203 KVDQA  207 (577)
Q Consensus       203 ~~a~~  207 (577)
                      .|+..
T Consensus        87 ~~a~~   91 (102)
T 1x4d_A           87 HLSQK   91 (102)
T ss_dssp             EEECC
T ss_pred             EECCC
Confidence            99875

>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=99.57  E-value=4.4e-15  Score=130.03  Aligned_cols=76  Identities=16%  Similarity=0.187  Sum_probs=70.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCeEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN--KFNIDGQELMLK  203 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Ln--g~~i~gr~i~V~  203 (577)
                      .+.++|||+|||+.+|+++|+.+|+.||.|..|.|+.+      +|||||+|.+.++|..||..|+  +..|.|+.|.|.
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~  102 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ  102 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEE
Confidence            45789999999999999999999999999999999875      6999999999999999999887  468999999999


Q ss_pred             Echh
Q 008117          204 VDQA  207 (577)
Q Consensus       204 ~a~~  207 (577)
                      |+..
T Consensus       103 ~a~~  106 (119)
T 2ad9_A          103 FSNH  106 (119)
T ss_dssp             ECSS
T ss_pred             EccC
Confidence            9865

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.57  E-value=1.8e-14  Score=135.73  Aligned_cols=82  Identities=16%  Similarity=0.232  Sum_probs=78.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+++++|+.+|+.||.|..|.|+.+. +|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
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  164 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            457899999999999999999999999999999999997 9999999999999999999999999999999999999998


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus       165 ~~~  167 (177)
T 2f3j_A          165 ASQ  167 (177)
T ss_dssp             SSG
T ss_pred             cCC
Confidence            664

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.57  E-value=5.2e-15  Score=125.89  Aligned_cols=75  Identities=20%  Similarity=0.348  Sum_probs=69.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..++|||+|||.++++++|+.+|+.||.|..|.|+      .++|||||+|.+.++|..||..|||..|+|+.|.|.|+.
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            46899999999999999999999999999999987      346999999999999999999999999999999998875


Q ss_pred             h
Q 008117          207 A  207 (577)
Q Consensus       207 ~  207 (577)
                      .
T Consensus       100 ~  100 (101)
T 2la4_A          100 E  100 (101)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=1.4e-14  Score=121.03  Aligned_cols=75  Identities=24%  Similarity=0.426  Sum_probs=70.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+|+++|+.+|+.||.|..|.|+.        +||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   78 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            45689999999999999999999999999999999874        4999999999999999999999999999999999


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        79 a~~   81 (92)
T 2dgt_A           79 STS   81 (92)
T ss_dssp             SSC
T ss_pred             ccC
Confidence            865

>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=99.57  E-value=8.7e-15  Score=126.38  Aligned_cols=77  Identities=19%  Similarity=0.317  Sum_probs=72.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||..+++++|+.+|+.||.|..|.|+.+      +|||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus        23 ~~~~~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           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            45789999999999999999999999999999999876      689999999999999999999999999999999988


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus        97 ~~~   99 (109)
T 1x4g_A           97 KES   99 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=1e-14  Score=123.21  Aligned_cols=77  Identities=17%  Similarity=0.285  Sum_probs=70.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.|. +.++.    +.++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            4578999999999999999999999999997 66654    467899999999999999999999999999999999988


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        92 ~~   93 (97)
T 2e5j_A           92 RQ   93 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.57  E-value=1.3e-14  Score=122.55  Aligned_cols=76  Identities=16%  Similarity=0.395  Sum_probs=70.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC--CeEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID--GQELMLK  203 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~--gr~i~V~  203 (577)
                      .+.++|||+|||+.+|+++|+.+|+.||.|..|.++.+      +|||||+|.+.++|..||..|||..|.  |+.|.|.
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            35689999999999999999999999999999998754      689999999999999999999999999  9999999


Q ss_pred             Echh
Q 008117          204 VDQA  207 (577)
Q Consensus       204 ~a~~  207 (577)
                      |+..
T Consensus        89 ~a~~   92 (97)
T 1why_A           89 FAKS   92 (97)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            9865

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.56  E-value=4.4e-15  Score=125.02  Aligned_cols=78  Identities=17%  Similarity=0.249  Sum_probs=71.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ..+.++|||+|||+.+|+++|+.+|+.||.|..+     ..+|.++|||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   87 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            4467999999999999999999999999988766     24789999999999999999999999999999999999998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        88 a~~   90 (96)
T 1fjc_A           88 TGE   90 (96)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            854

>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=99.55  E-value=1.7e-15  Score=137.52  Aligned_cols=84  Identities=15%  Similarity=0.269  Sum_probs=73.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEE--E---eecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWK--R---AQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQE  199 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~--i---~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~  199 (577)
                      ..+.++|||+|||+.+|+++|+.+|+.||.|..|.  +   +....+|.++|||||+|.+.++|..||..|||..|+|+.
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            34578999999999999999999999999987751  1   111247999999999999999999999999999999999


Q ss_pred             EEEEEchhh
Q 008117          200 LMLKVDQAT  208 (577)
Q Consensus       200 i~V~~a~~~  208 (577)
                      |.|.|+...
T Consensus       122 l~V~~a~~~  130 (143)
T 3egn_A          122 MVVQFARSA  130 (143)
T ss_dssp             CEEEECCCS
T ss_pred             EEEEECCCC
Confidence            999998664

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.55  E-value=4.1e-15  Score=126.76  Aligned_cols=80  Identities=26%  Similarity=0.377  Sum_probs=75.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+++++|+.+|+.||.|..|.|+.++ +|.++|||||+|.+.++|..||.  +|..|+|+.|.|.++
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            356899999999999999999999999999999999997 99999999999999999999998  999999999999887


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus        84 ~~~   86 (102)
T 2xs2_A           84 IRK   86 (102)
T ss_dssp             EEC
T ss_pred             CcC
Confidence            653

>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=2.1e-14  Score=119.39  Aligned_cols=75  Identities=17%  Similarity=0.322  Sum_probs=69.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+|+++|+.+|+.||.|..|.|+.        +||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34678999999999999999999999999999999974        4999999999999999999999999999999998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        78 a~~   80 (90)
T 2dnp_A           78 STK   80 (90)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            865

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.54  E-value=3.7e-14  Score=130.63  Aligned_cols=81  Identities=17%  Similarity=0.322  Sum_probs=77.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|..+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.|+
T Consensus        85 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  164 (166)
T 3md3_A           85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA  164 (166)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEec
Confidence            45789999999999999999999999999999999999889999999999999999999999999999999999999987


Q ss_pred             h
Q 008117          206 Q  206 (577)
Q Consensus       206 ~  206 (577)
                      .
T Consensus       165 ~  165 (166)
T 3md3_A          165 A  165 (166)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.54  E-value=1.9e-14  Score=123.38  Aligned_cols=76  Identities=16%  Similarity=0.208  Sum_probs=68.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC--ceeCCeEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNK--FNIDGQELMLK  203 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng--~~i~gr~i~V~  203 (577)
                      .+.++|||+|||+.+++++|+.+|+.||.|..|.|+.+      +|||||+|.+.++|..||..|++  ..|.|+.|.|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~   86 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            45789999999999999999999999999999998764      68999999999999999998865  45999999999


Q ss_pred             Echh
Q 008117          204 VDQA  207 (577)
Q Consensus       204 ~a~~  207 (577)
                      |+..
T Consensus        87 ~a~~   90 (104)
T 1wex_A           87 YSTS   90 (104)
T ss_dssp             ECSS
T ss_pred             EccC
Confidence            9865

>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=99.54  E-value=7.6e-15  Score=127.40  Aligned_cols=76  Identities=12%  Similarity=0.073  Sum_probs=70.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.|..|.|+.      ++|||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   81 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            3468999999999999999999999999999998864      4689999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        82 ~~   83 (111)
T 1whx_A           82 PI   83 (111)
T ss_dssp             ET
T ss_pred             CC
Confidence            65

>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=99.54  E-value=1.8e-14  Score=122.08  Aligned_cols=76  Identities=18%  Similarity=0.333  Sum_probs=71.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+.+|+++|+.+|+.||.|..|.|+.+      +|||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   86 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEc
Confidence            45789999999999999999999999999999998754      689999999999999999999999999999999988


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        87 ~~   88 (99)
T 2cpj_A           87 CH   88 (99)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>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=99.54  E-value=2.9e-14  Score=123.32  Aligned_cols=74  Identities=18%  Similarity=0.306  Sum_probs=69.2

Q ss_pred             CCCceEEEcCCCCC-CCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          126 KPQTKVYVGKIAPT-ADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       126 ~~~~tlfVgnLp~~-~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ...++|||+|||+. +++++|+.+|+.||.|..|.|        ++|||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   96 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM   96 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            45689999999999 999999999999999999988        468999999999999999999999999999999998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        97 a~~   99 (110)
T 1wf1_A           97 AGE   99 (110)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            864

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.30  E-value=5.3e-16  Score=135.64  Aligned_cols=83  Identities=13%  Similarity=0.216  Sum_probs=78.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKS--------WKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG  197 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~--------~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~g  197 (577)
                      .+.++|||+|||+.+++++|+.+|+.||.|..        |.|+.++.+|.++|||||+|.+.++|..||..|||..|.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            45789999999999999999999999999998        8999998899999999999999999999999999999999


Q ss_pred             eEEEEEEchhh
Q 008117          198 QELMLKVDQAT  208 (577)
Q Consensus       198 r~i~V~~a~~~  208 (577)
                      +.|.|.++...
T Consensus        85 ~~l~V~~a~~~   95 (116)
T 2lcw_A           85 NPIKVSFATRR   95 (116)
Confidence            99999988654

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=1.7e-14  Score=121.33  Aligned_cols=79  Identities=19%  Similarity=0.212  Sum_probs=71.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEE-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSW-KRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~-~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.|..| .|+.++.+|    .|||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            457899999999999999999999999999999 587775443    399999999999999999999999999999998


Q ss_pred             chhh
Q 008117          205 DQAT  208 (577)
Q Consensus       205 a~~~  208 (577)
                      +...
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            8653

>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=99.53  E-value=3.5e-14  Score=121.24  Aligned_cols=75  Identities=15%  Similarity=0.399  Sum_probs=69.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+|||+.+|+++|+.+|..||.|..|.|+.        +||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            4578999999999999999999999999999999863        59999999999999999999999999999999998


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus        81 ~~~   83 (103)
T 2dgu_A           81 KPP   83 (103)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=6e-14  Score=118.84  Aligned_cols=75  Identities=17%  Similarity=0.374  Sum_probs=69.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhc--CceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVC--GTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  202 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~--G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V  202 (577)
                      ..+.++|||+|||+.+|+++|+.+|+.|  |.|..|.+.        +|||||+|.+.++|..||..|||..|+|+.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            3467899999999999999999999999  999998874        479999999999999999999999999999999


Q ss_pred             EEchh
Q 008117          203 KVDQA  207 (577)
Q Consensus       203 ~~a~~  207 (577)
                      .|+..
T Consensus        84 ~~a~~   88 (99)
T 2cpd_A           84 TLAKP   88 (99)
T ss_dssp             ECCCC
T ss_pred             EECCC
Confidence            98865

>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=99.53  E-value=2.5e-14  Score=130.77  Aligned_cols=77  Identities=25%  Similarity=0.399  Sum_probs=72.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.|.+|.|+.+     ++|||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus        71 ~~~~~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           71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS  145 (150)
T ss_dssp             TTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            45789999999999999999999999999999999876     5799999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       146 ~~  147 (150)
T 2i2y_A          146 NG  147 (150)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.52  E-value=3e-14  Score=123.36  Aligned_cols=77  Identities=13%  Similarity=0.218  Sum_probs=69.3

Q ss_pred             CCCCceEEEcCCCCC-CCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCeEEE
Q 008117          125 EKPQTKVYVGKIAPT-ADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN--KFNIDGQELM  201 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~-~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Ln--g~~i~gr~i~  201 (577)
                      ..+.++|||+|||++ +|+++|+.+|+.||.|..|.|+.      ++|||||+|.+.++|..||..||  +..|.|+.|.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            345889999999998 99999999999999999999974      36999999999999999999885  5679999999


Q ss_pred             EEEchh
Q 008117          202 LKVDQA  207 (577)
Q Consensus       202 V~~a~~  207 (577)
                      |.|+..
T Consensus        96 V~~a~~  101 (112)
T 1x4f_A           96 VDLSEK  101 (112)
T ss_dssp             EEEECS
T ss_pred             EEECcc
Confidence            999865

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.52  E-value=1.7e-14  Score=121.57  Aligned_cols=74  Identities=18%  Similarity=0.425  Sum_probs=69.1

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          126 KPQTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       126 ~~~~tlfVgnLp~-~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      .+.++|||+|||+ .+|+++|+.+|+.||.|..|.|.        +|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus         8 ~~~~~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            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            4688999999999 99999999999999999999984        58999999999999999999999999999999998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        80 a~~   82 (96)
T 2kvi_A           80 SSS   82 (96)
T ss_dssp             EEC
T ss_pred             cCc
Confidence            865

>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=99.51  E-value=5.8e-14  Score=130.44  Aligned_cols=79  Identities=22%  Similarity=0.447  Sum_probs=76.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ..++|||+|||+.+|+++|+.+|+.||.|..|.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.||
T Consensus        93 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            3789999999999999999999999999999999999889999999999999999999999999999999999999986

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=4.1e-14  Score=118.74  Aligned_cols=76  Identities=17%  Similarity=0.234  Sum_probs=68.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.|..|  +.++.+|.   ||||+|.+.++|..||. |||..|+|+.|.|.++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            356899999999999999999999999999987  55555666   99999999999999999 9999999999999866


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        80 ~~   81 (94)
T 2e5g_A           80 EQ   81 (94)
T ss_dssp             CC
T ss_pred             Cc
Confidence            43

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=1.9e-14  Score=127.06  Aligned_cols=80  Identities=23%  Similarity=0.219  Sum_probs=73.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCce----EEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTV----KSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  201 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v----~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~  201 (577)
                      ...++|||+|||+++|+++|+.+|+.||.|    ..|.|+.+ .+|+++|||||+|.+.++|..||.. |+..|+|+.|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            457899999999999999999999999975    68999998 5899999999999999999999995 99999999999


Q ss_pred             EEEchh
Q 008117          202 LKVDQA  207 (577)
Q Consensus       202 V~~a~~  207 (577)
                      |..+..
T Consensus        99 V~~a~~  104 (123)
T 2dha_A           99 LFRSTA  104 (123)
T ss_dssp             CEEECH
T ss_pred             EEECCH
Confidence            987754

>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=99.51  E-value=2.2e-14  Score=127.07  Aligned_cols=79  Identities=15%  Similarity=0.113  Sum_probs=71.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceE--EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVK--SWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  203 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~--~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~  203 (577)
                      ...++|||+|||+.+|+++|+.+|+.| .|+  .|.|+.++. |.++|||||+|.+.++|.+||. +++..|+|+.|.|.
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~  116 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVF  116 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEE
Confidence            356889999999999999999999999 576  999999976 9999999999999999999998 48899999999998


Q ss_pred             Echh
Q 008117          204 VDQA  207 (577)
Q Consensus       204 ~a~~  207 (577)
                      .+..
T Consensus       117 ~a~~  120 (126)
T 2hgm_A          117 KSSQ  120 (126)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            7644

>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=99.50  E-value=4.1e-14  Score=118.35  Aligned_cols=75  Identities=15%  Similarity=0.332  Sum_probs=67.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCc-eEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC-ceeCCeEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGT-VKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNK-FNIDGQELMLK  203 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~-v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng-~~i~gr~i~V~  203 (577)
                      ...++|||+|||+++|+++|+.+|+.||. |..+.+.       ++|||||+|.+.++|..||..||| ..|+|+.|.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            45789999999999999999999999999 6655553       368999999999999999999999 99999999999


Q ss_pred             Echh
Q 008117          204 VDQA  207 (577)
Q Consensus       204 ~a~~  207 (577)
                      |+..
T Consensus        79 ~a~~   82 (93)
T 2cqh_A           79 YSVS   82 (93)
T ss_dssp             ECCC
T ss_pred             EccC
Confidence            9865

>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=99.50  E-value=4.1e-14  Score=117.23  Aligned_cols=74  Identities=15%  Similarity=0.302  Sum_probs=69.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..++|||+|||+.+++++|+.+|+.| .|..|.|.      .++|||||+|.+.++|..|+..|||..|+|+.|.|.++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            56899999999999999999999999 99999884      568999999999999999999999999999999999875


Q ss_pred             h
Q 008117          207 A  207 (577)
Q Consensus       207 ~  207 (577)
                      .
T Consensus        77 ~   77 (88)
T 1wg1_A           77 T   77 (88)
T ss_dssp             C
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=99.50  E-value=8.1e-15  Score=132.28  Aligned_cols=79  Identities=14%  Similarity=0.120  Sum_probs=72.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+++|+++|+.+|+.|| |+.|.|+.++. |+++|||||+|.+.++|..|| .||+..|+|+.|.|.++
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLN  120 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEEC
Confidence            4568999999999999999999999999 77999999975 999999999999999999999 68999999999999876


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       121 ~~  122 (139)
T 2hgn_A          121 ST  122 (139)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=1.4e-13  Score=116.06  Aligned_cols=74  Identities=15%  Similarity=0.284  Sum_probs=68.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .+.++|||+||  .+|+++|+.+|..||.|..|.|.      .++|||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a   84 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   84 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            35789999996  89999999999999999999984      45799999999999999999999999999999999988


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        85 ~~   86 (97)
T 1x5p_A           85 RK   86 (97)
T ss_dssp             SS
T ss_pred             CC
Confidence            65

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.49  E-value=1e-13  Score=134.28  Aligned_cols=81  Identities=17%  Similarity=0.361  Sum_probs=75.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ...+|||+|||+.+|+++|+.+|+.||.|..|.|+.+.  +.++|||||+|.+.++|..||..|||..|+|+.|.|.++.
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~  179 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK  179 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            35789999999999999999999999999999999983  5689999999999999999999999999999999999997


Q ss_pred             hhH
Q 008117          207 ATR  209 (577)
Q Consensus       207 ~~~  209 (577)
                      ...
T Consensus       180 ~~~  182 (213)
T 4f02_A          180 SRK  182 (213)
T ss_dssp             CHH
T ss_pred             CCc
Confidence            654

>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=99.49  E-value=3.8e-14  Score=123.72  Aligned_cols=74  Identities=23%  Similarity=0.322  Sum_probs=65.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeE-----E
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQE-----L  200 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~-----i  200 (577)
                      ...++|||+|||+++|+++|+.+|..||.|..|.|+.+       |||||+|.+.++|..||..|||..|+|+.     |
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEE
Confidence            35789999999999999999999999999999999765       89999999999999999999999999998     6


Q ss_pred             EEEEch
Q 008117          201 MLKVDQ  206 (577)
Q Consensus       201 ~V~~a~  206 (577)
                      .|..+.
T Consensus        87 ~v~~~~   92 (115)
T 3beg_B           87 RVKVDG   92 (115)
T ss_dssp             EEEECC
T ss_pred             EeccCC
Confidence            665443

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.49  E-value=9.1e-14  Score=134.06  Aligned_cols=83  Identities=29%  Similarity=0.492  Sum_probs=78.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||..+|+++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            35689999999999999999999999999999999999889999999999999999999999999999999999999988


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus       203 ~~~  205 (216)
T 2qfj_A          203 VTP  205 (216)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            653

>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=99.48  E-value=7e-14  Score=121.24  Aligned_cols=76  Identities=22%  Similarity=0.338  Sum_probs=68.4

Q ss_pred             CCCceEEE--cCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee-----CCe
Q 008117          126 KPQTKVYV--GKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI-----DGQ  198 (577)
Q Consensus       126 ~~~~tlfV--gnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i-----~gr  198 (577)
                      .+..+|||  |||++.+++++|+.+|+.||.|..|.|+.+      +|||||+|.+.++|..|+..|||..|     .|+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            45788999  789999999999999999999999987542      68999999999999999999999998     689


Q ss_pred             EEEEEEchh
Q 008117          199 ELMLKVDQA  207 (577)
Q Consensus       199 ~i~V~~a~~  207 (577)
                      .|.|.|+..
T Consensus        97 ~l~v~~a~~  105 (114)
T 2cq2_A           97 TLYLNFVEK  105 (114)
T ss_dssp             ECEEEEESC
T ss_pred             EEEEEeccc
Confidence            999988754

>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=99.48  E-value=1.1e-13  Score=115.07  Aligned_cols=74  Identities=15%  Similarity=0.214  Sum_probs=62.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee--CCeEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI--DGQELMLK  203 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i--~gr~i~V~  203 (577)
                      .+.++|||||||+++|+++|+.+|+.||.|.+|.|+.+     ++|||||+|.+.++|..    |+|..+  .|+.|.|.
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~   79 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHIS   79 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEE
Confidence            46889999999999999999999999999999999874     68999999999999873    466554  59999999


Q ss_pred             Echhh
Q 008117          204 VDQAT  208 (577)
Q Consensus       204 ~a~~~  208 (577)
                      ++...
T Consensus        80 ~a~~k   84 (89)
T 3d2w_A           80 NAEPK   84 (89)
T ss_dssp             ECC--
T ss_pred             EcCCC
Confidence            88654

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=1.1e-13  Score=114.53  Aligned_cols=71  Identities=18%  Similarity=0.309  Sum_probs=63.9

Q ss_pred             CceEEEcCCCCCCCHHH----HHHHHhhcC-ceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 008117          128 QTKVYVGKIAPTADSDF----VLSVLKVCG-TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  202 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~----L~~~F~~~G-~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V  202 (577)
                      .+.|||+|||+.++.++    |..+|+.|| .|.+|       +|   |||||.|.+.++|.+|+..|||..|.|+.|+|
T Consensus         9 ~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            9 HTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIV   78 (96)
T ss_dssp             SEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             ceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEE
Confidence            34499999999999987    558999995 99998       34   99999999999999999999999999999999


Q ss_pred             EEchhh
Q 008117          203 KVDQAT  208 (577)
Q Consensus       203 ~~a~~~  208 (577)
                      .|+...
T Consensus        79 ~~A~~~   84 (96)
T 2diu_A           79 SFTPKN   84 (96)
T ss_dssp             ESSCCS
T ss_pred             EecCCC
Confidence            988764

>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=99.47  E-value=1.5e-13  Score=126.47  Aligned_cols=78  Identities=15%  Similarity=0.123  Sum_probs=70.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG--QELMLKV  204 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~g--r~i~V~~  204 (577)
                      ...+|||+||++.+|+++|+.+|+.||.|..|.|+..    .++|||||+|.+.++|..|+..|||..|.|  +.|+|.|
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~  120 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  120 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEE
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEE
Confidence            4578999999999999999999999999999998654    257899999999999999999999999965  9999999


Q ss_pred             chhh
Q 008117          205 DQAT  208 (577)
Q Consensus       205 a~~~  208 (577)
                      +...
T Consensus       121 Ak~~  124 (164)
T 1sjr_A          121 SKLT  124 (164)
T ss_dssp             CSSS
T ss_pred             ecCC
Confidence            8653

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.47  E-value=2.4e-13  Score=129.28  Aligned_cols=82  Identities=21%  Similarity=0.443  Sum_probs=78.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+++++|+.+|+.||.|..|.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45799999999999999999999999999999999999889999999999999999999999999999999999999988


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       192 ~~  193 (198)
T 2yh0_A          192 SV  193 (198)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.46  E-value=6.9e-16  Score=165.41  Aligned_cols=64  Identities=9%  Similarity=0.061  Sum_probs=49.7

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++..++.+..+.. .+..+|.++|||||+|.+.++|..||..||+.
T Consensus       103 ~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~  167 (437)
T 3pgw_S          103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGK  167 (437)
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCC
Confidence            45699999999999999988552322211111 23568999999999999999999999999875

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.46  E-value=2.5e-13  Score=120.48  Aligned_cols=77  Identities=17%  Similarity=0.179  Sum_probs=69.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceE-EEEEeCCHHHHHHHHHHhCCceeCC--eEEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGF-GFCEFESAEGVLRALRLLNKFNIDG--QELMLK  203 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~-gFV~f~~~~~A~~Al~~Lng~~i~g--r~i~V~  203 (577)
                      ....|||+||++.+|+++|..+|+.||.|..|.|+..     .+|| |||+|.+.++|..|+..|||..|.|  +.|+|.
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~  101 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  101 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEE
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEE
Confidence            4567899999999999999999999999999988764     2577 9999999999999999999999988  899999


Q ss_pred             Echhh
Q 008117          204 VDQAT  208 (577)
Q Consensus       204 ~a~~~  208 (577)
                      |+...
T Consensus       102 ~ak~~  106 (130)
T 3zzy_A          102 FSKLT  106 (130)
T ss_dssp             ECSCS
T ss_pred             ecCCC
Confidence            88653

>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=113.22  Aligned_cols=71  Identities=24%  Similarity=0.418  Sum_probs=66.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhc----C-------ceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVC----G-------TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN  194 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~----G-------~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~  194 (577)
                      .+.++|||+|||+.+++++|+.+|+.|    |       .|.++.+..+      +|||||+|.+.++|..|+ .|||..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            457899999999999999999999999    8       8999998754      699999999999999999 899999


Q ss_pred             eCCeEEEEE
Q 008117          195 IDGQELMLK  203 (577)
Q Consensus       195 i~gr~i~V~  203 (577)
                      |+|+.|.|.
T Consensus        77 ~~g~~l~V~   85 (87)
T 2hzc_A           77 FQGQSLKIR   85 (87)
T ss_dssp             ETTEECEEE
T ss_pred             ECCeEEEEe
Confidence            999999985

>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=99.46  E-value=6.5e-14  Score=129.45  Aligned_cols=80  Identities=21%  Similarity=0.382  Sum_probs=76.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..++|||+|||+.+|+++|..+|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|+. |||..|+|+.|.|.|+.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            36799999999999999999999999999999999998899999999999999999999998 89999999999999986


Q ss_pred             h
Q 008117          207 A  207 (577)
Q Consensus       207 ~  207 (577)
                      +
T Consensus       165 p  165 (167)
T 2cjk_A          165 P  165 (167)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=1.2e-13  Score=120.33  Aligned_cols=78  Identities=21%  Similarity=0.328  Sum_probs=69.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCC---CCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSN---GTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  202 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~t---g~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V  202 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.|. +.++.+..+   |.++|||||+|.+.++|..||..|+  .++|+.|.|
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            4578999999999999999999999999999 888887766   7999999999999999999999884  478888887


Q ss_pred             EEch
Q 008117          203 KVDQ  206 (577)
Q Consensus       203 ~~a~  206 (577)
                      ..+.
T Consensus        83 ~~~~   86 (114)
T 2dnl_A           83 VSSP   86 (114)
T ss_dssp             ECCS
T ss_pred             ccCC
Confidence            6543

>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=99.46  E-value=3e-13  Score=124.98  Aligned_cols=79  Identities=22%  Similarity=0.379  Sum_probs=75.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG--QELMLKV  204 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~g--r~i~V~~  204 (577)
                      ..++|||+|||..+++++|+.+|+.||.|..+.++.+..+|.++|||||+|.+.++|..|+..|||..|.|  +.|.|.|
T Consensus        88 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~  167 (168)
T 1b7f_A           88 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL  167 (168)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEe
Confidence            46899999999999999999999999999999999998899999999999999999999999999999988  9999987


Q ss_pred             c
Q 008117          205 D  205 (577)
Q Consensus       205 a  205 (577)
                      |
T Consensus       168 A  168 (168)
T 1b7f_A          168 A  168 (168)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.45  E-value=2.4e-13  Score=128.97  Aligned_cols=81  Identities=15%  Similarity=0.343  Sum_probs=75.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..++|||+|||+.+|+++|+.+|+.||.|..|.|+.+..+|.++|||||+|.+.++|.+||.. +|..|+|+.|.|.++.
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~  181 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKAL  181 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecC
Confidence            468999999999999999999999999999999999988999999999999999999999986 8999999999999987


Q ss_pred             hh
Q 008117          207 AT  208 (577)
Q Consensus       207 ~~  208 (577)
                      ..
T Consensus       182 ~k  183 (196)
T 1l3k_A          182 SK  183 (196)
T ss_dssp             --
T ss_pred             Ch
Confidence            65

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.45  E-value=5.2e-13  Score=114.56  Aligned_cols=82  Identities=17%  Similarity=0.086  Sum_probs=73.0

Q ss_pred             CCCceEEEcCCCC-----CCCHHHHHHHHhhcCceEEEEEeecCCC-CCcceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 008117          126 KPQTKVYVGKIAP-----TADSDFVLSVLKVCGTVKSWKRAQYPSN-GTPKGFGFCEFESAEGVLRALRLLNKFNIDGQE  199 (577)
Q Consensus       126 ~~~~tlfVgnLp~-----~~te~~L~~~F~~~G~v~~~~i~~~~~t-g~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~  199 (577)
                      .++++|+|.||..     .-++++|+.+|++||.|.+|.|+.++.+ +.++|||||+|.+.++|..|+..|||..|+|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            3578999999963     2368899999999999999999988644 689999999999999999999999999999999


Q ss_pred             EEEEEchh
Q 008117          200 LMLKVDQA  207 (577)
Q Consensus       200 i~V~~a~~  207 (577)
                      |.|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999865

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.44  E-value=4.8e-13  Score=117.98  Aligned_cols=75  Identities=20%  Similarity=0.173  Sum_probs=66.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceE-EEEEeCCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGF-GFCEFESAEGVLRALRLLNKFNIDG--QELMLKV  204 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~-gFV~f~~~~~A~~Al~~Lng~~i~g--r~i~V~~  204 (577)
                      ...|||+||++.+|+++|+.+|+.||.|..|.|+..      .|| |||+|.+.++|..|+..|||..|.|  +.|.|.|
T Consensus        25 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           25 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEY   98 (124)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEEC
T ss_pred             EEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEE
Confidence            345789999999999999999999999999998652      276 9999999999999999999999987  6899988


Q ss_pred             chhh
Q 008117          205 DQAT  208 (577)
Q Consensus       205 a~~~  208 (577)
                      +...
T Consensus        99 Ak~~  102 (124)
T 2e5i_A           99 ARPT  102 (124)
T ss_dssp             CSCS
T ss_pred             ecCC
Confidence            8653

>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=99.44  E-value=3.8e-13  Score=123.87  Aligned_cols=79  Identities=18%  Similarity=0.288  Sum_probs=74.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeE--EEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQE--LMLKV  204 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~--i~V~~  204 (577)
                      ..++|||+|||..+++++|+.+|+.||.|..+.++.+..+|.++|||||+|.+.++|..|+..|||..|+|+.  |.|.|
T Consensus        87 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~  166 (167)
T 1fxl_A           87 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF  166 (167)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEe
Confidence            4678999999999999999999999999999999999889999999999999999999999999999999975  77776


Q ss_pred             c
Q 008117          205 D  205 (577)
Q Consensus       205 a  205 (577)
                      |
T Consensus       167 A  167 (167)
T 1fxl_A          167 A  167 (167)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.42  E-value=4.5e-13  Score=124.53  Aligned_cols=79  Identities=14%  Similarity=0.344  Sum_probs=73.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC---CeEEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID---GQELMLK  203 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~---gr~i~V~  203 (577)
                      ..++|||+|||+.+|+++|+.+|+.||.|..|.++.+. +|.++|||||+|.+.++|..|+..|||..|.   |+.|.|.
T Consensus        94 ~~~~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           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK  172 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEE
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEE
Confidence            46799999999999999999999999999999999985 6999999999999999999999999998776   4999999


Q ss_pred             Ech
Q 008117          204 VDQ  206 (577)
Q Consensus       204 ~a~  206 (577)
                      |+.
T Consensus       173 ~ad  175 (175)
T 3nmr_A          173 FAD  175 (175)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            873

>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=99.41  E-value=7.3e-13  Score=126.44  Aligned_cols=79  Identities=18%  Similarity=0.169  Sum_probs=72.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..++|||+|||+.+|+++|+.+|+.||.|..|.|+.+. +|.++|||||+|.+.++|..||..+ +..|+|+.|.|.++.
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~  185 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKD  185 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhH
Confidence            35899999999999999999999999999999999985 6999999999999999999999864 569999999998865


Q ss_pred             h
Q 008117          207 A  207 (577)
Q Consensus       207 ~  207 (577)
                      .
T Consensus       186 ~  186 (193)
T 2voo_A          186 D  186 (193)
T ss_dssp             T
T ss_pred             H
Confidence            4

>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=99.38  E-value=3.3e-13  Score=111.63  Aligned_cols=75  Identities=15%  Similarity=0.196  Sum_probs=63.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.|..|.|+.+     ++|||||+|.+.++|..|+.  .+..+.|+.|.|.++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEec
Confidence            35789999999999999999999999999999999764     67999999999999975432  234558999999877


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        76 ~~   77 (88)
T 1wf0_A           76 EP   77 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            55

>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=99.36  E-value=1.4e-12  Score=121.63  Aligned_cols=77  Identities=17%  Similarity=0.260  Sum_probs=71.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.|..+     ..+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  171 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT  171 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEEC
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEec
Confidence            357899999999999999999999999988766     368999999999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       172 ~~  173 (175)
T 1fje_B          172 GE  173 (175)
T ss_dssp             SS
T ss_pred             CC
Confidence            64

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.36  E-value=9e-13  Score=129.16  Aligned_cols=78  Identities=19%  Similarity=0.291  Sum_probs=71.2

Q ss_pred             CCCCceEEEcCCCCCC---------CHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 008117          125 EKPQTKVYVGKIAPTA---------DSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI  195 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~---------te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i  195 (577)
                      ....++||||||+..+         ++++|+.+|+.||.|.+|.|+.+      +|||||+|.+.++|..|+..|||..|
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            4568999999999998         79999999999999999999864      69999999999999999999999999


Q ss_pred             ------------CCeEEEEEEchhh
Q 008117          196 ------------DGQELMLKVDQAT  208 (577)
Q Consensus       196 ------------~gr~i~V~~a~~~  208 (577)
                                  .|+.|.|.||...
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~  229 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANED  229 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC--
T ss_pred             eccccccccccCCCCEEEEEEccCC
Confidence                        8999999999764

>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=99.33  E-value=2e-12  Score=124.55  Aligned_cols=78  Identities=17%  Similarity=0.207  Sum_probs=70.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCce--EEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe----E
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTV--KSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQ----E  199 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v--~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr----~  199 (577)
                      .+.++|||+|||+.+|+++|+.+|+.||.|  ..++++.+.  |..+|||||+|.+.++|..||..|||..|.|.    +
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p  198 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP  198 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcc
Confidence            357899999999999999999999999999  899988773  66679999999999999999999999999877    5


Q ss_pred             EEEEEc
Q 008117          200 LMLKVD  205 (577)
Q Consensus       200 i~V~~a  205 (577)
                      +.|+|+
T Consensus       199 ~~vk~~  204 (205)
T 3tyt_A          199 YTLKLC  204 (205)
T ss_dssp             EECEEE
T ss_pred             eEEEec
Confidence            777765

>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=99.29  E-value=8.6e-12  Score=106.93  Aligned_cols=83  Identities=17%  Similarity=0.077  Sum_probs=71.0

Q ss_pred             CCCceEEEcCCCC--CCC--------HHHHHHHHhhcCceEEEEEeecCCC--CCcceEEEEEeCCHHHHHHHHHHhCCc
Q 008117          126 KPQTKVYVGKIAP--TAD--------SDFVLSVLKVCGTVKSWKRAQYPSN--GTPKGFGFCEFESAEGVLRALRLLNKF  193 (577)
Q Consensus       126 ~~~~tlfVgnLp~--~~t--------e~~L~~~F~~~G~v~~~~i~~~~~t--g~~kg~gFV~f~~~~~A~~Al~~Lng~  193 (577)
                      .+++.|.|.|+-.  .+.        .++|+.+|++||.|.+|.|+.+..+  +.++|||||+|.+.++|.+|+..|||.
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            4578899999832  332        3689999999999999999988654  468999999999999999999999999


Q ss_pred             eeCCeEEEEEEchhh
Q 008117          194 NIDGQELMLKVDQAT  208 (577)
Q Consensus       194 ~i~gr~i~V~~a~~~  208 (577)
                      .|+|+.|.|.+....
T Consensus        83 ~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           83 KFANRVVVTKYCDPD   97 (105)
T ss_dssp             EETTEECEEEEECHH
T ss_pred             EeCCCEEEEEEeCHH
Confidence            999999999987553

>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=99.28  E-value=1.2e-11  Score=107.18  Aligned_cols=78  Identities=12%  Similarity=0.136  Sum_probs=67.6

Q ss_pred             CCCceEEEcCCCCCCC-----------HHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 008117          126 KPQTKVYVGKIAPTAD-----------SDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN  194 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~t-----------e~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~  194 (577)
                      .+.++|+|.||.....           +++|+.+|++||.|..|.| .+.   .++|||||+|.+.++|..||..|||..
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            3578999999954432           5799999999999999965 443   378999999999999999999999999


Q ss_pred             eCCeEEEEEEchh
Q 008117          195 IDGQELMLKVDQA  207 (577)
Q Consensus       195 i~gr~i~V~~a~~  207 (577)
                      |+|+.|.|.++..
T Consensus        89 ~~gr~l~v~~a~~  101 (112)
T 2dit_A           89 FGGRQITAQAWDG  101 (112)
T ss_dssp             ETTEECEEEECCS
T ss_pred             ECCcEEEEEEeCC
Confidence            9999999998765

>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=99.26  E-value=2.8e-12  Score=109.75  Aligned_cols=72  Identities=14%  Similarity=0.139  Sum_probs=64.7

Q ss_pred             EcCCCCCCCHHHHHHHH------------hhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 008117          133 VGKIAPTADSDFVLSVL------------KVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL  200 (577)
Q Consensus       133 VgnLp~~~te~~L~~~F------------~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i  200 (577)
                      +.||+..+++++|+.+|            ++||.|.+|.|+.+. +|.++|||||+|.+.++|.+|+..|||..|+|+.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56788888888777766            999999999999885 58999999999999999999999999999999999


Q ss_pred             EEEEc
Q 008117          201 MLKVD  205 (577)
Q Consensus       201 ~V~~a  205 (577)
                      .|.|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99876

>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=99.26  E-value=1.5e-11  Score=122.86  Aligned_cols=80  Identities=15%  Similarity=0.223  Sum_probs=73.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh-CCceeC---CeEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL-NKFNID---GQELML  202 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~L-ng~~i~---gr~i~V  202 (577)
                      +.++|||+|||+.+|+++|+.+|+.||.|..|.|+.+ .+|.++|||||+|.+.++|..||..| +|..+.   |+.|.|
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v  173 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIV  173 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEE
Confidence            4679999999999999999999999999999999999 59999999999999999999999999 555555   999999


Q ss_pred             EEchh
Q 008117          203 KVDQA  207 (577)
Q Consensus       203 ~~a~~  207 (577)
                      .++..
T Consensus       174 ~~~~~  178 (261)
T 3sde_A          174 EPMEQ  178 (261)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            88764

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.25  E-value=1.4e-11  Score=117.30  Aligned_cols=77  Identities=18%  Similarity=0.320  Sum_probs=71.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcC-ceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCG-TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID-GQELMLK  203 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G-~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~-gr~i~V~  203 (577)
                      .+.++|||+|||..+++++|+.+|+.|| .|..|.|+.+     .+|||||+|.+.++|..|+..|||..|+ |+.|.|.
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  192 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  192 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEE
Confidence            4579999999999999999999999999 9999998664     2689999999999999999999999999 9999999


Q ss_pred             Echh
Q 008117          204 VDQA  207 (577)
Q Consensus       204 ~a~~  207 (577)
                      |+..
T Consensus       193 ~a~~  196 (198)
T 1qm9_A          193 FSKS  196 (198)
T ss_dssp             EECC
T ss_pred             eecc
Confidence            9864

>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=99.24  E-value=2e-11  Score=106.78  Aligned_cols=81  Identities=17%  Similarity=0.080  Sum_probs=70.8

Q ss_pred             CCceEEEcCCCC--C---CCHHHHHHHHhhcCceEEEEEeecCC----CCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 008117          127 PQTKVYVGKIAP--T---ADSDFVLSVLKVCGTVKSWKRAQYPS----NGTPKGFGFCEFESAEGVLRALRLLNKFNIDG  197 (577)
Q Consensus       127 ~~~tlfVgnLp~--~---~te~~L~~~F~~~G~v~~~~i~~~~~----tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~g  197 (577)
                      ++++|+|.|+-.  .   --+++|+..|++||.|.+|.|+.+..    ++.++||+||+|.+.++|.+|+..|||..|+|
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            578999999842  1   23579999999999999999998864    45778999999999999999999999999999


Q ss_pred             eEEEEEEchh
Q 008117          198 QELMLKVDQA  207 (577)
Q Consensus       198 r~i~V~~a~~  207 (577)
                      +.|.|.|...
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999998755

>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=99.21  E-value=2.7e-11  Score=118.50  Aligned_cols=77  Identities=18%  Similarity=0.320  Sum_probs=71.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcC-ceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCG-TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID-GQELMLK  203 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G-~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~-gr~i~V~  203 (577)
                      .+.++|||+|||+.+++++|+.+|+.|| .|..|.|+..     .+|||||+|.+.++|..||..|||..|+ |+.|.|.
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~  223 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  223 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEE
Confidence            4579999999999999999999999999 9999998653     3689999999999999999999999999 9999999


Q ss_pred             Echh
Q 008117          204 VDQA  207 (577)
Q Consensus       204 ~a~~  207 (577)
                      |+..
T Consensus       224 ~a~~  227 (229)
T 2adc_A          224 FSKS  227 (229)
T ss_dssp             ECSS
T ss_pred             EecC
Confidence            9865

>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=99.12  E-value=1.1e-10  Score=120.22  Aligned_cols=77  Identities=23%  Similarity=0.355  Sum_probs=66.2

Q ss_pred             CCCCceEEEcC--CCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC---Ce-
Q 008117          125 EKPQTKVYVGK--IAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID---GQ-  198 (577)
Q Consensus       125 ~~~~~tlfVgn--Lp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~---gr-  198 (577)
                      ..++.+|||||  |++.+|+++|+.+|++||.|.+|.|..      ++|||||+|.+.++|.+||..|||..+.   |+ 
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            45688999999  588999999999999999999987743      4699999999999999999999999883   45 


Q ss_pred             -EEEEEEchh
Q 008117          199 -ELMLKVDQA  207 (577)
Q Consensus       199 -~i~V~~a~~  207 (577)
                       .|.|.|...
T Consensus        89 ~~ly~~~~~~   98 (345)
T 3tht_A           89 ITLYLNFVEK   98 (345)
T ss_dssp             EECEEEECSS
T ss_pred             eEEEEEEeec
Confidence             577777643

>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=99.11  E-value=3.2e-11  Score=110.87  Aligned_cols=131  Identities=10%  Similarity=0.021  Sum_probs=83.8

Q ss_pred             EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchhhHHHHHhhhhhhhhccccccccccccccC
Q 008117          157 SWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGK  236 (577)
Q Consensus       157 ~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~n  236 (577)
                      +++|+.+.  ..++|||||+|.+..+|.+|+..+++....+..+.+..........  .................+||+|
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~v~n   77 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVT--EGSHHHHHHMDVEGMTSLKVDN   77 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEE--CCCCCSSCCCCCCBCCEEEEES
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCcccccccc--ccccccccccCCCCCCEEEEeC
Confidence            56777774  4689999999999999999998887643333333332111100000  0000000111122234469999


Q ss_pred             CCcccchhhhcCCCC---CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          237 EDESVQSVEKNEPTK---SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       237 l~~~~~~~~l~e~~k---s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      |+..+++++|.+++.   .+......  .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus        78 l~~~~~~~~l~~~F~~~G~v~~~~i~--~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~  135 (158)
T 2kn4_A           78 LTYRTSPDTLRRVFEKYGRVGDVYIP--RDRYTKESRGFAFVRFHDKRDAEDAMDAMDGA  135 (158)
T ss_dssp             CCTTCCHHHHHHHHHHHSCEEEEECC--CCSSCTTSCCEEEEEESBHHHHHHHHHHSTTE
T ss_pred             CCCCCCHHHHHHHHHhcCCeEEEEEe--ecCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence            999999999998844   22111111  12468999999999999999999999998874

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.08  E-value=5.9e-10  Score=94.44  Aligned_cols=63  Identities=16%  Similarity=0.148  Sum_probs=56.3

Q ss_pred             CCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          138 PTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       138 ~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      ..+++++|+.+|++||.|..|.|+     +.++|||||+|.+.++|..||..+++  +.|+.|.|.|+..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~   89 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEG   89 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccC
Confidence            568999999999999999999987     46789999999999999999997554  6799999998755

>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=99.02  E-value=1.1e-09  Score=95.15  Aligned_cols=77  Identities=12%  Similarity=0.063  Sum_probs=64.7

Q ss_pred             CCceEEEcCCCCCCC----------HHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 008117          127 PQTKVYVGKIAPTAD----------SDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  196 (577)
Q Consensus       127 ~~~tlfVgnLp~~~t----------e~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~  196 (577)
                      +++.|.+.|+-....          .++|+..|++||.|.+|.|..+.    ++|||||+|.+.++|.+|+..|||..|+
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            466788888743221          24889999999999999986652    5899999999999999999999999999


Q ss_pred             CeEEEEEEchh
Q 008117          197 GQELMLKVDQA  207 (577)
Q Consensus       197 gr~i~V~~a~~  207 (577)
                      |+.|.|.|+..
T Consensus        82 GR~i~v~~~~~   92 (114)
T 3s6e_A           82 GKMITAAYVPL   92 (114)
T ss_dssp             TEECEEEEECH
T ss_pred             CEEEEEEEEcH
Confidence            99999999854

>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=98.95  E-value=1.5e-10  Score=105.56  Aligned_cols=129  Identities=17%  Similarity=0.112  Sum_probs=85.9

Q ss_pred             EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh-CCceeCCeEEEEEEchhhHHHHHhhhh-hhhhcccccccccccccc
Q 008117          158 WKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL-NKFNIDGQELMLKVDQATREYLERYVD-KKTENTKKLKETQDAGAG  235 (577)
Q Consensus       158 ~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~L-ng~~i~gr~i~V~~a~~~~~~~~~~~~-~k~~~~~~~~~~~~~~v~  235 (577)
                      +.+..+  ....+|+++|+|.+.++|.+|+..| ||..|+| .|.|.++............ ..............+||+
T Consensus         3 ~al~l~--g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~   79 (150)
T 2i2y_A            3 YKLILN--GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVG   79 (150)
T ss_dssp             EEEEEC--CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEE
T ss_pred             eEeeec--cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEe
Confidence            344443  4567899999999999999999999 9999999 9999876542111000000 000011122233446999


Q ss_pred             CCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          236 KEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       236 nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ||+..+++.+|.+++..++.+......    ..++|||||+|.+.++|..|+..|++.
T Consensus        80 nl~~~~t~~~l~~~F~~~G~i~~v~i~----~~~~g~afV~f~~~~~a~~A~~~l~g~  133 (150)
T 2i2y_A           80 NLGNNGNKTELERAFGYYGPLRSVWVA----RNPPGFAFVEFEDPRDAADAVRELDGR  133 (150)
T ss_dssp             SCCSCCSCHHHHHHHHHHSCEEEEEEC----SSSCSEEEEEESSHHHHHHHHHHHSSS
T ss_pred             CCCCCCCHHHHHHHHHhhCCEEEEEEe----eCCCcEEEEEECCHHHHHHHHHHcCCC
Confidence            999999999999884411111111010    016899999999999999999988874

>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=2.7e-09  Score=87.44  Aligned_cols=73  Identities=15%  Similarity=0.122  Sum_probs=62.3

Q ss_pred             CCCceEEEcCCC----CCCCH----HHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 008117          126 KPQTKVYVGKIA----PTADS----DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG  197 (577)
Q Consensus       126 ~~~~tlfVgnLp----~~~te----~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~g  197 (577)
                      ++..||+|.-++    .++-+    .+|...|..||.|..++|+.+        .+||+|.+.++|.+||. |||..|+|
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d--------~~fVtF~d~~sAlaAi~-mnG~~v~G   75 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED--------KMWVTFLEGSSALNVLS-LNGKELLN   75 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS--------SEEEEESSHHHHHHGGG-GTTCEETT
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC--------CEEEEECChHHHHHHHh-cCCeEeCC
Confidence            356788888776    23434    579999999999999999887        38999999999999999 99999999


Q ss_pred             eEEEEEEchh
Q 008117          198 QELMLKVDQA  207 (577)
Q Consensus       198 r~i~V~~a~~  207 (577)
                      +.|+|+++..
T Consensus        76 r~LkV~lkt~   85 (91)
T 2dnr_A           76 RTITIALKSP   85 (91)
T ss_dssp             EEEEEEECCC
T ss_pred             eEEEEEeCCC
Confidence            9999987654

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.87  E-value=8.9e-09  Score=89.72  Aligned_cols=87  Identities=15%  Similarity=0.136  Sum_probs=73.8

Q ss_pred             CCCCceEEEcCCCCC-CCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCC-HHHHHHHHHHhC--CceeCCeEE
Q 008117          125 EKPQTKVYVGKIAPT-ADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFES-AEGVLRALRLLN--KFNIDGQEL  200 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~-~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~-~~~A~~Al~~Ln--g~~i~gr~i  200 (577)
                      ..+++.|||+||++. ++.++|+.+|+.||.|.+|.++.+.      .+|||.|.+ ..+|..|+..||  |..|.|..+
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~------~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA------KEGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC------SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC------CEEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            456899999999999 9999999999999999999998874      369999999 899999999994  889999888


Q ss_pred             EEEEch--hhHHHHHhhhh
Q 008117          201 MLKVDQ--ATREYLERYVD  217 (577)
Q Consensus       201 ~V~~a~--~~~~~~~~~~~  217 (577)
                      .+.+..  .-+.|+.....
T Consensus        89 ~~evL~GeeE~~yw~Ki~e  107 (121)
T 1owx_A           89 TWEVLEGEVEKEALKKIIE  107 (121)
T ss_dssp             EEEECCHHHHHHHHHHHHH
T ss_pred             EEEECCCHHHHHHHHHHHH
Confidence            887654  34556665554

>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=98.71  E-value=2.2e-08  Score=82.43  Aligned_cols=70  Identities=17%  Similarity=0.243  Sum_probs=60.7

Q ss_pred             CCCceEEEcCCCCC-----C-CH---HHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 008117          126 KPQTKVYVGKIAPT-----A-DS---DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  196 (577)
Q Consensus       126 ~~~~tlfVgnLp~~-----~-te---~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~  196 (577)
                      ++..||+|.-++..     + .+   .+|.+.|..||.|..++|+.+.        +||+|.+.++|.+||. |||+.|+
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~   83 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVK   83 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEET
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeeeC
Confidence            45789999988743     3 32   4689999999999999999882        9999999999999999 9999999


Q ss_pred             CeEEEEEE
Q 008117          197 GQELMLKV  204 (577)
Q Consensus       197 gr~i~V~~  204 (577)
                      |+.|+|++
T Consensus        84 Gr~L~V~~   91 (95)
T 1ufw_A           84 GRAVKISG   91 (95)
T ss_dssp             TEEEEEEC
T ss_pred             CeEEEEec
Confidence            99999975

>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=98.53  E-value=1.6e-07  Score=91.12  Aligned_cols=69  Identities=19%  Similarity=0.072  Sum_probs=61.2

Q ss_pred             CCCHHHHHHHHhhcCceEEEEEeecC----CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          139 TADSDFVLSVLKVCGTVKSWKRAQYP----SNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       139 ~~te~~L~~~F~~~G~v~~~~i~~~~----~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      .-.+++|...|++||.|.++.|+.+.    .+|.++||+||+|.+.++|.+|+..|||..|+|+.|.|.+...
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            34557999999999999999998554    4558999999999999999999999999999999999998754

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=98.30  E-value=4.3e-07  Score=75.96  Aligned_cols=65  Identities=8%  Similarity=0.032  Sum_probs=50.0

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcc--cccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPEN--LKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~--~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+.+||+||+..+++++|.+++..++.  ..+.. ..+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~   76 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSL   76 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSS
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCC
Confidence            344799999999999999998552221  11111 123678999999999999999999999999874

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=98.24  E-value=3.5e-07  Score=75.75  Aligned_cols=62  Identities=11%  Similarity=0.021  Sum_probs=46.9

Q ss_pred             ccccccCCCcccchhhhcCCCCCCc-ccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPE-NLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLT  291 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~-~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~  291 (577)
                      +++||+|||..+++++|.+++...+ ....... .+..+|.++|||||+|.+.++|..|++.++
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~   65 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQ   65 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcC
Confidence            4579999999999999998844111 1111111 236789999999999999999999998764

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=98.24  E-value=1.8e-07  Score=83.63  Aligned_cols=107  Identities=6%  Similarity=0.017  Sum_probs=50.0

Q ss_pred             eEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCC
Q 008117          171 GFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPT  250 (577)
Q Consensus       171 g~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~  250 (577)
                      .|.|+.|.+...+..|+..++|....|+.- +.++..               .........+||+||+..+++.+|.+++
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~~~~---------------~~~~~~~~~l~V~nLp~~~te~~L~~~F   68 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSYGRP---------------PPDVEGMTSLKVDNLTYRTSPDTLRRVF   68 (135)
T ss_dssp             -------------------------------CCSCCS---------------CSSGGGCCCEEEECCCSSCHHHHHHHHH
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCCC-CCcCCC---------------CCCCCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            478899999999999999998877666431 111111               0112223346999999999999999884


Q ss_pred             CCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          251 KSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       251 ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..++.+.... ..+..+|.++|||||+|.+.++|..|+..|++.
T Consensus        69 ~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~  112 (135)
T 2lea_A           69 EKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGA  112 (135)
T ss_dssp             GGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTC
T ss_pred             HhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCC
Confidence            4222111111 122467899999999999999999999888764

>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=98.14  E-value=2.6e-07  Score=76.16  Aligned_cols=62  Identities=11%  Similarity=0.102  Sum_probs=46.6

Q ss_pred             ccccCCCcccchhhhcCCCCCCc--ccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPE--NLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~--~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++..++  ....... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         4 l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~   68 (90)
T 3p5t_L            4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKR   68 (90)
T ss_dssp             CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGS
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCC
Confidence            59999999999999988843222  1111111 23568999999999999999999999999984

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.13  E-value=1.4e-05  Score=66.98  Aligned_cols=74  Identities=9%  Similarity=0.056  Sum_probs=67.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhc-----CceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVC-----GTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL  200 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~-----G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i  200 (577)
                      ...++|-+-|||..+++..|+.|+..|     |.|+.+.++.+-      +-|+|+|.+...|.+|.-.|+|..|.|+.|
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~L   92 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVI   92 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEE
Confidence            347899999999999999999999999     999999998874      579999999999999998899999999999


Q ss_pred             EEEEc
Q 008117          201 MLKVD  205 (577)
Q Consensus       201 ~V~~a  205 (577)
                      +|...
T Consensus        93 r~gTv   97 (117)
T 2l9w_A           93 RSGTI   97 (117)
T ss_dssp             EEECH
T ss_pred             EecCH
Confidence            99643

>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=98.12  E-value=5.8e-07  Score=75.69  Aligned_cols=62  Identities=13%  Similarity=0.113  Sum_probs=47.4

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++..++...... ..+..+|.++|||||+|.+.++|.+|+..|++.
T Consensus        22 lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~   84 (99)
T 4fxv_A           22 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGL   84 (99)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCC
Confidence            59999999999999998843222111111 123678999999999999999999999998864

>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=98.11  E-value=6.4e-07  Score=82.67  Aligned_cols=119  Identities=18%  Similarity=0.079  Sum_probs=50.1

Q ss_pred             EEeCCHHHHHHHHHHhCCceeC--CeEEEEEEchhhH-HHHHhhh---hh-hhhccccccccccccccCCCcccchhhhc
Q 008117          175 CEFESAEGVLRALRLLNKFNID--GQELMLKVDQATR-EYLERYV---DK-KTENTKKLKETQDAGAGKEDESVQSVEKN  247 (577)
Q Consensus       175 V~f~~~~~A~~Al~~Lng~~i~--gr~i~V~~a~~~~-~~~~~~~---~~-k~~~~~~~~~~~~~~v~nl~~~~~~~~l~  247 (577)
                      .+|.+.++|..|+..|++....  |+.+.+.++.... ..+..+.   .. .............+||+||+..+++.+|.
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            7899999999999999987775  6666665532211 0111110   00 01111122334457999999999999999


Q ss_pred             CCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          248 EPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       248 e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .++..++.+..... .+..+|.++|||||+|.+.++|..||..|++.
T Consensus        91 ~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~  137 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGA  137 (165)
T ss_dssp             HHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             HHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCC
Confidence            88442221111111 22568899999999999999999999998874

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.07  E-value=5.3e-06  Score=67.21  Aligned_cols=64  Identities=11%  Similarity=0.084  Sum_probs=49.3

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++..++...... ..+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         6 ~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   70 (85)
T 1x4e_A            6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKAS   70 (85)
T ss_dssp             CEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHH
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCC
Confidence            3469999999999999999955332211111 123567999999999999999999999988875

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=98.07  E-value=1.4e-06  Score=74.83  Aligned_cols=64  Identities=8%  Similarity=0.123  Sum_probs=48.8

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++++|.+++..++.+..... .+..+|+++|||||+|.+.++|..|+..||+.
T Consensus         7 ~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~   71 (110)
T 3s8s_A            7 KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLT   71 (110)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             cEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCC
Confidence            34699999999999999998442221111111 23567999999999999999999999999875

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=97.94  E-value=1.9e-06  Score=72.54  Aligned_cols=65  Identities=8%  Similarity=-0.012  Sum_probs=47.9

Q ss_pred             cccccccCCCc------ccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDE------SVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~------~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+.+||+|||.      .+++.+|.+++..++...... ..+..+|+++|||||+|.+.++|..|+..|++.
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~   77 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK   77 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCc
Confidence            34569999999      999999988833222111111 122567999999999999999999999988864

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.91  E-value=6.5e-06  Score=70.56  Aligned_cols=60  Identities=12%  Similarity=-0.085  Sum_probs=45.0

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      .+||+||+..+++++|.+++..+.+ .......+..|+++|||||+|.+.++|.+|| .+++
T Consensus        18 ~v~V~nLp~~~te~dl~~~F~~~~v-~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~   77 (109)
T 2dnn_A           18 YVSVHGMPFSAMENDVRDFFHGLRV-DAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNR   77 (109)
T ss_dssp             EEEEECCCSSCCHHHHHHHTTTSCC-CEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTT
T ss_pred             EEEEeCCCCCCCHHHHHHHhccCCe-eEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCC
Confidence            3699999999999999998653322 1111122345999999999999999999999 4543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.90  E-value=6.9e-06  Score=68.95  Aligned_cols=63  Identities=13%  Similarity=0.085  Sum_probs=49.1

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|.+++..+......  .+..++.++|||||+|.+.++|..||..|++.
T Consensus        15 ~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~--~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~   77 (102)
T 2fc8_A           15 SKTLFVKGLSEDTTEETLKESFDGSVRARIV--TDRETGSSKGFGFVDFNSEEDAKAAKEAMEDG   77 (102)
T ss_dssp             CSSEEEECCCTTCCHHHHHHTSTTCSEEEEE--ECSSSCSEEEEEEEECSSHHHHHHHHHHHTTC
T ss_pred             CCEEEEeCCCCccCHHHHHHHhcCCeEEEEE--ecCCCCCcCcEEEEEECCHHHHHHHHHHhCCC
Confidence            3446999999999999999995522222111  12567899999999999999999999998874

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.89  E-value=7.7e-06  Score=70.44  Aligned_cols=63  Identities=11%  Similarity=0.054  Sum_probs=46.6

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCC---CCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKES---HDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~---g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++++|.+++..++........+..+   |.++|||||+|.+.++|..||..|+++
T Consensus        10 ~lfVgnLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~~   75 (114)
T 2dnl_A           10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEE   75 (114)
T ss_dssp             CEEEECCCTTCCHHHHHHHTTTTCCCCEECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEEE
T ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCEEEEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhhc
Confidence            359999999999999998855222111111112333   899999999999999999999988554

>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=97.89  E-value=2.7e-06  Score=76.27  Aligned_cols=106  Identities=8%  Similarity=-0.033  Sum_probs=46.1

Q ss_pred             eEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCC
Q 008117          171 GFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPT  250 (577)
Q Consensus       171 g~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~  250 (577)
                      ++||..|..+..+..++..+... .+|...--......      +       .........+||+||+..+++++|.+++
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~g~~~------~-------~~~~~~~~~lfV~nLp~~~te~dL~~~F   67 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGSGDSE------F-------TVQSTTGHCVHMRGLPYKATENDIYNFF   67 (139)
T ss_dssp             ---------------------------------------------------------CCCCEECCSCCTTCCHHHHHHHH
T ss_pred             CcccccccCccccchhcccchhc-cCCCCCCCCCCCcc------c-------CCCCCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            67888888887777776654322 23322211100000      0       0011222346999999999999999995


Q ss_pred             CCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          251 KSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       251 ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      ..+++. ......+.+|+++|||||+|.+.++|.+|| .+++
T Consensus        68 ~~~Gi~-~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g  107 (139)
T 2hgn_A           68 SPLNPV-RVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDR  107 (139)
T ss_dssp             CSCCCS-EEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCS
T ss_pred             HhcCCe-EEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCC
Confidence            533322 222222345999999999999999999998 4543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.85  E-value=1.2e-05  Score=67.53  Aligned_cols=65  Identities=14%  Similarity=0.078  Sum_probs=48.7

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|.+++..++....... .+..++.++|||||+|.+.++|..|+..|++.
T Consensus        12 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~   77 (102)
T 2cqb_A           12 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES   77 (102)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCC
Confidence            344699999999999999988442221111111 23567899999999999999999999998864

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.84  E-value=1.1e-05  Score=69.17  Aligned_cols=64  Identities=19%  Similarity=0.065  Sum_probs=48.7

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccc--------cCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLK--------DNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k--------~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++..++...        .... .+..+|.++|||||+|.+.++|..||..|++.
T Consensus        16 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   88 (113)
T 2cpe_A           16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   88 (113)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCC
Confidence            3469999999999999998844222111        1111 23478999999999999999999999998875

>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=97.84  E-value=4.8e-06  Score=70.37  Aligned_cols=65  Identities=8%  Similarity=-0.021  Sum_probs=48.3

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|.+++..++.+.......+.+|.++|||||+|.+.++|..|+..|++.
T Consensus        15 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   79 (105)
T 2dnh_A           15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGS   79 (105)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCC
Confidence            34469999999999999998844222111111111346899999999999999999999988875

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.84  E-value=7.6e-06  Score=67.84  Aligned_cols=63  Identities=8%  Similarity=0.100  Sum_probs=47.6

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccC-CC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDN-ET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~-~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|..++..++..... .. .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         7 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~   71 (96)
T 1x5t_A            7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQ   71 (96)
T ss_dssp             EEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCC
Confidence            46999999999999999884322211111 11 22478999999999999999999999988764

>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=97.84  E-value=9.7e-06  Score=68.97  Aligned_cols=62  Identities=11%  Similarity=-0.168  Sum_probs=46.3

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcc---cccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPEN---LKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~---~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      ..+||+||+..+++.+|.+++..++.   ........+..|.++|||||+|.+.++|..||. +++
T Consensus        12 ~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~   76 (107)
T 2lmi_A           12 FLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHR   76 (107)
T ss_dssp             CEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTT
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCc
Confidence            34699999999999999998653222   222222223349999999999999999999988 554

>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=97.84  E-value=7e-06  Score=68.23  Aligned_cols=63  Identities=6%  Similarity=0.005  Sum_probs=47.3

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|.+++..++....... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         4 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   67 (96)
T 2x1f_A            4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGY   67 (96)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence            3599999999999999888432221111111 22467899999999999999999999998874

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.84  E-value=4e-06  Score=71.09  Aligned_cols=60  Identities=5%  Similarity=-0.122  Sum_probs=43.2

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLT  291 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~  291 (577)
                      .+||+||+..+++++|.+++..++.+.......+..|.++|||||+|.+.++|..|+. ++
T Consensus        13 ~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~   72 (103)
T 1s79_A           13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TP   72 (103)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SS
T ss_pred             EEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cC
Confidence            3699999999999999988432221111111112338999999999999999999987 44

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.84  E-value=1e-05  Score=68.16  Aligned_cols=65  Identities=9%  Similarity=0.127  Sum_probs=49.5

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|.+++..++.+..... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~   80 (103)
T 2cq0_A           15 NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGF   80 (103)
T ss_dssp             SEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCC
Confidence            344699999999999999999553221111111 22467899999999999999999999998874

>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=97.83  E-value=6e-06  Score=71.45  Aligned_cols=63  Identities=8%  Similarity=0.025  Sum_probs=47.1

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++++|.+++..++.+.......+.+|.++|||||+|.+.++|..|+..|++.
T Consensus         9 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~   71 (116)
T 2fy1_A            9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGK   71 (116)
T ss_dssp             EEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCC
Confidence            359999999999999998843222111111112338999999999999999999999988764

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.83  E-value=9.1e-06  Score=68.39  Aligned_cols=62  Identities=8%  Similarity=0.097  Sum_probs=48.0

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|.+++..++.+.......+ +|.++|||||+|.+.++|..|+..|++.
T Consensus        17 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~   78 (103)
T 2d9p_A           17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGR   78 (103)
T ss_dssp             CEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCC
Confidence            3699999999999999998553332221112113 7899999999999999999999998874

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=97.83  E-value=3.5e-06  Score=67.75  Aligned_cols=61  Identities=3%  Similarity=-0.081  Sum_probs=44.3

Q ss_pred             ccccCCCccc------chhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESV------QSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~------~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+      ++.+|.+++..++......-. ..+|.++|||||+|.+.++|..|+..|++.
T Consensus         4 l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~   70 (81)
T 2krb_A            4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGY   70 (81)
T ss_dssp             EEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSC
T ss_pred             EEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCc
Confidence            5999999988      568887773322211111111 467899999999999999999999887764

>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=97.82  E-value=1e-05  Score=67.87  Aligned_cols=61  Identities=18%  Similarity=0.070  Sum_probs=47.4

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCC-CC-CCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETG-NK-ESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~-~~-~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++++|.+++..++ .....-. +. .+|+++|||||+|.+.++|..|+ .+++.
T Consensus        21 ~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~   83 (100)
T 2j76_E           21 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEE   83 (100)
T ss_dssp             EEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCC
Confidence            359999999999999999866444 2222221 22 58999999999999999999999 77764

>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=97.82  E-value=9.1e-06  Score=67.81  Aligned_cols=64  Identities=9%  Similarity=-0.033  Sum_probs=47.9

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++..++....... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         9 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   73 (99)
T 1whw_A            9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQ   73 (99)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCC
Confidence            34699999999999999988432221111111 22458899999999999999999999998874

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.82  E-value=1.2e-05  Score=66.40  Aligned_cols=63  Identities=13%  Similarity=0.145  Sum_probs=47.6

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|.+++..++...... ..+..++.++|||||+|.+.++|..|+..|++.
T Consensus         7 ~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   70 (95)
T 2dnz_A            7 GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGF   70 (95)
T ss_dssp             EEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCC
Confidence            359999999999999998844222111111 123567899999999999999999999998874

>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=97.81  E-value=8.1e-06  Score=69.06  Aligned_cols=60  Identities=12%  Similarity=-0.097  Sum_probs=46.2

Q ss_pred             ccccccCCCcccchhhhcCCCCCCccccc-CCCCCCCCCCCCceEEEEeCCHHHHHHHHHH
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKD-NETGNKESHDPTNFGVVTEEDRKADQEALEK  289 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~-~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~  289 (577)
                      ..+||+||+..+++.+|.+++..++.... .....+.+|+++|||||+|.+.++|..||..
T Consensus        16 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~   76 (104)
T 1wg5_A           16 GFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK   76 (104)
T ss_dssp             CEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh
Confidence            34699999999999999999663332221 1122246899999999999999999999886

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=97.81  E-value=6.8e-06  Score=72.65  Aligned_cols=62  Identities=6%  Similarity=-0.022  Sum_probs=47.9

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcc-----cccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPEN-----LKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~-----~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+.+||+||+..+++++|.+++..++.     ++..  .+..+|.++|||||+|.+. +|.+|+..|++.
T Consensus        23 ~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~--~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~   89 (131)
T 2m2b_A           23 NDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVI--KDKQTQLNRGFAFIQLSTI-EAAQLLQILQAL   89 (131)
T ss_dssp             CCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECC--BCSSSSSBCSCEEEECCHH-HHHHHHHHHTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEE--EcCCCCCcceEEEEEECCH-HHHHHHHHhcCC
Confidence            344699999999999999988442211     1111  2256899999999999999 999999999984

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.81  E-value=7e-06  Score=68.70  Aligned_cols=65  Identities=18%  Similarity=0.132  Sum_probs=48.2

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|.+++..++.........+.+|.++|||||+|.+.++|..|+..|++.
T Consensus        17 ~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~   81 (100)
T 2do4_A           17 KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGM   81 (100)
T ss_dssp             CSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCC
Confidence            33469999999999999998844222111111111337899999999999999999999998863

>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=97.80  E-value=1e-05  Score=66.91  Aligned_cols=63  Identities=16%  Similarity=-0.040  Sum_probs=48.1

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccc-cCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLK-DNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k-~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|.+++..++... .....+..+|.++|||||+|.+.++|.+|+..|++.
T Consensus        17 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~   80 (95)
T 2ek1_A           17 VIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDR   80 (95)
T ss_dssp             EEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCC
Confidence            369999999999999998855222111 111122567899999999999999999999988764

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=97.80  E-value=7.9e-06  Score=68.31  Aligned_cols=65  Identities=12%  Similarity=0.030  Sum_probs=48.7

Q ss_pred             cccccccCCCcccchhhhcCCCCCCccccc--------CCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKD--------NET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~--------~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++++|.+++..++....        ... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus        13 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~   86 (99)
T 2la6_A           13 NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   86 (99)
T ss_dssp             CSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            334699999999999999988442221111        111 22467999999999999999999999988874

>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=97.80  E-value=1.1e-05  Score=67.27  Aligned_cols=64  Identities=16%  Similarity=-0.030  Sum_probs=48.8

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccC-CCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDN-ETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~-~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++..++..... ...+..+|.++|||||+|.+.++|.+|+..|++.
T Consensus        16 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~   80 (98)
T 2cqp_A           16 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDR   80 (98)
T ss_dssp             EEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            336999999999999999885522221111 1123578899999999999999999999998864

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=97.80  E-value=2.9e-06  Score=73.33  Aligned_cols=61  Identities=18%  Similarity=0.207  Sum_probs=44.4

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++..++.+...... ...+.++|||||+|.+.++|..||..|++.
T Consensus         8 lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~-~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~   68 (115)
T 4f25_A            8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVV-CDENGSKGYGFVHFETQEAAERAIEKMNGM   68 (115)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEE-EETTEEEEEEEEEESCHHHHHHHHHHHTTC
T ss_pred             EEECCCCCCCCHHHHHHHHhccCCEEEEEEe-ecCCCCCceEEEEECCHHHHHHHHHHcCCC
Confidence            4999999999999999984422211111110 112447999999999999999999998875

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.79  E-value=1.6e-05  Score=66.56  Aligned_cols=62  Identities=10%  Similarity=0.034  Sum_probs=49.1

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|.+++..++.+..   ..+.+|.++|||||+|.+.++|..|+..|++.
T Consensus        15 ~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~---~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~   76 (101)
T 2fc9_A           15 SKTLVLSNLSYSATEETLQEVFEKATFIKV---PQNQNGKSKGYAFIEFASFEDAKEALNSCNKR   76 (101)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHCSSCSEEEC---CBCSSSCBCSEEEEECSSHHHHHHHHHHTSSE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCEEEE---EECCCCCEeeEEEEEECCHHHHHHHHHHhCCC
Confidence            344699999999999999998653332221   11367899999999999999999999988864

>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=97.79  E-value=1e-05  Score=69.67  Aligned_cols=60  Identities=5%  Similarity=-0.134  Sum_probs=45.9

Q ss_pred             ccccccCCCcccchhhhcCCCCCCccc-ccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHH
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENL-KDNETGNKESHDPTNFGVVTEEDRKADQEALEK  289 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~-k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~  289 (577)
                      ..+||+||+..+++.+|.+++..++.. .......+.+|.++|||||+|.+.++|..||..
T Consensus        16 ~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~   76 (114)
T 2cpy_A           16 VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL   76 (114)
T ss_dssp             CEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG
T ss_pred             cEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh
Confidence            346999999999999999986533322 222222234899999999999999999999876

>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=97.78  E-value=1.6e-05  Score=70.17  Aligned_cols=66  Identities=17%  Similarity=0.062  Sum_probs=49.5

Q ss_pred             ccccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          228 ETQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       228 ~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ....+||+||+..+++.+|.+++..++.+..... .+..+|.++|||||+|.+.++|..||..|++.
T Consensus        45 ~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~  111 (129)
T 2kxn_B           45 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGM  111 (129)
T ss_dssp             CSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence            3445799999999999999988442221111111 23567899999999999999999999998874

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.78  E-value=1.8e-05  Score=65.31  Aligned_cols=65  Identities=6%  Similarity=0.005  Sum_probs=48.8

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|.+++..++...... ..+..++.++|||||+|.+.++|..|+..|++.
T Consensus        16 ~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~   81 (94)
T 2e5h_A           16 KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNK   81 (94)
T ss_dssp             TTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCC
Confidence            33469999999999999998855222111111 123567899999999999999999999988763

>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=97.76  E-value=1.6e-05  Score=67.27  Aligned_cols=62  Identities=10%  Similarity=-0.029  Sum_probs=48.1

Q ss_pred             ccccccCCCcccchhhhcCCCC---CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTK---SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~k---s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++.   .+......  .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus        14 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~--~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~   78 (106)
T 2dgp_A           14 IKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVL--KDRFTGMHKGCAFLTYCERESALKAQSALHEQ   78 (106)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHHHSCCCEEECC--CCSSSCSCCSEEEEEESSHHHHHHHHHHHTTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEE--ecCCCCCcceEEEEEECCHHHHHHHHHHhcCC
Confidence            3469999999999999998844   22211111  22567999999999999999999999999874

>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=97.76  E-value=6.5e-06  Score=72.42  Aligned_cols=62  Identities=11%  Similarity=-0.125  Sum_probs=46.6

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccc-cCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLK-DNETGNKESHDPTNFGVVTEEDRKADQEALEKLT  291 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k-~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~  291 (577)
                      ..+||+||+..+++++|.+++..+.+.. ......+..|+++|||||+|.+.++|.+||...+
T Consensus        43 ~~lfVgnLp~~~te~dL~~~F~~~~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~~~  105 (126)
T 2hgm_A           43 GFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKHK  105 (126)
T ss_dssp             CEEEEECCCTTCCHHHHHHHTTTSCEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTTTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHHCC
Confidence            3469999999999999999966333321 1222223449999999999999999999988543

>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=97.75  E-value=1.2e-05  Score=69.03  Aligned_cols=64  Identities=9%  Similarity=0.013  Sum_probs=48.6

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhH
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMV  294 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i  294 (577)
                      .+||+||+..+++.+|..++..++.........+.+|.++|||||+|.+.++|..|+..|++..
T Consensus        27 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~   90 (114)
T 1x5o_A           27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKF   90 (114)
T ss_dssp             EEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCE
Confidence            3699999999999999998553322221111113378999999999999999999999888753

>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=97.75  E-value=9.3e-06  Score=65.27  Aligned_cols=62  Identities=11%  Similarity=0.133  Sum_probs=46.8

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++...+....... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         4 l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~   66 (83)
T 3md1_A            4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQ   66 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCC
Confidence            599999999999999988442221111111 12467899999999999999999999988865

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=97.75  E-value=4.3e-06  Score=76.48  Aligned_cols=62  Identities=11%  Similarity=0.051  Sum_probs=47.4

Q ss_pred             ccccCCCcccchhhhcCCCCCCc--ccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPE--NLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~--~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++..++  .+..... .+..+|.++|||||+|.+.++|..||..|++.
T Consensus        58 lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~  122 (156)
T 3n9u_C           58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGK  122 (156)
T ss_dssp             EEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCC
Confidence            49999999999999998844222  1111111 23578999999999999999999999998764

>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=97.75  E-value=6.7e-06  Score=69.47  Aligned_cols=61  Identities=5%  Similarity=-0.184  Sum_probs=45.9

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      ..+||+||+..+++++|.+++..++.. ......+.+|+++|||||+|.+.++|.+||. +++
T Consensus        16 ~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~   76 (102)
T 1wez_A           16 HCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDK   76 (102)
T ss_dssp             CEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCC
Confidence            346999999999999999996633322 1122123489999999999999999999985 443

>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=97.74  E-value=6.1e-06  Score=72.18  Aligned_cols=62  Identities=11%  Similarity=-0.116  Sum_probs=47.2

Q ss_pred             ccccccCCCcccchhhhcCCCCCCccccc-CCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKD-NETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~-~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      ..+||+||+..+++.+|.+++..++.+.. .......+|.++|||||+|.+.++|..||. +++
T Consensus        26 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g   88 (124)
T 1wel_A           26 FCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHK   88 (124)
T ss_dssp             CEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCS
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCC
Confidence            34699999999999999998653332211 111235689999999999999999999998 655

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.74  E-value=8.8e-06  Score=69.80  Aligned_cols=65  Identities=12%  Similarity=0.017  Sum_probs=48.2

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|.+++..++.+.......+.+|.++|||||+|.+.++|..|+..|++.
T Consensus        15 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~   79 (114)
T 2do0_A           15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQ   79 (114)
T ss_dssp             CSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            34469999999999999998844222111111111345889999999999999999999998874

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=97.74  E-value=8.3e-06  Score=68.72  Aligned_cols=64  Identities=14%  Similarity=0.012  Sum_probs=48.1

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|.+++..+++....-..+..+|.++|||||+|.+.++|..|+ .|++.
T Consensus        15 ~~~l~V~nLp~~~t~~~l~~~F~~~gi~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~   78 (103)
T 2dng_A           15 PYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGA   78 (103)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHTTTSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhCCceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCC
Confidence            33469999999999999999855333221111123567899999999999999999999 77763

>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=97.73  E-value=8.1e-06  Score=72.85  Aligned_cols=62  Identities=6%  Similarity=-0.208  Sum_probs=46.5

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcc---cccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPEN---LKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~---~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      ..+||+||+..+++++|.+++..++.   ........+..|+++|||||+|.+.++|.+||. +++
T Consensus        45 ~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g  109 (136)
T 2hgl_A           45 FVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDR  109 (136)
T ss_dssp             CEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCC
Confidence            33699999999999999998653332   222222223349999999999999999999998 665

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.73  E-value=1.6e-05  Score=66.42  Aligned_cols=63  Identities=19%  Similarity=0.195  Sum_probs=46.4

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++..++.+.... ..+..+|.++|||||+|.+.++|..|+. +++.
T Consensus        11 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~   74 (99)
T 2dgs_A           11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFH   74 (99)
T ss_dssp             CEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCC
Confidence            3469999999999999998844222111111 1225678999999999999999999998 6653

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=97.73  E-value=8.7e-06  Score=70.66  Aligned_cols=62  Identities=8%  Similarity=-0.172  Sum_probs=46.4

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcc---cccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPEN---LKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~---~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      ..+||+||+..+++++|.+++..++.   +.......+..|+++|||||+|.+.++|.+||. +++
T Consensus        18 ~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g   82 (118)
T 2db1_A           18 YVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDR   82 (118)
T ss_dssp             CEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTT
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCC
Confidence            33699999999999999998653322   222222223348999999999999999999998 654

>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=97.73  E-value=1.6e-05  Score=67.12  Aligned_cols=62  Identities=18%  Similarity=0.062  Sum_probs=47.4

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCC-CCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKES-HDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~-g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++..++ +..... .+..+ |.++|||||+|.+.++|.+|| .|++.
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~   79 (104)
T 1wi8_A           16 YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEE   79 (104)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCC
Confidence            3469999999999999999866433 222222 22444 899999999999999999999 77764

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.73  E-value=1.6e-05  Score=67.34  Aligned_cols=64  Identities=16%  Similarity=0.086  Sum_probs=47.3

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCC-CC-CCCCCCCceEEEEeCCHHHHHHHHHHH-hh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GN-KESHDPTNFGVVTEEDRKADQEALEKL-TC  292 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~-~~~g~~kgfgfV~f~~~e~a~~Al~~l-~~  292 (577)
                      ...+||+||+..+++.+|.+++..++.+..... .+ ..+|.++|||||+|.+.++|..|+..| ++
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~   81 (107)
T 2cph_A           15 TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHS   81 (107)
T ss_dssp             CCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccC
Confidence            344699999999999999988442221111111 12 347899999999999999999999998 54

>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=97.72  E-value=7e-06  Score=69.58  Aligned_cols=65  Identities=14%  Similarity=0.031  Sum_probs=48.2

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|.+++..++.+.......+.+|.++|||||+|.+.++|..|+..|++.
T Consensus        29 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~   93 (107)
T 3ulh_A           29 GGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGV   93 (107)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCC
Confidence            34469999999999999988844222111111111338899999999999999999999998874

>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=97.71  E-value=1e-05  Score=65.38  Aligned_cols=64  Identities=14%  Similarity=0.079  Sum_probs=47.6

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++..++....... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         8 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   72 (85)
T 3mdf_A            8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES   72 (85)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCC
Confidence            34699999999999999988442221111111 12467889999999999999999999988864

>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=97.71  E-value=1.3e-05  Score=68.40  Aligned_cols=65  Identities=17%  Similarity=0.028  Sum_probs=48.6

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|..++..++....... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus        26 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~   91 (110)
T 1oo0_B           26 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGA   91 (110)
T ss_dssp             BEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCC
Confidence            344699999999999999988442221111111 22467899999999999999999999998874

>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=97.71  E-value=1.1e-05  Score=68.04  Aligned_cols=64  Identities=13%  Similarity=0.096  Sum_probs=47.8

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++..++.+..... .+..++.++|||||+|.+.++|..|+..|++.
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   80 (105)
T 1x5u_A           16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMI   80 (105)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCC
Confidence            34699999999999999888442221111111 22457899999999999999999999988763

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.71  E-value=1.5e-05  Score=67.00  Aligned_cols=65  Identities=12%  Similarity=0.075  Sum_probs=48.6

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|.+++..++.+.... ..+..+|.++|||||+|.+.++|..|+..|++.
T Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~   78 (103)
T 2dnm_A           13 MITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGA   78 (103)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCC
Confidence            34469999999999999998844222111111 123567899999999999999999999998874

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=97.71  E-value=7e-06  Score=69.60  Aligned_cols=64  Identities=3%  Similarity=-0.091  Sum_probs=46.6

Q ss_pred             cccccccCCCccc------chhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESV------QSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~------~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+.+||+||+..+      ++.+|..++..++........ ..+|.++|||||+|.+.++|..|+..|++.
T Consensus        15 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~   84 (105)
T 2nlw_A           15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGY   84 (105)
T ss_dssp             CSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSE
T ss_pred             CCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCc
Confidence            3446999999998      667788774422211111111 467899999999999999999999988764

>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=97.71  E-value=1.5e-05  Score=68.00  Aligned_cols=63  Identities=10%  Similarity=-0.011  Sum_probs=47.3

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLT  291 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~  291 (577)
                      ...+||+||+..+++.+|.+++..++.+..... .+..+|.++|||||+|.+.++|..|+..++
T Consensus        15 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~   78 (111)
T 1x4h_A           15 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAAS   78 (111)
T ss_dssp             CCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhc
Confidence            344699999999999999988432221111111 225678999999999999999999999987

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.69  E-value=7.6e-06  Score=68.97  Aligned_cols=64  Identities=13%  Similarity=0.020  Sum_probs=47.7

Q ss_pred             ccccccCCCcccchhhhcCCCCC-CcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKS-PENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks-~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++.. ++.........+.+|.++|||||+|.+.++|..|+..|++.
T Consensus        10 ~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~   74 (104)
T 2dhg_A           10 YSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGA   74 (104)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCC
Confidence            34699999999999999887432 33221111111338899999999999999999999998874

>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=97.69  E-value=9.8e-06  Score=65.77  Aligned_cols=62  Identities=8%  Similarity=0.131  Sum_probs=46.7

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++..++....... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         9 l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~   71 (87)
T 3bs9_A            9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQ   71 (87)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCC
Confidence            599999999999999988442221111111 12467899999999999999999999998863

>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=97.69  E-value=1.2e-05  Score=69.25  Aligned_cols=64  Identities=11%  Similarity=0.075  Sum_probs=47.8

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++++|.+++..++.+..... .+..++.++|||||+|.+.++|..|+..|++.
T Consensus        26 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~   90 (115)
T 2cpz_A           26 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGF   90 (115)
T ss_dssp             CCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCC
Confidence            34699999999999999988442211111111 12457899999999999999999999998874

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=97.69  E-value=4.8e-06  Score=69.90  Aligned_cols=62  Identities=19%  Similarity=0.132  Sum_probs=45.9

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|.+++..++........+..+|.++|||||+|.+.++|..|+. |++.
T Consensus        19 ~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~   80 (101)
T 1fj7_A           19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGL   80 (101)
T ss_dssp             EEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCc
Confidence            3699999999999999988441111100111225678999999999999999999998 8764

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.69  E-value=2.1e-05  Score=65.89  Aligned_cols=62  Identities=13%  Similarity=0.105  Sum_probs=47.8

Q ss_pred             ccccccCCCcccchhhhcCCCC---CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTK---SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~k---s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++.   .+......  .+..++.++|||||+|.+.++|..|+..|++.
T Consensus        13 ~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~--~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~   77 (102)
T 1x5s_A           13 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVV--KDRETQRSRGFGFVTFENIDDAKDAMMAMNGK   77 (102)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHHHSCCCEEEEC--CCSSSCSCCSEEEEECSSHHHHHHHHHHHTTC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEE--eCCCCCCcccEEEEEECCHHHHHHHHHHhCCC
Confidence            3469999999999999988844   22211111  22567889999999999999999999998875

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.68  E-value=1.3e-05  Score=66.29  Aligned_cols=66  Identities=17%  Similarity=0.065  Sum_probs=48.4

Q ss_pred             ccccccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          228 ETQDAGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       228 ~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ....+||+||+..+++.+|.+++..++...... ..+..++.++|||||+|.+.++|..|+..|++.
T Consensus        14 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~   80 (95)
T 2cqc_A           14 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGM   80 (95)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCC
Confidence            344569999999999999988843222111111 122566889999999999999999999998763

>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=97.67  E-value=3.5e-05  Score=66.20  Aligned_cols=60  Identities=7%  Similarity=-0.063  Sum_probs=45.2

Q ss_pred             ccccccccCCCcc-cchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          228 ETQDAGAGKEDES-VQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       228 ~~~~~~v~nl~~~-~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      ....+||+||+.. +++.+|.+++..++.+....     ..+++|||||+|.+.++|..|+..|++
T Consensus        24 p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~-----i~~~kg~aFVef~~~~~A~~Ai~~l~~   84 (112)
T 1x4f_A           24 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYI-----LMRMKSQAFIEMETREDAMAMVDHCLK   84 (112)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEE-----EETTTTEEEEECSSHHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEE-----EecCCCEEEEEECCHHHHHHHHHHhcc
Confidence            3445799999998 99999999955333222111     124689999999999999999998865

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=97.67  E-value=1.9e-05  Score=68.93  Aligned_cols=64  Identities=16%  Similarity=0.057  Sum_probs=47.9

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++..++.+.......+.+|.++|||||+|.+.++|..|+..|++.
T Consensus        36 ~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   99 (124)
T 2kt5_A           36 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGV   99 (124)
T ss_dssp             EEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCC
Confidence            3469999999999999988844222111111111338899999999999999999999998875

>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=97.66  E-value=2.2e-05  Score=68.55  Aligned_cols=65  Identities=14%  Similarity=0.038  Sum_probs=48.5

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|.+++..++.+..... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus        22 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   87 (126)
T 3ex7_B           22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQ   87 (126)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence            344699999999999999988432221111111 22458899999999999999999999988874

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.65  E-value=1.3e-05  Score=63.35  Aligned_cols=60  Identities=15%  Similarity=0.045  Sum_probs=44.9

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLT  291 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~  291 (577)
                      +||+||+..+++.+|..++...+......- .+..+|.++|||||.|.+.++|..|+..++
T Consensus         3 l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~   63 (77)
T 1uaw_A            3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR   63 (77)
T ss_dssp             EEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC
Confidence            499999999999999888432221111111 224678999999999999999999998776

>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=97.65  E-value=2.9e-05  Score=66.45  Aligned_cols=64  Identities=13%  Similarity=-0.029  Sum_probs=46.0

Q ss_pred             ccccccCCCcccchhhhc---CCCCCCc---ccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKN---EPTKSPE---NLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~---e~~ks~~---~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +.+||+||+..+++++|.   +++..++   ......+ ....++.++|||||+|.+.++|..|+..|++.
T Consensus        16 ~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~   86 (111)
T 2cpi_A           16 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNV   86 (111)
T ss_dssp             SCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCC
Confidence            346999999999999998   7744222   1111111 11224567799999999999999999998875

>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=97.65  E-value=1.9e-05  Score=67.24  Aligned_cols=63  Identities=13%  Similarity=0.123  Sum_probs=46.7

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++++|.+++..++.+.....  ..++.++|||||+|.+.++|..|+..|++.
T Consensus        22 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i--~~~~~~~g~afV~f~~~~~A~~A~~~l~g~   84 (109)
T 1x4a_A           22 DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL--KNRRGGPPFAFVEFEDPRDAEDAVYGRDGY   84 (109)
T ss_dssp             SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEE--CCSSSSSCCEEEEESCHHHHHHHHHHHTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEE--EECCCCCcEEEEEECCHHHHHHHHHHcCCC
Confidence            344699999999999999988442221111111  234568999999999999999999998874

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=97.65  E-value=2.2e-05  Score=61.80  Aligned_cols=57  Identities=16%  Similarity=0.090  Sum_probs=41.9

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHH
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALE  288 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~  288 (577)
                      +||+||+..+++++|.+++...+....... .+..+|.++|||||+|.+.++|..|+.
T Consensus         2 l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~   59 (75)
T 2mss_A            2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE   59 (75)
T ss_dssp             EEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS
T ss_pred             EEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH
Confidence            489999999999999888332221111111 224578999999999999999999876

>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=97.64  E-value=1.4e-05  Score=68.53  Aligned_cols=62  Identities=10%  Similarity=0.048  Sum_probs=46.9

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|.+++..++.+..... .+..+|.++|||||+|.+.++|..|| .|++.
T Consensus        27 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~   89 (114)
T 2cq4_A           27 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQ   89 (114)
T ss_dssp             EEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTE
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCC
Confidence            4699999999999999988442221111111 23566899999999999999999999 88764

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=97.64  E-value=1.2e-05  Score=67.93  Aligned_cols=64  Identities=14%  Similarity=0.045  Sum_probs=47.8

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++..++....... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus        24 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   88 (106)
T 1p27_B           24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQ   88 (106)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCC
Confidence            34699999999999999988442221111111 22567899999999999999999999998874

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=97.64  E-value=1.6e-05  Score=68.69  Aligned_cols=62  Identities=11%  Similarity=0.076  Sum_probs=47.5

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++..++....... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus        43 l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~  105 (118)
T 2khc_A           43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGF  105 (118)
T ss_dssp             EEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCC
Confidence            489999999999999988553332111111 23567899999999999999999999988764

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=97.63  E-value=9.3e-06  Score=66.33  Aligned_cols=57  Identities=7%  Similarity=-0.078  Sum_probs=43.2

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++..++......     ...++|||||+|.+.++|.+|+..||+.
T Consensus        10 L~VgNL~~~~te~~L~~lF~q~G~V~~~~-----l~~~kGfaFVey~~~~eA~~Ai~~Ln~~   66 (89)
T 2wbr_A           10 LLLKNLTAQIDGPTLRTLCMQHGPLVSFH-----PYLNQGIALCKYTTREEANKAQMALNNC   66 (89)
T ss_dssp             EEEECCCTTCCCHHHHHHHHHHSCEEEEE-----EETTTTEEEEEESSHHHHHHHHHHHTTE
T ss_pred             EEEeCCCccCCHHHHHHHHHhhCCEEEEE-----EcCCCcEEEEEECCHHHHHHHHHHhcCC
Confidence            58999999999999999944111111111     1237999999999999999999999873

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.62  E-value=1e-05  Score=67.52  Aligned_cols=62  Identities=13%  Similarity=0.076  Sum_probs=47.6

Q ss_pred             ccccccCCCcccchhhhcCCCC---CCc-ccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTK---SPE-NLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~k---s~~-~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++.   .+. ..+..  .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus        10 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~--~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~   75 (99)
T 2div_A           10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKII--RNRLTGIPAGYCFVEFADLATAEKCLHKINGK   75 (99)
T ss_dssp             SEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEE--ECSSSCCEEEEEEEECSCHHHHHHHHHTTTTS
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEe--ecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCC
Confidence            3469999999999999988843   222 11111  22568899999999999999999999988864

>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=97.62  E-value=9.8e-06  Score=67.02  Aligned_cols=64  Identities=16%  Similarity=0.128  Sum_probs=46.8

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++..++.........+.+|.++|||||+|.+.++|..|+..|++.
T Consensus        17 ~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~   80 (95)
T 2ywk_A           17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGI   80 (95)
T ss_dssp             GEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCC
Confidence            3469999999999999998844222111111111334889999999999999999999988764

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.62  E-value=1.2e-05  Score=65.98  Aligned_cols=61  Identities=10%  Similarity=-0.033  Sum_probs=46.1

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|.+++..+.+. ......+.+|.++|||||+|.+.++|..|+. +++.
T Consensus        12 ~l~v~nLp~~~t~~~l~~~F~~~~i~-~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~   72 (91)
T 2dgw_A           12 TVKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNRE   72 (91)
T ss_dssp             EEEEECCCSSCCHHHHHHHHTTSCCS-EEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSE
T ss_pred             EEEEECCCCCCCHHHHHHHHhhCCce-EEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCc
Confidence            36999999999999999884422211 1111113678999999999999999999999 7764

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=97.62  E-value=1.1e-05  Score=66.92  Aligned_cols=60  Identities=8%  Similarity=0.024  Sum_probs=47.9

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|..++..++.+...    ..+|.++|||||+|.+.++|..|+..|++.
T Consensus        17 ~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   76 (96)
T 1fjc_A           17 RTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGA   76 (96)
T ss_dssp             GEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCC
Confidence            346999999999999999885533322211    457889999999999999999999988863

>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=97.61  E-value=2.7e-05  Score=65.42  Aligned_cols=63  Identities=19%  Similarity=0.110  Sum_probs=45.1

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++..++.+.......+. +.++|||||+|.+.++|..|+..|++.
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~   78 (103)
T 2cq3_A           16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-RGSKGFGFVTFENSADADRAREKLHGT   78 (103)
T ss_dssp             CEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT-TTTCCEEEEEESCHHHHHHHHHHHTTC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-CCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            346999999999999999884422211111111122 238999999999999999999998874

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=97.60  E-value=1.6e-05  Score=65.25  Aligned_cols=62  Identities=11%  Similarity=-0.002  Sum_probs=46.3

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|..++..++........ ..+|.++|||||+|.+.++|..|+..|++.
T Consensus        10 ~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~-~~~g~~~g~afV~f~~~~~a~~a~~~l~g~   71 (92)
T 2dgv_A           10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIK-MENGKSKGCGVVKFESPEVAERACRMMNGM   71 (92)
T ss_dssp             EEEECSCCTTCCHHHHHHHHHTTSCEEEEEEE-ESSSCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-ccCCCcceEEEEEECCHHHHHHHHHHhCCC
Confidence            36999999999999998884322211111111 247889999999999999999999998874

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=97.60  E-value=1.9e-05  Score=67.36  Aligned_cols=63  Identities=14%  Similarity=0.026  Sum_probs=46.8

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      ..+||+||+..+++.+|..++..++....... .+..+|.++|||||+|.+.++|..|+..++.
T Consensus        26 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~   89 (109)
T 2rs2_A           26 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRH   89 (109)
T ss_dssp             CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCC
Confidence            34699999999999999988442221111111 2356799999999999999999999987653

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=97.60  E-value=1.5e-05  Score=68.55  Aligned_cols=64  Identities=8%  Similarity=0.125  Sum_probs=48.0

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++..++.+..... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   80 (115)
T 2dgo_A           16 FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQ   80 (115)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCC
Confidence            34699999999999999988442221111111 12457899999999999999999999998874

>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=97.59  E-value=1.8e-05  Score=67.45  Aligned_cols=65  Identities=14%  Similarity=0.138  Sum_probs=48.4

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|.+++..++....... .+..+|.++|||||.|.+.++|..|+..+++.
T Consensus        26 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~   91 (108)
T 2jrs_A           26 PMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGF   91 (108)
T ss_dssp             CEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCC
Confidence            344699999999999999988442221111111 12467889999999999999999999988874

>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=97.59  E-value=4.8e-05  Score=64.12  Aligned_cols=61  Identities=8%  Similarity=-0.068  Sum_probs=44.6

Q ss_pred             cccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          227 KETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       227 ~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      .+...+||+||+..+++++|.+++..++.......     ...+|||||+|.+.++|..|+..++.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i-----~~~kg~aFVef~~~~~A~~Ai~~l~~   73 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILM-----LKGKNQAFLELATEEAAITMVNYYSA   73 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEE-----ETTTTEEEEEESSHHHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE-----ECCCCEEEEEECCHHHHHHHHHHhcc
Confidence            34455799999999999999998553332221111     11289999999999999999987753

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.58  E-value=1.8e-05  Score=68.21  Aligned_cols=67  Identities=12%  Similarity=0.164  Sum_probs=49.6

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhHHH
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEE  296 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i~e  296 (577)
                      ..+||+||+..+++++|.+++..++.+.... ..+..++.++|||||+|.+.++|..||..+++.+..
T Consensus        18 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g   85 (116)
T 2cqd_A           18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDG   85 (116)
T ss_dssp             SEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCCcCCC
Confidence            3469999999999999998844222111111 123567999999999999999999999998875443

>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=97.58  E-value=4.8e-05  Score=64.26  Aligned_cols=60  Identities=7%  Similarity=-0.054  Sum_probs=44.6

Q ss_pred             ccccccccCCCc-ccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          228 ETQDAGAGKEDE-SVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       228 ~~~~~~v~nl~~-~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      +...+||+||+. .+++.+|.+++..++.+.....     -..+|||||+|++.++|..|+..|++
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i-----~~~kg~aFVef~~~~~A~~Ai~~l~~   74 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLI-----LNKINEAFIEMATTEDAQAAVDYYTT   74 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEE-----CSSSSCEEEEESSHHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEE-----EcCCCEEEEEECCHHHHHHHHHHHcC
Confidence            344569999999 9999999999653222211111     12368999999999999999999886

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=97.57  E-value=2.5e-05  Score=65.66  Aligned_cols=62  Identities=10%  Similarity=-0.092  Sum_probs=45.6

Q ss_pred             cccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          227 KETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       227 ~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+..++||+||+..+++.+|.+++...+.......     -+.||||||+|++.++|..|+..+++.
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i-----~~~kg~AFVef~~~~~A~~Av~~ln~~   80 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVV-----MPKKRQALVEFEDVLGACNAVNYAADN   80 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEE-----ETTTTEEEEEESSHHHHHHHHHHHHHS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEE-----EcCCCEEEEEECCHHHHHHHHHHhcCC
Confidence            34556799999999999999988442221111100     135899999999999999999998763

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=97.56  E-value=3.3e-05  Score=68.57  Aligned_cols=65  Identities=14%  Similarity=0.082  Sum_probs=48.3

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|.+++...+...... ..+..+|.++|||||+|.+.++|.+|+..|++.
T Consensus        63 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~  128 (140)
T 2ku7_A           63 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES  128 (140)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEE
T ss_pred             CcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCC
Confidence            34469999999999999998844221111111 122567899999999999999999999988764

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.55  E-value=3.6e-05  Score=65.61  Aligned_cols=64  Identities=17%  Similarity=0.091  Sum_probs=45.5

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++++|.+++..++.........+ .+.++|||||+|.+.++|..|+..|++.
T Consensus        29 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-~~~~kg~afV~f~~~~~A~~Ai~~l~g~   92 (109)
T 2err_A           29 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGSKGFGFVTFENSADADRAREKLHGT   92 (109)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCB-TTBCTTEEEEECCCSHHHHHHHHHHTTC
T ss_pred             CCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEEC-CCCCceEEEEEECCHHHHHHHHHHcCCC
Confidence            334699999999999999888442221111111111 2348999999999999999999988864

>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=97.55  E-value=3.4e-05  Score=67.01  Aligned_cols=61  Identities=10%  Similarity=-0.066  Sum_probs=44.1

Q ss_pred             cccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          227 KETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       227 ~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      .....+||+||+..+++.+|.+++..++.+.....     -..+|||||+|++.++|..|+..+++
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i-----~~~kG~AFVeF~~~e~A~~Ai~~l~~   89 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM-----LKGKNQAFIEMNTEEAANTMVNYYTS   89 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEE-----EGGGTEEEEECSCHHHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE-----eCCCCEEEEEECCHHHHHHHHHHhcc
Confidence            34455799999999999999988442221111111     01279999999999999999998875

>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=97.55  E-value=8.3e-06  Score=79.44  Aligned_cols=62  Identities=11%  Similarity=0.102  Sum_probs=48.1

Q ss_pred             ccccCCCcccchhhhcCCCCCCc--ccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPE--NLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~--~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++..++  .+..+.. .+..+|+++|||||+|.+.++|.+||..|++.
T Consensus        71 lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~  135 (229)
T 3q2s_C           71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKR  135 (229)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTS
T ss_pred             EEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCC
Confidence            59999999999999998844333  1221111 23578999999999999999999999988754

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.54  E-value=2e-05  Score=66.88  Aligned_cols=58  Identities=10%  Similarity=-0.066  Sum_probs=41.7

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      ..+||+||+..+++++|.+++..++.......     -..||||||+|++.++|..|+..+++
T Consensus        17 ~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i-----~~~kGfaFVeF~~~~~A~~Ai~~l~~   74 (105)
T 1sjq_A           17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM-----LKGKNQAFIEMNTEEAANTMVNYYTS   74 (105)
T ss_dssp             CEEEECSCCTTSCHHHHHHHHHHHCCEEEEEE-----ETTTTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE-----EcCCCEEEEEECCHHHHHHHHHHhcc
Confidence            34699999999999999988441111111100     01279999999999999999998763

>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=97.53  E-value=1.9e-05  Score=67.72  Aligned_cols=65  Identities=8%  Similarity=-0.113  Sum_probs=47.8

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccc-cCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLK-DNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k-~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++++|.+++..++... ........+|.++|||||+|.+.++|..|+..|++.
T Consensus        25 ~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~   90 (115)
T 2cpx_A           25 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGY   90 (115)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence            34579999999999999998855211110 000111337899999999999999999999998874

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=97.53  E-value=4.2e-05  Score=65.65  Aligned_cols=59  Identities=14%  Similarity=0.090  Sum_probs=44.2

Q ss_pred             ccccCCCcccchhhhcCCCCCCc-ccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPE-NLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~-~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++..++ .+....   -..+.++|||||+|.+.++|.+|+..|++.
T Consensus        31 l~VgnLp~~~te~dL~~~F~~~G~~v~~v~---i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~   90 (111)
T 2jvr_A           31 ITMKNLPEGCSWQDLKDLARENSLETTFSS---VNTRDFDGTGALEFPSEEILVEALERLNNI   90 (111)
T ss_dssp             EEEECSSCCCCHHHHHHHHHHHTCCCSEEE---CSSCSSSCCEEEEESSHHHHHHHHHHTTTE
T ss_pred             EEEECCCCCCCHHHHHHHHHHhCCeeEEEE---EEcCCCCCEEEEEECCHHHHHHHHHHcCCC
Confidence            59999999999999998844222 111111   112358999999999999999999998874

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=97.53  E-value=2e-05  Score=69.46  Aligned_cols=63  Identities=13%  Similarity=0.049  Sum_probs=44.8

Q ss_pred             cccccccCCCcccchhhhcC----CCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNE----PTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e----~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++++|+.    ++..++.+.....  ..+|.++|||||+|.+.++|..|+..|++.
T Consensus        29 ~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i--~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~   95 (127)
T 2a3j_A           29 SQVVLITNINPEVPKEKLQALLYALASSQGDILDIVV--DLSDDNSGKAYIVFATQESAQAFVEAFQGY   95 (127)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEE--CCCCSSCCCEEEEESSHHHHHHHHHHSTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEe--ccCCCcCCEEEEEECCHHHHHHHHHHHCCC
Confidence            34479999999999988652    3221111111111  346889999999999999999999998874

>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=97.52  E-value=1.3e-05  Score=67.40  Aligned_cols=63  Identities=11%  Similarity=0.132  Sum_probs=46.6

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|.+++..++....... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus        10 ~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~   73 (104)
T 1p1t_A           10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGR   73 (104)
T ss_dssp             CEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSB
T ss_pred             EEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence            3599999999999999888332221111111 12457889999999999999999999988764

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.52  E-value=1.4e-05  Score=70.06  Aligned_cols=59  Identities=14%  Similarity=-0.161  Sum_probs=44.4

Q ss_pred             cccccCCCcccchhhhcCCCCCCc-c---cccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHH
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPE-N---LKDNETGNKESHDPTNFGVVTEEDRKADQEALEK  289 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~-~---~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~  289 (577)
                      .+||+||+..+++++|.+++..++ +   ........+.+|+++|||||+|.+.++|.+||..
T Consensus        25 ~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~   87 (123)
T 2dha_A           25 IVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK   87 (123)
T ss_dssp             EEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh
Confidence            369999999999999999844221 1   1112222235799999999999999999999975

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=96.66  E-value=1.3e-05  Score=69.10  Aligned_cols=63  Identities=13%  Similarity=0.024  Sum_probs=48.2

Q ss_pred             cccccCCCcccchhhhcCCCCCCccccc--------CCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKD--------NET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~--------~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|.+++..++....        ... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         9 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   80 (116)
T 2lcw_A            9 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   80 (116)
Confidence            3699999999999999998552221111        111 22467899999999999999999999988874

>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=97.51  E-value=2.5e-05  Score=71.01  Aligned_cols=66  Identities=12%  Similarity=0.035  Sum_probs=48.7

Q ss_pred             ccccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          228 ETQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       228 ~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ....+||+||+..+++.+|.+++..++.+..+.. .+..++.++|||||+|.+.++|..||..|++.
T Consensus        38 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~  104 (156)
T 1h2v_Z           38 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGT  104 (156)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence            3445799999999999999988442211111111 22557889999999999999999999988764

>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=97.48  E-value=2.1e-05  Score=64.07  Aligned_cols=61  Identities=16%  Similarity=0.144  Sum_probs=45.3

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++..++....... .+..+|.++|||||+|.+.++|..|+ .+++.
T Consensus         9 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~   70 (89)
T 3ucg_A            9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDES   70 (89)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCC
Confidence            599999999999999888442221111111 12457899999999999999999999 77764

>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=97.48  E-value=3.9e-05  Score=65.80  Aligned_cols=63  Identities=10%  Similarity=0.019  Sum_probs=45.9

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|..++..++.......  ..++.++|||||+|.+.++|..|+..|++.
T Consensus         8 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i--~~~~~~~g~afV~f~~~~~A~~A~~~l~g~   70 (115)
T 3lqv_A            8 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV--GNTPETRGTAYVVYEDIFDAKNAVDHLSGF   70 (115)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEE--ECSTTTTTCEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEE--eeCCCCCcEEEEEECCHHHHHHHHHHcCCC
Confidence            344699999999999999888432221111111  123566999999999999999999988874

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.48  E-value=1.7e-05  Score=65.94  Aligned_cols=62  Identities=15%  Similarity=0.016  Sum_probs=45.7

Q ss_pred             ccccccCCCcccchhhhcCCCCC------CcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKS------PENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks------~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++++|.+++..      +.+..+..  ...++.++|||||+|.+.++|..|+..|++.
T Consensus         6 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~   73 (98)
T 2cpf_A            6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKN--KAGVLLSMGFGFVEYKKPEQAQKALKQLQGH   73 (98)
T ss_dssp             CCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEEC--TTCCEEEEEEEEEEESSHHHHHHHHHHSTTC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCCCcCcccEEEEEECCHHHHHHHHHHhCCC
Confidence            34699999999999999988332      12221100  0114588999999999999999999998874

>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=97.47  E-value=3.2e-05  Score=63.18  Aligned_cols=59  Identities=25%  Similarity=0.224  Sum_probs=45.5

Q ss_pred             ccccCCCcccchhhhcCCCC---CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTK---SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~k---s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++.   .+......  .+..+|.++|||||+|.+.+ |..|+..|++.
T Consensus         4 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~--~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~   65 (90)
T 2ki2_A            4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLI--YDRETKKPKGFGFVEMQEES-VSEAIAKLDNT   65 (90)
T ss_dssp             EEEEEECTTSSHHHHTTTHHHHTCCSEEEEC--CCSSSCCCCEEEEEEECTTH-HHHHHHTSCSS
T ss_pred             EEECCCCCCCCHHHHHHHHHhcCCEEEEEEE--EcCCCCCcceEEEEEECCHH-HHHHHHHhCCC
Confidence            49999999999999998844   22211111  22567899999999999999 99999988765

>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=97.46  E-value=1.8e-05  Score=66.55  Aligned_cols=60  Identities=8%  Similarity=0.008  Sum_probs=44.5

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHH
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEK  289 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~  289 (577)
                      ..+||+||+..+++.+|.+++..++.+..... .+..+|.++|||||+|.+.++|..||..
T Consensus        16 ~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~   76 (103)
T 2cqg_A           16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ   76 (103)
T ss_dssp             CCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS
T ss_pred             CEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc
Confidence            34699999999999999988442221111111 2246799999999999999999999985

>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=97.46  E-value=6e-05  Score=63.85  Aligned_cols=61  Identities=11%  Similarity=-0.082  Sum_probs=44.6

Q ss_pred             cccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          227 KETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       227 ~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      .+..++||+||+..+++.+|.+++..++.......     ...||||||+|.+.++|..|+..|++
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i-----~~~kg~aFVef~~~~~A~~Ai~~l~~   73 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM-----MPFKRQALVEFENIDSAKECVTFAAD   73 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEE-----ETTTTEEEEEESSHHHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEE-----ECCCCEEEEEECCHHHHHHHHHHhcc
Confidence            34556799999999999999988442222111111     11389999999999999999998865

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.45  E-value=2.5e-05  Score=65.88  Aligned_cols=62  Identities=16%  Similarity=0.070  Sum_probs=45.7

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      ..+||+||+..+++.+|.+++..++.+..... .+..+|.++|||||+|.+.++|..||.. ++
T Consensus        17 ~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~   79 (105)
T 2dh8_A           17 GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RP   79 (105)
T ss_dssp             SEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CC
Confidence            34699999999999999988432221111111 1246789999999999999999999987 54

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=97.45  E-value=1.7e-05  Score=70.66  Aligned_cols=61  Identities=16%  Similarity=0.207  Sum_probs=46.7

Q ss_pred             cccccCCCcccchhhhcCCCC---CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTK---SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~k---s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++++|.+++.   .+..+...  .+..+|.++|||||+|.+.++|.+|+..|++.
T Consensus        44 ~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~--~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~  107 (139)
T 1u6f_A           44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIV--CDRETRQSRGYGFVKFQSGSSAQQAIAGLNGF  107 (139)
T ss_dssp             EEEEESCSTTCCHHHHHHHHHHHSCEEEEEEE--EETTTTEEEEEEEEEESSHHHHHHHHHHTTTE
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--EcCCCCCcceEEEEEECCHHHHHHHHHHhCCC
Confidence            359999999999999988844   22111111  12457889999999999999999999998874

>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=97.44  E-value=0.0002  Score=59.88  Aligned_cols=75  Identities=12%  Similarity=0.026  Sum_probs=63.0

Q ss_pred             CCceEEEcCCCCCC-CH----HHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 008117          127 PQTKVYVGKIAPTA-DS----DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  201 (577)
Q Consensus       127 ~~~tlfVgnLp~~~-te----~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~  201 (577)
                      -+++|+|.||+..+ ..    ..++.+|..|+.+..+.....      -.=..|.|.+.++|.+|-..||+..|+|..|+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS------FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc------ceEEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            36789999998754 32    467899999999998877653      23468999999999999999999999999999


Q ss_pred             EEEchh
Q 008117          202 LKVDQA  207 (577)
Q Consensus       202 V~~a~~  207 (577)
                      |.|++.
T Consensus        78 ~YFgq~   83 (104)
T 1wey_A           78 LYFAQT   83 (104)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            999874

>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=97.44  E-value=1.9e-05  Score=70.74  Aligned_cols=65  Identities=9%  Similarity=-0.045  Sum_probs=48.1

Q ss_pred             cccccccCCCcccchhhhcCCCCCCccccc------CCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKD------NETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~------~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|..++..++.+..      .+.....+|.++|||||+|.+.++|..|+..|++.
T Consensus        45 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~  115 (143)
T 3egn_A           45 NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGY  115 (143)
T ss_dssp             CSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCC
Confidence            344699999999999999988442221110      00011357899999999999999999999999874

>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=97.44  E-value=4e-05  Score=62.19  Aligned_cols=61  Identities=10%  Similarity=0.085  Sum_probs=44.8

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHH
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEK  289 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~  289 (577)
                      ...+||+||+..+++.+|.+++..++....... .+..+|.++|||||+|.+.++|..|+..
T Consensus        11 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~   72 (87)
T 3s7r_A           11 AGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ   72 (87)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh
Confidence            334699999999999999988442221111111 2256799999999999999999999865

>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=97.43  E-value=2.7e-05  Score=66.11  Aligned_cols=60  Identities=17%  Similarity=0.059  Sum_probs=45.9

Q ss_pred             cccccCCCcccchhhhcCCCC---C-CcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHh
Q 008117          231 DAGAGKEDESVQSVEKNEPTK---S-PENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLT  291 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~k---s-~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~  291 (577)
                      .+||+||+..+++++|.+++.   . +...... ..+..+|.++|||||+|.+.++|..|+..|+
T Consensus        10 ~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~-~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~   73 (109)
T 2dis_A           10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVY-ASAADKMKNRGFAFVEYESHRAAAMARRKLM   73 (109)
T ss_dssp             EEEEECCCTTSCHHHHHHHHHHHSTTEEEEECC-SSSCTTTTTCCEEEEEESSHHHHHHHHTTTT
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEE-ccCCCCCCcCcEEEEEecCHHHHHHHHHHhh
Confidence            359999999999999988744   1 2222111 1235678999999999999999999999885

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=97.42  E-value=3.6e-05  Score=71.80  Aligned_cols=62  Identities=16%  Similarity=0.057  Sum_probs=46.6

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++..++.+.......+.+|.++|||||+|.+.++|..|+..|++.
T Consensus        91 l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~  152 (177)
T 2f3j_A           91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGV  152 (177)
T ss_dssp             EEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCC
Confidence            49999999999999998844222111111112337899999999999999999999988875

>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=97.41  E-value=4.2e-05  Score=64.27  Aligned_cols=58  Identities=12%  Similarity=0.060  Sum_probs=44.8

Q ss_pred             cccccccCCCcccchhhhcCCCC------CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTK------SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~k------s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|.+++.      ++.+..      + .+.++|||||+|.+.++|..|+..|++.
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~------~-~~~~~g~afV~f~~~~~a~~A~~~l~g~   78 (103)
T 2cqi_A           15 PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMIT------E-HTSNDPYCFVEFYEHRDAAAALAAMNGR   78 (103)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEEC------C-CCSSCCEEEEEESSHHHHHHHHHHHTTE
T ss_pred             CCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEe------c-CCCCCCEEEEEECCHHHHHHHHHHhCCC
Confidence            34469999999999999998844      222222      1 2336899999999999999999988875

>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=97.38  E-value=4e-05  Score=63.63  Aligned_cols=60  Identities=17%  Similarity=0.075  Sum_probs=42.1

Q ss_pred             ccccCCCcccchhhhc----CCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKN----EPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~----e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.    +++..++.........+..+  +|||||+|.+.++|..|+..|++.
T Consensus        12 l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~   75 (96)
T 2dgx_A           12 VQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRY   75 (96)
T ss_dssp             EEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTE
T ss_pred             EEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCC
Confidence            5999999999999998    66331111111111112222  899999999999999999999875

>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=97.38  E-value=2.3e-05  Score=64.93  Aligned_cols=62  Identities=11%  Similarity=0.024  Sum_probs=45.4

Q ss_pred             ccccccCCCcccchhhhc----CCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKN----EPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~----e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.    +++..++.......  ..+|.++|||||+|.+.++|..|+..|++.
T Consensus         9 ~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i--~~~~~~~g~afV~f~~~~~A~~A~~~l~g~   74 (97)
T 1nu4_A            9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV--SRSLKMRGQAFVIFKEVSSATNALRSMQGF   74 (97)
T ss_dssp             SEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEEC--CHHHHHTTCEEEEESSHHHHHHHHHHHTTC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEE--EcCCCcCcEEEEEeCCHHHHHHHHHHhCCC
Confidence            446999999999999888    66332221111111  135778999999999999999999998874

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.37  E-value=8.1e-05  Score=63.97  Aligned_cols=59  Identities=15%  Similarity=0.043  Sum_probs=44.4

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHH
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEK  289 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~  289 (577)
                      .+||+||+..+++.+|.+++..++.+.... ..+..+|.++|||||+|.+.++|..||..
T Consensus        29 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~   88 (116)
T 1x4b_A           29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA   88 (116)
T ss_dssp             EEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh
Confidence            359999999999999998844222111111 12356789999999999999999999876

>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=97.36  E-value=4.7e-05  Score=61.71  Aligned_cols=62  Identities=15%  Similarity=0.112  Sum_probs=44.2

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCC-CCCCC-CCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKES-HDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~-g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++..++....... .+..+ +.++|||||+|.+.++|..|+..|++.
T Consensus         7 l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   70 (88)
T 4a8x_A            7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGG   70 (88)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCC
Confidence            599999999999999888332221111110 11223 338999999999999999999998874

>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=97.35  E-value=4.4e-05  Score=59.98  Aligned_cols=56  Identities=13%  Similarity=0.118  Sum_probs=42.5

Q ss_pred             ccccCCCcccchhhhcCCCC---CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHH
Q 008117          232 AGAGKEDESVQSVEKNEPTK---SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEK  289 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~k---s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~  289 (577)
                      +||+||+..+++++|..++.   .+....-  ..+..+|.++|||||+|.+.++|..|+..
T Consensus         2 l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i--~~~~~~~~~~g~afV~f~~~~~a~~Ai~~   60 (75)
T 1iqt_A            2 IFVGGLSPDTPEEKIREYFGGFGEVESIEL--PMDNKTNKRRGFCFITFKEEEPVKKIMEK   60 (75)
T ss_dssp             EEESCCCSSCCHHHHHHHHHHHSCCSEECC--CCSCCCSSSCCCEEEECSSSHHHHHHHTT
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEE--EecCCCCCcCCEEEEEECCHHHHHHHHHh
Confidence            48999999999999988843   2211111  12256789999999999999999999874

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.35  E-value=4.7e-05  Score=63.26  Aligned_cols=60  Identities=13%  Similarity=0.121  Sum_probs=45.3

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|..++..++... .   ...++.++|||||+|.+.++|..|+..|++.
T Consensus        20 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~---~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   79 (97)
T 2e5j_A           20 ADVYVGNLPRDARVSDLKRALRELGSVP-L---RLTWQGPRRRAFLHYPDSAAAQQAVSCLQGL   79 (97)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCC-S---EEEEETTTTEEEEECSSHHHHHHHHHHHTTC
T ss_pred             CEEEEeCCCCcCcHHHHHHHHHhcCCEE-E---EEEcCCCCcEEEEEECCHHHHHHHHHHhCCC
Confidence            3469999999999999988844221111 0   0224578999999999999999999988864

>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=97.33  E-value=8.4e-05  Score=60.54  Aligned_cols=56  Identities=11%  Similarity=-0.034  Sum_probs=44.0

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++....+.. ...     ..++|||||+|.+.++|..|+..|++.
T Consensus         8 l~V~nLp~~~t~~~l~~~F~~~~v~~-~~i-----~~~~g~afV~f~~~~~a~~Ai~~l~g~   63 (88)
T 1wg1_A            8 ILVKNLPQDSNCQEVHDLLKDYDLKY-CYV-----DRNKRTAFVTLLNGEQAQNAIQMFHQY   63 (88)
T ss_dssp             EEEESCCSSCCHHHHHHHTCSSCCCC-EEE-----EGGGTEEEECCSCHHHHHHHHHHHTTE
T ss_pred             EEEeCCCCCCCHHHHHHHHhhCCeEE-EEE-----eCCCcEEEEEECCHHHHHHHHHHhCCC
Confidence            59999999999999998855332211 111     167999999999999999999998875

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=97.33  E-value=2.8e-05  Score=67.76  Aligned_cols=62  Identities=13%  Similarity=0.127  Sum_probs=45.7

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++++|.+++..++.+..... .+..+|.++|||||+|.+.++|..|+ .|++.
T Consensus        38 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~  100 (124)
T 2jwn_A           38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDET  100 (124)
T ss_dssp             EEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCC
Confidence            3599999999999999988442221111111 12467899999999999999999999 67764

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=97.30  E-value=6.9e-05  Score=62.63  Aligned_cols=58  Identities=7%  Similarity=-0.040  Sum_probs=43.9

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++++|..++..++.....     ....++|||||+|.+.++|..|+..|++.
T Consensus        29 ~l~V~nlp~~~~~~~l~~~f~~~G~i~~~-----~~~~~~g~afV~f~~~~~A~~Ai~~l~g~   86 (101)
T 2la4_A           29 TAYIGNIPHFATEADLIPLFQNFGFILDF-----KHYPEKGCCFIKYDTHEQAAVCIVALANF   86 (101)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHTTSCCSEE-----EEETTTTEEEEECSSHHHHHHHHHHHTTC
T ss_pred             EEEEcCCCcccCHHHHHHHHHhCCCEEEE-----EEecCCCEEEEEECCHHHHHHHHHHhCCC
Confidence            36999999999999999884422211111     11257899999999999999999988864

>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=97.28  E-value=6.4e-05  Score=64.76  Aligned_cols=56  Identities=13%  Similarity=0.012  Sum_probs=41.4

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++..++.+.......+      |||||+|.+.++|..||..|++.
T Consensus        19 l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~   74 (115)
T 3beg_B           19 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNT   74 (115)
T ss_dssp             EEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCC
Confidence            599999999999999988442221111111001      89999999999999999988764

>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=97.28  E-value=5.7e-05  Score=65.05  Aligned_cols=62  Identities=10%  Similarity=-0.035  Sum_probs=44.7

Q ss_pred             cccccccc--cCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          227 KETQDAGA--GKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       227 ~~~~~~~v--~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+++.+||  +||+..+++++|++++...+......-   .  ..+|||||+|.+.++|.+|+..||+.
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i---~--~~rgfaFV~f~~~~~A~~Ai~~lnG~   86 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM---P--PNKPYSFARYRTTEESKRAYVTLNGK   86 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEEC---C--TTCSCEEEEESSHHHHHHHHHHTTTC
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEE---e--CCCCEEEEEECCHHHHHHHHHHhCCC
Confidence            34555799  679999999999988441111111111   1  13799999999999999999999885

>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=97.25  E-value=0.00011  Score=60.94  Aligned_cols=60  Identities=13%  Similarity=0.076  Sum_probs=43.6

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|.+++..++.......   ..  .+|||||+|.+.++|..|+..|++.
T Consensus        17 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~---~~--~~g~afV~f~~~~~A~~A~~~l~g~   76 (97)
T 1why_A           17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDH---VK--GDSFAYIQYESLDAAQAACAKMRGF   76 (97)
T ss_dssp             CSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEE---CS--SSCCEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEE---eC--CCCEEEEEECCHHHHHHHHHHHCCC
Confidence            344699999999999999988442221111111   11  2789999999999999999998864

>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=97.23  E-value=0.00011  Score=62.81  Aligned_cols=58  Identities=12%  Similarity=-0.049  Sum_probs=44.1

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|.+++..++.+.....     ..++|||||+|.+.++|..|+..|++.
T Consensus        12 ~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i-----~~~~g~afV~f~~~~~A~~Ai~~l~g~   69 (111)
T 1whx_A           12 VILAKNLPAGTLAAEIQETFSRFGSLGRVLL-----PEGGITAIVEFLEPLEARKAFRHLAYS   69 (111)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHTTSCEEEEEC-----CSSSSCEEEEESCHHHHHHHHHHHTTC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE-----eCCCCEEEEEeCCHHHHHHHHHHhCCC
Confidence            4699999999999999988442222111111     136899999999999999999999874

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=97.23  E-value=0.00015  Score=61.74  Aligned_cols=58  Identities=19%  Similarity=0.106  Sum_probs=43.8

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|..++..++.......       .+|||||+|.+.++|..|+..|++.
T Consensus        31 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i-------~kg~afV~f~~~~~A~~Ai~~l~g~   88 (108)
T 2jvo_A           31 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI-------LNGFAFVEFEEAESAAKAIEEVHGK   88 (108)
T ss_dssp             CSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEE-------ETTEEEEECSSHHHHHHHHHHHTTC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEE-------ECCEEEEEECCHHHHHHHHHHcCCC
Confidence            344699999999999999988442222211111       1799999999999999999998875

>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=97.20  E-value=0.00016  Score=60.24  Aligned_cols=59  Identities=17%  Similarity=0.120  Sum_probs=44.4

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|..++..++......     ....+|||||+|.+.++|..|+..|++.
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~-----~~~~kg~afV~f~~~~~a~~a~~~l~g~   74 (99)
T 2cpj_A           16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVF-----IHKDKGFGFIRLETRTLAEIAKVELDNM   74 (99)
T ss_dssp             TEEEEESCCTTCCHHHHHHHTSTTCCCSEEE-----EETTTTEEEEECSSSHHHHHHHHHHTTC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCCeEEEE-----EecCCCEEEEEECCHHHHHHHHHHhCCC
Confidence            3469999999999999998855332211111     1234899999999999999999998875

>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=97.20  E-value=8.2e-05  Score=63.19  Aligned_cols=57  Identities=12%  Similarity=0.010  Sum_probs=41.6

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|.+++..++.+.......+      |||||+|.+.++|..||..|++.
T Consensus        17 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~   73 (108)
T 1x4c_A           17 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNT   73 (108)
T ss_dssp             EEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSE
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcC
Confidence            3599999999999999988442221111111001      89999999999999999988764

>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=97.17  E-value=7.2e-05  Score=61.49  Aligned_cols=56  Identities=14%  Similarity=0.093  Sum_probs=42.5

Q ss_pred             cccccCCCcccchhhhcCCCCCCcc-cccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPEN-LKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~-~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      .+||+||+..+++++|.+++..++. ....      .-.++|||||+|.+.++|..|+..|++
T Consensus        10 ~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~------~~~~~g~afV~f~~~~~A~~A~~~l~g   66 (93)
T 2cqh_A           10 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQ------VLLKSGYAFVDYPDQNWAIRAIETLSG   66 (93)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHHTTCCCSSC------EEEETTEEEECCSCHHHHHHHHHHHTT
T ss_pred             EEEEeCCCCCCCHHHHHHHHHHcCCceEEE------EEcCCCEEEEEECCHHHHHHHHHHccC
Confidence            3599999999999999888441111 1100      013589999999999999999999987

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=97.17  E-value=9.1e-05  Score=61.88  Aligned_cols=55  Identities=16%  Similarity=0.157  Sum_probs=42.0

Q ss_pred             ccccCCCcccchhhhcCCCC---CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTK---SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~k---s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++.   .+......   .+    ++|||||+|.+.++|..|+..|++.
T Consensus         3 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~---~~----~~g~afV~f~~~~~a~~A~~~l~g~   60 (101)
T 2hvz_A            3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIA---RN----PPGFAFVEFEDPRDAEDAVRGLDGK   60 (101)
T ss_dssp             EEEECCCSSCSHHHHHHHHHHHCCCSEEEEE---SS----SSSEEEEECSSHHHHHHHHHHHHHS
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEe---eC----CCCEEEEEECCHHHHHHHHHHHCCC
Confidence            49999999999999988843   22211100   01    7899999999999999999988874

>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=97.17  E-value=0.00013  Score=60.63  Aligned_cols=58  Identities=10%  Similarity=0.060  Sum_probs=43.7

Q ss_pred             cccccccCCCc-ccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDE-SVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~-~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+. .+++++|..++..++.......       ++|||||+|.+.++|..|+..+++.
T Consensus        22 ~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~Ai~~l~g~   80 (97)
T 2xnq_A           22 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEXESQE   80 (97)
T ss_dssp             TCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE-------CSSEEEEEESSHHHHHHHHHHHTTS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCC
Confidence            34469999998 9999999888543322211111       3899999999999999999988774

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=97.13  E-value=0.00016  Score=59.82  Aligned_cols=58  Identities=10%  Similarity=0.030  Sum_probs=43.6

Q ss_pred             cccccccCCCc-ccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDE-SVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~-~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+. .+++.+|..++..++......       -++|||||+|.+.++|..|+..|++.
T Consensus        10 ~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~-------i~~g~afV~f~~~~~A~~A~~~l~g~   68 (96)
T 2kvi_A           10 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQIN-------IKNAFGFIQFDNPQSVRDAIECESQE   68 (96)
T ss_dssp             CEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEE-------EETTEEEEEESCHHHHHHHHHHHTCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEE-------EeCCEEEEEECCHHHHHHHHHHcCCC
Confidence            33469999998 999999998844232221111       13899999999999999999998765

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=97.12  E-value=1.9e-05  Score=66.34  Aligned_cols=57  Identities=14%  Similarity=0.074  Sum_probs=42.3

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHH
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALE  288 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~  288 (577)
                      +||+||+..+++++|..++..++.........+.+|.++|||||+|.+.++|..|+.
T Consensus        12 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~   68 (102)
T 2xs2_A           12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE   68 (102)
T ss_dssp             EEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT
T ss_pred             EEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh
Confidence            599999999999999988442221111111112388999999999999999999988

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.09  E-value=0.00014  Score=59.42  Aligned_cols=56  Identities=18%  Similarity=0.209  Sum_probs=42.4

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|..++..++.......       .+|||||+|.+.++|..|+..|++.
T Consensus        10 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~-------~~g~afV~f~~~~~A~~A~~~l~g~   65 (90)
T 2dnq_A           10 KLFIGNLPREATEQEIRSLFEQYGKVLECDI-------IKNYGFVHIEDKTAAEDAIRNLHHY   65 (90)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHTSSCEEEEEE-------ETTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhCCCEEEEEE-------ECCEEEEEECCHHHHHHHHHHhcCC
Confidence            3599999999999999888442221111111       1789999999999999999998874

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.08  E-value=0.00014  Score=60.53  Aligned_cols=58  Identities=10%  Similarity=0.006  Sum_probs=44.3

Q ss_pred             cccccccCCCcccchhhhcCCCCCC--cccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSP--ENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~--~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++.+|..++..+  +.....       ..++|||||+|.+.++|..|+..|++.
T Consensus        15 ~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~-------~~~~g~afV~f~~~~~A~~A~~~l~g~   74 (99)
T 2cpd_A           15 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-------KKIRDYAFVHFSNREDAVEAMKALNGK   74 (99)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEE-------EECSSEEEEEESSHHHHHHHHHHHSSE
T ss_pred             cCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEE-------EEeCCeEEEEeCCHHHHHHHHHHhCCC
Confidence            3446999999999999998884422  222111       235789999999999999999988875

>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=97.08  E-value=0.00026  Score=57.91  Aligned_cols=52  Identities=19%  Similarity=0.074  Sum_probs=36.9

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHH
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQE  285 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~  285 (577)
                      ..+||+||+..+++++|.+++..++........    ..++|||||+|.+.++|..
T Consensus        12 ~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~----~~srGfaFV~F~~~~~A~~   63 (89)
T 3d2w_A           12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIP----KPFRAFAFVTFADDKVAQS   63 (89)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHTTTSCEEEEECC----SSCCSEEEEEESCHHHHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEe----eCCCCEEEEEECCHHHHHH
Confidence            346999999999999999884422222111111    1379999999999999873

>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=97.00  E-value=0.00015  Score=61.62  Aligned_cols=56  Identities=7%  Similarity=0.033  Sum_probs=42.8

Q ss_pred             cccccCCCcc-cchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDES-VQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~-~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+.. +++++|.+++..++.......       ++|||||+|.+.++|..|+..|++.
T Consensus        29 ~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A~~~l~g~   85 (110)
T 1wf1_A           29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGENGR   85 (110)
T ss_dssp             EEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHHHHHHTTC
T ss_pred             EEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCC
Confidence            4699999999 999999888442221111111       5899999999999999999998874

>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=96.99  E-value=0.00015  Score=68.49  Aligned_cols=108  Identities=9%  Similarity=-0.010  Sum_probs=63.5

Q ss_pred             CHHHHHHHHHHh--CCceeCCeEEEEEEchhhHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCccc
Q 008117          179 SAEGVLRALRLL--NKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENL  256 (577)
Q Consensus       179 ~~~~A~~Al~~L--ng~~i~gr~i~V~~a~~~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~  256 (577)
                      +...+..|+...  ....+.+..+.|.-.....  ...+..   .. ........+||+||+..++.++|.+++..++..
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p--~p~~~~---~~-~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v  136 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKP--LPEVTD---EY-KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQV  136 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSC--CCCCCH---HH-HHHHHHTEEEEECCCTTCCHHHHHHHHTTSCCE
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCC--Ccccch---hh-hhccccCEEEecCCCCcCCHHHHHHHHhcCCCE
Confidence            567788888776  5556665544553321100  000000   00 001112336999999999999999884422211


Q ss_pred             ccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          257 KDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       257 k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      ....-....+|.++|||||+|.+.++|..|+..++.
T Consensus       137 ~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~~  172 (193)
T 2voo_A          137 LNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQ  172 (193)
T ss_dssp             EEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTTC
T ss_pred             EEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCCC
Confidence            111111134588999999999999999999976543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.98  E-value=0.00033  Score=57.38  Aligned_cols=57  Identities=12%  Similarity=0.105  Sum_probs=42.5

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|..++..++......       ..++||||+|.+.++|..|+..|++.
T Consensus        11 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~-------~~~~~afV~f~~~~~a~~A~~~l~g~   67 (92)
T 2dgt_A           11 TKLHVGNISPTCTNQELRAKFEEYGPVIECD-------IVKDYAFVHMERAEDAVEAIRGLDNT   67 (92)
T ss_dssp             EEEEEESCCSSCCHHHHHHHHHTTSCCCEEE-------ECSSEEEEEESCHHHHHHHHHHHTTE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE-------EECCEEEEEECCHHHHHHHHHHhCCC
Confidence            3469999999999999998844222111111       12569999999999999999998874

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.96  E-value=0.00026  Score=58.33  Aligned_cols=58  Identities=16%  Similarity=0.043  Sum_probs=42.3

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|..++..++..... ..+..+|.   ||||+|.+.++|..|+. |++.
T Consensus        10 ~l~V~nl~~~~t~~~l~~~F~~~G~v~~v-~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~   67 (94)
T 2e5g_A           10 SVFVSGFPRGVDSAQLSEYFLAFGPVASV-VMDKDKGV---FAIVEMGDVGAREAVLS-QSQH   67 (94)
T ss_dssp             EEEEECCCTTCCHHHHHHHGGGTSCEEEE-EECSSSCC---EEEEEESSHHHHHHHHT-CSCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCCeEEE-EEcCCCCc---EEEEEECCHHHHHHHHh-cCCe
Confidence            35999999999999999885533222111 12234444   99999999999999999 7764

>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=96.95  E-value=0.00019  Score=60.21  Aligned_cols=57  Identities=9%  Similarity=0.087  Sum_probs=42.7

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++..++.+....       ..+|||||+|.+.++|..|+..|++.
T Consensus        12 ~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~-------~~~~~afV~f~~~~~a~~A~~~l~g~   68 (103)
T 2dgu_A           12 KVLFVRNLANTVTEEILEKAFSQFGKLERVK-------KLKDYAFIHFDERDGAVKAMEEMNGK   68 (103)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHHSCEEEEE-------ECSSCEEEEESSHHHHHHHHHHHTTE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE-------EECCEEEEEeCCHHHHHHHHHHHCCC
Confidence            3469999999999999998844222111110       12679999999999999999998875

>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=96.94  E-value=0.00015  Score=61.47  Aligned_cols=58  Identities=5%  Similarity=0.029  Sum_probs=42.2

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|..++..++.+.....     ...+|||||+|.+.++|..|+..|++.
T Consensus        27 ~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i-----~~~~g~afV~f~~~~~a~~A~~~l~g~   84 (109)
T 1x4g_A           27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRV-----FPEKGYSFVRFSTHESAAHAIVSVNGT   84 (109)
T ss_dssp             EEEEECCSSCCCHHHHHHHHHHHSCEEEEEE-----ETTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeEEEEE-----eCCCCEEEEEECCHHHHHHHHHHcCCC
Confidence            3699999999999999888441111110000     011899999999999999999998874

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=96.88  E-value=9.6e-05  Score=64.61  Aligned_cols=48  Identities=8%  Similarity=0.010  Sum_probs=35.7

Q ss_pred             ccccCC----CcccchhhhcCCCCCCcccccC-CCCCCCCCCCCceEEEEeCC
Q 008117          232 AGAGKE----DESVQSVEKNEPTKSPENLKDN-ETGNKESHDPTNFGVVTEED  279 (577)
Q Consensus       232 ~~v~nl----~~~~~~~~l~e~~ks~~~~k~~-~~~~~~~g~~kgfgfV~f~~  279 (577)
                      +||+||    +..+++..|++++.+++-+... ...+..||.++|||||+|.+
T Consensus         5 I~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d   57 (136)
T 2j8a_A            5 IVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYAS   57 (136)
T ss_dssp             EEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC-
T ss_pred             EEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECC
Confidence            399999    9999999999985533322211 12448999999999999996

>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=96.86  E-value=0.00043  Score=56.15  Aligned_cols=52  Identities=17%  Similarity=0.044  Sum_probs=37.4

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHH
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEA  286 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~A  286 (577)
                      .+||+||+..+++++|.+++..++........    ..++|||||+|.+.++|..|
T Consensus         7 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~----~~~~g~afV~f~~~~~a~~~   58 (88)
T 1wf0_A            7 GVFVGRCTGDMTEDELREFFSQYGDVMDVFIP----KPFRAFAFVTFADDQIAQSL   58 (88)
T ss_dssp             EEEEESCCSSSCHHHHHHHSTTTSCCCEEECC----SSCCSCCEEECSCHHHHHHT
T ss_pred             EEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEe----cCCCCEEEEEECCHHHHHHH
Confidence            35999999999999999885533322211111    12799999999999998754

>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=96.85  E-value=0.00015  Score=58.65  Aligned_cols=62  Identities=6%  Similarity=-0.000  Sum_probs=42.1

Q ss_pred             cccccCCCcccchhhhcCCCCCC----cccc-cC-CCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSP----ENLK-DN-ETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~----~~~k-~~-~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++++|.+++...    ++.. .+ ...+-.....+|||||+|.+.++|..|+ .|++.
T Consensus         8 ~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~kg~afV~f~~~~~a~~A~-~l~g~   75 (87)
T 2hzc_A            8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGI   75 (87)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSSSSEEEEEESSHHHHHHHG-GGTTC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCCCcEEEEEcCCHHHHHHHH-hcCCC
Confidence            35999999999999998874422    2100 00 0000122345899999999999999999 88764

>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=96.85  E-value=0.00024  Score=57.07  Aligned_cols=58  Identities=10%  Similarity=0.060  Sum_probs=41.6

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHH-hh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKL-TC  292 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l-~~  292 (577)
                      ..+||+||+..+++.+|.+++...+.......     ..++|||||+|.+.++|..|+..| ++
T Consensus        13 ~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~-----~~~kg~afV~f~~~~~A~~a~~~l~~~   71 (85)
T 2ytc_A           13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITV-----VQRQQCAFIQFATRQAAEVAAEKSFNK   71 (85)
T ss_dssp             CCEEEECCTTTSCHHHHHHHHHTTSCEEEEEE-----EGGGTEEEEEESSHHHHHHHHHTTTTT
T ss_pred             cEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEE-----ECCCCEEEEEECCHHHHHHHHHHhcCC
Confidence            34699999999999999888332221111100     124799999999999999999987 54

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.80  E-value=0.00031  Score=57.30  Aligned_cols=57  Identities=12%  Similarity=0.103  Sum_probs=42.0

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|..++..++......       ..++||||+|.+.++|..|+..|++.
T Consensus        10 ~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~-------~~~~~afV~f~~~~~a~~A~~~l~g~   66 (90)
T 2dnp_A           10 WKIFVGNVSAACTSQELRSLFERRGRVIECD-------VVKDYAFVHMEKEADAKAAIAQLNGK   66 (90)
T ss_dssp             CCEEEESCCTTCCHHHHHHHHHHHSCEEEEE-------ECSSCEEEEESCHHHHHHHHHHHTTC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHcCCCEEEEE-------EECCEEEEEECCHHHHHHHHHHhCCC
Confidence            3469999999999999988844221111110       12569999999999999999998874

>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=96.79  E-value=0.0045  Score=50.69  Aligned_cols=68  Identities=12%  Similarity=0.169  Sum_probs=57.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCc--ceEEEEEeCCHHHHHHHHHHhCCceeC
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTP--KGFGFCEFESAEGVLRALRLLNKFNID  196 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~--kg~gFV~f~~~~~A~~Al~~Lng~~i~  196 (577)
                      +.|.|.+||+++|++++...++.++.+..+..+....+.++  -+-|||.|.+.+++......++|+.|.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            57899999999999999999999998887777766544443  356899999999999999999999873

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=96.75  E-value=0.00059  Score=56.44  Aligned_cols=57  Identities=18%  Similarity=0.110  Sum_probs=41.7

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+|+  .+++.+|.+++..++.+...     ..+.++|||||+|.+.++|..|+..|++.
T Consensus        16 ~~l~V~n~--~~t~~~l~~~F~~~G~i~~v-----~i~~~~g~afV~f~~~~~a~~Ai~~l~g~   72 (97)
T 1x5p_A           16 NTLYVYGE--DMTPTLLRGAFSPFGNIIDL-----SMDPPRNCAFVTYEKMESADQAVAELNGT   72 (97)
T ss_dssp             SEEEEECS--SCCHHHHHHHHTTTSCEEEE-----EEETTTTEEEEEESSHHHHHHHHHHTTTE
T ss_pred             CEEEEcCC--CCCHHHHHHHHhhCCCEEEE-----EecCCCCEEEEEECCHHHHHHHHHHhCCC
Confidence            34699996  78889998884422211111     11467999999999999999999998875

>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=96.72  E-value=0.00028  Score=64.61  Aligned_cols=59  Identities=10%  Similarity=-0.162  Sum_probs=42.8

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++..++.+.....   ....++|||||+|.+.++|..|+..|++.
T Consensus        49 l~VgNL~~~vted~L~~~Fs~fG~V~~V~i---~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~  107 (164)
T 1sjr_A           49 IIVENLFYPVTLDVLHQIFSKFGTVLKIIT---FTKNNQFQALLQYADPVSAQHAKLSLDGQ  107 (164)
T ss_dssp             EEECSCCSCCCHHHHHHHHHHHSCEEEEEE---EESSSCEEEEEEESCHHHHHHHHHHSTTB
T ss_pred             EEEeCcCCCCCHHHHHHHHHhcCCEEEEEE---EeCCCCCEEEEEECCHHHHHHHHHHhCCC
Confidence            589999999999999988441111110000   01225789999999999999999999875

>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=96.71  E-value=0.0005  Score=70.67  Aligned_cols=63  Identities=8%  Similarity=-0.071  Sum_probs=45.7

Q ss_pred             ccccccccccC--CCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          226 LKETQDAGAGK--EDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       226 ~~~~~~~~v~n--l~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+++.+||+|  |+..+++++|.+++...+.+....-     ..+||||||+|.+.++|.+|++.||+.
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~-----~~~kgfaFV~f~~~~~A~~Ai~~lnG~   79 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-----PPNKPYSFARYRTTEESKRAYVTLNGK   79 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEEC-----CTTCSEEEEEESSHHHHHHHHHHTTTC
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEE-----eCCCCEEEEEECCHHHHHHHHHHhCCC
Confidence            44566679999  5788999999888442221111111     125899999999999999999999985

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=96.61  E-value=0.00063  Score=59.87  Aligned_cols=58  Identities=12%  Similarity=-0.116  Sum_probs=42.5

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCce-EEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNF-GVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgf-gfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++...+........    .+.+|| |||+|.+.++|..|+..|++.
T Consensus        31 I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~----~~~~gfqAFVef~~~~~A~~Ai~~LnG~   89 (130)
T 3zzy_A           31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITF----TKNNQFQALLQYADPVSAQHAKLSLDGQ   89 (130)
T ss_dssp             EEEESCCSCCCHHHHHHHHTTSSCEEEEEEE----EETTEEEEEEEESCHHHHHHHHHHHTTC
T ss_pred             EEECCCCCCCCHHHHHHHHhCcCCEEEEEEE----cCCCCcEEEEEECCHHHHHHHHHHcCCC
Confidence            4899999999999999984422211111110    123688 999999999999999999875

>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=96.61  E-value=0.0093  Score=49.00  Aligned_cols=54  Identities=11%  Similarity=0.070  Sum_probs=45.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL  190 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~L  190 (577)
                      ...++| ++|..+...+|..+|+.||. ..|.++.|       .-|||.|.+++.|..|+..+
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidD-------TsAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDD-------TSAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEET-------TEEEEECSCHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcC-------CeEEEEecCHHHHHHHHHhc
Confidence            455666 99999999999999999994 44666666       48999999999999999876

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.57  E-value=0.00088  Score=55.24  Aligned_cols=53  Identities=2%  Similarity=-0.081  Sum_probs=39.9

Q ss_pred             ccccCCCcccchhhhc----CCCCCC-cccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKN----EPTKSP-ENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~----e~~ks~-~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||.||+..++.+.|.    +++..+ +.+.+      -+|   |||||.|.+.++|..|++.|++.
T Consensus        12 lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~------Vtg---G~AfV~F~~~esA~~A~~~l~G~   69 (96)
T 2diu_A           12 LYVYNLPANKDGKSVSNRLRRLSDNCGGKVLS------ITG---CSAILRFINQDSAERAQKRMENE   69 (96)
T ss_dssp             EEEESCCTTSCHHHHHHHHHHHHHTTTCCEEE------CCT---TCEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEE------Eec---CEEEEEECCHHHHHHHHHHhcCC
Confidence            6999999999988754    453333 12221      133   99999999999999999999874

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=96.57  E-value=0.00083  Score=58.67  Aligned_cols=57  Identities=11%  Similarity=-0.074  Sum_probs=41.5

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCce-EEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNF-GVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgf-gfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++...+........ .   + .|| |||+|.+.++|..|+..|++.
T Consensus        28 l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~-~---~-~Gf~aFVef~~~~~A~~A~~~LnG~   85 (124)
T 2e5i_A           28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIF-K---R-NGIQAMVEFESVLCAQKAKAALNGA   85 (124)
T ss_dssp             EEEESCCSCCCHHHHHHHHTTTSCEEEEEEE-E---S-SSEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEcCcCCCCCHHHHHHHHHhcCCEEEEEEE-e---C-CCCEEEEEECCHHHHHHHHHHhCCC
Confidence            5899999999999999884422211111111 1   1 286 999999999999999999875

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.46  E-value=0.00049  Score=57.73  Aligned_cols=53  Identities=13%  Similarity=-0.019  Sum_probs=34.9

Q ss_pred             cccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhHH
Q 008117          239 ESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVE  295 (577)
Q Consensus       239 ~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i~  295 (577)
                      ..+++.+|.+++..++.+.....    .+.++|||||+|.+.++|..|+..++++..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i----~~~~rGfaFVeF~~~~~A~~Ai~~~~~~~g   79 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVL----SSKKPGTAVVEFATVKAAELAVQNEVGLVD   79 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEE----ESSSSSEEEEEESCHHHHHHHHHTCCBCSS
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEE----ccCCCCEEEEEECCHHHHHHHHHhcCCCCC
Confidence            45677777776332221111111    147899999999999999999998766543

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.27  E-value=0.019  Score=47.70  Aligned_cols=69  Identities=22%  Similarity=0.355  Sum_probs=57.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhh---c--CceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKV---C--GTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL  200 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~---~--G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i  200 (577)
                      ....+|.|.|||+.+.++.|.-+|..   .  |.|..|....        +-|+|+|.+...|.+.|.. ..+.|+|..|
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~L   76 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQL   76 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEE
Confidence            34689999999999999999999986   2  4777776633        4789999999999999873 4788889888


Q ss_pred             EEE
Q 008117          201 MLK  203 (577)
Q Consensus       201 ~V~  203 (577)
                      .|.
T Consensus        77 sV~   79 (104)
T 2dhx_A           77 SLR   79 (104)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            884

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=96.18  E-value=0.0021  Score=54.28  Aligned_cols=28  Identities=14%  Similarity=0.000  Sum_probs=25.7

Q ss_pred             CCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          266 SHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       266 ~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ++.++|||||.|.+.++|.+|+..||+.
T Consensus        52 ~~~~~G~~FV~f~~~~~A~~Ai~~lnG~   79 (105)
T 2pe8_A           52 PDDEAVRIFLEFERVESAIKAVVDLNGR   79 (105)
T ss_dssp             CTTTSEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCCcEEEEEEECCHHHHHHHHHHHCCC
Confidence            4688999999999999999999999875

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=96.17  E-value=0.0013  Score=64.11  Aligned_cols=59  Identities=12%  Similarity=0.025  Sum_probs=41.9

Q ss_pred             ccccccCCCccc---------chhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESV---------QSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~---------~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+         ++.+|..++..++.+.....     ..++|||||+|.+.++|..|++.|++.
T Consensus       135 rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v-----~~~kG~AFV~F~~~~~Ae~A~~am~g~  202 (240)
T 3u1l_A          135 KTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRY-----VESKNCGFVKFKYQANAEFAKEAMSNQ  202 (240)
T ss_dssp             CEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEE-----EGGGTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             ceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEE-----ECCCCEEEEEeCCHHHHHHHHHHhCCC
Confidence            346999999988         68888777332221111111     135899999999999999999998874

>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=96.10  E-value=0.00069  Score=57.19  Aligned_cols=30  Identities=10%  Similarity=-0.037  Sum_probs=26.5

Q ss_pred             CCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          264 KESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       264 ~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +.+|.++|||||.|.+.++|.+|+..||+.
T Consensus        62 ~~~~~~~G~~fV~f~~~~~A~~A~~~lng~   91 (104)
T 1jmt_A           62 NLGDHLVGNVYVKFRREEDAEKAVIDLNNR   91 (104)
T ss_dssp             SSSSSSEEEEEEEESCHHHHHHHHHHHTTC
T ss_pred             CCCCCccEEEEEEECCHHHHHHHHHHHCCC
Confidence            344789999999999999999999999874

>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=95.82  E-value=0.028  Score=48.17  Aligned_cols=70  Identities=13%  Similarity=0.090  Sum_probs=56.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC-eEEEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG-QELMLKV  204 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~g-r~i~V~~  204 (577)
                      ..+-|.|-+.|+.. -..|...|..||.|+......      ...|-.|.|.+..+|.+||. .||..|+| -.|-|..
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p   93 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKP   93 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEE
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEE
Confidence            46778888999875 567888999999999887621      23699999999999999999 49999985 5666654

>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=95.77  E-value=0.011  Score=48.83  Aligned_cols=54  Identities=11%  Similarity=0.050  Sum_probs=45.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN  191 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Ln  191 (577)
                      ..++| ++|..+...+|..+|+.|| -..|.++.|       .-|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidD-------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDD-------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEET-------TEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcC-------CeEEEEecCHHHHHHHHHhcc
Confidence            34555 9999999999999999999 556777777       489999999999999999764

>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=95.75  E-value=0.0073  Score=50.87  Aligned_cols=27  Identities=19%  Similarity=-0.103  Sum_probs=24.9

Q ss_pred             CCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          267 HDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       267 g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +.++|||||.|.+.++|.+|+..||+.
T Consensus        56 ~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A           56 VPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             CTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             cCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            578999999999999999999999874

>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=95.60  E-value=0.0055  Score=52.10  Aligned_cols=25  Identities=16%  Similarity=0.233  Sum_probs=23.4

Q ss_pred             CCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          269 PTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       269 ~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ++|||||+|.+.++|..|+..|++.
T Consensus        63 ~~G~afV~f~~~~~A~~Ai~~lng~   87 (112)
T 2dit_A           63 PDGVASVSFRDPEEADYCIQTLDGR   87 (112)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCEEEEEEECCHHHHHHHHHHcCCC
Confidence            7999999999999999999999874

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=95.37  E-value=0.0023  Score=52.53  Aligned_cols=61  Identities=15%  Similarity=0.052  Sum_probs=41.1

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|..++..++.......  -......|.|||+|.+.++|..|+..|++.
T Consensus        17 ~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~--i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~   77 (96)
T 2e44_A           17 KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQ--VNTDSETAVVNVTYSSKDQARQALDKLNGF   77 (96)
T ss_dssp             CEEEEEECSSSCHHHHHHHHHHHSCEEEEEE--ECCSSSSEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEEEcCCCCCCHHHHHHHHHhcCCeEEEEE--eecCCCCCEEEEEECCHHHHHHHHHHhCCC
Confidence            3699999999999999988441111111100  001122344999999999999999988874

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=94.66  E-value=0.034  Score=45.85  Aligned_cols=69  Identities=9%  Similarity=0.096  Sum_probs=52.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCc--ceEEEEEeCCHHHHHHHHHHhCCceeC
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTP--KGFGFCEFESAEGVLRALRLLNKFNID  196 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~--kg~gFV~f~~~~~A~~Al~~Lng~~i~  196 (577)
                      +-.|.|..||+++|++++.+.++.+-.+.....+....+-++  -+-|||.|.+.+++......++|+.|-
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~   79 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFL   79 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            567999999999999999888887666544444333323222  245899999999999999999998873

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=94.13  E-value=0.064  Score=46.60  Aligned_cols=76  Identities=13%  Similarity=0.053  Sum_probs=53.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCC-------------CC-CcceEEEEEeCCHHHHHHHHHHhCCc
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPS-------------NG-TPKGFGFCEFESAEGVLRALRLLNKF  193 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~-------------tg-~~kg~gFV~f~~~~~A~~Al~~Lng~  193 (577)
                      ..-|.|-+.|+..+ ..+...|++||.|..-.-.....             .+ ...+|-.|.|.+..+|.+||.. ||.
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-NGA   84 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-TTC
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-CCe
Confidence            45677778876554 56678999999987621111100             00 1246889999999999999994 999


Q ss_pred             eeCCeEEEEEEc
Q 008117          194 NIDGQELMLKVD  205 (577)
Q Consensus       194 ~i~gr~i~V~~a  205 (577)
                      .|+|..|-|...
T Consensus        85 ii~G~mIGV~Py   96 (132)
T 3p3d_A           85 VFNGVLLGVIPY   96 (132)
T ss_dssp             EETTEECEEEEC
T ss_pred             EeCcEEEEEEEC
Confidence            999987777654

>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=93.78  E-value=0.032  Score=47.99  Aligned_cols=28  Identities=11%  Similarity=-0.065  Sum_probs=25.5

Q ss_pred             CCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          266 SHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       266 ~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ++.++||+||+|.+.++|.+|+..||+.
T Consensus        67 ~~~~~G~~FV~F~~~e~A~~Ai~~LnGr   94 (118)
T 3ue2_A           67 DAEIIVKIFVEFSIASETHKAIQALNGR   94 (118)
T ss_dssp             TCEEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCcceEEEEEEECCHHHHHHHHHHHCCC
Confidence            5678899999999999999999999875

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.18  E-value=0.082  Score=56.12  Aligned_cols=55  Identities=16%  Similarity=0.144  Sum_probs=42.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR  188 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~  188 (577)
                      .++|||. ++..+++.+|..+|+.||.|.++.+..+.  |   .|+.|+|.+.+++..++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~--g---~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF--G---LYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS--S---EEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC--C---eEEEEEeCCHHHHHHHHh
Confidence            5899997 79999999999999999999999886542  2   799999999999987764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=91.95  E-value=0.1  Score=45.03  Aligned_cols=55  Identities=5%  Similarity=-0.085  Sum_probs=37.7

Q ss_pred             cccccCCCcc-cchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCC-HHHHHHHHHHH
Q 008117          231 DAGAGKEDES-VQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEED-RKADQEALEKL  290 (577)
Q Consensus       231 ~~~v~nl~~~-~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~-~e~a~~Al~~l  290 (577)
                      +++|+||+.. ++..+|++++...+.+..++-   ..|  ..+|||.|.+ ..+|..|+.++
T Consensus        20 il~v~~l~~~~~sredLke~F~~~G~V~~Vd~---~~g--~~tgfVrf~~~~~~A~~av~~l   76 (121)
T 1owx_A           20 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDF---VRG--AKEGIILFKEKAKEALGKAKDA   76 (121)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEEC---CTT--CSEEEEEESSCHHHHHHHHHHT
T ss_pred             EEEEecCCCCcCCHHHHHHHHHhcCCEEEEEE---ecC--CCEEEEEECCChHHHHHHHHHh
Confidence            4688999999 999999988552222221111   111  2269999999 78999988875

>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=91.68  E-value=0.11  Score=44.29  Aligned_cols=25  Identities=16%  Similarity=-0.053  Sum_probs=23.4

Q ss_pred             CCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          269 PTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       269 ~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ++|||||.|.+.++|.+|+..||+.
T Consensus        54 ~~G~~fV~f~~~e~A~~Ai~~lnG~   78 (114)
T 3s6e_A           54 AQGNVYVKCPSIAAAIAAVNALHGR   78 (114)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHTTC
T ss_pred             CcEEEEEEECCHHHHHHHHHHhCCC
Confidence            5899999999999999999999975

>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=86.70  E-value=0.37  Score=45.65  Aligned_cols=30  Identities=13%  Similarity=-0.007  Sum_probs=27.1

Q ss_pred             CCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          264 KESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       264 ~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+|.++||+||+|.+.++|.+|+..|++.
T Consensus       169 ~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr  198 (222)
T 3dxb_A          169 EEDAEIIVKIFVEFSIASETHKAIQALNGR  198 (222)
T ss_dssp             STTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             ccCcCceeEEEEEECCHHHHHHHHHHhcCc
Confidence            456789999999999999999999999875

>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=80.55  E-value=3.5  Score=44.29  Aligned_cols=55  Identities=11%  Similarity=0.067  Sum_probs=45.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN  191 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Ln  191 (577)
                      ...++|+ +|..+...+|..+|+.||. ..|.++.+       ..|||.|.+.+.|..++..+.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widd-------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDD-------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSS-------SEEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcC-------CeEEEEECCHHHHHHHHHHHH
Confidence            4566676 8889999999999999994 45666655       489999999999999999884

---

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	577
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	5e-10
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-09
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-09
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-09
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-09
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-09
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-08
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-08
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-08
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	6e-08
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	6e-08
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	8e-08
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-07
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	2e-07
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	3e-07
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-07
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	5e-07
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-07
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	7e-07
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	7e-07
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	7e-07
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	9e-07
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	5e-05
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-06
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-06
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-06
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-06
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	3e-06
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	5e-04
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	0.002
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	4e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	7e-06
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	7e-06
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	8e-06
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-05
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-05
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-04
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-05
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-05
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-05
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-05
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	3e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	4e-05
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	5e-05
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-05
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	5e-05
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	5e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	7e-05
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-04
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-04
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	4e-04
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	4e-04
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	7e-04
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	7e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	0.002
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	0.002
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	0.002
d1ij5a_	321	a.39.1.9 (A:) Cbp40 (plasmodial specific CaII-bind	0.002

>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 = 60.0 bits (145), Expect = 4e-12
 Identities = 18/79 (22%), Positives = 30/79 (37%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
           T +YV  +  T   D + ++    G++      +    G P+G  F  +   E    A+ 
Sbjct: 7   TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 66

Query: 189 LLNKFNIDGQELMLKVDQA 207
            LN    +G    L V  A
Sbjct: 67  ALNNVIPEGGSQPLSVRLA 85

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.8 bits (139), Expect = 3e-11
 Identities = 15/79 (18%), Positives = 27/79 (34%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
             +YV  +  T     +  +    G + + +       G  +G GF  F+       A++
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 189 LLNKFNIDGQELMLKVDQA 207
            LN     G    + V  A
Sbjct: 67  GLNGQKPSGATEPITVKFA 85

>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 = 55.0 bits (132), Expect = 5e-10
 Identities = 18/103 (17%), Positives = 40/103 (38%), Gaps = 3/103 (2%)

Query: 126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 185
           +    +Y+  +     ++ +  +    G ++     +  +    +G  +  +E       
Sbjct: 5   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDAKN 61

Query: 186 ALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKE 228
           A   L+ FN+  + L++    A R + +    KK E  K LKE
Sbjct: 62  ACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKE 104

>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 = 53.1 bits (127), Expect = 1e-09
 Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 2/80 (2%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
           T + V  +        + ++ +  G + + +  +    G   G+ F +F S     RA++
Sbjct: 3   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

Query: 189 LLNKFNIDGQELMLKVDQAT 208
           +LN   +  +   LKV  A 
Sbjct: 63  VLNGITVRNKR--LKVSYAR 80

>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 = 52.7 bits (126), Expect = 1e-09
 Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
           K+++G ++     + +       G VK     + P     +GFGF  F    GV + L  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA- 60

Query: 190 LNKFNIDGQELMLKV 204
            ++  +D + +  KV
Sbjct: 61  QSRHELDSKTIDPKV 75

>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 = 52.6 bits (126), Expect = 2e-09
 Identities = 15/81 (18%), Positives = 31/81 (38%), Gaps = 2/81 (2%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
            +YVG + P      +       G + S +  +        G+ +  F+      RAL  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 190 LNKFNIDGQELMLKVDQATRE 210
           +N   I G+   +++  + R+
Sbjct: 62  MNFDVIKGKP--VRIMWSQRD 80

>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 = 51.6 bits (123), Expect = 4e-09
 Identities = 17/83 (20%), Positives = 30/83 (36%)

Query: 122 TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 181
           +  +   T + V  +  T   D +L        +      +Y   G P G     FES +
Sbjct: 3   SSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD 62

Query: 182 GVLRALRLLNKFNIDGQELMLKV 204
               A+  LN   I  +++ L +
Sbjct: 63  EATAAVIDLNDRPIGSRKVKLVL 85

>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 = 50.8 bits (121), Expect = 6e-09
 Identities = 19/79 (24%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
           K+++G +    + D V  +L   G +K++   +  + G  KG+ FCE+       +A+  
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 190 LNKFNIDGQELMLKVDQAT 208
           LN   +  ++  L V +A+
Sbjct: 63  LNGMQLGDKK--LLVQRAS 79

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (121), Expect = 1e-08
 Identities = 20/88 (22%), Positives = 41/88 (46%), Gaps = 3/88 (3%)

Query: 123 PAEKPQ-TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 181
            +E+ Q   VYVG +        +  +    G V +    +    G  +G+GF EF S E
Sbjct: 3   ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 62

Query: 182 GVLRALRLLNKFNIDGQELMLKVDQATR 209
               A+++++   + G+   ++V++A+ 
Sbjct: 63  DADYAIKIMDMIKLYGKP--IRVNKASA 88

>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 = 49.7 bits (118), Expect = 2e-08
 Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 2/80 (2%)

Query: 128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRAL 187
           +T + V  +      +   S+    G ++S K  +    G   G+GF  +   +   +A+
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 188 RLLNKFNIDGQELMLKVDQA 207
             LN   +  +   +KV  A
Sbjct: 62  NTLNGLRLQTKT--IKVSYA 79

>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 = 49.6 bits (118), Expect = 2e-08
 Identities = 18/85 (21%), Positives = 32/85 (37%)

Query: 126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 185
           K    +YVG ++     + +  +    G +K           T  GF F E+ S      
Sbjct: 5   KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 64

Query: 186 ALRLLNKFNIDGQELMLKVDQATRE 210
           A+R +N   +D + +    D   +E
Sbjct: 65  AMRYINGTRLDDRIIRTDWDAGFKE 89

>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 = 47.7 bits (113), Expect = 6e-08
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 1/75 (1%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
           K++VG ++P    + +       G V+S +          +GF F  F+  E V + +  
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 190 LNKFNIDGQELMLKV 204
               N+   +  +KV
Sbjct: 61  KYH-NVGLSKCEIKV 74

>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 = 48.6 bits (115), Expect = 6e-08
 Identities = 17/82 (20%), Positives = 29/82 (35%), Gaps = 3/82 (3%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
           TK++VG +        +    +  G ++          G  +G+GF          RA +
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 70

Query: 189 LLNKFNIDGQELMLKVDQATRE 210
             N   IDG+     V+ A   
Sbjct: 71  DPNPI-IDGR--KANVNLAYLG 89

>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 = 48.5 bits (115), Expect = 8e-08
 Identities = 20/101 (19%), Positives = 44/101 (43%), Gaps = 3/101 (2%)

Query: 109 MPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGT 168
           M   +  VPL      ++   K+++G ++     + + +  +  G +      + P++  
Sbjct: 1   MEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKR 60

Query: 169 PKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATR 209
            +GFGF  F S   V  A+      +IDG+  +++  +A  
Sbjct: 61  SRGFGFVTFSSMAEVDAAMA-ARPHSIDGR--VVEPKRAVA 98

>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 = 47.8 bits (113), Expect = 1e-07
 Identities = 18/87 (20%), Positives = 34/87 (39%), Gaps = 3/87 (3%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
           PA     ++YVG + P   +  +  V    G ++        +      F F EFE    
Sbjct: 9   PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDI---DLKNRRGGPPFAFVEFEDPRD 65

Query: 183 VLRALRLLNKFNIDGQELMLKVDQATR 209
              A+   + ++ DG  L ++  ++ R
Sbjct: 66  AEDAVYGRDGYDYDGYRLRVEFPRSGR 92

>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 = 47.2 bits (112), Expect = 1e-07
 Identities = 19/90 (21%), Positives = 41/90 (45%), Gaps = 4/90 (4%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQ-YPSNGTPKGFGFCEFESAE 181
           P ++  +K+ V  I   A+   +  +    G +K+ +  +     G  +GFGF +F + +
Sbjct: 3   PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 62

Query: 182 GVLRALR-LLNKFNIDGQELMLKVDQATRE 210
              +A   L +  ++ G+   L ++ A  E
Sbjct: 63  DAKKAFNALCHSTHLYGRR--LVLEWADSE 90

>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 = 47.0 bits (111), Expect = 2e-07
 Identities = 19/82 (23%), Positives = 40/82 (48%), Gaps = 2/82 (2%)

Query: 128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRAL 187
           + K++VG ++   +   +  V    G +      +       +GFGF  FE+ +    A+
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 188 RLLNKFNIDGQELMLKVDQATR 209
             +N  ++DG++  ++VDQA +
Sbjct: 65  MAMNGKSVDGRQ--IRVDQAGK 84

>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 = 46.6 bits (110), Expect = 3e-07
 Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 2/82 (2%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
            +++V  ++ T+  + +  +    G +             PKGF F  F   E  ++A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 189 LLNKFNIDGQELMLKVDQATRE 210
            ++     G+  ML V  +T +
Sbjct: 69  EVDGQVFQGR--MLHVLPSTIK 88

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.6 bits (110), Expect = 3e-07
 Identities = 13/92 (14%), Positives = 27/92 (29%), Gaps = 4/92 (4%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
             + P  ++ V  +      D +  +    GTV         +    +     ++     
Sbjct: 2   AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN----QFQALLQYADPVS 57

Query: 183 VLRALRLLNKFNIDGQELMLKVDQATREYLER 214
              A   L+  NI      L++D +    L  
Sbjct: 58  AQHAKLSLDGQNIYNACCTLRIDFSKLTSLNV 89

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.0 bits (109), Expect = 4e-07
 Identities = 15/89 (16%), Positives = 31/89 (34%), Gaps = 11/89 (12%)

Query: 122 TPAEKPQTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESA 180
           T      ++V++G +         V ++    G +              KGF F ++ + 
Sbjct: 9   TDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCS--------VHKGFAFVQYVNE 60

Query: 181 EGVLRALRLLNKFNIDGQELMLKVDQATR 209
                A+   +   I GQ  +L ++ A  
Sbjct: 61  RNARAAVAGEDGRMIAGQ--VLDINLAAE 87

>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 = 45.5 bits (107), Expect = 5e-07
 Identities = 13/74 (17%), Positives = 25/74 (33%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
           P   + V  ++       +  V    G +          +   +GF F  FE+ +    A
Sbjct: 8   PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 67

Query: 187 LRLLNKFNIDGQEL 200
               N   +DG+ +
Sbjct: 68  KERANGMELDGRRI 81

>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 = 45.4 bits (107), Expect = 6e-07
 Identities = 18/82 (21%), Positives = 35/82 (42%), Gaps = 5/82 (6%)

Query: 132 YVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP---SNGTPKGFGFCEFESAEGVLRALR 188
           ++  +  +   + +  V    G +KS   ++           GFGF E++  E   +AL+
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 189 LLNKFNIDGQELMLKVDQATRE 210
            L    +DG +  L+V  + R 
Sbjct: 62  QLQGHTVDGHK--LEVRISERA 81

>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 = 44.9 bits (106), Expect = 7e-07
 Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 3/79 (3%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
           K+ V  +        +  +    GT+K      Y  +G   G     FE     L+A++ 
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKA-AVHYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 190 LNKFNIDGQELMLKVDQAT 208
            N   +DG+   + +   T
Sbjct: 61  YNGVPLDGRP--MNIQLVT 77

>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 = 45.4 bits (107), Expect = 7e-07
 Identities = 18/85 (21%), Positives = 35/85 (41%)

Query: 126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 185
             +  +YVG +A   D   + +     G +   +          +GF F EFE AE    
Sbjct: 3   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62

Query: 186 ALRLLNKFNIDGQELMLKVDQATRE 210
           A+  +N+  + G+ + + + +  R 
Sbjct: 63  AIDNMNESELFGRTIRVNLAKPMRI 87

>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 = 45.0 bits (106), Expect = 7e-07
 Identities = 16/78 (20%), Positives = 37/78 (47%), Gaps = 3/78 (3%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
           K+++G ++     + + S  +  GT+      + P+    +GFGF  + + E V  A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 190 LNKFNIDGQELMLKVDQA 207
                +DG+  +++  +A
Sbjct: 68  RPH-KVDGR--VVEPKRA 82

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.6 bits (115), Expect = 9e-07
 Identities = 26/145 (17%), Positives = 64/145 (44%), Gaps = 6/145 (4%)

Query: 381 RDLKREKEREIDRYEREAERERVRKE-----REQRRKIEEAEREYERCLKDWEYR-ERER 434
           R   ++ +    +Y  E  +    +E      + +  + +A  + ++ L + E   E ER
Sbjct: 151 RLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVER 210

Query: 435 EKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADE 494
            K    +   +   E +RK E + +++E       +     +E  R + ++E+E  LA +
Sbjct: 211 VKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALK 270

Query: 495 VREEEEIAVAKRRAEEEQLQQQQRD 519
           ++E+E++     + E   ++ + +D
Sbjct: 271 LQEQEQLLKEGFQKESRIMKNEIQD 295

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (101), Expect = 5e-05
 Identities = 24/140 (17%), Positives = 56/140 (40%), Gaps = 5/140 (3%)

Query: 377 RDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREK 436
            ++ R   + +E      + +        + +Q    +E E E ER   +      +   
Sbjct: 165 YEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLH 224

Query: 437 ERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVR 496
           E Q + E+  E++ +  +E L    E  ++ R +  +   E     +++E+E+ L +  +
Sbjct: 225 EMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKE-QERTLALKLQEQEQLLKEGFQ 283

Query: 497 EEEEIAVAKRRAEEEQLQQQ 516
           +E        + E + LQ +
Sbjct: 284 KESR----IMKNEIQDLQTK 299

>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 = 45.1 bits (106), Expect = 1e-06
 Identities = 16/84 (19%), Positives = 30/84 (35%), Gaps = 2/84 (2%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
               +++  +        +L +    G V S K          K FGF  +++      A
Sbjct: 17  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 76

Query: 187 LRLLNKFNIDGQELMLKVDQATRE 210
           ++ +N F I  +   LKV     +
Sbjct: 77  IQSMNGFQIGMKR--LKVQLKRSK 98

>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 = 44.2 bits (104), Expect = 2e-06
 Identities = 17/84 (20%), Positives = 30/84 (35%), Gaps = 2/84 (2%)

Query: 121 VTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESA 180
           V  A +  + + V  +        +       G V   +  +    G  KGFGF  F   
Sbjct: 1   VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEY 60

Query: 181 EGVLRALRLLNKFNIDGQELMLKV 204
           E  ++ +   +   IDG+    K+
Sbjct: 61  ETQVKVMSQRHM--IDGRWCDCKL 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 = 43.6 bits (102), Expect = 2e-06
 Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 3/80 (3%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKR-AQYPSNGTPKGFGFCEFESAEGVLRALRL 189
           +++G + P  D   +       G +    +  + P  G  KG+ F  F S +    A+  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 190 LNKFNIDGQELMLKVDQATR 209
           +N   +  +   + V  A +
Sbjct: 61  MNGQYLCNRP--ITVSYAFK 78

>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 = 43.4 bits (102), Expect = 2e-06
 Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 3/78 (3%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
           K+++G ++       +       G V        P  G  +GFGF  F+ +E V + +  
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD- 59

Query: 190 LNKFNIDGQELMLKVDQA 207
             +  ++G+   +   +A
Sbjct: 60  QKEHKLNGKV--IDPKRA 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 = 43.6 bits (102), Expect = 3e-06
 Identities = 20/80 (25%), Positives = 31/80 (38%), Gaps = 2/80 (2%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
             ++V  I   A  D +       G +K+         G  KG+   E+E+ +  L A  
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 189 LLNKFNIDGQELMLKVDQAT 208
            LN   I GQ   ++VD   
Sbjct: 68  ALNGAEIMGQT--IQVDWCF 85

>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 = 43.6 bits (102), Expect = 4e-06
 Identities = 28/88 (31%), Positives = 42/88 (47%), Gaps = 2/88 (2%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
             ++    V+VG I   A  + +  +    G V S++       G PKG+GFCE++  E 
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 183 VLRALRLLNKFNIDGQELMLKVDQATRE 210
            L A+R LN     G+   L+VD A  E
Sbjct: 63  ALSAMRNLNGREFSGRA--LRVDNAASE 88

>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 = 44.5 bits (104), Expect = 4e-06
 Identities = 24/96 (25%), Positives = 40/96 (41%), Gaps = 2/96 (2%)

Query: 114 RPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFG 173
           + +P   + P       + V  I  T D   +  + +  G ++S K          +G+G
Sbjct: 28  QHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYG 87

Query: 174 FCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATR 209
           F +F+S     +A+  LN FNI  +   LKV  A  
Sbjct: 88  FVKFQSGSSAQQAIAGLNGFNILNKR--LKVALAAS 121

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.7 bits (100), Expect = 7e-06
 Identities = 15/84 (17%), Positives = 31/84 (36%), Gaps = 6/84 (7%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
           P T+++VG + P      +            +   +   +     F + ++ES +    A
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFD------RFGSIRTIDHVKGDSFAYIQYESLDAAQAA 69

Query: 187 LRLLNKFNIDGQELMLKVDQATRE 210
              +  F + G +  L+VD A   
Sbjct: 70  CAKMRGFPLGGPDRRLRVDFAKSG 93

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.3 bits (99), Expect = 7e-06
 Identities = 12/86 (13%), Positives = 28/86 (32%), Gaps = 3/86 (3%)

Query: 126 KPQTKVYVGKIAPTADSDFV-LSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 184
           +P   +Y+  +      D +  S+  +              +   +G  F  F+      
Sbjct: 1   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 60

Query: 185 RALRLLNKFNIDGQELMLKVDQATRE 210
            ALR +  F    +   +++  A  +
Sbjct: 61  NALRSMQGFPFYDKP--MRIQYAKTD 84

>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 = 42.4 bits (99), Expect = 8e-06
 Identities = 17/84 (20%), Positives = 28/84 (33%), Gaps = 2/84 (2%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGT--PKGFGFCEFESAEGVLRA 186
            ++++G I      + +L  +               +      +GF F E+ES      A
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 187 LRLLNKFNIDGQELMLKVDQATRE 210
            R L    I      + VD A  E
Sbjct: 62  RRKLMPGRIQLWGHQIAVDWAEPE 85

>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 = 41.3 bits (96), Expect = 1e-05
 Identities = 16/78 (20%), Positives = 33/78 (42%), Gaps = 3/78 (3%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
           K++VG ++     + V    +  G V         +    +GFGF  FES + V +    
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE- 59

Query: 190 LNKFNIDGQELMLKVDQA 207
           ++   I+ +   ++  +A
Sbjct: 60  IHFHEINNKM--VECKKA 75

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.8 bits (102), Expect = 1e-05
 Identities = 14/88 (15%), Positives = 34/88 (38%), Gaps = 1/88 (1%)

Query: 123 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 182
            A     K++VG I    +   +    +  G ++  +      +G  +GF F  F+  + 
Sbjct: 92  GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 151

Query: 183 VLRALRLLNKFNIDGQELMLKVDQATRE 210
           V + +       ++G    ++   + +E
Sbjct: 152 VDKIVI-QKYHTVNGHNCEVRKALSKQE 178

>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 = 40.8 bits (94), Expect = 1e-04
 Identities = 13/65 (20%), Positives = 28/65 (43%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
           K+++G ++     + + S  +  GT+      + P+    +GFGF  + + E V  A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 190 LNKFN 194
                
Sbjct: 68  RPHKV 72

>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 = 41.6 bits (97), Expect = 2e-05
 Identities = 17/87 (19%), Positives = 37/87 (42%), Gaps = 4/87 (4%)

Query: 122 TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 181
           + ++    +++V  I        +  +    G +   +          KGFGF  FE++ 
Sbjct: 5   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSA 62

Query: 182 GVLRALRLLNKFNIDGQELMLKVDQAT 208
              RA   L+   ++G++  ++V+ AT
Sbjct: 63  DADRAREKLHGTVVEGRK--IEVNNAT 87

>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 = 41.2 bits (96), Expect = 2e-05
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 2/81 (2%)

Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
               + V  ++       +  + +  G++     A+  + G  KGF F  F   E   RA
Sbjct: 7   DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 66

Query: 187 LRLLNKFNIDGQELMLKVDQA 207
           +  ++ F  D     L V+ A
Sbjct: 67  IAGVSGFGYDHLI--LNVEWA 85

>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 = 41.2 bits (96), Expect = 2e-05
 Identities = 13/91 (14%), Positives = 30/91 (32%), Gaps = 7/91 (7%)

Query: 119 PTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFE 178
           P  +   +    +    ++     D +  V +    ++   +     +G  KG  + EF+
Sbjct: 7   PCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFK 61

Query: 179 SAEGVLRALRLLNKFNIDGQELMLKVDQATR 209
           S     + L       IDG+   + +     
Sbjct: 62  SEADAEKNLEEKQGAEIDGRS--VSLYYTGE 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 = 41.1 bits (96), Expect = 2e-05
 Identities = 14/80 (17%), Positives = 30/80 (37%), Gaps = 8/80 (10%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
           ++++VG + P    + +  + +  G        +         FGF   E+      A  
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKV 62

Query: 189 LLNKFNIDGQELMLKVDQAT 208
            L+   + G++  L+V  A 
Sbjct: 63  ELDNMPLRGKQ--LRVRFAC 80

>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 = 40.8 bits (95), Expect = 3e-05
 Identities = 21/86 (24%), Positives = 34/86 (39%), Gaps = 4/86 (4%)

Query: 125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 184
           +     +YVG ++       +L +    G  KS K      + +   + F EF       
Sbjct: 5   DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCK--MITEHTSNDPYCFVEFYEHRDAA 62

Query: 185 RALRLLNKFNIDGQELMLKVDQATRE 210
            AL  +N   I G+E  +KV+ AT  
Sbjct: 63  AALAAMNGRKILGKE--VKVNWATTP 86

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 4e-05
 Identities = 11/82 (13%), Positives = 29/82 (35%), Gaps = 9/82 (10%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
           + + V  +   ++   V  +LK       +           K   F    + E    A++
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCYVD-------RNKRTAFVTLLNGEQAQNAIQ 58

Query: 189 LLNKFNIDGQELMLKVDQATRE 210
           + ++++  G++  L V     +
Sbjct: 59  MFHQYSFRGKD--LIVQLQPTD 78

>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 = 40.0 bits (93), Expect = 5e-05
 Identities = 12/80 (15%), Positives = 21/80 (26%), Gaps = 9/80 (11%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
           + V+VG+       D +       G V      +       + F F  F   +       
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLCG 60

Query: 189 LLNKFNIDGQELMLKVDQAT 208
                 I G    + +  A 
Sbjct: 61  --EDLIIKGIS--VHISNAE 76

>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 = 40.1 bits (93), Expect = 5e-05
 Identities = 14/79 (17%), Positives = 26/79 (32%), Gaps = 6/79 (7%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKS-----WKRAQYPSNGTPKGFGFCEFESAEGVL 184
           ++YVG I      + ++        +                   K F F EF S +   
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 185 RALRLLNKFNIDGQELMLK 203
           +A+   +     GQ L ++
Sbjct: 63  QAMA-FDGIIFQGQSLKIR 80

>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 = 39.7 bits (92), Expect = 5e-05
 Identities = 14/80 (17%), Positives = 34/80 (42%), Gaps = 9/80 (11%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
           K+Y+G ++P   +D +  +        + +           G+ F ++      +RA+  
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQV------LLKSGYAFVDYPDQNWAIRAIET 56

Query: 190 LN-KFNIDGQELMLKVDQAT 208
           L+ K  + G+   ++VD + 
Sbjct: 57  LSGKVELHGKI--MEVDYSV 74

>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 = 39.4 bits (91), Expect = 5e-05
 Identities = 14/70 (20%), Positives = 29/70 (41%)

Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
           +Y+  + P      ++ + +  G + S K     +    KG+GF +F+S     +A+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 191 NKFNIDGQEL 200
               +  Q  
Sbjct: 61  KASGVQAQMA 70

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.5 bits (92), Expect = 7e-05
 Identities = 11/81 (13%), Positives = 22/81 (27%), Gaps = 9/81 (11%)

Query: 128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRAL 187
            T V V      + S  +L      G +     +          +    ++S     +AL
Sbjct: 4   DTWVTVFGFPQASASY-ILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKAL 56

Query: 188 RLLNKFNIDGQELMLKVDQAT 208
               +       +M+ V    
Sbjct: 57  SKDGRI-FGES-IMIGVKPCI 75

>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 = 38.9 bits (90), Expect = 1e-04
 Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 3/78 (3%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
           K++VG I    +   +    +  G ++  +      +G  +GF F  F+  + V + +  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI- 62

Query: 190 LNKFNIDGQELMLKVDQA 207
                ++G     +V +A
Sbjct: 63  QKYHTVNGH--NCEVRKA 78

>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 = 38.5 bits (89), Expect = 2e-04
 Identities = 15/81 (18%), Positives = 34/81 (41%), Gaps = 4/81 (4%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
             +++  +  + D+  +       G + S K     +    KG+GF  FE+ E   RA+ 
Sbjct: 9   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIE 66

Query: 189 LLNKFNIDGQELMLKVDQATR 209
            +N   ++ ++  + V +   
Sbjct: 67  KMNGMLLNDRK--VFVGRFKS 85

>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 = 37.6 bits (87), Expect = 4e-04
 Identities = 15/90 (16%), Positives = 25/90 (27%), Gaps = 8/90 (8%)

Query: 120 TVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFES 179
            V  +      VY G IA       +       G +   +            + F  F +
Sbjct: 10  VVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFST 63

Query: 180 AEGVLRALRLLNKFNIDGQELMLKVDQATR 209
            E    A+  +N   I+G    +K      
Sbjct: 64  HESAAHAIVSVNGTTIEGHV--VKCYWGKE 91

>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 = 37.9 bits (87), Expect = 4e-04
 Identities = 14/87 (16%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

Query: 124 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 183
               +   ++  I  +     VL  L+     ++       +NG   G    +F++ +  
Sbjct: 4   VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 63

Query: 184 LRALRLLNKFNIDGQELMLKVDQATRE 210
            ++ R L++  ++G+     V   T E
Sbjct: 64  RKSER-LHRKKLNGR--EAFVHVVTLE 87

>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 = 36.6 bits (84), Expect = 7e-04
 Identities = 13/83 (15%), Positives = 30/83 (36%), Gaps = 5/83 (6%)

Query: 129 TKVYVGKIAPTADSDFVLSVL--KVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
            ++ +  ++     + +L           K    A    +       F  FE+ +   RA
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 187 LRLLNKFNIDGQELMLKVDQATR 209
           L+ +N+  +  +E  + V  A +
Sbjct: 65  LQ-MNRSLLGNRE--ISVSLADK 84

>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 = 37.1 bits (85), Expect = 7e-04
 Identities = 24/96 (25%), Positives = 35/96 (36%), Gaps = 11/96 (11%)

Query: 123 PAEKPQ-TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP--------SNGTPKGFG 173
           P E    + +YV  +  +   D +    K CG VK  KR   P          G PKG  
Sbjct: 2   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 61

Query: 174 FCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATR 209
              +E       A+   +  +  G +  LKV  A +
Sbjct: 62  TVSYEDPPTAKAAVEWFDGKDFQGSK--LKVSLARK 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 = 35.2 bits (80), Expect = 0.002
 Identities = 18/80 (22%), Positives = 28/80 (35%), Gaps = 5/80 (6%)

Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
           T V V  +  + + + V    K CG +     A          F   EF   +G L A+ 
Sbjct: 1   TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT 58

Query: 189 LLNKFNIDGQELMLKVDQAT 208
             +K  +   E  + V   T
Sbjct: 59  KTHKV-VGQNE--IIVSHLT 75

>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 = 35.4 bits (81), Expect = 0.002
 Identities = 12/78 (15%), Positives = 27/78 (34%), Gaps = 8/78 (10%)

Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
            +YV  +  +   + +             +          + + F  F + E  + A++ 
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVER------VKKIRDYAFVHFSNREDAVEAMKA 63

Query: 190 LNKFNIDGQELMLKVDQA 207
           LN   +DG    ++V  A
Sbjct: 64  LNGKVLDGSP--IEVTLA 79

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.6 bits (81), Expect = 0.002
 Identities = 20/91 (21%), Positives = 41/91 (45%), Gaps = 5/91 (5%)

Query: 123 PAEKPQ-TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 181
           P++  +   V++  ++  ++ + +  VL+  G +K  +   +P     KG  F +F + E
Sbjct: 2   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 182 GVLRALRLLN-KFNIDGQELM---LKVDQAT 208
              + L   + +    G +L    LKVD A 
Sbjct: 62  AAQKCLAAASLEAEGGGLKLDGRQLKVDLAV 92

>d1ij5a_ a.39.1.9 (A:) Cbp40 (plasmodial specific CaII-binding protein LAV1-2) {Physarum polycephalum [TaxId: 5791]} Length = 321

class: All alpha proteins
fold: EF Hand-like
superfamily: EF-hand
family: Cbp40 (plasmodial specific CaII-binding protein LAV1-2)
domain: Cbp40 (plasmodial specific CaII-binding protein LAV1-2)
species: Physarum polycephalum [TaxId: 5791]

 Score = 38.1 bits (87), Expect = 0.002
 Identities = 17/117 (14%), Positives = 48/117 (41%), Gaps = 2/117 (1%)

Query: 408 EQRRKIEEAEREYERCLKDWEYREREREKERQYEKE--KEKERERKRKKEILYDEEEDED 465
           ++   +++     E   K  ++     +++R   +    +KE+E+K K      + ++E 
Sbjct: 9   QREANVKKVHENLEELQKKLDHTSFAHKEDRDRLEAQIAQKEQEQKAKLAEYDQKVQNEF 68

Query: 466 DSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALK 522
           D+R+R  R     +      ++      +  E++     + R  +  L ++  + L+
Sbjct: 69  DARERAEREREAARGDAAAEKQRLASLLKDLEDDASGYNRLRPSKPMLSEEDTNILR 125

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	577
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.79
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.78
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.77
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.77
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.77
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.76
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.76
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.76
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.76
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.76
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.75
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.75
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.75
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.75
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.74
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.74
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.74
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.73
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.73
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.72
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.72
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.72
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.72
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.72
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.71
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.71
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.71
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.7
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.7
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.7
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.7
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.69
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.69
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.69
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.68
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.67
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.67
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.67
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.66
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.66
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.65
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.64
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.64
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.63
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.63
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.63
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.63
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.62
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.62
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.61
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.61
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.61
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.6
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.6
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.59
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.59
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.59
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.58
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.58
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.57
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.57
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.56
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.56
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.56
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.56
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.55
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.54
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.54
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.54
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.54
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.53
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.53
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.53
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.51
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.47
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.46
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.45
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.42
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.41
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	99.38
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.3
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.28
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.16
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.13
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.06
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	98.3
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	98.27
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	98.23
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	98.18
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	98.17
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	98.14
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	98.13
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	98.13
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	98.12
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	98.11
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	98.1
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.08
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	98.08
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.05
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	98.05
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	98.03
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	98.03
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	98.01
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	98.01
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.0
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	98.0
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	97.99
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	97.99
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	97.98
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	97.98
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	97.98
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	97.98
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	97.96
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	97.96
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	97.95
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	97.95
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	97.92
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	97.92
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	97.9
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	97.88
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	97.86
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	97.86
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	97.86
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	97.86
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	97.86
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	97.84
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	97.83
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	97.82
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	97.82
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	97.82
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	97.8
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	97.79
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	97.77
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	97.75
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	97.74
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	97.72
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	97.71
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	97.69
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	97.68
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	97.68
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	97.68
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	97.67
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	97.66
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	97.65
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	97.61
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	97.57
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	97.55
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	97.54
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	97.52
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	97.48
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	97.48
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	97.47
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	97.47
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	97.43
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	97.33
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	97.26
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	97.26
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	97.25
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	97.2
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	97.17
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.15
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.07
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	97.03
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	96.98
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	96.85
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	96.85
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.83
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	96.69
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	96.64
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	96.51
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	96.17
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	93.32
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	92.26
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	88.97

>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=99.79  E-value=1.9e-19  Score=168.18  Aligned_cols=153  Identities=16%  Similarity=0.218  Sum_probs=119.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      .++|||||||+.+|+++|+.+|+.||.|.++.++.+..+|.++|||||+|.+.++|..|+. +++..++++.+.+.....
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            4799999999999999999999999999999999999999999999999999999999998 478888898888876543


Q ss_pred             hHHHHHhhhhhhhhccccccccccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHH
Q 008117          208 TREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEA  286 (577)
Q Consensus       208 ~~~~~~~~~~~k~~~~~~~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~A  286 (577)
                      ......         .......+.+||+||+..+++.+|.+++..++....... .+..+|.++|||||.|.+.++|.+|
T Consensus        85 ~~~~~~---------~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~A  155 (183)
T d1u1qa_          85 REDSQR---------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI  155 (183)
T ss_dssp             TTGGGS---------TTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHH
T ss_pred             cccccc---------cccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHH
Confidence            321111         011122233599999999999999988442221111111 1256789999999999999999999


Q ss_pred             HHHH
Q 008117          287 LEKL  290 (577)
Q Consensus       287 l~~l  290 (577)
                      |...
T Consensus       156 l~~~  159 (183)
T d1u1qa_         156 VIQK  159 (183)
T ss_dssp             HTSS
T ss_pred             HHhC
Confidence            8643

>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=99.78  E-value=3.5e-19  Score=144.26  Aligned_cols=80  Identities=16%  Similarity=0.346  Sum_probs=77.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      .++|||+|||+.+|+++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|+|.|+.+
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            57899999999999999999999999999999999999999999999999999999999999999999999999999864

>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=99.77  E-value=5.2e-19  Score=148.97  Aligned_cols=84  Identities=17%  Similarity=0.273  Sum_probs=78.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.|.+|.|+.+..+|.++|||||+|.+.++|..||. |||..|+|+.|.|.++
T Consensus        16 ~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a   94 (101)
T d2cq4a1          16 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQAS   94 (101)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEH
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEEC
Confidence            345799999999999999999999999999999999999999999999999999999999996 9999999999999998


Q ss_pred             hhhHH
Q 008117          206 QATRE  210 (577)
Q Consensus       206 ~~~~~  210 (577)
                      .+.+.
T Consensus        95 ~~~~n   99 (101)
T d2cq4a1          95 QAEKN   99 (101)
T ss_dssp             HHHHH
T ss_pred             CCCCC
Confidence            76544

>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=99.77  E-value=1.3e-18  Score=142.85  Aligned_cols=82  Identities=22%  Similarity=0.237  Sum_probs=77.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|..+|+.||.|.+|+|+.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.|+
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            35789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        85 ~~   86 (88)
T d1rk8a_          85 FV   86 (88)
T ss_dssp             EE
T ss_pred             cC
Confidence            64

>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=99.77  E-value=8.5e-19  Score=141.27  Aligned_cols=77  Identities=19%  Similarity=0.343  Sum_probs=75.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       130 tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      +|||||||+.+|+++|..+|+.||.|.+|+|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|+|.|+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999885

>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=99.76  E-value=1.3e-18  Score=144.30  Aligned_cols=82  Identities=21%  Similarity=0.307  Sum_probs=78.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ..+++|||+|||+++|+++|+.+|+.||.|.+|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
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            45789999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        85 ~~   86 (93)
T d1h2vz_          85 AG   86 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>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=1.6e-18  Score=140.25  Aligned_cols=80  Identities=16%  Similarity=0.320  Sum_probs=76.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      .++|||+|||+.+++++|+.+|+.||.|..|.|+.+..+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.|+.+
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            46899999999999999999999999999999999989999999999999999999999999999999999999999864

>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=99.76  E-value=6.3e-19  Score=145.06  Aligned_cols=81  Identities=21%  Similarity=0.363  Sum_probs=78.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..++|||+|||+++|+++|+.+|+.||.|.+|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+.
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             h
Q 008117          207 A  207 (577)
Q Consensus       207 ~  207 (577)
                      +
T Consensus        84 p   84 (89)
T d2cqba1          84 P   84 (89)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.76  E-value=4.3e-18  Score=151.95  Aligned_cols=82  Identities=23%  Similarity=0.338  Sum_probs=78.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||||||+++|+++|+.+|+.||.|.+|.|+.++.||.++|||||+|.+.++|..||..|||+.|+|+.|+|.|+
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            34678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus       120 ~~  121 (139)
T d1u6fa1         120 AS  121 (139)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=99.76  E-value=1.4e-18  Score=144.17  Aligned_cols=82  Identities=21%  Similarity=0.400  Sum_probs=78.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..++|||+|||+.+|+++|+.+|+.||.|.+|.|+.++.+|.++|||||+|.+.++|..||..|||+.|+|+.|+|.+|.
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            35799999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             hh
Q 008117          207 AT  208 (577)
Q Consensus       207 ~~  208 (577)
                      ..
T Consensus        88 ~~   89 (93)
T d1x5ua1          88 AH   89 (93)
T ss_dssp             TT
T ss_pred             CC
Confidence            63

>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=99.75  E-value=2.3e-18  Score=145.39  Aligned_cols=82  Identities=17%  Similarity=0.284  Sum_probs=78.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      +.++|||+|||+++++++|+.+|+.||.|.+|.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+.
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            45789999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             hh
Q 008117          207 AT  208 (577)
Q Consensus       207 ~~  208 (577)
                      ..
T Consensus        97 ~k   98 (102)
T d2cpza1          97 SK   98 (102)
T ss_dssp             CS
T ss_pred             CC
Confidence            53

>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=99.75  E-value=2.2e-18  Score=142.01  Aligned_cols=82  Identities=18%  Similarity=0.295  Sum_probs=78.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||..+++++|..+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
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            35689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      .+
T Consensus        86 kp   87 (90)
T d2cq0a1          86 KP   87 (90)
T ss_dssp             SC
T ss_pred             eC
Confidence            65

>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=99.75  E-value=3e-18  Score=138.96  Aligned_cols=76  Identities=17%  Similarity=0.242  Sum_probs=73.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  202 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V  202 (577)
                      +.++|||+|||+.+|+++|+.+|+.||.|.+|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|+|
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            4689999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.75  E-value=2.8e-18  Score=139.84  Aligned_cols=79  Identities=18%  Similarity=0.294  Sum_probs=74.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG--QELMLKV  204 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~g--r~i~V~~  204 (577)
                      ..++|||+|||+.+|+++|+.+|+.||.|.+|+|+.++.+|.++|||||+|.+.++|..|+..|||..|+|  ++|.|+|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            35789999999999999999999999999999999999999999999999999999999999999999998  5589987


Q ss_pred             c
Q 008117          205 D  205 (577)
Q Consensus       205 a  205 (577)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.74  E-value=1.4e-18  Score=141.58  Aligned_cols=79  Identities=22%  Similarity=0.456  Sum_probs=76.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      .+|||+|||+++|+++|+.+|+.||.|..|+|+.++.||.++|||||+|.+.++|..|+..|||..|+|+.|.|.++..
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~~   80 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASV   80 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            4799999999999999999999999999999999999999999999999999999999999999999999999999865

>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=4.2e-18  Score=138.81  Aligned_cols=79  Identities=22%  Similarity=0.379  Sum_probs=75.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG--QELMLKV  204 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~g--r~i~V~~  204 (577)
                      ..++|||+|||+++++++|+.+|+.||.|..|+|+.++.+|.++|||||+|.+.++|..||..|||..+.|  ++|.|.|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            46789999999999999999999999999999999999999999999999999999999999999999976  8899988


Q ss_pred             c
Q 008117          205 D  205 (577)
Q Consensus       205 a  205 (577)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.74  E-value=3.6e-18  Score=141.91  Aligned_cols=84  Identities=20%  Similarity=0.402  Sum_probs=77.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHh-CCceeCCeEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP-SNGTPKGFGFCEFESAEGVLRALRLL-NKFNIDGQELML  202 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~-~tg~~kg~gFV~f~~~~~A~~Al~~L-ng~~i~gr~i~V  202 (577)
                      ....++|||+|||+.+++++|+.+|+.||.|.+|.|+.+. .+|.++|||||+|.+.++|..||..| ||..|+|+.|.|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            3457889999999999999999999999999999998875 48999999999999999999999988 999999999999


Q ss_pred             EEchhh
Q 008117          203 KVDQAT  208 (577)
Q Consensus       203 ~~a~~~  208 (577)
                      .||...
T Consensus        85 ~~A~~~   90 (94)
T d2cpha1          85 EWADSE   90 (94)
T ss_dssp             EECCCC
T ss_pred             EEcCCC
Confidence            998653

>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=99.73  E-value=6.4e-18  Score=141.78  Aligned_cols=82  Identities=16%  Similarity=0.258  Sum_probs=78.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|..||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|+|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        86 ~~   87 (99)
T d1whwa_          86 TI   87 (99)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.73  E-value=8.5e-18  Score=136.60  Aligned_cols=79  Identities=20%  Similarity=0.359  Sum_probs=74.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..++|||||||+++|+++|..+|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||. ++++.|+|+.|.|+.|.
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            35799999999999999999999999999999999999999999999999999999999998 69999999999998764

>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=4.3e-18  Score=137.38  Aligned_cols=79  Identities=19%  Similarity=0.267  Sum_probs=69.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      +||||+|||+++|+++|..+|+.||.|..+.++.+..+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++.+
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            6999999999999999999999999999998888888999999999999999999999999999999999999999864

>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=99.72  E-value=9.6e-18  Score=134.31  Aligned_cols=76  Identities=18%  Similarity=0.257  Sum_probs=73.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       130 tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      .|||+|||+.+++++|+.+|+.||.|.+|.|+.++ +|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            69999999999999999999999999999999985 89999999999999999999999999999999999999875

>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=99.72  E-value=1.1e-17  Score=141.32  Aligned_cols=82  Identities=18%  Similarity=0.290  Sum_probs=76.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      +...++|||+|||+.+|+++|+++|+.||.|.+|.|+.++.||.++|||||+|.+.++|..||..+|+ .|+|+.|.|.+
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            34567899999999999999999999999999999999999999999999999999999999998876 79999999998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        86 a~~   88 (103)
T d2cqda1          86 AYL   88 (103)
T ss_dssp             STT
T ss_pred             cCC
Confidence            765

>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=99.72  E-value=7e-18  Score=138.97  Aligned_cols=82  Identities=18%  Similarity=0.361  Sum_probs=77.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ....+|||||||+++|+.+|..+|+.||.|..|.++.+..+|.++|||||+|.+.++|..||..|||+.|+|+.|.|.++
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            34678999999999999999999999999999999998899999999999999999999999999999999999999987


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        83 ~~   84 (90)
T d1x5sa1          83 GK   84 (90)
T ss_dssp             EC
T ss_pred             CC
Confidence            65

>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=99.72  E-value=2.4e-18  Score=137.48  Aligned_cols=76  Identities=22%  Similarity=0.383  Sum_probs=73.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ++|||+|||+++|+++|+.+|+.||.|.+|.|+.++.||.++|||||+|.+.++|.+||. +|++.|+|+.|.|++|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            579999999999999999999999999999999999999999999999999999999998 7999999999999875

>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=99.72  E-value=5.3e-18  Score=143.63  Aligned_cols=82  Identities=29%  Similarity=0.532  Sum_probs=78.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..++|||+|||+++|+++|..+|+.||.|.+|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++.
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            35789999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             hh
Q 008117          207 AT  208 (577)
Q Consensus       207 ~~  208 (577)
                      ..
T Consensus        87 ~~   88 (104)
T d1p1ta_          87 SE   88 (104)
T ss_dssp             CT
T ss_pred             CC
Confidence            53

>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=2.4e-17  Score=135.61  Aligned_cols=81  Identities=19%  Similarity=0.256  Sum_probs=75.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+++|+++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||.  ++..|+|+.|.|+++
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 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh--cCCccCCEEeEEEeC
Confidence            356889999999999999999999999999999999999999999999999999999999998  455899999999988


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus        84 ~~k   86 (90)
T d2cqga1          84 NSK   86 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            653

>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=99.71  E-value=2.1e-17  Score=136.04  Aligned_cols=80  Identities=21%  Similarity=0.317  Sum_probs=74.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||||||.++|+++|+.+|+.||.|..|.|+.+..++  +|||||+|.+.++|..|+..|||..|+|+.|+|.|+
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            456899999999999999999999999999999999886544  789999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        84 ~~   85 (90)
T d2cqia1          84 TT   85 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.71  E-value=2.6e-17  Score=132.03  Aligned_cols=77  Identities=16%  Similarity=0.362  Sum_probs=73.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .++|||||||+++|+++|+.+|+.||.|..+.++.++.++.++|||||+|.+.++|.+|+. |||..|+|+.|.|+.|
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            5789999999999999999999999999999999999999999999999999999999996 8999999999999865

>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=1.4e-17  Score=135.52  Aligned_cols=77  Identities=21%  Similarity=0.469  Sum_probs=72.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNG---TPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       131 lfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg---~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      |||+|||+++|+++|+.+|+.||.|.+|.|+.++.++   .++|||||+|.+.++|..||..|||..|+|+.|.|.|+..
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            8999999999999999999999999999999887665   4689999999999999999999999999999999998754

>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=99.70  E-value=1.3e-17  Score=140.72  Aligned_cols=79  Identities=22%  Similarity=0.341  Sum_probs=75.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      .++|||||||+++|+++|+.+|+.||.|..+.|+.++.++.++|||||+|.+.++|..||. ++|+.|+|+.|.|.++.+
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            4799999999999999999999999999999999999999999999999999999999997 799999999999988765

>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=99.70  E-value=1.2e-17  Score=132.64  Aligned_cols=74  Identities=20%  Similarity=0.375  Sum_probs=70.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       130 tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      .|||||||+++|+++|..+|++||.|..|.|+.++.+|+++|||||+|.+.++|..||. +++..|+|+.|.|+.
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKR   74 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeE
Confidence            48999999999999999999999999999999999999999999999999999999998 799999999999853

>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=99.70  E-value=5.7e-17  Score=134.29  Aligned_cols=81  Identities=19%  Similarity=0.245  Sum_probs=75.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+.+++++|+.+|+.||.|.+|.|+.+.  +.++|||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   85 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            3457789999999999999999999999999999999884  45789999999999999999999999999999999999


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        86 A~~   88 (93)
T d2cq3a1          86 ATA   88 (93)
T ss_dssp             CCS
T ss_pred             cCc
Confidence            865

>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=1.3e-17  Score=135.15  Aligned_cols=77  Identities=18%  Similarity=0.397  Sum_probs=72.9

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCceEEE-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          131 VYVGKIAPTADSDFVLSVLKVCGTVKSW-KRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       131 lfVgnLp~~~te~~L~~~F~~~G~v~~~-~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      |||+|||+++|+++|+.+|+.||.|..+ .|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+..
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~   78 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFK   78 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecC
Confidence            8999999999999999999999998764 7888889999999999999999999999999999999999999999864

>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=99.69  E-value=2.1e-17  Score=135.74  Aligned_cols=79  Identities=18%  Similarity=0.365  Sum_probs=73.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      ..+|||+|||+++|+++|..+|+.||.|..|.|+.+.  +.++|||||+|.+.++|..||..|||..|+|+.|.|.++..
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            5689999999999999999999999999999999884  45789999999999999999999999999999999998865


Q ss_pred             h
Q 008117          208 T  208 (577)
Q Consensus       208 ~  208 (577)
                      .
T Consensus        86 ~   86 (89)
T d1cvja2          86 R   86 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=6.1e-17  Score=139.29  Aligned_cols=79  Identities=13%  Similarity=0.234  Sum_probs=73.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      .+++|||+|||+.+|+++|..+|+.||.|.+|.+..   ++.++|||||+|.+.++|..||..|||+.|+|+.|.|.|+.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            468999999999999999999999999999999875   46779999999999999999999999999999999999986


Q ss_pred             hh
Q 008117          207 AT  208 (577)
Q Consensus       207 ~~  208 (577)
                      ..
T Consensus        83 ~~   84 (114)
T d2f9da1          83 AN   84 (114)
T ss_dssp             HH
T ss_pred             CC
Confidence            53

>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=99.69  E-value=1.2e-17  Score=132.58  Aligned_cols=75  Identities=21%  Similarity=0.345  Sum_probs=71.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       130 tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .|||||||+++|+++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||. ++++.|+|+.|.|+.|
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            59999999999999999999999999999999999999999999999999999999998 4888999999999754

>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=99.68  E-value=3.1e-17  Score=130.10  Aligned_cols=75  Identities=21%  Similarity=0.313  Sum_probs=72.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       130 tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .|||||||+++|+++|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..||. |||+.|+|+.|.|.+|
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            48999999999999999999999999999999999999999999999999999999997 8999999999999865

>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=99.67  E-value=1e-16  Score=133.85  Aligned_cols=81  Identities=19%  Similarity=0.363  Sum_probs=76.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC------CceeCCeEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN------KFNIDGQEL  200 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Ln------g~~i~gr~i  200 (577)
                      ..++|||||||+++|+++|+.+|..||.|..+.++.+..++.++|||||+|.+.++|..||..||      |..|+|+.|
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            46799999999999999999999999999999999999999999999999999999999999886      678999999


Q ss_pred             EEEEchh
Q 008117          201 MLKVDQA  207 (577)
Q Consensus       201 ~V~~a~~  207 (577)
                      .|.++..
T Consensus        87 ~v~~a~~   93 (98)
T d1x4ha1          87 KVDLAVT   93 (98)
T ss_dssp             EEECCCC
T ss_pred             EEEECCC
Confidence            9998765

>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=99.67  E-value=9e-17  Score=135.08  Aligned_cols=83  Identities=19%  Similarity=0.331  Sum_probs=76.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceE--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVK--------SWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  196 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~--------~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~  196 (577)
                      ....++|||+|||+.+|+++|+.+|..||.|.        .+.+..+..+|.++|||||+|.+.++|..||..|||+.|+
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            34578999999999999999999999999874        5667778889999999999999999999999999999999


Q ss_pred             CeEEEEEEchh
Q 008117          197 GQELMLKVDQA  207 (577)
Q Consensus       197 gr~i~V~~a~~  207 (577)
                      |+.|.|.++..
T Consensus        85 gr~i~V~~a~~   95 (101)
T d2cpea1          85 GSKLKVSLARK   95 (101)
T ss_dssp             TEECEEECSSC
T ss_pred             CEEEEEEEcCC
Confidence            99999998865

>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=99.67  E-value=5.8e-17  Score=132.18  Aligned_cols=80  Identities=11%  Similarity=0.225  Sum_probs=70.0

Q ss_pred             CCceEEEcCCCCCCC-HHHHHHHHhhcCceEEEEEeec-CCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          127 PQTKVYVGKIAPTAD-SDFVLSVLKVCGTVKSWKRAQY-PSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       127 ~~~tlfVgnLp~~~t-e~~L~~~F~~~G~v~~~~i~~~-~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ..++|||+|||+.+| ++.|+.+|+.||.|.+|.|+.+ ..+|.++|||||+|.+.++|..||. |||..|+|+.|.|.+
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            468999999999886 5569999999999999998764 5789999999999999999999996 999999999999999


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        82 a~~   84 (86)
T d2ghpa3          82 ADK   84 (86)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            864

>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=99.66  E-value=2.4e-17  Score=138.93  Aligned_cols=82  Identities=20%  Similarity=0.322  Sum_probs=77.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      .++++|||+|||..+++++|..+|+.||.|..+.++.+..+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
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            35789999999999999999999999999999999888889999999999999999999999999999999999999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        96 k~   97 (102)
T d2cpxa1          96 KN   97 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.66  E-value=2.5e-16  Score=130.89  Aligned_cols=79  Identities=19%  Similarity=0.365  Sum_probs=72.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+++|+++|+.+|+.||.|..+.+..   ++.++|||||+|.+.++|..||..|||+.|+|+.|.|.|+
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~---~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecc---cccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            4567899999999999999999999999999988754   4567899999999999999999999999999999999988


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        89 ~~   90 (95)
T d1x4aa1          89 RS   90 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            65

>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=99.65  E-value=2.7e-16  Score=127.81  Aligned_cols=77  Identities=18%  Similarity=0.185  Sum_probs=72.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      .++|||+|||.++|+++|..+|+.||.|..|.|..+ .+|.++|||||+|.+.++|.+||. ++|..|.|+.|.|.|..
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 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEEC-TTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeee-ccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            579999999999999999999999999999999887 489999999999999999999997 79999999999998764

>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=99.64  E-value=1.6e-16  Score=133.57  Aligned_cols=81  Identities=23%  Similarity=0.295  Sum_probs=74.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+++|+++|+.+|+.||.|..+.++.+ .++.++|||||+|.+.++|..||..|||..|.|++|.|.++
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            45689999999999999999999999999999999888 58999999999999999999999999999999999888665


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      .+
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            43

>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=99.64  E-value=4.4e-17  Score=134.36  Aligned_cols=80  Identities=21%  Similarity=0.386  Sum_probs=73.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.|.++.|+.+ .+|.++|||||+|.+.++|..||. |||..|+|+.|.|.++
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            35679999999999999999999999999999988765 689999999999999999999996 8999999999999987


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.63  E-value=4e-16  Score=129.80  Aligned_cols=75  Identities=20%  Similarity=0.321  Sum_probs=70.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..++|||+|||..+++++|+.+|+.||.|.+|+|+.+      +|||||+|.+.++|..||..|||..|+|+.|+|.|+.
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4578999999999999999999999999999999876      5899999999999999999999999999999999986


Q ss_pred             h
Q 008117          207 A  207 (577)
Q Consensus       207 ~  207 (577)
                      .
T Consensus        91 ~   91 (96)
T d1x4ga1          91 E   91 (96)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=4.9e-16  Score=125.72  Aligned_cols=76  Identities=12%  Similarity=0.214  Sum_probs=69.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID-GQELMLKV  204 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~-gr~i~V~~  204 (577)
                      +++++|||+|||.++|+++|..+|+.||.|..|.++.+     .+|||||+|.+.++|..|+..|||..|. |+.|.|.|
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~   80 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITF   80 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEE
Confidence            45789999999999999999999999999999999754     3689999999999999999999999984 78999999


Q ss_pred             ch
Q 008117          205 DQ  206 (577)
Q Consensus       205 a~  206 (577)
                      +.
T Consensus        81 ak   82 (83)
T d2b0ga1          81 AK   82 (83)
T ss_dssp             CC
T ss_pred             ec
Confidence            85

>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=99.63  E-value=2.6e-16  Score=131.01  Aligned_cols=79  Identities=16%  Similarity=0.250  Sum_probs=71.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ....++|||+|||+++|+++|+.+|..||.|..+..     +|.++|||||+|.+.++|..||..|||..|+|+.|.|.|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345789999999999999999999999998866542     788999999999999999999999999999999999999


Q ss_pred             chhh
Q 008117          205 DQAT  208 (577)
Q Consensus       205 a~~~  208 (577)
                      +...
T Consensus        88 a~~k   91 (96)
T d1fjca_          88 TGEK   91 (96)
T ss_dssp             CSSS
T ss_pred             eCCC
Confidence            8653

>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=99.63  E-value=7.8e-17  Score=126.78  Aligned_cols=71  Identities=20%  Similarity=0.359  Sum_probs=68.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 008117          131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  201 (577)
Q Consensus       131 lfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~  201 (577)
                      |||+|||+++|+++|+.+|+.||.|..+.++.++.++.++|||||+|.+.++|..||..|||..|+|+.|+
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            89999999999999999999999999999999999999999999999999999999999999999998764

>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=99.62  E-value=3.3e-16  Score=127.63  Aligned_cols=79  Identities=22%  Similarity=0.235  Sum_probs=70.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ..++|||+|||+++++++|.++|..||.|..+.++....+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++
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            4678999999999999999999999999876433344468999999999999999999999999999999999999864

>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=99.62  E-value=7e-16  Score=130.31  Aligned_cols=79  Identities=20%  Similarity=0.436  Sum_probs=70.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP-SNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~-~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      +.++|||+|||+++|+++|+.+|+.|| |+.+.++.+. .+|.++|||||+|.+.++|.+|+. ||++.|+|+.|.|.++
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-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEEC
Confidence            468999999999999999999999999 7777777654 578999999999999999987775 8999999999999987


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        92 ~~   93 (104)
T d1wi8a_          92 DQ   93 (104)
T ss_dssp             CC
T ss_pred             CC
Confidence            55

>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=99.61  E-value=6.1e-16  Score=126.55  Aligned_cols=77  Identities=14%  Similarity=0.253  Sum_probs=69.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee-CCeEEEEEEc
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI-DGQELMLKVD  205 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i-~gr~i~V~~a  205 (577)
                      ++++|||+|||+.+|+++|+.+|..||.|..+.+..    ++.+|||||+|.+.++|..|+..|||..| +|+.|+|.|+
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            478999999999999999999999999998887654    34578999999999999999999999998 5899999998


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ++
T Consensus        85 k~   86 (88)
T d2adca2          85 KS   86 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            65

>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=99.61  E-value=3.7e-16  Score=128.15  Aligned_cols=76  Identities=17%  Similarity=0.233  Sum_probs=69.6

Q ss_pred             CceEEEcCCCCCCCHHHH---HHHHhhcCceEEEEEeecCCCCCc---ceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 008117          128 QTKVYVGKIAPTADSDFV---LSVLKVCGTVKSWKRAQYPSNGTP---KGFGFCEFESAEGVLRALRLLNKFNIDGQELM  201 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L---~~~F~~~G~v~~~~i~~~~~tg~~---kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~  201 (577)
                      .++|||+|||+.+++++|   .++|++||.|..|.|+.++.++.+   .|||||+|.+.++|..||..|||..|+|+.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            567999999999999999   678999999999999998766654   49999999999999999999999999999999


Q ss_pred             EE
Q 008117          202 LK  203 (577)
Q Consensus       202 V~  203 (577)
                      |.
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            73

>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=120.81  Aligned_cols=73  Identities=21%  Similarity=0.281  Sum_probs=67.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ++|||+|||+++++++|+.+|+.||.|..|.|+.++.  ..++||||+|.+.++|.+||. ||+..|+|+.|.|..
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~   73 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSH   73 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEE
Confidence            5899999999999999999999999999999998853  445899999999999999996 899999999999964

>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=99.60  E-value=7.2e-16  Score=131.72  Aligned_cols=75  Identities=12%  Similarity=0.054  Sum_probs=69.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..++|||+|||+.+++++|+.+|+.||.|..|.|.      ..+|||||+|.+.++|..||..|||..|.|+.|.|.|+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            46899999999999999999999999999999874      346899999999999999999999999999999999875


Q ss_pred             h
Q 008117          207 A  207 (577)
Q Consensus       207 ~  207 (577)
                      .
T Consensus        83 ~   83 (111)
T d1whxa_          83 I   83 (111)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=6.6e-16  Score=127.20  Aligned_cols=79  Identities=14%  Similarity=0.300  Sum_probs=71.4

Q ss_pred             CCceEEEcCCCCCCCHHHHH----HHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVL----SVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  202 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~----~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V  202 (577)
                      |+++|||||||+.+++++|+    .+|+.||.|.+|.+..   ++.++|||||+|.+.++|..|+..|||..|+|+.|.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            57899999999999999886    4689999999998754   5778999999999999999999999999999999999


Q ss_pred             EEchhh
Q 008117          203 KVDQAT  208 (577)
Q Consensus       203 ~~a~~~  208 (577)
                      .|+...
T Consensus        79 ~~ak~~   84 (91)
T d1nu4a_          79 QYAKTD   84 (91)
T ss_dssp             EECSSC
T ss_pred             EEeCCC
Confidence            998764

>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=99.59  E-value=8.4e-16  Score=125.15  Aligned_cols=75  Identities=19%  Similarity=0.337  Sum_probs=70.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..++|||+|||.++++++|+.+|+.||.|.+|.+..+      +|||||+|.+.++|..|+..|||..|+|+.|.|.||.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3568999999999999999999999999999999765      5899999999999999999999999999999999986


Q ss_pred             h
Q 008117          207 A  207 (577)
Q Consensus       207 ~  207 (577)
                      .
T Consensus        81 ~   81 (86)
T d2cpja1          81 H   81 (86)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.59  E-value=1.2e-15  Score=126.85  Aligned_cols=80  Identities=18%  Similarity=0.287  Sum_probs=72.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCc-eEEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCeEEEEE
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGT-VKSWKRAQYP-SNGTPKGFGFCEFESAEGVLRALRLLN--KFNIDGQELMLK  203 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~-v~~~~i~~~~-~tg~~kg~gFV~f~~~~~A~~Al~~Ln--g~~i~gr~i~V~  203 (577)
                      .+.|||||||..+|+++|+.+|+.||. |..+.|+.+. .+|.++|||||+|.+.++|..||..|+  +..++|+.|.|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            368999999999999999999999995 8999998875 578999999999999999999999886  456689999999


Q ss_pred             Echh
Q 008117          204 VDQA  207 (577)
Q Consensus       204 ~a~~  207 (577)
                      ||..
T Consensus        81 ~A~p   84 (96)
T d2disa1          81 WAEP   84 (96)
T ss_dssp             ESCS
T ss_pred             EcCC
Confidence            9865

>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=99.59  E-value=1.8e-15  Score=126.32  Aligned_cols=74  Identities=18%  Similarity=0.294  Sum_probs=67.3

Q ss_pred             CCCceEEEcCCC-CCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 008117          126 KPQTKVYVGKIA-PTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  204 (577)
Q Consensus       126 ~~~~tlfVgnLp-~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~  204 (577)
                      ...++|||+||+ ..+++.+|+.+|++||.|..|.|        ++|||||+|.+.++|..||..|||+.|.|+.|.|.|
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            445789999997 57888999999999999999998        358999999999999999999999999999999998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        85 a~~   87 (98)
T d1wf2a_          85 AAE   87 (98)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            754

>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=99.58  E-value=3.2e-15  Score=121.67  Aligned_cols=75  Identities=13%  Similarity=0.272  Sum_probs=68.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..++|||+|||+++|+++|+.+|+.||.|..+.+..      ++|||||+|.+.++|..||..|||..|+|+.|.|.|+.
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            457999999999999999999999999988877643      46899999999999999999999999999999999986


Q ss_pred             h
Q 008117          207 A  207 (577)
Q Consensus       207 ~  207 (577)
                      +
T Consensus        81 P   81 (86)
T d2cpda1          81 P   81 (86)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.58  E-value=1.8e-15  Score=128.83  Aligned_cols=75  Identities=15%  Similarity=0.256  Sum_probs=69.3

Q ss_pred             CceEEEcCCCC-CCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          128 QTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       128 ~~tlfVgnLp~-~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      +++|||+||++ .+|+++|..+|+.||.|..|.|+.++     +|||||+|.+.++|.+||..|||..|.|+.|.|.|+.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            57999999965 69999999999999999999998763     6899999999999999999999999999999999875


Q ss_pred             h
Q 008117          207 A  207 (577)
Q Consensus       207 ~  207 (577)
                      .
T Consensus        77 ~   77 (109)
T d2adca1          77 H   77 (109)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.57  E-value=1.3e-15  Score=122.34  Aligned_cols=74  Identities=15%  Similarity=0.308  Sum_probs=66.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc-eeCCeEEEEEEchh
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKF-NIDGQELMLKVDQA  207 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~-~i~gr~i~V~~a~~  207 (577)
                      .+|||||||+++|+++|+.+|+.||.|.++.+...      +|||||+|.+.++|..||..|||. .|+|+.|.|.|+.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            47999999999999999999999999887766554      689999999999999999999995 69999999999865


Q ss_pred             h
Q 008117          208 T  208 (577)
Q Consensus       208 ~  208 (577)
                      .
T Consensus        76 k   76 (80)
T d2cqha1          76 K   76 (80)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.57  E-value=1.9e-15  Score=127.32  Aligned_cols=81  Identities=16%  Similarity=0.196  Sum_probs=72.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ....+|||+|||+++|+++|..+|..||.|..+.++....+|.++|||||+|.+.++|..||. |||..|+|+.|.|.++
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            346789999999999999999999999998775555555799999999999999999999997 8999999999999886


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        85 ~~   86 (103)
T d2cpya1          85 TL   86 (103)
T ss_dssp             CH
T ss_pred             CH
Confidence            54

>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=99.56  E-value=2.9e-15  Score=119.83  Aligned_cols=73  Identities=14%  Similarity=0.225  Sum_probs=67.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      .+++|||+||+  +|+++|+.+|+.||.|.+|.+..+      +|||||+|.+.++|..|+..|||..|+|+.|+|.|+.
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            56899999996  899999999999999999998654      5899999999999999999999999999999999986


Q ss_pred             h
Q 008117          207 A  207 (577)
Q Consensus       207 ~  207 (577)
                      .
T Consensus        76 ~   76 (79)
T d2bz2a1          76 K   76 (79)
T ss_dssp             S
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=9.8e-16  Score=125.04  Aligned_cols=71  Identities=20%  Similarity=0.198  Sum_probs=65.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      .+|||+|||+++|+++|..+|+.||.|..|.|+.+       |||||+|.+.++|..||..|||..|+|+.|.|.++.
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~   71 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   71 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEe
Confidence            36999999999999999999999999999998765       899999999999999999999999999999987653

>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=99.56  E-value=5.5e-15  Score=124.70  Aligned_cols=80  Identities=15%  Similarity=0.101  Sum_probs=73.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ...+|||+|||+++|+++|+++|..||.|..+.++.+..++.++|||||+|.+.++|.+|+. ||+..|+|+.|.|.++.
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~   92 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECC
Confidence            45679999999999999999999999999887777777899999999999999999999997 89999999999998775


Q ss_pred             h
Q 008117          207 A  207 (577)
Q Consensus       207 ~  207 (577)
                      .
T Consensus        93 ~   93 (104)
T d1wg5a_          93 R   93 (104)
T ss_dssp             T
T ss_pred             H
Confidence            4

>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=99.56  E-value=4.7e-15  Score=123.71  Aligned_cols=75  Identities=19%  Similarity=0.222  Sum_probs=68.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ....+|||+|||+.+++.+|+.+|+.||.|..|.|..+       |||||+|.+.++|..||..|||..|.|+.|.|.+.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD-------GMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhccccccccccc-------ceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            35678999999999999999999999999999998643       89999999999999999999999999999999876


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        86 ~~   87 (98)
T d1wg4a_          86 RV   87 (98)
T ss_dssp             EE
T ss_pred             ec
Confidence            43

>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=99.55  E-value=4.2e-15  Score=121.47  Aligned_cols=74  Identities=15%  Similarity=0.304  Sum_probs=65.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      ..++|||+|||+++++++|+.+|..|| +..+.+      +..+|||||+|.+.++|..||..|||+.|+|+.|.|.|+.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            467899999999999999999999999 333333      3457999999999999999999999999999999999875


Q ss_pred             h
Q 008117          207 A  207 (577)
Q Consensus       207 ~  207 (577)
                      .
T Consensus        77 ~   77 (88)
T d1wg1a_          77 T   77 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.54  E-value=7.6e-15  Score=122.20  Aligned_cols=75  Identities=17%  Similarity=0.426  Sum_probs=69.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG--QELMLKV  204 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~g--r~i~V~~  204 (577)
                      +.++|||+|||+++++++|+++|+.||.|..|.++.+      ++||||+|.+.++|..|+..|||..|.|  +.|+|.|
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            4689999999999999999999999999999998765      5899999999999999999999999986  5899998


Q ss_pred             chh
Q 008117          205 DQA  207 (577)
Q Consensus       205 a~~  207 (577)
                      +..
T Consensus        90 ak~   92 (97)
T d1whya_          90 AKS   92 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            865

>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=99.54  E-value=2.3e-15  Score=123.03  Aligned_cols=75  Identities=15%  Similarity=0.199  Sum_probs=67.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.|..|.+.     ..++|||||+|.+.++|..||.  +++.|+|+.|.|.++
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            357899999999999999999999999999999864     3467999999999999999985  899999999999987


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        76 ~~   77 (88)
T d1wf0a_          76 EP   77 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.54  E-value=4.8e-15  Score=125.95  Aligned_cols=78  Identities=14%  Similarity=0.113  Sum_probs=70.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee--CCeEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI--DGQELMLK  203 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i--~gr~i~V~  203 (577)
                      .+..+|||+|||+.+|+++|+.+|+.||.|..|.|+.+    +.+|||||+|.+.++|..||..|||..|  .|+.|.|.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~----~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEee----CCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            45788999999999999999999999999999999876    3579999999999999999999999998  47888888


Q ss_pred             Echh
Q 008117          204 VDQA  207 (577)
Q Consensus       204 ~a~~  207 (577)
                      |+..
T Consensus        81 ~s~~   84 (108)
T d2adba1          81 FSKL   84 (108)
T ss_dssp             ECSS
T ss_pred             ecCC
Confidence            7754

>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=99.54  E-value=1.1e-14  Score=115.30  Aligned_cols=70  Identities=14%  Similarity=0.184  Sum_probs=63.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEchh
Q 008117          131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  207 (577)
Q Consensus       131 lfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~~  207 (577)
                      |||+|||+++++++|+.+|..|| +..+.+      +.++|||||+|.+.++|..|+..|||..|.|+.|.|.|+..
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~   70 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPT   70 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCS
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCC
Confidence            79999999999999999999999 444443      45679999999999999999999999999999999999854

>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=99.53  E-value=5.8e-15  Score=126.30  Aligned_cols=82  Identities=21%  Similarity=0.247  Sum_probs=73.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|..+|+.||.|..+.++.+..+|.++|||||+|.+.++|.+|+. |||..|+|+.|.|..+
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEc
Confidence            356789999999999999999999999998776566556799999999999999999999997 8999999999999877


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus        95 ~~~   97 (112)
T d1wela1          95 TKK   97 (112)
T ss_dssp             CHH
T ss_pred             ChH
Confidence            543

>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=99.53  E-value=5.9e-15  Score=124.04  Aligned_cols=79  Identities=14%  Similarity=0.105  Sum_probs=71.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ....+|||+|||+++|+++|+.+|..|| |..+.++.+ .+|.++|||||+|.+.++|..||. ||+..|+|+.|.|.++
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~-~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIG-PDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEES-SSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEe-cCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            4567999999999999999999999998 457777777 478999999999999999999997 8999999999999887


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        90 ~~   91 (102)
T d1weza_          90 ST   91 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.53  E-value=1.9e-14  Score=117.45  Aligned_cols=77  Identities=13%  Similarity=0.167  Sum_probs=69.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCceeCCeEEEE
Q 008117          125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL--NKFNIDGQELML  202 (577)
Q Consensus       125 ~~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~L--ng~~i~gr~i~V  202 (577)
                      ..++++|||+|||+.+++++|..+|+.||.|..+.+..+      ++||||+|.+.++|..|+..|  ++..|+|+.|.|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            457899999999999999999999999999999998765      489999999999999999855  688999999999


Q ss_pred             EEchh
Q 008117          203 KVDQA  207 (577)
Q Consensus       203 ~~a~~  207 (577)
                      .|+..
T Consensus        79 ~~sk~   83 (88)
T d2cq1a1          79 QYSNH   83 (88)
T ss_dssp             EECSC
T ss_pred             EECCC
Confidence            99865

>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=99.51  E-value=9.1e-15  Score=122.17  Aligned_cols=78  Identities=14%  Similarity=0.244  Sum_probs=69.6

Q ss_pred             CCCCceEEEcCCCC-CCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH--HhCCceeCCeEEE
Q 008117          125 EKPQTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR--LLNKFNIDGQELM  201 (577)
Q Consensus       125 ~~~~~tlfVgnLp~-~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~--~Lng~~i~gr~i~  201 (577)
                      ...+++|||+|||. .+|+++|..+|+.||.|..+.++.+      +|||||+|.+.++|..||.  .+++..|+|+.|.
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            34578999999998 4899999999999999999999765      5899999999999999997  4789999999999


Q ss_pred             EEEchhh
Q 008117          202 LKVDQAT  208 (577)
Q Consensus       202 V~~a~~~  208 (577)
                      |.|+...
T Consensus        89 V~~s~~~   95 (99)
T d1x4fa1          89 VDLSEKY   95 (99)
T ss_dssp             EEEECSC
T ss_pred             EEEcCCc
Confidence            9998653

>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=99.47  E-value=1.2e-13  Score=116.33  Aligned_cols=76  Identities=16%  Similarity=0.195  Sum_probs=68.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCceeCCeEEEEE
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL--NKFNIDGQELMLK  203 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~L--ng~~i~gr~i~V~  203 (577)
                      .++.+|||+|||+.+|+++|..+|..||.|..|.+..+      ++||||+|.+.++|..||..|  ++..|+|+.|.|.
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~   86 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEE
Confidence            45889999999999999999999999999999998654      589999999999999999877  6778899999999


Q ss_pred             Echh
Q 008117          204 VDQA  207 (577)
Q Consensus       204 ~a~~  207 (577)
                      |+..
T Consensus        87 ~s~~   90 (104)
T d1wexa_          87 YSTS   90 (104)
T ss_dssp             ECSS
T ss_pred             EcCC
Confidence            8854

>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=99.46  E-value=6.1e-14  Score=114.64  Aligned_cols=76  Identities=12%  Similarity=0.106  Sum_probs=68.9

Q ss_pred             CCCceEEEcCCCCC-CCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCceeCCeEEEE
Q 008117          126 KPQTKVYVGKIAPT-ADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL--NKFNIDGQELML  202 (577)
Q Consensus       126 ~~~~tlfVgnLp~~-~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~L--ng~~i~gr~i~V  202 (577)
                      .++++|||+|||.. +|+++|..+|+.||.|..|.++.+      ++||||.|.+.++|..|+..|  ++..|.|++|.|
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            46889999999986 789999999999999999999765      379999999999999999866  788999999999


Q ss_pred             EEchh
Q 008117          203 KVDQA  207 (577)
Q Consensus       203 ~~a~~  207 (577)
                      .|+..
T Consensus        80 ~~s~~   84 (89)
T d1x4da1          80 HLSQK   84 (89)
T ss_dssp             EEECC
T ss_pred             EECCC
Confidence            99865

>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=99.45  E-value=2.1e-13  Score=126.39  Aligned_cols=82  Identities=15%  Similarity=0.331  Sum_probs=77.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ...++|||+|||+.+|+++|+.+|+.||.|..+.|+.+..+|.++|||||+|.+.++|.+||. +++..|+|+.|.|.+|
T Consensus        95 ~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A  173 (183)
T d1u1qa_          95 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA  173 (183)
T ss_dssp             CCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEEC
T ss_pred             cccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEec
Confidence            356799999999999999999999999999999999998899999999999999999999997 7999999999999988


Q ss_pred             hhh
Q 008117          206 QAT  208 (577)
Q Consensus       206 ~~~  208 (577)
                      ...
T Consensus       174 ~~k  176 (183)
T d1u1qa_         174 LSK  176 (183)
T ss_dssp             CCH
T ss_pred             CCc
Confidence            654

>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=99.42  E-value=2.6e-15  Score=123.28  Aligned_cols=75  Identities=20%  Similarity=0.336  Sum_probs=66.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEe-----ecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRA-----QYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  203 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~-----~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~  203 (577)
                      ++|||||||+.+|+++|+++|+.||.|..+.++     .+..++.++|||||+|.+.++|..|+. |||+.|.|+.|+|.
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            689999999999999999999999988766553     344678899999999999999999996 99999999999995


Q ss_pred             E
Q 008117          204 V  204 (577)
Q Consensus       204 ~  204 (577)
                      .
T Consensus        81 r   81 (90)
T d1u2fa_          81 R   81 (90)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.41  E-value=7.3e-14  Score=117.56  Aligned_cols=76  Identities=12%  Similarity=0.036  Sum_probs=67.6

Q ss_pred             CCCceEEEcCCCCCC-CH----HHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 008117          126 KPQTKVYVGKIAPTA-DS----DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL  200 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~-te----~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i  200 (577)
                      ....+|||+||+..+ ++    ++|..+|+.||.|.+|.+..      +++||||+|.+.++|..||..|||..|+|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            457899999999976 33    46999999999999999874      36899999999999999999999999999999


Q ss_pred             EEEEchh
Q 008117          201 MLKVDQA  207 (577)
Q Consensus       201 ~V~~a~~  207 (577)
                      +|.|+..
T Consensus        77 ~v~~a~~   83 (104)
T d1weya_          77 KLYFAQT   83 (104)
T ss_dssp             EEECCCC
T ss_pred             EEeeccc
Confidence            9999854

>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=99.38  E-value=3.8e-14  Score=119.35  Aligned_cols=76  Identities=14%  Similarity=0.126  Sum_probs=71.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      +.++|.+++..+++++|.++|++||.|.+|.|+.+ .+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.|+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            56889999999999999999999999999999877 58999999999999999999999999999999999999875

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.30  E-value=3.2e-12  Score=109.08  Aligned_cols=75  Identities=11%  Similarity=0.030  Sum_probs=65.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCH-HHHHHHHHHhCCceeCCeEEEEEEc
Q 008117          127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESA-EGVLRALRLLNKFNIDGQELMLKVD  205 (577)
Q Consensus       127 ~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~-~~A~~Al~~Lng~~i~gr~i~V~~a  205 (577)
                      ....+||||||+.+|+++|+.+|+.||.|.+|.|+.+      +|||||.|.+. ++|..|+..||+..|.++.+.|.|+
T Consensus        10 g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          10 GCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             CCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            3567799999999999999999999999999999754      58999999985 7899999999999988777777766


Q ss_pred             hh
Q 008117          206 QA  207 (577)
Q Consensus       206 ~~  207 (577)
                      ..
T Consensus        84 ~~   85 (113)
T d1owxa_          84 VL   85 (113)
T ss_dssp             EC
T ss_pred             ec
Confidence            43

>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=99.28  E-value=4.7e-12  Score=105.66  Aligned_cols=64  Identities=22%  Similarity=0.344  Sum_probs=58.0

Q ss_pred             CCCceEEEc--CCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 008117          126 KPQTKVYVG--KIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI  195 (577)
Q Consensus       126 ~~~~tlfVg--nLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i  195 (577)
                      .+..+|||+  |||..+|+++|+.+|++||.|..|.++.+      ++||||+|.+.++|..|+..|||..|
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            456788885  59999999999999999999999988765      47999999999999999999999987

>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=99.16  E-value=2.6e-11  Score=100.73  Aligned_cols=79  Identities=11%  Similarity=0.148  Sum_probs=67.2

Q ss_pred             CCCceEEEcCC--CCCCC---------HHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 008117          126 KPQTKVYVGKI--APTAD---------SDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN  194 (577)
Q Consensus       126 ~~~~tlfVgnL--p~~~t---------e~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~  194 (577)
                      ...++|+|.||  |..+.         .++|+..|++||.|..|.+..+    .++|||||.|.+.++|..|+..|||..
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            46889999999  44321         2578899999999999988654    567999999999999999999999999


Q ss_pred             eCCeEEEEEEchhh
Q 008117          195 IDGQELMLKVDQAT  208 (577)
Q Consensus       195 i~gr~i~V~~a~~~  208 (577)
                      |+|+.|.|.+....
T Consensus        82 ~~gr~i~v~~~~g~   95 (99)
T d2dita1          82 FGGRQITAQAWDGT   95 (99)
T ss_dssp             ETTEECEEEECCSC
T ss_pred             ECCEEEEEEEeCCc
Confidence            99999999987653

>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=99.13  E-value=5.2e-11  Score=94.89  Aligned_cols=71  Identities=13%  Similarity=0.018  Sum_probs=59.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeE-EEEEEch
Q 008117          128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQE-LMLKVDQ  206 (577)
Q Consensus       128 ~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~-i~V~~a~  206 (577)
                      .+.|||+|||+++++..| .+|+.||.|.++.+.      ..++||||.|.+.++|.+||. |||..|+|+. |.|.-+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            467999999999987655 579999999999874      346899999999999999997 8999999975 5576543

>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=99.06  E-value=8.5e-11  Score=98.44  Aligned_cols=82  Identities=17%  Similarity=0.086  Sum_probs=68.7

Q ss_pred             CCCceEEEcCC--CCCCC--------HHHHHHHHhhcCceEEEEEeecCCC--CCcceEEEEEeCCHHHHHHHHHHhCCc
Q 008117          126 KPQTKVYVGKI--APTAD--------SDFVLSVLKVCGTVKSWKRAQYPSN--GTPKGFGFCEFESAEGVLRALRLLNKF  193 (577)
Q Consensus       126 ~~~~tlfVgnL--p~~~t--------e~~L~~~F~~~G~v~~~~i~~~~~t--g~~kg~gFV~f~~~~~A~~Al~~Lng~  193 (577)
                      ++++.|+|.||  +..+.        .++|+..|++||.|.+|.|..+..+  ....||+||+|.+.++|..|+..|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            35788999999  44332        2468999999999999999876543  344689999999999999999999999


Q ss_pred             eeCCeEEEEEEchh
Q 008117          194 NIDGQELMLKVDQA  207 (577)
Q Consensus       194 ~i~gr~i~V~~a~~  207 (577)
                      .|+|+.|.|.|...
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999998754

>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=98.30  E-value=3.7e-07  Score=70.14  Aligned_cols=62  Identities=11%  Similarity=0.078  Sum_probs=49.1

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccC-CCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDN-ETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~-~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++..++..... -..+..++.++|||||+|.+.++|..|+..||+.
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~   63 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKAS   63 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHH
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCC
Confidence            4899999999999999996633322111 1133678899999999999999999999999875

>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=98.27  E-value=2.9e-07  Score=74.00  Aligned_cols=65  Identities=14%  Similarity=0.078  Sum_probs=49.3

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+++||+||+..+++.+|.+++..++....... .+..+|.++|||||.|.+.++|..|+..|++.
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~   70 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES   70 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTE
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCC
Confidence            345799999999999999988442221111111 23677999999999999999999999998864

>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=98.23  E-value=1.9e-07  Score=74.32  Aligned_cols=65  Identities=14%  Similarity=0.149  Sum_probs=49.5

Q ss_pred             ccccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          228 ETQDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       228 ~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .++ +||+||+..+++++|.+++..++....... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         6 ~t~-lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   71 (85)
T d1b7fa2           6 DTN-LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNV   71 (85)
T ss_dssp             TCE-EEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCE-EEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCC
Confidence            344 599999999999999998442222111111 23578999999999999999999999999874

>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=98.18  E-value=4.6e-07  Score=72.92  Aligned_cols=64  Identities=9%  Similarity=0.127  Sum_probs=50.0

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +.+||+||+..+++.+|.+++..++....... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         9 ~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~   73 (90)
T d2cq0a1           9 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGF   73 (90)
T ss_dssp             EEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCC
Confidence            34699999999999999999663332221111 23568999999999999999999999999863

>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=98.17  E-value=2.4e-07  Score=72.56  Aligned_cols=62  Identities=15%  Similarity=0.041  Sum_probs=47.2

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++..++.........+.+|+++|||||+|.+.++|..|+..+++.
T Consensus         3 l~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   64 (78)
T d1no8a_           3 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGV   64 (78)
T ss_dssp             EEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTC
T ss_pred             EEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCC
Confidence            49999999999999998844221111111122468999999999999999999999998864

>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=98.14  E-value=5e-07  Score=71.44  Aligned_cols=62  Identities=10%  Similarity=0.090  Sum_probs=46.9

Q ss_pred             ccccCCCcccchhhhcCCCCCCc-ccccC-CCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPE-NLKDN-ETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~-~~k~~-~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++...+ +.... --.+..+|+++|||||+|.+.++|..|+..+++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~   64 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQ   64 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCc
Confidence            48999999999999998833222 11110 0123577999999999999999999999988764

>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=98.13  E-value=1.1e-07  Score=78.84  Aligned_cols=66  Identities=14%  Similarity=0.187  Sum_probs=49.7

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhHHHH
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEER  297 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i~e~  297 (577)
                      +||+||+..+++++|.+++..++...... -.+..+|.++|||||+|.+.++|..||+.++..|..+
T Consensus        13 lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr   79 (103)
T d2cqda1          13 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGR   79 (103)
T ss_dssp             EEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTE
T ss_pred             EEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCE
Confidence            59999999999999999844222111111 1236779999999999999999999999888765443

>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=98.13  E-value=4.7e-07  Score=74.52  Aligned_cols=63  Identities=10%  Similarity=0.002  Sum_probs=49.8

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhH
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMV  294 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i  294 (577)
                      +||+||+..+++++|.+++..++...........++.++|||||+|.+.++|..|+..||+..
T Consensus        21 lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~   83 (101)
T d1x5oa1          21 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKF   83 (101)
T ss_dssp             EEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCC
T ss_pred             EEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCE
Confidence            599999999999999999663332222222234678899999999999999999999998753

>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=98.12  E-value=3e-07  Score=73.18  Aligned_cols=62  Identities=10%  Similarity=0.061  Sum_probs=47.7

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++..++....... .+..+|.++|||||+|.+.++|..|+..||+.
T Consensus         9 lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~   71 (85)
T d1fxla2           9 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ   71 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCC
Confidence            499999999999999998442221111111 12567999999999999999999999998864

>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=98.11  E-value=3.4e-07  Score=72.49  Aligned_cols=65  Identities=17%  Similarity=0.069  Sum_probs=48.9

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...+||+||+..+++++|.+++..++...... ..+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         9 ~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~   74 (83)
T d2cqca1           9 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGM   74 (83)
T ss_dssp             GGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCC
Confidence            34579999999999999998843222111111 123567899999999999999999999998864

>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=98.10  E-value=5e-07  Score=71.24  Aligned_cols=62  Identities=8%  Similarity=0.015  Sum_probs=47.5

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++...+....... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         5 l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~   67 (82)
T d1b7fa1           5 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGI   67 (82)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCC
Confidence            599999999999999988432221111111 22578899999999999999999999998864

>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=98.08  E-value=8.5e-07  Score=71.95  Aligned_cols=62  Identities=15%  Similarity=0.058  Sum_probs=46.7

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCC--CCCCCCCCCceEEEEeCCHHHHHHHHHHH-hh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNET--GNKESHDPTNFGVVTEEDRKADQEALEKL-TC  292 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~--~~~~~g~~kgfgfV~f~~~e~a~~Al~~l-~~  292 (577)
                      .+||+||+..+++++|.+++..++.......  ....+|.++|||||.|.+.++|..||..| ++
T Consensus        10 ~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~   74 (94)
T d2cpha1          10 KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHS   74 (94)
T ss_dssp             CEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCC
Confidence            3699999999999999988442221111111  12457999999999999999999999988 44

>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=98.08  E-value=3e-07  Score=71.40  Aligned_cols=58  Identities=9%  Similarity=0.051  Sum_probs=44.2

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHH
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEK  289 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~  289 (577)
                      +||+||+..+++++|.+++..++...... ..+..+|+++|||||+|.+.++|.+||..
T Consensus         2 lfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~   60 (75)
T d1hd0a_           2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ   60 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHT
T ss_pred             EEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhc
Confidence            49999999999999998844222111111 12367899999999999999999999874

>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=98.05  E-value=4.6e-07  Score=72.12  Aligned_cols=62  Identities=15%  Similarity=0.060  Sum_probs=48.0

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++..++....... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         4 lfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~   66 (85)
T d2u2fa_           4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM   66 (85)
T ss_dssp             EEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSC
T ss_pred             EEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCC
Confidence            499999999999999998442221111111 23678999999999999999999999988764

>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=98.05  E-value=6.7e-07  Score=75.18  Aligned_cols=62  Identities=10%  Similarity=-0.001  Sum_probs=47.8

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .++||+||+..+++++|.+++..++.+.....  ..++.++|||||+|.+.++|..|+..|++.
T Consensus         8 r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~--~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~   69 (114)
T d2f9da1           8 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRV--GNTPETRGTAYVVYEDIFDAKNACDHLSGF   69 (114)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEE--ECSTTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhhcCCeEeecc--cccCCcCCeEEEEECCHHHHHHHHHHhCCC
Confidence            34699999999999999998543332222222  345678999999999999999999999864

>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=98.03  E-value=6.2e-07  Score=73.82  Aligned_cols=62  Identities=10%  Similarity=0.050  Sum_probs=47.6

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++++|.+++..++.+..... .+..+|.++|||||+|.+.++|..|+. |++.
T Consensus        20 tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~   82 (101)
T d2cq4a1          20 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQ   82 (101)
T ss_dssp             EEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTE
T ss_pred             EEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCC
Confidence            3699999999999999999553332222222 236789999999999999999999985 7653

>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=98.03  E-value=5.6e-07  Score=74.21  Aligned_cols=62  Identities=10%  Similarity=0.017  Sum_probs=48.2

Q ss_pred             ccccCCCcccchhhhcCCCCCCc-ccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPE-NLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~-~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++..++ +.......+..+|.++|||||+|.+.++|..||..|++.
T Consensus        21 l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~   83 (102)
T d2cpza1          21 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGF   83 (102)
T ss_dssp             EEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCC
Confidence            69999999999999998844222 111111133678999999999999999999999999864

>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=98.01  E-value=4.1e-07  Score=73.30  Aligned_cols=61  Identities=8%  Similarity=-0.007  Sum_probs=45.8

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLT  291 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~  291 (577)
                      .+||+||+..+++++|.+++..++....... .+..+|.++|||||+|.+.++|.+||...+
T Consensus        10 ~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~   71 (90)
T d2cqga1          10 DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH   71 (90)
T ss_dssp             CEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCE
T ss_pred             eEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCC
Confidence            3599999999999999988442221111111 225689999999999999999999998654

>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=98.01  E-value=6.8e-07  Score=71.58  Aligned_cols=64  Identities=17%  Similarity=0.034  Sum_probs=48.3

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .++||+||+..+++++|.+++..++....... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         8 ~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~   72 (88)
T d1rk8a_           8 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGA   72 (88)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCC
Confidence            34699999999999999988442211111111 22578999999999999999999999998864

>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=98.00  E-value=1.5e-06  Score=70.99  Aligned_cols=62  Identities=10%  Similarity=-0.016  Sum_probs=47.7

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++..++...... ..+..+|.++|||||+|.+.++|..||..|++.
T Consensus        11 lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~   73 (99)
T d1whwa_          11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQ   73 (99)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTE
T ss_pred             EEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCC
Confidence            59999999999999998843222111111 123678999999999999999999999999864

>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=98.00  E-value=7.1e-07  Score=70.30  Aligned_cols=62  Identities=15%  Similarity=0.123  Sum_probs=47.7

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++..++....... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         5 l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~   67 (82)
T d1fxla1           5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGL   67 (82)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCC
Confidence            599999999999999988442221111111 23567899999999999999999999999874

>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=97.99  E-value=8e-07  Score=71.94  Aligned_cols=63  Identities=13%  Similarity=0.035  Sum_probs=48.0

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++++|.+++...+....... .+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         9 tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~   72 (93)
T d1h2vz_           9 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGT   72 (93)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTS
T ss_pred             EEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCC
Confidence            4699999999999999988442221111111 23667899999999999999999999998864

>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=97.99  E-value=1e-06  Score=69.24  Aligned_cols=62  Identities=8%  Similarity=-0.004  Sum_probs=42.3

Q ss_pred             ccccCCCcccchhhhcCCCCCCc-ccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPE-NLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~-~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++..++ +....-..+..+|.++|||||+|.+.++|..|+..|++.
T Consensus         4 l~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~   66 (81)
T d2ghpa1           4 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGL   66 (81)
T ss_dssp             EEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTC
T ss_pred             EEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCC
Confidence            59999999999999998844111 111111123567899999999999999999999998874

>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=97.98  E-value=4e-07  Score=73.50  Aligned_cols=61  Identities=20%  Similarity=0.122  Sum_probs=46.3

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++..++...........+|+++|||||+|.+.++|..||+ +++.
T Consensus        16 ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~   76 (91)
T d1fjeb1          16 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGL   76 (91)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGE
T ss_pred             EEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCc
Confidence            599999999999999998552221111111236689999999999999999999995 7664

>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=97.98  E-value=1.7e-06  Score=68.73  Aligned_cols=63  Identities=16%  Similarity=-0.044  Sum_probs=49.3

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccc-cCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLK-DNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k-~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ++||+|||..+++++|.+++...+... ...-....+|.++|||||.|.+.++|.+|+..|++.
T Consensus        11 ~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~   74 (86)
T d2cqpa1          11 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDR   74 (86)
T ss_dssp             EEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTC
T ss_pred             EEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCC
Confidence            469999999999999999966333221 111233567999999999999999999999998764

>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=97.98  E-value=8.7e-07  Score=71.71  Aligned_cols=63  Identities=13%  Similarity=0.099  Sum_probs=48.3

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCC-CCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNET-GNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~-~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|.+++..++....... .+..+|.++|||||.|.+.++|..|+..|++.
T Consensus        11 tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~   74 (93)
T d1x5ua1          11 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMI   74 (93)
T ss_dssp             EEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCC
Confidence            3699999999999999988442221111111 23678999999999999999999999998764

>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=97.98  E-value=4.7e-07  Score=71.13  Aligned_cols=57  Identities=12%  Similarity=0.079  Sum_probs=46.6

Q ss_pred             ccccCCCcccchhhhcCCCC------CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTK------SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~k------s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++.      ++.+..     +..+|.++|||||+|.+.++|..|+..|++.
T Consensus         3 lfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~-----d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~   65 (80)
T d1cvja1           3 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCR-----DMITRRSLGYAYVNFQQPADAERALDTMNFD   65 (80)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEE-----CTTTCCEEEEEEEEESSHHHHHHHHTTSTTC
T ss_pred             EEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEe-----cccccCCCCceEEEECCHHHHHHHHHHcCCC
Confidence            59999999999999998843      222322     3577999999999999999999999888763

>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=97.96  E-value=1.6e-06  Score=67.18  Aligned_cols=56  Identities=11%  Similarity=-0.092  Sum_probs=46.6

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+|||..+++.+|.+++...++..      ...++++|||||.|.+.++|.+|+..||+.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g~~~------~~~~~~~g~afv~f~~~~~A~~Ai~~ln~~   56 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYELKY------CFVDKYKGTAFVTLLNGEQAEAAINTFHQS   56 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSCEEE------EEEETTTTEEEEEESSHHHHHHHHHHHTTE
T ss_pred             CEEeCCCCcCCHHHHHHHHhcccccc------eeecccceeEEEEECCHHHHHHHHHHhCCc
Confidence            38999999999999999966444322      334678999999999999999999999864

>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=97.96  E-value=1.8e-06  Score=69.21  Aligned_cols=62  Identities=13%  Similarity=0.064  Sum_probs=47.5

Q ss_pred             ccccCCCcccchhhhcCCCCCCc-ccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPE-NLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~-~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++..++ +.....-....+|.++|||||+|.+.++|..|+..|++.
T Consensus         8 ifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~   70 (90)
T d1x5sa1           8 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGK   70 (90)
T ss_dssp             EEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTC
T ss_pred             EEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCC
Confidence            59999999999999998844111 111111123677899999999999999999999998764

>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=97.95  E-value=1.4e-06  Score=69.74  Aligned_cols=57  Identities=11%  Similarity=-0.045  Sum_probs=47.3

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|.+++..+++..      ...+.++|||||+|.+.++|..|+..|++.
T Consensus         7 ~i~V~nLp~~~t~~~l~~lF~~~G~~~------~~~~~~kg~afV~f~~~~~A~~Ai~~ln~~   63 (88)
T d1wg1a_           7 GILVKNLPQDSNCQEVHDLLKDYDLKY------CYVDRNKRTAFVTLLNGEQAQNAIQMFHQY   63 (88)
T ss_dssp             CEEEESCCSSCCHHHHHHHTCSSCCCC------EEEEGGGTEEEECCSCHHHHHHHHHHHTTE
T ss_pred             EEEEeCCCCccChHHHHHHHHhcCcee------eeeeccCCceEEEECCHHHHHHHHHHhCCC
Confidence            369999999999999999976444221      334667999999999999999999999886

>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=97.95  E-value=2.3e-07  Score=72.15  Aligned_cols=59  Identities=10%  Similarity=0.053  Sum_probs=43.9

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccC-CCCCCCCCCCCceEEEEeCCHHHHHHHHHHH
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDN-ETGNKESHDPTNFGVVTEEDRKADQEALEKL  290 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~-~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l  290 (577)
                      +||+||+..+++++|.+++..++..... -..+..+|+++|||||+|.+.++|..||+..
T Consensus         2 lfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~   61 (75)
T d1x0fa1           2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK   61 (75)
T ss_dssp             EEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCS
T ss_pred             EEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhC
Confidence            4999999999999999884422211111 1123678999999999999999999997643

>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=97.92  E-value=1.5e-06  Score=67.70  Aligned_cols=57  Identities=16%  Similarity=0.048  Sum_probs=43.3

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHH
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALE  288 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~  288 (577)
                      +||+||+..+++++|.+++...+...... -.+..+|+++|||||+|.+.++|.+||.
T Consensus         3 lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~   60 (77)
T d1uawa_           3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA   60 (77)
T ss_dssp             EEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH
T ss_pred             EEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH
Confidence            49999999999999998844222111111 1336779999999999999999999986

>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=97.92  E-value=3.2e-06  Score=68.67  Aligned_cols=63  Identities=6%  Similarity=-0.118  Sum_probs=47.4

Q ss_pred             cccccCCCcccchhhhcCCCCCCc-ccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPE-NLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~-~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++++|.+++..++ +.......+..++.++|||||+|.+.++|..|+..+++.
T Consensus        10 tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~   73 (98)
T d1x4ha1          10 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLE   73 (98)
T ss_dssp             CEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTT
T ss_pred             EEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccc
Confidence            469999999999999998843222 111111123667889999999999999999999988743

>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=97.90  E-value=8.9e-07  Score=70.27  Aligned_cols=60  Identities=17%  Similarity=0.024  Sum_probs=44.8

Q ss_pred             ccccCCCcccchhhhcCCCC------CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTK------SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~k------s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++.      ++.+..+.  .....+.++|||||+|.+.++|..|+..+++.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~--~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~   66 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKK--NKAGVLLSMGFGFVEYKKPEQAQKALKQLQGH   66 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEE--CTTCCEEEEEEEEEEESSHHHHHHHHHHSTTC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceeccc--ccccccccceEEEEEECCHHHHHHHHHHhCCC
Confidence            48999999999999998833      22232211  11233467999999999999999999998864

>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=97.88  E-value=4.3e-06  Score=66.87  Aligned_cols=63  Identities=11%  Similarity=-0.051  Sum_probs=45.2

Q ss_pred             cccccccCCCcccchhhh---cCCCC------CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEK---NEPTK------SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l---~e~~k------s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+.+||+||+..++++++   .+++.      .+.+.++.  .....+.++|||||+|.+.++|..|+..||+.
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~--~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~   79 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNST--SYAGSQGPSASAYVTYIRSEDALRAIQCVNNV   79 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCS--SCCSSSCCCEEEEEEESSHHHHHHHHHHHTTE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeecc--CcCCCCCcceEEEEecccchhHHHHHHHhCCC
Confidence            345699999999999998   55533      22222211  11333456699999999999999999999874

>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=97.86  E-value=9.5e-07  Score=72.98  Aligned_cols=62  Identities=11%  Similarity=0.138  Sum_probs=47.1

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++..++...... -.+..+|.++|||||+|.+.++|..|+..|++.
T Consensus        11 l~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~   73 (104)
T d1p1ta_          11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGR   73 (104)
T ss_dssp             EEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSB
T ss_pred             EEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCC
Confidence            59999999999999998844222111111 122567899999999999999999999988764

>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=97.86  E-value=3.6e-06  Score=67.92  Aligned_cols=62  Identities=18%  Similarity=0.085  Sum_probs=45.3

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++++|.+++..++.........+ .+.++|||||+|.+.++|..|+..|++.
T Consensus        13 ~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~-~~~~kg~afV~f~~~~~a~~Ai~~l~~~   74 (93)
T d2cq3a1          13 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGSKGFGFVTFENSADADRAREKLHGT   74 (93)
T ss_dssp             EEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECC-TTTTCCEEEEEESCHHHHHHHHHHHTTC
T ss_pred             EEEEECCCCCCCHHHHHHHHhhcceeeecccccc-ccCCcceeEEEECCHHHHHHHHHHcCCC
Confidence            3599999999999999998552222111111112 2336999999999999999999998875

>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=97.86  E-value=5.1e-06  Score=67.89  Aligned_cols=63  Identities=17%  Similarity=0.035  Sum_probs=48.1

Q ss_pred             cccccCCCcccchhhhcCCCCCCccc---------ccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENL---------KDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~---------k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|.+++..++..         ......+..+|.++|||||+|.+.++|..|+..|++.
T Consensus        10 ~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~   81 (101)
T d2cpea1          10 AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   81 (101)
T ss_dssp             EEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             EEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCC
Confidence            46999999999999999884422211         1111123567899999999999999999999999874

>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=97.86  E-value=8.6e-07  Score=70.33  Aligned_cols=60  Identities=13%  Similarity=0.049  Sum_probs=44.9

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHHh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKLT  291 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~  291 (577)
                      +||+||+..+++++|.+++..++...... ..+..+|.++|||||+|.+.++|.+||...+
T Consensus         9 lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~   69 (84)
T d1l3ka1           9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP   69 (84)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCS
T ss_pred             EEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCC
Confidence            59999999999999998844222111111 1236779999999999999999999987533

>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=97.86  E-value=4e-06  Score=64.50  Aligned_cols=60  Identities=13%  Similarity=0.008  Sum_probs=44.8

Q ss_pred             ccccCCCcccchhhhcCCCCCCc-ccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPE-NLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~-~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      +||+||+..+++++|.+++..++ +....-..+..+|.++|||||+|.+.++|..|+. +++
T Consensus         2 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~   62 (75)
T d2msta_           2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHF   62 (75)
T ss_dssp             EEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSS
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCC
Confidence            49999999999999998843222 1111112336678999999999999999999985 654

>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=97.84  E-value=1.9e-06  Score=68.41  Aligned_cols=57  Identities=5%  Similarity=-0.124  Sum_probs=43.5

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHH
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALE  288 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~  288 (577)
                      +||+|||..+++.+|.+++..++.........+.+|.++|||||+|.+.++|..||.
T Consensus         9 vfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~   65 (85)
T d1zh5a2           9 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE   65 (85)
T ss_dssp             EEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT
T ss_pred             EEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH
Confidence            599999999999999998442221111122225678999999999999999999985

>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=97.83  E-value=3.9e-06  Score=69.00  Aligned_cols=60  Identities=7%  Similarity=-0.072  Sum_probs=47.4

Q ss_pred             ccccCCCcccchhhhcCCCCCCccccc-CCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKD-NETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~-~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      +||+||+..+++.+|.+++...+.... .....+.+|.++|||||.|.+.++|..||. +++
T Consensus        11 v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~   71 (103)
T d2cpya1          11 AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHR   71 (103)
T ss_dssp             EEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCS
T ss_pred             EEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCC
Confidence            699999999999999999664443221 122346789999999999999999999986 554

>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=97.82  E-value=2e-06  Score=67.37  Aligned_cols=57  Identities=12%  Similarity=0.031  Sum_probs=44.8

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++...+...     ....+.++|||||+|.+.++|..|++.|++.
T Consensus         4 l~V~nLp~~~te~~L~~~F~~~G~i~-----~~~~~~~rg~aFV~f~~~~~A~~Ai~~lng~   60 (80)
T d2cqha1           4 LYIGNLSPAVTADDLRQLFGDRKLPL-----AGQVLLKSGYAFVDYPDQNWAIRAIETLSGK   60 (80)
T ss_dssp             EEEECCCTTCCHHHHHHHHHHTTCCC-----SSCEEEETTEEEECCSCHHHHHHHHHHHTTT
T ss_pred             EEEECCCCCCCHHHHHHHHHHhCcEE-----EeEEecccceEEEEECCHHHHHHHHHHhCCC
Confidence            59999999999999999844222211     1233456899999999999999999999863

>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=97.82  E-value=2e-06  Score=70.99  Aligned_cols=69  Identities=12%  Similarity=-0.089  Sum_probs=49.5

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccc-cCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhHHHH
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLK-DNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEER  297 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k-~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i~e~  297 (577)
                      ..++||+|||..+++.+|.+++..++... ......+.++.++|||||+|.+.++|.+|+...+..|..+
T Consensus        15 ~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR   84 (104)
T d1wg5a_          15 DGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHR   84 (104)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSS
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcce
Confidence            34469999999999999999966332211 1122336678999999999999999999986433344433

>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=97.82  E-value=1.1e-06  Score=70.54  Aligned_cols=61  Identities=18%  Similarity=0.207  Sum_probs=44.0

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++..++........ ...+.++|||||+|.+.++|..|+..|++.
T Consensus        11 l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~-~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~   71 (89)
T d1cvja2          11 IFIKNLDKSIDNKALYDTFSAFGNILSCKVV-CDENGSKGYGFVHFETQEAAERAIEKMNGM   71 (89)
T ss_dssp             EEEESCCSSCCHHHHHHHHHTTSCEEEEEEC-CBTTBCCSCEEEEESCHHHHHHHTTSSSEE
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCceEEEEE-eecCCCcceeEEEECCHHHHHHHHHHcCCC
Confidence            5999999999999999884422211111111 112447899999999999999999988764

>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=97.80  E-value=4.5e-06  Score=68.76  Aligned_cols=59  Identities=15%  Similarity=0.027  Sum_probs=44.8

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCC-CCCCCCCCCCceEEEEeCCHHHHHHHHHHH
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNE-TGNKESHDPTNFGVVTEEDRKADQEALEKL  290 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~-~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l  290 (577)
                      +||+||+..+++++|.+++..++...... ..+..++.++|||||+|.+.++|..||...
T Consensus        23 lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~   82 (103)
T d1x4ba1          23 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR   82 (103)
T ss_dssp             EEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSC
T ss_pred             EEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhC
Confidence            59999999999999999844222211111 133677899999999999999999998643

>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=97.79  E-value=2.2e-06  Score=70.40  Aligned_cols=66  Identities=8%  Similarity=-0.114  Sum_probs=49.0

Q ss_pred             ccccccccCCCcccchhhhcCCCCCCcccc-cCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          228 ETQDAGAGKEDESVQSVEKNEPTKSPENLK-DNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       228 ~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k-~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +.+.+||+||+..+++.+|.+++..++... ..-..+..+|.++|||||.|.+.++|..|+..|++.
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~   83 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGY   83 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCC
Confidence            345579999999999999998855111111 000122467899999999999999999999998774

>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=97.77  E-value=2.5e-06  Score=69.30  Aligned_cols=62  Identities=8%  Similarity=0.027  Sum_probs=48.8

Q ss_pred             ccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          228 ETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       228 ~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+.+||+||+..+++++|.+++..++.....    ..+|.++|||||+|.+.++|..|+..|++.
T Consensus        15 ~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~----~~~~~~~~~afV~f~~~~~A~~A~~~l~~~   76 (96)
T d1fjca_          15 AARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGA   76 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcccceee----eecCccccEEEEEeCCHHHHHHHHHHcCCC
Confidence            34557999999999999999995533322211    346788999999999999999999998764

>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=97.75  E-value=4e-06  Score=68.00  Aligned_cols=60  Identities=17%  Similarity=0.043  Sum_probs=44.9

Q ss_pred             ccccCCCcccchhhhcCCCCC----CcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKS----PENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks----~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      +||+||+..+++++|.+++..    +...... .....+|.++|||||+|.++++|..|+..|++
T Consensus         4 LyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~-~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~   67 (96)
T d2disa1           4 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVY-ASAADKMKNRGFAFVEYESHRAAAMARRKLMP   67 (96)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHSTTEEEEECC-SSSCTTTTTCCEEEEEESSHHHHHHHHTTTTT
T ss_pred             EEEcCCCCcCCHHHHHHHHHHhCCcceEEEEe-eeccccccCCCeEEEEEcCHHHHHHHHHHHcC
Confidence            599999999999999988441    1111111 11245688999999999999999999988753

>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=97.74  E-value=1.4e-06  Score=75.96  Aligned_cols=57  Identities=16%  Similarity=0.200  Sum_probs=47.0

Q ss_pred             ccccCCCcccchhhhcCCCC------CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTK------SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~k------s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++.      ++.+..     +..+|.++|||||+|.+.++|..||..|++.
T Consensus        45 l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~-----d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~  107 (139)
T d1u6fa1          45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVC-----DRETRQSRGYGFVKFQSGSSAQQAIAGLNGF  107 (139)
T ss_dssp             EEEESCSTTCCHHHHHHHHHHHSCEEEEEEEE-----ETTTTEEEEEEEEEESSHHHHHHHHHHTTTE
T ss_pred             EEEeCCCCCCCHHHHHHHHHhhcccccccccc-----ccccccccceeeEEECCHHHHHHHHHHhCCC
Confidence            49999999999999998844      222222     2577899999999999999999999999864

>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=97.72  E-value=5e-06  Score=67.32  Aligned_cols=60  Identities=13%  Similarity=0.144  Sum_probs=45.7

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++..++.......  ..++.++|||||.|.+.++|..||..|++.
T Consensus        17 l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~--~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~   76 (95)
T d1x4aa1          17 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDL--KNRRGGPPFAFVEFEDPRDAEDAVYGRDGY   76 (95)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEE--CCSSSSSCCEEEEESCHHHHHHHHHHHTTC
T ss_pred             EEEECCCCCCCHHHHHHHHhcCCceEEEEe--cccccccceEEEEECCHHHHHHHHHHhCCC
Confidence            699999999999999999552221111111  334567899999999999999999999875

>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=97.71  E-value=3.9e-06  Score=66.79  Aligned_cols=56  Identities=13%  Similarity=-0.003  Sum_probs=42.8

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++..++......      ....|||||+|.+.++|..||..|++.
T Consensus         3 vfV~nlp~~~~~~~l~~~F~~~G~v~~~~------i~~~g~afV~f~~~~~a~~Ai~~l~g~   58 (87)
T d3begb1           3 VVVSGLPPSGSWQDLKDHMREAGDVCYAD------VYRDGTGVVEFVRKEDMTYAVRKLDNT   58 (87)
T ss_dssp             EEEEECCSSCCTTHHHHHHGGGSCEEEEE------ECTTSEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEECCCCcCCHHHHHHHHhhhccccccc------ccccceeeEEeCCHHHHHHHHHHhCCC
Confidence            59999999999999999955333222111      123589999999999999999988765

>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=97.69  E-value=5.8e-06  Score=64.35  Aligned_cols=57  Identities=12%  Similarity=0.085  Sum_probs=43.2

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccc-cCCCCCCCCCCCCceEEEEeCCHHHHHHHHH
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLK-DNETGNKESHDPTNFGVVTEEDRKADQEALE  288 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k-~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~  288 (577)
                      +||+||+..+++++|.+++..++... ..-..+..++.++|||||.|.+.+++..|+.
T Consensus         5 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~   62 (79)
T d1l3ka2           5 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI   62 (79)
T ss_dssp             EEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH
T ss_pred             EEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH
Confidence            59999999999999999944222111 1111236788999999999999999888875

>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=97.68  E-value=4.4e-06  Score=66.26  Aligned_cols=59  Identities=10%  Similarity=-0.029  Sum_probs=45.9

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +++||+||+..+++.+|.+++..++....     ...+.++|||||.|.+.++|..|+..|++.
T Consensus         9 k~l~V~nLp~~~te~~l~~~F~~~g~i~~-----~~~~~~rg~afV~f~~~~~A~~Ai~~l~~~   67 (86)
T d2cpda1           9 KILYVRNLMLSTSEEMIEKEFNNIKPGAV-----ERVKKIRDYAFVHFSNREDAVEAMKALNGK   67 (86)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHTTSTTCE-----EEEEECSSEEEEEESSHHHHHHHHHHHSSE
T ss_pred             CEEEEcCCCCCCCHHHHHHhhcccceeee-----EEEccccEEEEEEeCCHHHHHHHHHHcCCC
Confidence            45699999999999999888442222111     223567999999999999999999999874

>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=97.68  E-value=2.3e-06  Score=70.39  Aligned_cols=68  Identities=7%  Similarity=-0.102  Sum_probs=49.1

Q ss_pred             cccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhhHHHH
Q 008117          229 TQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEER  297 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~i~e~  297 (577)
                      ..++||+|||..+++.+|.+++..+.... .....+.+|.++|||||+|.+.++|..|+..-+.+|..+
T Consensus        15 ~~~v~v~nLp~~~te~dl~~~F~~~~~~~-v~~~~~~~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR   82 (102)
T d1weza_          15 GHCVHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHR   82 (102)
T ss_dssp             SCEEEEESCCTTCCHHHHHHSSCSCCCSE-EEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHhccCcce-eeeEEecCCcceEEEEEEECCHHHHHHHHHcCCCEECCE
Confidence            34579999999999999999966333211 111124568899999999999999999987433344444

>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=97.68  E-value=8.2e-06  Score=64.93  Aligned_cols=62  Identities=13%  Similarity=0.005  Sum_probs=46.8

Q ss_pred             ccccccccCCCcccchhhhcCCCCCCc-ccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          228 ETQDAGAGKEDESVQSVEKNEPTKSPE-NLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       228 ~~~~~~v~nl~~~~~~~~l~e~~ks~~-~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +++++||+||+..+++++|.+++...+ +....    ...++++|||||+|.+.++|..|+..|++.
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~----~~~~~~~~~afV~f~~~~~A~~A~~~l~~~   71 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF----KFFQKDRKMALIQMGSVEEAVQALIDLHNH   71 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEE----EECSSSTTCEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEE----EeeecccceeEEEECCHHHHHHHHHhccCC
Confidence            455679999999999999998844222 21100    223456899999999999999999998874

>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=97.67  E-value=6.3e-06  Score=68.50  Aligned_cols=58  Identities=12%  Similarity=-0.054  Sum_probs=45.0

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ++||+||+..+++.+|.+++..++.+...     ...+++|||||.|.+.++|..|+..||+.
T Consensus        12 ~l~V~nLp~~~t~~~L~~~F~~fG~I~~v-----~l~~~kg~afV~f~~~~~A~~A~~~lng~   69 (111)
T d1whxa_          12 VILAKNLPAGTLAAEIQETFSRFGSLGRV-----LLPEGGITAIVEFLEPLEARKAFRHLAYS   69 (111)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHTTSCEEEE-----ECCSSSSCEEEEESCHHHHHHHHHHHTTC
T ss_pred             EEEEECCCCCCCHHHHHhhhhccCCccEE-----EeeccCceEEEEEcCHHHHHHHHHHHcCC
Confidence            35999999999999999994422221111     12356899999999999999999999876

>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=97.66  E-value=6e-06  Score=66.08  Aligned_cols=62  Identities=11%  Similarity=0.004  Sum_probs=43.6

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|.+++..++.........+ ....+|||||+|.+.++|..|+..+++.
T Consensus        10 tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d-~~~~~~~afV~f~~~~~A~~A~~~l~~~   71 (90)
T d2cqia1          10 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE-HTSNDPYCFVEFYEHRDAAAALAAMNGR   71 (90)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECC-CCSSCCEEEEEESSHHHHHHHHHHHTTE
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCCceeeeeecc-cCccceeeEEEECCHHHHHHHHHHcCCC
Confidence            4699999999999999988441111111111001 1223799999999999999999998874

>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=97.65  E-value=6.9e-06  Score=67.55  Aligned_cols=63  Identities=17%  Similarity=0.014  Sum_probs=45.6

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccC-CCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDN-ETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~-~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ..+||+||+..+++.+|.+++..++..... --....+|.++|||||+|.+.++|.+|+ .+++.
T Consensus        16 ~~v~V~nLp~~~te~~l~~~f~~~g~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~   79 (104)
T d1wi8a_          16 YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEE   79 (104)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTTTSCEEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhccccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCC
Confidence            346999999999999999996633321110 1122467889999999999999997666 46553

>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=97.61  E-value=5.6e-06  Score=65.68  Aligned_cols=62  Identities=11%  Similarity=0.089  Sum_probs=40.4

Q ss_pred             cccccCCCcccch-hhhcCCCCCCcccccCC--CCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQS-VEKNEPTKSPENLKDNE--TGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~-~~l~e~~ks~~~~k~~~--~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++ +.|.+++..++......  -....+|.++|||||+|.+.++|..|+. +++.
T Consensus         6 ~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~   70 (86)
T d2ghpa3           6 EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRS   70 (86)
T ss_dssp             EEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTE
T ss_pred             EEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCC
Confidence            3599999998764 55877733222111111  1225688999999999999999999985 6654

>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=97.57  E-value=9.1e-06  Score=67.86  Aligned_cols=65  Identities=11%  Similarity=-0.122  Sum_probs=48.2

Q ss_pred             ccccccccCCCcccchhhhcCCCCCCccccc-CCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          228 ETQDAGAGKEDESVQSVEKNEPTKSPENLKD-NETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       228 ~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~-~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ...++||+||+..+++++|.+++..++.... ..-....+|.++|||||+|.+.++|.+||. +++.
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~   82 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQ   82 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSB
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCC
Confidence            3445799999999999999999653332221 111236789999999999999999999886 5543

>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=97.55  E-value=5.4e-06  Score=66.12  Aligned_cols=55  Identities=16%  Similarity=0.032  Sum_probs=42.1

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHH
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALE  288 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~  288 (577)
                      +.+||+||+..+++++|++++..++...+.    .....++|||||+|.+.++|..||.
T Consensus         6 ~~lfV~nLp~~~te~~L~~~F~~~G~v~~v----~~~~~~~gfafV~f~~~~~a~~a~~   60 (88)
T d1wf0a_           6 SGVFVGRCTGDMTEDELREFFSQYGDVMDV----FIPKPFRAFAFVTFADDQIAQSLCG   60 (88)
T ss_dssp             CEEEEESCCSSSCHHHHHHHSTTTSCCCEE----ECCSSCCSCCEEECSCHHHHHHTTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCCceEE----EEeeccCceEEEEECCHHHHHHHHh
Confidence            346999999999999999996533322211    2345678999999999999999875

>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=97.54  E-value=4e-06  Score=67.31  Aligned_cols=63  Identities=11%  Similarity=0.037  Sum_probs=45.1

Q ss_pred             cccccccCCCcccchhhhcCC----CCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          229 TQDAGAGKEDESVQSVEKNEP----TKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       229 ~~~~~v~nl~~~~~~~~l~e~----~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+.+||+||+..+++++|.+.    +..++......  ...+++++|||||+|.+.++|..|+..+++.
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~--~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~   69 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDIL--VSRSLKMRGQAFVIFKEVSSATNALRSMQGF   69 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEE--CCHHHHHTTCEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceE--EeeeccCCCceEEEECCHHHHHHHHHHhCCC
Confidence            345799999999999988643    12222111111  1345678999999999999999999999864

>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=97.52  E-value=1.2e-05  Score=65.46  Aligned_cols=56  Identities=13%  Similarity=0.030  Sum_probs=44.0

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++.+|.+++..++.....      ....+|||||+|.+.++|..||++||+.
T Consensus        18 i~V~Nlp~~~~~~~L~~~F~~~G~v~~~------~i~~~g~afV~f~~~~~a~~Ai~~lng~   73 (98)
T d1wg4a_          18 VLVSGLPPSGSWQDLKDHMREAGDVCYA------DVQKDGMGMVEYLRKEDMEYALRKLDDT   73 (98)
T ss_dssp             EEEECCCSSCCHHHHHHHHTTSSCEEEE------EEETTTEEEEEESSHHHHHHHHHHHSSE
T ss_pred             EEEECCCCCCCHHHHHHHHHhhcccccc------cccccceEEEEECCHHHHHHHHHHhCCC
Confidence            6999999999999999995533322211      1235799999999999999999998865

>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=97.48  E-value=1.8e-05  Score=62.62  Aligned_cols=57  Identities=18%  Similarity=0.125  Sum_probs=44.9

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++..++.....     ...+.+|||||+|.+.++|..|+..|++.
T Consensus        11 l~V~nLp~~~~~~~l~~~F~~~G~i~~i-----~~~~~k~~afV~f~~~~~A~~A~~~l~g~   67 (86)
T d2cpja1          11 LFVGNLPPDITEEEMRKLFEKYGKAGEV-----FIHKDKGFGFIRLETRTLAEIAKVELDNM   67 (86)
T ss_dssp             EEEESCCTTCCHHHHHHHTSTTCCCSEE-----EEETTTTEEEEECSSSHHHHHHHHHHTTC
T ss_pred             EEEECCCCCCCHHHHHHHHHHhCCceEe-----eeecccceEEEEECCHHHHHHHHHHhCCC
Confidence            6999999999999999986644322211     11245899999999999999999999865

>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=97.48  E-value=2.6e-06  Score=68.24  Aligned_cols=61  Identities=8%  Similarity=0.024  Sum_probs=44.7

Q ss_pred             ccccCCCcccchhhhcCCCC------CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTK------SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~k------s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++.      +..+.......+..++.++|||||+|.+.++|..|+. |++.
T Consensus         4 lyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~   70 (90)
T d1u2fa_           4 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGI   70 (90)
T ss_dssp             EEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSC
T ss_pred             EEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCc
Confidence            59999999999999988843      2222211111235678899999999999999998874 6654

>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=97.47  E-value=1.7e-05  Score=65.70  Aligned_cols=59  Identities=10%  Similarity=-0.162  Sum_probs=43.7

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+..+++++|.+++..++.......   ...+++|||||+|.+.++|..|+..|++.
T Consensus        10 v~V~NL~~~vte~~L~~~F~~~G~i~~~~i---~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~   68 (108)
T d2adba1          10 IIVENLFYPVTLDVLHQIFSKFGTVLKIIT---FTKNNQFQALLQYADPVSAQHAKLSLDGQ   68 (108)
T ss_dssp             EESCSCCSTTHHHHHHHHHTTTSCEEEEEE---EEETTEEEEEEEESCHHHHHHHHHHHHSC
T ss_pred             EEEeCcCCCCCHHHHHHHHccCCcEEEEEE---EeeCCCCeEEEEECCHHHHHHHHHHHCCC
Confidence            599999999999999998442221111000   11245899999999999999999998875

>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=97.47  E-value=2.8e-05  Score=61.02  Aligned_cols=62  Identities=11%  Similarity=-0.040  Sum_probs=45.1

Q ss_pred             ccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          228 ETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       228 ~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +.+++||+||+..+++++|..++...+........    ...+|||||.|.+.++|..|+..|++.
T Consensus         7 P~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~----~~~~g~afV~f~~~~~A~~A~~~l~g~   68 (83)
T d2b0ga1           7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLV----PNRHDIAFVEFTTELQSNAAKEALQGF   68 (83)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEC----TTTCSCEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhccCccEEEeeee----cccceeEEEecCCHHHHHHHHHHhCCc
Confidence            34567999999999999999884422211111111    124789999999999999999998873

>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=97.43  E-value=5.3e-05  Score=60.04  Aligned_cols=61  Identities=8%  Similarity=-0.099  Sum_probs=46.1

Q ss_pred             ccccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHh
Q 008117          226 LKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLT  291 (577)
Q Consensus       226 ~~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~  291 (577)
                      ..+..++||+||+..+++.+|.+++...+.....     ...+.+|||||+|.+.++|..|+..++
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v-----~~~~~~~~afV~f~~~e~A~~a~~~~~   65 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNI-----LMLKGKNQAFLELATEEAAITMVNYYS   65 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEE-----EEETTTTEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccc-----cccccceEEEEEeCCHHHHHHHHHHHc
Confidence            3456678999999999999999995533322211     123457899999999999999998765

>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=97.33  E-value=2.5e-05  Score=63.43  Aligned_cols=55  Identities=9%  Similarity=0.006  Sum_probs=41.3

Q ss_pred             ccccCCC-cccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKED-ESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~-~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +||+||+ ..+++.+|.+++..++.+....       .++|||||+|.+.++|..|+..|++.
T Consensus        18 lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~-------i~rg~aFV~f~~~~~A~~Ai~~lng~   73 (98)
T d1wf2a_          18 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCS-------VHKGFAFVQYVNERNARAAVAGEDGR   73 (98)
T ss_dssp             EEEEEECTTTCCHHHHHHSSTTSSCEEEEE-------EETEEEEEEESSHHHHHHHHHTTTTC
T ss_pred             EEEeCCCcccCCHHHHHHHHhhcCCEEEEE-------EeCCeEEEEECCHHHHHHHHHHcCCC
Confidence            6999997 5677888988855333222111       15899999999999999999999874

>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=97.26  E-value=5.6e-05  Score=61.09  Aligned_cols=61  Identities=13%  Similarity=0.074  Sum_probs=45.2

Q ss_pred             ccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          228 ETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       228 ~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +++.+||+||+..+++++|.+++..++......     ..+.++||||+|.+.++|..|+..|++.
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~   76 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTID-----HVKGDSFAYIQYESLDAAQAACAKMRGF   76 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEE-----ECSSSCCEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEe-----eeccccEEEeccCCHHHHHHHHHHhCCC
Confidence            445679999999999999998843222111111     1234789999999999999999998874

>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=97.26  E-value=7e-05  Score=58.02  Aligned_cols=57  Identities=19%  Similarity=0.140  Sum_probs=41.6

Q ss_pred             ccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +.+||+|++  +++++|.+++...+....     -...+.+|||||+|.+.++|..|+..|++.
T Consensus         6 ~ti~V~~~~--~te~~L~~~F~~~G~I~~-----v~~~~~~~~afV~f~~~~~A~~Ai~~lng~   62 (79)
T d2bz2a1           6 NTLYVYGED--MTPTLLRGAFSPFGNIID-----LSMDPPRNCAFVTYEKMESADQAVAELNGT   62 (79)
T ss_dssp             CEEEEECSS--CCHHHHHHHHSTTCCCSC-----EEEETTTTEEEEECSSHHHHHHHHHHHTTC
T ss_pred             CEEEEECCC--CCHHHHHHHHhccCccce-----eeeccCCCEEEEEEcccHHHHHHHHHhCCC
Confidence            346999986  788899888442222111     112356899999999999999999999865

>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=97.25  E-value=7.9e-05  Score=61.01  Aligned_cols=61  Identities=11%  Similarity=-0.083  Sum_probs=45.8

Q ss_pred             cccccccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhh
Q 008117          227 KETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTC  292 (577)
Q Consensus       227 ~~~~~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~  292 (577)
                      .+.+++||+||+..+++.+|.+++..++....     ....+.+|||||+|.+.++|..|+..++.
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~-----~~~~~~k~~AfV~f~~~e~A~~ai~~~~~   73 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICY-----VMMMPFKRQALVEFENIDSAKECVTFAAD   73 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEE-----EEEETTTTEEEEEESSHHHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceE-----EEEEecceeEEEEeCCHHHHHHHHHHHcC
Confidence            45667899999999999999998552222111     11235689999999999999999987753

>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=97.20  E-value=2.9e-05  Score=62.77  Aligned_cols=58  Identities=5%  Similarity=0.029  Sum_probs=42.8

Q ss_pred             cccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+||+||+..+++.+|.+++..++.......     ...+|||||.|.+.++|..|+..|++.
T Consensus        20 ~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i-----~~~kg~afV~f~~~~~A~~Ai~~l~~~   77 (96)
T d1x4ga1          20 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRV-----FPEKGYSFVRFSTHESAAHAIVSVNGT   77 (96)
T ss_dssp             EEEEECCSSCCCHHHHHHHHHHHSCEEEEEE-----ETTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEEcCCCCCCCHHHHHHHHHHhCCceEEEE-----EecceEEEEEECCHHHHHHHHHHhCCC
Confidence            3699999999999999988441111110000     123899999999999999999998875

>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=97.17  E-value=4e-05  Score=63.24  Aligned_cols=59  Identities=10%  Similarity=-0.059  Sum_probs=41.1

Q ss_pred             cccccCCCc-ccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          231 DAGAGKEDE-SVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       231 ~~~v~nl~~-~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ++||+||+. .+++++|.+++..++.+......    -..+|||||+|.+.++|.+|+..|++.
T Consensus         4 ~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~----~~~kg~afV~f~~~~~A~~ai~~lng~   63 (109)
T d2adca1           4 VLLVSNLNPERVTPQSLFILFGVYGDVQRVKIL----FNKKENALVQMADGNQAQLAMSHLNGH   63 (109)
T ss_dssp             EEEEESCCTTTCCHHHHHHHHHHHTCEEEEEEC----CTTSCCEEEEESCHHHHHHHHHHHTTC
T ss_pred             EEEEeCCCcccCCHHHHHHHHhhccccceEEEE----ecccceEEEEECCHHHHHHHHHHhCCC
Confidence            469999964 58999998884411111111000    013799999999999999999998865

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.15  E-value=0.00046  Score=53.71  Aligned_cols=69  Identities=17%  Similarity=0.245  Sum_probs=56.6

Q ss_pred             CCCceEEEcCCCCCC------CH---HHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 008117          126 KPQTKVYVGKIAPTA------DS---DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  196 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~------te---~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~  196 (577)
                      ++..||.|.-..+..      .+   .+|.+.|..||.|.-++++.+        -..|+|.+-.+|.+|+. |+|..|.
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v~   83 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKVK   83 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEET
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEEc
Confidence            346677776554333      33   367888999999999999876        78999999999999999 7999999


Q ss_pred             CeEEEEE
Q 008117          197 GQELMLK  203 (577)
Q Consensus       197 gr~i~V~  203 (577)
                      |+.|.|.
T Consensus        84 G~~l~It   90 (95)
T d1ufwa_          84 GRAVKIS   90 (95)
T ss_dssp             TEEEEEE
T ss_pred             ceEEEEe
Confidence            9999985

>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=97.07  E-value=0.0014  Score=48.42  Aligned_cols=60  Identities=13%  Similarity=0.261  Sum_probs=51.7

Q ss_pred             HHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEch
Q 008117          144 FVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  206 (577)
Q Consensus       144 ~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Lng~~i~gr~i~V~~a~  206 (577)
                      .|..+|..+|.|.++.|... ..|.  -.|-|...+..+|..|+..||...|++++|.|.++.
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 LLQEAFARHGKVKSVELSPH-TDYQ--LKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSC-CSTT--CCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEec-cCCc--EEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            56678999999999998765 2343  478999999999999999999999999999998764

>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=97.03  E-value=4.3e-05  Score=58.74  Aligned_cols=57  Identities=9%  Similarity=-0.030  Sum_probs=39.9

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHH
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEK  289 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~  289 (577)
                      +||+||+..+++++|++++..++.........+.. ..++||||+|.+.++|.+||..
T Consensus         3 v~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~-~~~~~afV~F~~~~~a~~Al~~   59 (75)
T d2ghpa2           3 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK-KNFRFARIEFARYDGALAAITK   59 (75)
T ss_dssp             EEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT-SSSEEEEEEESSHHHHHHHHTT
T ss_pred             EEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc-ccceEEEEEEcchHHhHHHHHh
Confidence            49999999999999999954222222111111222 3457999999999999999853

>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=96.98  E-value=0.00034  Score=56.57  Aligned_cols=58  Identities=7%  Similarity=-0.042  Sum_probs=42.4

Q ss_pred             ccccccccCCCcc-cchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHH
Q 008117          228 ETQDAGAGKEDES-VQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKL  290 (577)
Q Consensus       228 ~~~~~~v~nl~~~-~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l  290 (577)
                      ...++||+||+.. +++.+|.+++..++.....     ...+.+|||||.|.+.++|..|+..+
T Consensus        17 ~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v-----~~~~~k~~afV~f~~~~~A~~Ai~~~   75 (99)
T d1x4fa1          17 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNY-----ILMRMKSQAFIEMETREDAMAMVDHC   75 (99)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEE-----EEETTTTEEEEECSSHHHHHHHHHHH
T ss_pred             CCCEEEEeCCcCCccCHHHHHhhhccccceeEE-----EEeecCCcEEEEecchHHHHHHHHHH
Confidence            3455799999875 7999999986644422211     12345899999999999999998744

>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=96.85  E-value=0.00011  Score=59.81  Aligned_cols=62  Identities=10%  Similarity=-0.043  Sum_probs=44.0

Q ss_pred             cccccccc--cCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          227 KETQDAGA--GKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       227 ~~~~~~~v--~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+++..+|  ++|+..+++++|..++...+......     ....++||||.|.+.++|..|+..|++.
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~-----~~~~k~~aFV~f~~~e~A~~A~~~lng~   79 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALL-----MPPNKPYSFARYRTTEESKRAYVTLNGK   79 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEE-----CCTTCSCEEEEESSHHHHHHHHHHTTTC
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEe-----eccCccEEEEEECCHHHHHHHHHHhCCC
Confidence            44555566  55999999999998844222111110     1234789999999999999999999874

>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=96.85  E-value=0.00025  Score=58.85  Aligned_cols=56  Identities=9%  Similarity=0.014  Sum_probs=39.9

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCH-HHHHHHHHHHhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDR-KADQEALEKLTC  292 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~-e~a~~Al~~l~~  292 (577)
                      .||+||+..+++++|.+++..++.+...+.     -+.+|||||.|.+. ++|..|+..+++
T Consensus        14 ~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i-----~~~kg~gfV~F~~~~~~A~~a~~~~~~   70 (113)
T d1owxa_          14 KFSGDLDDQTCREDLHILFSNHGEIKWIDF-----VRGAKEGIILFKEKAKEALGKAKDANN   70 (113)
T ss_dssp             EEEESCCSSCCHHHHHHHTCSSCCEEEEEC-----CTTCSEEEEEESSCHHHHHHHHHHTTT
T ss_pred             EEECCCCCCCCHHHHHHHHHhcCChheEEE-----ecCCceEEEEecCcHHHHHHHHHHhcC
Confidence            599999999999999998653332221111     13489999999985 677778776654

>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=96.83  E-value=0.0019  Score=50.83  Aligned_cols=68  Identities=12%  Similarity=0.182  Sum_probs=58.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcc--eEEEEEeCCHHHHHHHHHHhCCceeC
Q 008117          129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPK--GFGFCEFESAEGVLRALRLLNKFNID  196 (577)
Q Consensus       129 ~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~k--g~gFV~f~~~~~A~~Al~~Lng~~i~  196 (577)
                      +.|.|..||+++|++++.+.++..|.+..+..+....+-++.  +-|||.|.+.+++......++|+.+.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            578999999999999999999999999888777765444433  56899999999999999999999883

>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=96.69  E-value=6.5e-05  Score=61.63  Aligned_cols=55  Identities=9%  Similarity=-0.079  Sum_probs=40.1

Q ss_pred             cccCCCcccchhhhcCC-CC-----CCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          233 GAGKEDESVQSVEKNEP-TK-----SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       233 ~v~nl~~~~~~~~l~e~-~k-----s~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ++.++...++++++.++ .+     ++.+.+      +.+|.++|||||.|.+.++|.+|+..|++.
T Consensus        31 ~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~------~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~   91 (104)
T d1jmta_          31 EMQEHYDEFFEEVFTEMEEKYGEVEEMNVCD------NLGDHLVGNVYVKFRREEDAEKAVIDLNNR   91 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTCCEEEEEECC------SSSSSSEEEEEEEESCHHHHHHHHHHHTTC
T ss_pred             HhhhhhhhhhHHHHHHHhccCCCEEEEEeec------CCCCCEeeEEEEEEechhHHHHHHHHHCCC
Confidence            55555556666666666 22     222332      567899999999999999999999999864

>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=96.64  E-value=0.00067  Score=53.59  Aligned_cols=60  Identities=7%  Similarity=-0.049  Sum_probs=43.3

Q ss_pred             cccccccccCCCcc-cchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHh
Q 008117          227 KETQDAGAGKEDES-VQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLT  291 (577)
Q Consensus       227 ~~~~~~~v~nl~~~-~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~  291 (577)
                      ....++||+||+.. +++.+|.+++..++.....     .....++||||.|++.++|..|+..++
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i-----~i~~~k~~afV~f~~~~~A~~A~~~l~   66 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNH-----LILNKINEAFIEMATTEDAQAAVDYYT   66 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEE-----EECSSSSCEEEEESSHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEE-----EeeccceEEEEEEcchhhHHHHHHHHh
Confidence            34556799999985 7899999996633322211     112346899999999999999998764

>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=96.51  E-value=0.00027  Score=57.77  Aligned_cols=59  Identities=7%  Similarity=-0.071  Sum_probs=39.9

Q ss_pred             ccccccCCCccc-chh----hhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          230 QDAGAGKEDESV-QSV----EKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       230 ~~~~v~nl~~~~-~~~----~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +.+||+||+..+ +++    +|+.++..++....     -...++++||||.|.+.++|..|+..|++.
T Consensus         6 ~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~-----~~~~k~~~~afV~f~~~~~A~~Ai~~lng~   69 (104)
T d1weya_           6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTT-----FQYFKSFKRVRINFSNPLSAADARLRLHKT   69 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCE-----EEEETTTTEEEEECSSTTHHHHHHHTSTTS
T ss_pred             ceEEEEeCCchhcCcHHHHHHHHHHhcccccceE-----EEEecCCCEEEEEECCHHHHHHHHHHhccc
Confidence            346999999986 333    24444222221111     112357899999999999999999999985

>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=96.17  E-value=0.00076  Score=52.30  Aligned_cols=55  Identities=11%  Similarity=-0.051  Sum_probs=39.6

Q ss_pred             ccccCCCcccchhhhcCCCCCCcccccCCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          232 AGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       232 ~~v~nl~~~~~~~~l~e~~ks~~~~k~~~~~~~~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      .+|.+++...++..++.|+.-..+..      ...+..+|||||.|.+.++|.+||. +|+.
T Consensus         7 V~V~G~p~~~~~~il~~F~~~G~I~~------~~~~~~~~~~fV~f~~~~~A~~Al~-~nG~   61 (81)
T d1wwha1           7 VTVFGFPQASASYILLQFAQYGNILK------HVMSNTGNWMHIRYQSKLQARKALS-KDGR   61 (81)
T ss_dssp             EEEECCCGGGHHHHHHHHHTTSCEEE------EEECSSSSEEEEEESSHHHHHHHHT-TTTC
T ss_pred             EEEECCChHHHHHHHHHHHhhhhhhe------EEecCCCCEEEEEEcccHHHHHHHh-cCCC
Confidence            47888999988877765543212221      2345678999999999999999995 6653

>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=93.32  E-value=0.025  Score=45.38  Aligned_cols=29  Identities=17%  Similarity=-0.115  Sum_probs=24.8

Q ss_pred             CCCCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          265 ESHDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       265 ~~g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      ......||+||.|.+.++|..|+..|++.
T Consensus        53 ~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_          53 VEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             SSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            34456789999999999999999999874

>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=92.26  E-value=0.047  Score=43.28  Aligned_cols=27  Identities=15%  Similarity=0.228  Sum_probs=24.2

Q ss_pred             CCCCceEEEEeCCHHHHHHHHHHHhhh
Q 008117          267 HDPTNFGVVTEEDRKADQEALEKLTCM  293 (577)
Q Consensus       267 g~~kgfgfV~f~~~e~a~~Al~~l~~~  293 (577)
                      +..+||+||.|.+.++|.+|+..||+.
T Consensus        54 ~~~~G~~fV~f~~~e~A~~A~~~lng~   80 (99)
T d2dita1          54 RHPDGVASVSFRDPEEADYCIQTLDGR   80 (99)
T ss_dssp             TCTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCccEEEEEECCHHHHHHHHHHhCCc
Confidence            456899999999999999999999874

>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=88.97  E-value=0.75  Score=35.71  Aligned_cols=58  Identities=10%  Similarity=0.091  Sum_probs=46.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCceEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 008117          126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN  191 (577)
Q Consensus       126 ~~~~tlfVgnLp~~~te~~L~~~F~~~G~v~~~~i~~~~~tg~~kg~gFV~f~~~~~A~~Al~~Ln  191 (577)
                      +....||.-..|..+.-.+|..+|+.||.|.- ..+.+       .-|||...+.+.|..++..+.
T Consensus        13 p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~V-swIdd-------TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          13 PKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQI-SWIDD-------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEEECCTTCCHHHHHHHHTTTCSCCC-EEEET-------TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCcceeEEEeCCcccchhHHHHHhcCCCceEE-EEecC-------ceEEEEecCHHHHHHHHHHhc
Confidence            34567999999999999999999999997643 23344       279999999999988887653