Citrus Sinensis ID: 025068

---

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-------26
Protein Sequence
MAYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQGIYNPYQQYVPIYGVPGTVNTAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGGPNLNAITTSPLPTVQAPYPTVHARWRF
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHcccEEEEEEEEcccccccccccEEEEccHHHHHHHHcccccEEccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccHHHHHcccccccEEEcccccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHcccccEEccEEEEEcccccccccccccccEEEEccccccccHHHHHHHHHHcccEEEEEEEEcccccccEEEEEEcccHHHHHHHHHHHcccccEEcccEEEEEccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mayqsipgpgsgsssssgfqylnspfgdttyTKVFVGGLAWETQSETMRRYFEQFGEILEAVVItdkntgrskgygfvtfrepeaarracadptpfidgrrancnlaslgrprpqvlygrlrpatlfsgstqatrgpyigsfgyqqplpynyqqgmvypsygyatygpeyvypqgiynpyqqyvpiygvpgtvntavypygqlgqtipgshaytpvqgygmpghqimqfggpnlnaittsplptvqapyptvharwrf
Flexible Loop (DISEMBL)
mayqsipgpgsgsssssGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVvitdkntgrskgygfvtfrepeaarraCADPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQGIYNPYQQYVPIYGVPGTVNTAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGGPNLNAITTsplptvqapyptvharwrf
Low Complexity Region (SEG)
MAYQSIpgpgsgsssssgFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQGIYNPYQQYVPIYGVPGTVNTAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGGPNLNAITTSPLPTVQAPYPTVHARWRF
Disordered region (IsUnstruct)
***********************SPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQGIYNPYQQYVPIYGVPGTVNTAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGGPNLNAITTSPLPTVQA*Y*********
Disordered Region (DISOPRED)
*********************************VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRAN**********************LFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQGIYNPYQQYVPIYG*******************************************************************W*F
Disordered Region (DISEMBL)
*****************GFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQGIYNPYQQYVPIYGVPGTVNTAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGGPNLNAITTSPLPTVQAPYPTVHARWRF
Disordered Region (DISPRO)
*****************************TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASL******VLYGRLRPATLFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQGIYNPYQQYVPIYGVPGTVNTAVY*****GQTIPGSHAYTPVQGYGMPGHQIMQFGGPNLNAITTSPLPTVQAPYPTVHARWRF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQGIYNPYQQYVPIYGVPGTVNTAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGGPNLNAITTSPLPTVQAPYPTVHARWRF
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	258	2.2.26 [Sep-21-2011]
Q76LC6	230	RNA-binding protein 24 OS	no	no	0.344	0.386	0.633	1e-27
Q5ZJX4	215	RNA-binding protein 38 OS	yes	no	0.472	0.567	0.448	2e-27
Q9I8B3	224	RNA-binding protein 24-B	N/A	no	0.356	0.410	0.602	2e-27
Q9BX46	236	RNA-binding protein 24 OS	yes	no	0.333	0.364	0.655	2e-27
Q6P8A7	226	RNA-binding protein 24 OS	yes	no	0.333	0.380	0.643	3e-27
Q6GQD3	225	RNA-binding protein 24-A	N/A	no	0.333	0.382	0.643	3e-27
Q9H0Z9	239	RNA-binding protein 38 OS	no	no	0.472	0.510	0.448	3e-27
D3Z4I3	236	RNA-binding protein 24 OS	yes	no	0.333	0.364	0.643	5e-27
Q5ZMA3	225	RNA-binding protein 24 OS	yes	no	0.333	0.382	0.643	6e-27
Q6DIV4	219	RNA-binding protein 38 OS	no	no	0.333	0.392	0.632	6e-27

>sp|Q76LC6|RBM24_DANRE RNA-binding protein 24 OS=Danio rerio GN=rbm24 PE=2 SV=1

 Score =  123 bits (308), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 57/90 (63%), Positives = 70/90 (77%), Gaps = 1/90 (1%)

Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
           DTTYTK+FVGGL + T   ++R+YFE FGEI EAVVITD+ TG+S+GYGFVT  +  AA 
Sbjct: 7   DTTYTKIFVGGLPYHTTDSSLRKYFEVFGEIEEAVVITDRQTGKSRGYGFVTMADRSAAD 66

Query: 88  RACADPTPFIDGRRANCNLASLGRPRPQVL 117
           RAC DP P IDGR+AN NLA LG  +P+V+
Sbjct: 67  RACKDPNPIIDGRKANVNLAYLG-AKPRVM 95

Plays a role in myogenic differentiation by regulating myog levels. May bind to the 3'-UTR of myog mRNA and regulate its stability.
Danio rerio (taxid: 7955)

>sp|Q5ZJX4|RBM38_CHICK RNA-binding protein 38 OS=Gallus gallus GN=RBM38 PE=2 SV=1

 Score =  123 bits (308), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 69/154 (44%), Positives = 90/154 (58%), Gaps = 32/154 (20%)

Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
           DTT+TK+FVGGL + T   ++R+YFE FG+I EAVVITD+ TG+S+GYGFVT  +  AA 
Sbjct: 7   DTTFTKIFVGGLPYHTTDSSLRKYFEVFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 66

Query: 88  RACADPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSGSTQATRGPYIGSFGYQQP 147
           RAC DP P IDGR+AN NLA LG           +P ++ +G T           G QQ 
Sbjct: 67  RACKDPNPIIDGRKANVNLAYLG----------AKPRSIQTGFT----------IGVQQ- 105

Query: 148 LPYNYQQGMVYPSYGYATYG--PEYVYPQGIYNP 179
                    ++P++    +G  P YVYPQ I  P
Sbjct: 106 ---------LHPAFIQRPFGLTPHYVYPQAIIQP 130

RNA-binding protein that specifically bind the 3'-UTR of some transcripts, leading to maintain their stability. Also acts as a mRNA splicing factor. May play a role in myogenic differentiation.

Gallus gallus (taxid: 9031)

>sp|Q9I8B3|RB24B_XENLA RNA-binding protein 24-B OS=Xenopus laevis GN=rbm24-b PE=2 SV=1

 Score =  122 bits (307), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 56/93 (60%), Positives = 71/93 (76%), Gaps = 1/93 (1%)

Query: 22  LNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFR 81
           +++   DTTYTK+FVGGL + T   ++R+YFE FG+I EAVVITD+ TG+S+GYGFVT  
Sbjct: 1   MHTTQKDTTYTKIFVGGLPYHTTDSSLRKYFEVFGDIEEAVVITDRQTGKSRGYGFVTMA 60

Query: 82  EPEAARRACADPTPFIDGRRANCNLASLG-RPR 113
           +  AA RAC DP P IDGR+AN NLA LG +PR
Sbjct: 61  DRAAAERACKDPNPIIDGRKANVNLAYLGAKPR 93

Plays a role in myogenic differentiation by regulating myog levels. May bind to the 3'-UTR of myog mRNA and regulate its stability.

Xenopus laevis (taxid: 8355)

>sp|Q9BX46|RBM24_HUMAN RNA-binding protein 24 OS=Homo sapiens GN=RBM24 PE=1 SV=1

 Score =  122 bits (306), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 57/87 (65%), Positives = 68/87 (78%), Gaps = 1/87 (1%)

Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
           DTTYTK+FVGGL + T   ++R+YFE FGEI EAVVITD+ TG+S+GYGFVT  +  AA 
Sbjct: 7   DTTYTKIFVGGLPYHTTDASLRKYFEVFGEIEEAVVITDRQTGKSRGYGFVTMADRAAAE 66

Query: 88  RACADPTPFIDGRRANCNLASLG-RPR 113
           RAC DP P IDGR+AN NLA LG +PR
Sbjct: 67  RACKDPNPIIDGRKANVNLAYLGAKPR 93

Plays a role in myogenic differentiation by regulating MYOG levels. Binds to the 3'-UTR of MYOG mRNA and regulates its stability.

Homo sapiens (taxid: 9606)

>sp|Q6P8A7|RBM24_XENTR RNA-binding protein 24 OS=Xenopus tropicalis GN=rbm24 PE=2 SV=1

 Score =  122 bits (305), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 56/87 (64%), Positives = 68/87 (78%), Gaps = 1/87 (1%)

Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
           DTTYTK+FVGGL + T   ++R+YFE FG+I EAVVITD+ TG+S+GYGFVT  +  AA 
Sbjct: 7   DTTYTKIFVGGLPYHTTDSSLRKYFEVFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 66

Query: 88  RACADPTPFIDGRRANCNLASLG-RPR 113
           RAC DP P IDGR+AN NLA LG +PR
Sbjct: 67  RACKDPNPIIDGRKANVNLAYLGAKPR 93

Plays a role in myogenic differentiation by regulating myog levels. May bind to the 3'-UTR of myog mRNA and regulate its stability.

Xenopus tropicalis (taxid: 8364)

>sp|Q6GQD3|RB24A_XENLA RNA-binding protein 24-A OS=Xenopus laevis GN=rbm24-a PE=2 SV=1

 Score =  122 bits (305), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 56/87 (64%), Positives = 68/87 (78%), Gaps = 1/87 (1%)

Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
           DTTYTK+FVGGL + T   ++R+YFE FG+I EAVVITD+ TG+S+GYGFVT  +  AA 
Sbjct: 7   DTTYTKIFVGGLPYHTTDSSLRKYFEVFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 66

Query: 88  RACADPTPFIDGRRANCNLASLG-RPR 113
           RAC DP P IDGR+AN NLA LG +PR
Sbjct: 67  RACKDPNPIIDGRKANVNLAYLGAKPR 93

Plays a role in myogenic differentiation by regulating myog levels. May bind to the 3'-UTR of myog mRNA and regulate its stability.

Xenopus laevis (taxid: 8355)

>sp|Q9H0Z9|RBM38_HUMAN RNA-binding protein 38 OS=Homo sapiens GN=RBM38 PE=1 SV=2

 Score =  122 bits (305), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 69/154 (44%), Positives = 89/154 (57%), Gaps = 32/154 (20%)

Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
           DTT+TK+FVGGL + T   ++R+YFE FG+I EAVVITD+ TG+S+GYGFVT  +  AA 
Sbjct: 30  DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 89

Query: 88  RACADPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSGSTQATRGPYIGSFGYQQP 147
           RAC DP P IDGR+AN NLA LG           +P +L +G           + G QQ 
Sbjct: 90  RACKDPNPIIDGRKANVNLAYLG----------AKPRSLQTGF----------AIGVQQ- 128

Query: 148 LPYNYQQGMVYPSYGYATYG--PEYVYPQGIYNP 179
                    ++P+    TYG  P Y+YP  I  P
Sbjct: 129 ---------LHPTLIQRTYGLTPHYIYPPAIVQP 153

RNA-binding protein that specifically bind the 3'-UTR of CDKN1A transcripts, leading to maintain the stability of CDKN1A transcripts, thereby acting as a mediator of the p53/TP53 family to regulate CDKN1A. CDKN1A is a cyclin-dependent kinase inhibitor transcriptionally regulated by the p53/TP53 family to induce cell cycle arrest. Isoform 1, but not isoform 2, has the ability to induce cell cycle arrest in G1 and maintain the stability of CDKN1A transcripts induced by p53/TP53. Also acts as a mRNA splicing factor. Specifically regulates the expression of FGFR2-IIIb, an epithelial cell-specific isoform of FGFR2. Plays a role in myogenic differentiation.

Homo sapiens (taxid: 9606)

>sp|D3Z4I3|RBM24_MOUSE RNA-binding protein 24 OS=Mus musculus GN=Rbm24 PE=3 SV=1

 Score =  121 bits (304), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 56/87 (64%), Positives = 68/87 (78%), Gaps = 1/87 (1%)

Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
           DTTYTK+FVGGL + T   ++R+YFE FG+I EAVVITD+ TG+S+GYGFVT  +  AA 
Sbjct: 7   DTTYTKIFVGGLPYHTTDASLRKYFEVFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 66

Query: 88  RACADPTPFIDGRRANCNLASLG-RPR 113
           RAC DP P IDGR+AN NLA LG +PR
Sbjct: 67  RACKDPNPIIDGRKANVNLAYLGAKPR 93

Plays a role in myogenic differentiation by regulating MYOG levels. Binds to the 3'-UTR of MYOG mRNA and regulates its stability.

Mus musculus (taxid: 10090)

>sp|Q5ZMA3|RBM24_CHICK RNA-binding protein 24 OS=Gallus gallus GN=RBM24 PE=2 SV=2

 Score =  121 bits (303), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 56/87 (64%), Positives = 68/87 (78%), Gaps = 1/87 (1%)

Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
           DTTYTK+FVGGL + T   ++R+YFE FG+I EAVVITD+ TG+S+GYGFVT  +  AA 
Sbjct: 7   DTTYTKIFVGGLPYHTTDSSLRKYFEVFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 66

Query: 88  RACADPTPFIDGRRANCNLASLG-RPR 113
           RAC DP P IDGR+AN NLA LG +PR
Sbjct: 67  RACKDPNPIIDGRKANVNLAYLGAKPR 93

Plays a role in myogenic differentiation by regulating MYOG levels. Binds to the 3'-UTR of MYOG mRNA and regulates its stability.

Gallus gallus (taxid: 9031)

>sp|Q6DIV4|RBM38_XENTR RNA-binding protein 38 OS=Xenopus tropicalis GN=rbm38 PE=2 SV=1

 Score =  121 bits (303), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 55/87 (63%), Positives = 68/87 (78%), Gaps = 1/87 (1%)

Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
           DTT+TK+FVGGL + T   ++R+YFE FG+I EAVVITD+ TG+S+GYGFVT  +  AA 
Sbjct: 7   DTTFTKIFVGGLPYHTTDASLRKYFEVFGDIDEAVVITDRQTGKSRGYGFVTMSDRAAAE 66

Query: 88  RACADPTPFIDGRRANCNLASLG-RPR 113
           RAC DP P IDGR+AN NLA LG +PR
Sbjct: 67  RACKDPNPIIDGRKANVNLAYLGAKPR 93

RNA-binding protein that specifically bind the 3'-UTR of VegT transcripts, leading to maintain their stability and stimulate their translation, thereby playing a role in germ layer formation. VegT is a localized maternal determinant essentially required for endoderm formation. Also has some proneural function in the open neural plate and in the context of retinogenesis. May also act as a mRNA splicing factor. May play a role in myogenic differentiation.

Xenopus tropicalis (taxid: 8364)

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	258
359491921	346	PREDICTED: uncharacterized protein LOC10	0.972	0.725	0.826	1e-110
224061833	287	predicted protein [Populus trichocarpa]	0.972	0.874	0.8	1e-103
357467185	371	RNA-binding protein 24-B [Medicago trunc	0.972	0.676	0.771	1e-103
224086108	286	predicted protein [Populus trichocarpa]	0.972	0.877	0.779	1e-101
356508471	286	PREDICTED: RNA-binding protein 24-like [	0.972	0.877	0.755	1e-101
356517913	293	PREDICTED: 40S ribosomal protein S19, mi	0.972	0.856	0.750	1e-100
449458055	286	PREDICTED: RNA-binding protein Musashi h	0.972	0.877	0.745	3e-97
22330665	285	RNA recognition motif-containing protein	0.937	0.849	0.683	2e-92
297842407	283	RNA recognition motif-containing protein	0.937	0.855	0.679	5e-92
23505939	274	At1g20880/F9H16_14 [Arabidopsis thaliana	0.910	0.857	0.633	1e-81

>gi|359491921|ref|XP_002273353.2| PREDICTED: uncharacterized protein LOC100258188 [Vitis vinifera]

 Score =  404 bits (1037), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 209/253 (82%), Positives = 228/253 (90%), Gaps = 2/253 (0%)

Query: 1   MAYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE 60
           MAYQ IPGP SGSSSSSGFQ+LNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE
Sbjct: 1   MAYQPIPGPSSGSSSSSGFQFLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE 60

Query: 61  AVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQVLYGR 120
           AVVITDKNTGRSKGYGFVTFR+PE+ARRAC DP P IDGRRANCNLASLGRPRP + YGR
Sbjct: 61  AVVITDKNTGRSKGYGFVTFRDPESARRACLDPAPIIDGRRANCNLASLGRPRPSMSYGR 120

Query: 121 LRPATLFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQGIYNPY 180
           LRP T + GS  ATRG Y+G+FGYQQP+ Y+YQQG +YPSYGYA YGPEYVYPQG+YNPY
Sbjct: 121 LRPVTPYLGSVPATRGSYVGNFGYQQPVSYSYQQGFMYPSYGYAAYGPEYVYPQGVYNPY 180

Query: 181 --QQYVPIYGVPGTVNTAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGGPNLNAIT 238
             QQY+ IYGVPGTVNTA+YPYGQLGQT+P SH YT VQGY MPGHQ MQFGG ++NAI+
Sbjct: 181 PGQQYLQIYGVPGTVNTAIYPYGQLGQTLPSSHGYTTVQGYAMPGHQFMQFGGSSVNAIS 240

Query: 239 TSPLPTVQAPYPT 251
           TSP+PT+QAPYPT
Sbjct: 241 TSPIPTIQAPYPT 253

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224061833|ref|XP_002300621.1| predicted protein [Populus trichocarpa] gi|222842347|gb|EEE79894.1| predicted protein [Populus trichocarpa]

 Score =  382 bits (980), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 204/255 (80%), Positives = 221/255 (86%), Gaps = 4/255 (1%)

Query: 1   MAYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE 60
           MAYQ++PGP SGSSSSSGFQY+NSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFG+ILE
Sbjct: 1   MAYQAVPGPSSGSSSSSGFQYMNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGDILE 60

Query: 61  AVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPR-PQVLYG 119
           AVVITDKNTGRSKGYGFVTFREPEAARRACADPTP IDGRRANCNLASLGRPR PQ   G
Sbjct: 61  AVVITDKNTGRSKGYGFVTFREPEAARRACADPTPMIDGRRANCNLASLGRPRPPQPYVG 120

Query: 120 RLRPATLFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQGIYNP 179
           RLRPA  +  S Q  RG Y GSFGYQQP+ Y YQQG++Y  YGYA YGPEYVY QG+YNP
Sbjct: 121 RLRPAPPYIASVQTPRGTYAGSFGYQQPVSYGYQQGLMYHPYGYAAYGPEYVYQQGVYNP 180

Query: 180 Y---QQYVPIYGVPGTVNTAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGGPNLNA 236
           Y   QQY+ IYGVPGTVNT +YPYGQ GQ +PG H YT +QGY +PGH IMQFGGP +NA
Sbjct: 181 YAAGQQYLQIYGVPGTVNTGMYPYGQFGQNVPGGHGYTTMQGYAVPGHHIMQFGGPGVNA 240

Query: 237 ITTSPLPTVQAPYPT 251
           +TTSPLPT+QAPYPT
Sbjct: 241 MTTSPLPTIQAPYPT 255

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357467185|ref|XP_003603877.1| RNA-binding protein 24-B [Medicago truncatula] gi|355492925|gb|AES74128.1| RNA-binding protein 24-B [Medicago truncatula]

 Score =  379 bits (973), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 199/258 (77%), Positives = 220/258 (85%), Gaps = 7/258 (2%)

Query: 1   MAYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE 60
           MAYQ   GP SGSSSSSGFQ LNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFG+ILE
Sbjct: 1   MAYQ---GPSSGSSSSSGFQLLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGDILE 57

Query: 61  AVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPR-PQVLYG 119
           AVVITDKNTGRSKGYGFVTFR+PEAARRACADP+P IDGRRANCNLAS GRPR P + YG
Sbjct: 58  AVVITDKNTGRSKGYGFVTFRDPEAARRACADPSPVIDGRRANCNLASHGRPRGPPISYG 117

Query: 120 RLRPATLFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQGIYNP 179
           R+RPA+ + GS Q  RG Y+G +GYQQPL Y YQQGMVYP YGY TYGPEYVYPQG+YNP
Sbjct: 118 RVRPASPYVGSLQPARGAYVGGYGYQQPLSYGYQQGMVYPPYGYTTYGPEYVYPQGMYNP 177

Query: 180 Y---QQYVPIYGVPGTVNTAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGGPNLNA 236
           Y   QQY+ IYGVPG +NT +YPYGQLGQ IPG H YT +QGY +PGHQI+ +GG N+NA
Sbjct: 178 YAGQQQYLQIYGVPGAMNTTIYPYGQLGQAIPGGHGYTAMQGYTVPGHQIVPYGGSNVNA 237

Query: 237 ITTSPLPTVQAPYPTVHA 254
           ITTSP+P +Q PYP + A
Sbjct: 238 ITTSPVPAIQVPYPRIAA 255

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224086108|ref|XP_002307819.1| predicted protein [Populus trichocarpa] gi|222857268|gb|EEE94815.1| predicted protein [Populus trichocarpa]

 Score =  373 bits (958), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 198/254 (77%), Positives = 219/254 (86%), Gaps = 3/254 (1%)

Query: 1   MAYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE 60
           MAYQ+IPGP SGSSSSSGFQY+NSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFG+ILE
Sbjct: 1   MAYQAIPGPSSGSSSSSGFQYMNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGDILE 60

Query: 61  AVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQVLYGR 120
           AVVITDKNTGRSKGYGFVTFREP+AARRACADPTP IDGRRANCNLASLGRPRP + YGR
Sbjct: 61  AVVITDKNTGRSKGYGFVTFREPDAARRACADPTPIIDGRRANCNLASLGRPRPPLPYGR 120

Query: 121 LRPATLFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQGIYNPY 180
            RPA  +  S Q  RG Y+GSFGYQQP+ Y YQQG++Y  YGYA YGPEYVY QG YNPY
Sbjct: 121 PRPAAPYITSVQTPRGTYVGSFGYQQPVSYGYQQGLMYNPYGYAAYGPEYVYQQGAYNPY 180

Query: 181 ---QQYVPIYGVPGTVNTAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGGPNLNAI 237
               QY+ IYGVPGTVN+ +YPYGQL Q +PG H YT + GY +PGHQI+QFGGP++NAI
Sbjct: 181 ATGHQYLQIYGVPGTVNSGMYPYGQLSQNVPGGHGYTSMPGYAVPGHQIVQFGGPSVNAI 240

Query: 238 TTSPLPTVQAPYPT 251
           TTS +PT+QAPY T
Sbjct: 241 TTSSMPTIQAPYHT 254

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356508471|ref|XP_003522980.1| PREDICTED: RNA-binding protein 24-like [Glycine max]

 Score =  372 bits (956), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 192/254 (75%), Positives = 220/254 (86%), Gaps = 3/254 (1%)

Query: 1   MAYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE 60
           MAYQ++ GP SGSSSSSGFQ LNSPFGDTTYTKVFVGGLAWETQSETMRRYF+QFGEILE
Sbjct: 1   MAYQAMQGPSSGSSSSSGFQLLNSPFGDTTYTKVFVGGLAWETQSETMRRYFDQFGEILE 60

Query: 61  AVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQVLYGR 120
           AVVITDKNTGRSKGYGFVTFR+PEAARRACADP+P IDGRRANCNLASLGRPRP + YGR
Sbjct: 61  AVVITDKNTGRSKGYGFVTFRDPEAARRACADPSPVIDGRRANCNLASLGRPRPPLPYGR 120

Query: 121 LRPATLFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQGIYNPY 180
           +RPA+ + GS Q  RG Y+G FGYQQP+ Y+YQQG+VYP YGY +YGPEY+YPQ +YNPY
Sbjct: 121 IRPASPYVGSLQPARGAYVGGFGYQQPVSYSYQQGLVYPPYGYTSYGPEYIYPQSLYNPY 180

Query: 181 --QQYVPIYGVPGTVN-TAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGGPNLNAI 237
             QQY+ IYGVPG VN T +YPYGQ+GQ I   H Y+ +QGY +PGHQI+ +GG N+NAI
Sbjct: 181 MGQQYLQIYGVPGAVNTTTIYPYGQVGQAITSGHGYSAMQGYTVPGHQIVPYGGSNVNAI 240

Query: 238 TTSPLPTVQAPYPT 251
           TTSP+P +QA YP+
Sbjct: 241 TTSPMPAIQASYPS 254

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356517913|ref|XP_003527630.1| PREDICTED: 40S ribosomal protein S19, mitochondrial-like [Glycine max]

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 196/261 (75%), Positives = 220/261 (84%), Gaps = 10/261 (3%)

Query: 1   MAYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE 60
           MAYQ+I  P SGSSSSSGFQ LNSPFGDTTYTKVFVGGLAWETQSETMRRYF+QFGEILE
Sbjct: 1   MAYQAIQVPSSGSSSSSGFQLLNSPFGDTTYTKVFVGGLAWETQSETMRRYFDQFGEILE 60

Query: 61  AVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQVLYG- 119
           AVVITDKNTGRSKGYGFVTFR+PEAARRACADPTP IDGRRANCNLASLGRPRP + YG 
Sbjct: 61  AVVITDKNTGRSKGYGFVTFRDPEAARRACADPTPVIDGRRANCNLASLGRPRPPLPYGI 120

Query: 120 ------RLRPATLFSGSTQATRGPYIGSFGY-QQPLPYNYQQGMVYPSYGYATYGPEYVY 172
                 R+RPA+ + GS Q  RG Y+G FGY QQP+ Y+YQQG+VYP YGY TYGPEY+Y
Sbjct: 121 VLCLIRRIRPASPYVGSLQPARGAYVGGFGYQQQPVSYSYQQGLVYPPYGYTTYGPEYIY 180

Query: 173 PQGIYNPY--QQYVPIYGVPGTVNTAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFG 230
           PQ +YNPY  QQY+ IYGVPG VNT VYPYGQ+GQ IP  H Y+ +QGY +PGHQI+ +G
Sbjct: 181 PQSLYNPYMGQQYLQIYGVPGAVNTTVYPYGQVGQAIPSGHGYSAIQGYTVPGHQIVPYG 240

Query: 231 GPNLNAITTSPLPTVQAPYPT 251
           G N+NAITTSP+P +QA YP+
Sbjct: 241 GSNVNAITTSPMPAIQASYPS 261

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449458055|ref|XP_004146763.1| PREDICTED: RNA-binding protein Musashi homolog 2-like [Cucumis sativus] gi|449531145|ref|XP_004172548.1| PREDICTED: RNA-binding protein Musashi homolog 2-like [Cucumis sativus]

 Score =  360 bits (924), Expect = 3e-97,   Method: Compositional matrix adjust.
 Identities = 190/255 (74%), Positives = 212/255 (83%), Gaps = 4/255 (1%)

Query: 1   MAYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE 60
           MAYQ  PGP S S SSS   +LNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE
Sbjct: 1   MAYQHGPGPSSISGSSSSSGFLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE 60

Query: 61  AVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQVLY-- 118
           AVVITDKNTGRSKGYGFVTFR+PE+ARRACADPTP IDGRRANCNLASLGRPRP + Y  
Sbjct: 61  AVVITDKNTGRSKGYGFVTFRDPESARRACADPTPIIDGRRANCNLASLGRPRPPLSYGT 120

Query: 119 GRLRPATLFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQGIYN 178
           GRLR   ++ G  Q  RG YIG+FGYQQP+ Y YQQG+ YP YGYATYGPEYVYPQG YN
Sbjct: 121 GRLRQPAVYVGGMQPNRGTYIGNFGYQQPVSYAYQQGLAYPPYGYATYGPEYVYPQGGYN 180

Query: 179 PY--QQYVPIYGVPGTVNTAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGGPNLNA 236
           P+  QQY+ IYGVPG+ +  +Y YGQLGQT+PG H Y  V GY MP  QI+QF GPN+NA
Sbjct: 181 PFVGQQYLQIYGVPGSASPTIYHYGQLGQTVPGGHGYGAVHGYAMPSPQILQFSGPNVNA 240

Query: 237 ITTSPLPTVQAPYPT 251
           +T+SP+PT+QAPYP+
Sbjct: 241 LTSSPMPTIQAPYPS 255

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22330665|ref|NP_565132.2| RNA recognition motif-containing protein [Arabidopsis thaliana] gi|332197724|gb|AEE35845.1| RNA recognition motif-containing protein [Arabidopsis thaliana]

 Score =  344 bits (883), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 179/262 (68%), Positives = 207/262 (79%), Gaps = 20/262 (7%)

Query: 1   MAYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE 60
           MAYQ +PG        SGF YLNSPFGDTT+TKVFVGGLAWETQSET+R++FEQ+GEILE
Sbjct: 1   MAYQPVPG--------SGFHYLNSPFGDTTFTKVFVGGLAWETQSETLRQHFEQYGEILE 52

Query: 61  AVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQVLY-- 118
           AVVI DKNTGRSKGYGFVTFR+PEAARRACADPTP IDGRRANCNLASLGRPRP + Y  
Sbjct: 53  AVVIADKNTGRSKGYGFVTFRDPEAARRACADPTPIIDGRRANCNLASLGRPRPPLPYAV 112

Query: 119 -----GRLRPATLFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVY- 172
                GRLRPA+ + G+ Q  RG  IG++ YQQPLPYNYQQG+VYP YG   YGPEY+Y 
Sbjct: 113 IPNMPGRLRPASPYIGNVQGPRGSLIGNYPYQQPLPYNYQQGVVYP-YGVTAYGPEYMYS 171

Query: 173 -PQGIYNPY--QQYVPIYGVPGTVNTAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQF 229
             QG+Y+PY  QQY+ +YGVPG VN+ VY YGQL QTIP  H YT VQGY +PG  I+Q 
Sbjct: 172 QSQGLYSPYMGQQYLQVYGVPGAVNSPVYQYGQLSQTIPNGHGYTAVQGYSVPGSHILQL 231

Query: 230 GGPNLNAITTSPLPTVQAPYPT 251
           GGP ++ +TTS +P +QAPYP+
Sbjct: 232 GGPTVSTMTTSSMPALQAPYPS 253

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297842407|ref|XP_002889085.1| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297334926|gb|EFH65344.1| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  343 bits (879), Expect = 5e-92,   Method: Compositional matrix adjust.
 Identities = 178/262 (67%), Positives = 205/262 (78%), Gaps = 20/262 (7%)

Query: 1   MAYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE 60
           MAYQS+PG        SGF YLNSPFGDTT+TKVFVGGLAWETQSET+RR+FEQFGEILE
Sbjct: 1   MAYQSVPG--------SGFHYLNSPFGDTTFTKVFVGGLAWETQSETLRRHFEQFGEILE 52

Query: 61  AVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQVLY-- 118
           AVVI DKNTGRSKGYGFVTFR+PEAARRACADPTP IDGRRANCNLASLGRPRP + Y  
Sbjct: 53  AVVIADKNTGRSKGYGFVTFRDPEAARRACADPTPIIDGRRANCNLASLGRPRPPLPYAL 112

Query: 119 -----GRLRPATLFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVY- 172
                GRLRPA+ + G+ Q  RG  IG++ YQQPLPYNYQQG+VYP YG   YGPEY+Y 
Sbjct: 113 IPNMPGRLRPASPYIGNVQGPRGSLIGNYPYQQPLPYNYQQGVVYP-YGVTAYGPEYMYS 171

Query: 173 -PQGIYNPY--QQYVPIYGVPGTVNTAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQF 229
             QG+Y PY  QQY+ +YGVPG VN+ +Y YGQL QTIP  H Y  VQGY +PG  ++Q 
Sbjct: 172 QSQGLYGPYMGQQYLQVYGVPGAVNSPIYQYGQLSQTIPSGHGYPAVQGYSVPGSHVLQL 231

Query: 230 GGPNLNAITTSPLPTVQAPYPT 251
           GGP ++A+TTS +  +Q PYP+
Sbjct: 232 GGPTVSAMTTSSMSALQGPYPS 253

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|23505939|gb|AAN28829.1| At1g20880/F9H16_14 [Arabidopsis thaliana]

 Score =  308 bits (790), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 166/262 (63%), Positives = 192/262 (73%), Gaps = 27/262 (10%)

Query: 1   MAYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE 60
           MAY SIP        SSGF YLNSPFGDTT+TKVFVGGLAWETQSET+RR+F+Q+G+ILE
Sbjct: 1   MAYHSIP--------SSGFHYLNSPFGDTTFTKVFVGGLAWETQSETLRRHFDQYGDILE 52

Query: 61  AVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQVLY-- 118
           AVVITDKNTGRSKGYGFVTFR+PEAARRAC DPTP IDGRRANCNLASLGR RP + Y  
Sbjct: 53  AVVITDKNTGRSKGYGFVTFRDPEAARRACVDPTPIIDGRRANCNLASLGRSRPPMQYAV 112

Query: 119 -----GRLRPATLFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYP 173
                GR+RP + + GS Q+ RG + GS  Y QP  YNYQQG+VYP YG   YGP+Y+Y 
Sbjct: 113 IPHAPGRVRPHSPYVGSVQSPRGLHFGSHPYHQPPTYNYQQGVVYP-YGVTPYGPDYMYS 171

Query: 174 Q--GIYNPY--QQYVPIYGVPGTVNTAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQF 229
           Q  G Y PY  QQY+ +YGVPG VN+  Y YGQL  TIPG+H YT  QGY  PG  ++Q 
Sbjct: 172 QSQGFYGPYMGQQYLQVYGVPGAVNSPGYQYGQLSHTIPGAHGYTAGQGYSHPGSHVLQL 231

Query: 230 GGPNLNAITTSPLPTVQAPYPT 251
           G        TSP+  +Q+PYP+
Sbjct: 232 G-------ATSPMSAIQSPYPS 246

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	258
TAIR|locus:2011726	285	AT1G76460 [Arabidopsis thalian	0.899	0.814	0.700	2.4e-92
TAIR|locus:2037370	274	AT1G20880 [Arabidopsis thalian	0.883	0.832	0.639	1.2e-81
TAIR|locus:2032120	287	AT1G78260 [Arabidopsis thalian	0.806	0.724	0.502	1.1e-48
TAIR|locus:2196521	291	AT1G22330 [Arabidopsis thalian	0.864	0.766	0.467	4.4e-45
TAIR|locus:2044370	336	AT2G46780 [Arabidopsis thalian	0.682	0.523	0.515	2.8e-41
TAIR|locus:2017779	347	AT1G22910 [Arabidopsis thalian	0.755	0.561	0.495	3.3e-40
TAIR|locus:2006998	245	AT1G33470 [Arabidopsis thalian	0.837	0.881	0.417	1.1e-39
TAIR|locus:2102435	261	ARP1 "ABA-regulated RNA-bindin	0.806	0.796	0.411	1.6e-31
ZFIN|ZDB-GENE-030131-5923	246	rbm38 "RNA binding motif prote	0.779	0.817	0.389	3.8e-30
ZFIN|ZDB-GENE-040628-1	230	rbm24a "RNA binding motif prot	0.740	0.830	0.392	2.7e-29

TAIR|locus:2011726 AT1G76460 [Arabidopsis thaliana (taxid:3702)]

 Score = 920 (328.9 bits), Expect = 2.4e-92, P = 2.4e-92
 Identities = 171/244 (70%), Positives = 198/244 (81%)

Query:    19 FQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFV 78
             F YLNSPFGDTT+TKVFVGGLAWETQSET+R++FEQ+GEILEAVVI DKNTGRSKGYGFV
Sbjct:    11 FHYLNSPFGDTTFTKVFVGGLAWETQSETLRQHFEQYGEILEAVVIADKNTGRSKGYGFV 70

Query:    79 TFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQVLY-------GRLRPATLFSGST 131
             TFR+PEAARRACADPTP IDGRRANCNLASLGRPRP + Y       GRLRPA+ + G+ 
Sbjct:    71 TFRDPEAARRACADPTPIIDGRRANCNLASLGRPRPPLPYAVIPNMPGRLRPASPYIGNV 130

Query:   132 QATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQ--GIYNPY--QQYVPIY 187
             Q  RG  IG++ YQQPLPYNYQQG+VYP YG   YGPEY+Y Q  G+Y+PY  QQY+ +Y
Sbjct:   131 QGPRGSLIGNYPYQQPLPYNYQQGVVYP-YGVTAYGPEYMYSQSQGLYSPYMGQQYLQVY 189

Query:   188 GVPGTVNTAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGGPNLNAITTSPLPTVQA 247
             GVPG VN+ VY YGQL QTIP  H YT VQGY +PG  I+Q GGP ++ +TTS +P +QA
Sbjct:   190 GVPGAVNSPVYQYGQLSQTIPNGHGYTAVQGYSVPGSHILQLGGPTVSTMTTSSMPALQA 249

Query:   248 PYPT 251
             PYP+
Sbjct:   250 PYPS 253

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0048573 "photoperiodism, flowering" evidence=RCA

TAIR|locus:2037370 AT1G20880 [Arabidopsis thaliana (taxid:3702)]

 Score = 819 (293.4 bits), Expect = 1.2e-81, P = 1.2e-81
 Identities = 158/247 (63%), Positives = 184/247 (74%)

Query:    19 FQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFV 78
             F YLNSPFGDTT+TKVFVGGLAWETQSET+RR+F+Q+G+ILEAVVITDKNTGRSKGYGFV
Sbjct:    11 FHYLNSPFGDTTFTKVFVGGLAWETQSETLRRHFDQYGDILEAVVITDKNTGRSKGYGFV 70

Query:    79 TFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQVLY-------GRLRPATLFSGST 131
             TFR+PEAARRAC DPTP IDGRRANCNLASLGR RP + Y       GR+RP + + GS 
Sbjct:    71 TFRDPEAARRACVDPTPIIDGRRANCNLASLGRSRPPMQYAVIPHAPGRVRPPSPYVGSV 130

Query:   132 QATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQ--GIYNPY--QQYVPIY 187
             Q+ RG + GS  Y QP  YNYQQG+VYP YG   YGP+Y+Y Q  G Y PY  QQY+ +Y
Sbjct:   131 QSPRGLHFGSHPYHQPPTYNYQQGVVYP-YGVTPYGPDYMYSQSQGFYGPYMGQQYLQVY 189

Query:   188 GVPGTVNTAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGGPNLNAITTSPLPTVQA 247
             GVPG VN+  Y YGQL  TIPG+H YT  QGY  PG  ++Q G        TSP+  +Q+
Sbjct:   190 GVPGAVNSPGYQYGQLSHTIPGAHGYTAGQGYSHPGSHVLQLGA-------TSPMSAIQS 242

Query:   248 PYPTVHA 254
             PYP+  A
Sbjct:   243 PYPSPSA 249

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2032120 AT1G78260 [Arabidopsis thaliana (taxid:3702)]

 Score = 508 (183.9 bits), Expect = 1.1e-48, P = 1.1e-48
 Identities = 116/231 (50%), Positives = 139/231 (60%)

Query:    21 YLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 80
             Y  SPFGDTTYTKVFVGGLAWET ++ MRRYFEQFGEILEAV+ITDKNTG+SKGYGFVTF
Sbjct:     6 YYRSPFGDTTYTKVFVGGLAWETPTDEMRRYFEQFGEILEAVIITDKNTGKSKGYGFVTF 65

Query:    81 REPEAARRACADPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSGSTQATRGPYIG 140
             RE ++A RA ADP P IDGR+ANCN+AS GRPRP    GR +     S S   + GP   
Sbjct:    66 RESDSATRAVADPNPVIDGRKANCNIASFGRPRPSPPRGRGQTG---SPSQYQSGGPSTY 122

Query:   141 SFGYQQPLPYNYQQGMVYPSYGYATYGPE-YVYPQGIYNP-------YQQYVPIYG---- 188
             + G   PLP      ++YPSYGY TY P+ + Y Q +YN        YQQ   +YG    
Sbjct:   123 T-GMAAPLPPAAAPQLMYPSYGY-TYNPDQFGYHQALYNTQLQQAQYYQQQQQLYGGGAT 180

Query:   189 VPGTVNTAVYP----YGQLGQT--IPGSHAYTPVQGYGMPGHQIMQFGGPN 233
              P +    + P    YG   Q   +P  H +   Q Y    H   +F  P+
Sbjct:   181 SPSSSGATIMPSPYYYGYSLQAPRVPYQHHHHLPQPYNPQQHHHQRFSSPS 231

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2196521 AT1G22330 [Arabidopsis thaliana (taxid:3702)]

 Score = 474 (171.9 bits), Expect = 4.4e-45, P = 4.4e-45
 Identities = 115/246 (46%), Positives = 142/246 (57%)

Query:    21 YLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 80
             Y  SPFGDTT+TKVFVGGLAWET ++ MRRYF+QFGEILEAV+ITDK TG+SKGYGFVTF
Sbjct:     6 YYRSPFGDTTHTKVFVGGLAWETPTDEMRRYFDQFGEILEAVIITDKATGKSKGYGFVTF 65

Query:    81 REPEAARRACADPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSGSTQATRGPYIG 140
             R+ ++A RA ADP P IDGR+ANCN+AS GRPRP    GR +      GS    +G    
Sbjct:    66 RDSDSATRAVADPNPVIDGRKANCNIASFGRPRPSTPRGRGQ-----GGSPSQYQGGGQS 120

Query:   141 SF-GYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQGIYNPY---QQYVP--IYG-----V 189
             S+ G   P+       ++YPSYGY TY  EY Y Q +YN      QY    +YG      
Sbjct:   121 SYTGMAAPVQQAAAAQLMYPSYGY-TYNSEYGYHQALYNAQLQQAQYYQQQMYGGGGATS 179

Query:   190 PGTVNTAVYPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGG----PNLNAITTSPLPTV 245
             P + N    PY  L    P  + +   Q Y    HQ  Q       P+ ++    P   V
Sbjct:   180 PSSSNIMPSPYYYLQAPSPRPYLHHQ-QHYQYHHHQQQQQQQQQRLPSASSYLIYP-SNV 237

Query:   246 QAPYPT 251
             +AP P+
Sbjct:   238 EAPTPS 243

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2044370 AT2G46780 [Arabidopsis thaliana (taxid:3702)]

 Score = 438 (159.2 bits), Expect = 2.8e-41, P = 2.8e-41
 Identities = 98/190 (51%), Positives = 119/190 (62%)

Query:    23 NSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFRE 82
             N+   DT  TK+FVGGLAWETQ +TMRRYFEQFGEI+EAVVITDKNTGRSKGYGFVTF+E
Sbjct:    13 NNNTTDTKLTKIFVGGLAWETQRDTMRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFKE 72

Query:    83 PEAARRACADPTPFIDGRRANCNLASLG--RPRPQVL----YGRLR-PAT---LFSGSTQ 132
              EAA RAC +  P IDGRRANCNLA LG  +PRP        GR R P +   L + S Q
Sbjct:    73 AEAAMRACQNMNPVIDGRRANCNLACLGAQKPRPPTSPRHGTGRFRSPGSGVGLVAPSPQ 132

Query:   133 ATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQGIYNPY----QQYVPIYG 188
                     +F +QQ   +  Q    Y +YG++ Y  E +YP   YN +    QQ+ P  G
Sbjct:   133 FRGSSSSSAFVHQQQQQHTAQFPFPYSTYGFSGYSQEGMYPMNYYNHHLYGGQQFSPYMG 192

Query:   189 VPGTVNTAVY 198
              P   +T ++
Sbjct:   193 HPSAGSTGMF 202

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2017779 AT1G22910 [Arabidopsis thaliana (taxid:3702)]

 Score = 428 (155.7 bits), Expect = 3.3e-40, P = 3.3e-40
 Identities = 106/214 (49%), Positives = 125/214 (58%)

Query:    27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
             GDTTYTKVFVGGLAWET  ETM+++FEQFGEILEAVVITDK +GRSKGYGFVTFRE EAA
Sbjct:     8 GDTTYTKVFVGGLAWETHKETMKKHFEQFGEILEAVVITDKASGRSKGYGFVTFREAEAA 67

Query:    87 RRACADPTPFIDGRRANCNLASLG--RPRPQVLY----GRLRPATLFSGSTQATRGPYIG 140
             R AC D TP IDGRRANCNLASLG  R +P        GR+    +   + Q   GP   
Sbjct:    68 RSACVDATPVIDGRRANCNLASLGLQRSKPSTPNHGGGGRINNMRVMMSTMQTGFGPPPP 127

Query:   141 SFGYQQPLPYNYQQGMVYPSYGYATYGPEYV-YPQGIYNPYQ-QYVPIYGVPGTVNTAVY 198
                  QP  + +   +    +GY+ Y P+Y  +P  +Y  Y       YGV G  N+   
Sbjct:   128 P----QPPTFTHYPHLPLNLFGYSPYSPDYSSFPTNLYGMYGCTSGGQYGVYGNRNS--- 180

Query:   199 PYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGGP 232
               G  G T   + A TP    G  GH  +QF  P
Sbjct:   181 --GGGGLTAAAASA-TPFYPCG-GGHGGVQFSQP 210

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

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

TAIR|locus:2006998 AT1G33470 [Arabidopsis thaliana (taxid:3702)]

 Score = 423 (154.0 bits), Expect = 1.1e-39, P = 1.1e-39
 Identities = 101/242 (41%), Positives = 135/242 (55%)

Query:    28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
             DTT+TKVFVGGLAWET   ++R YFEQFG+I+EAVVITDK++GRSKGYGFVTF +PEAA+
Sbjct:     3 DTTFTKVFVGGLAWETHKVSLRNYFEQFGDIVEAVVITDKSSGRSKGYGFVTFCDPEAAQ 62

Query:    88 RACADPTPFIDGRRANCNLASLG--RPRPQV-LYGRLRPATLFSGSTQATRGPYIGSFG- 143
             +AC DP P IDGRRANCNLA+ G  R +P   ++G +       G       P+   FG 
Sbjct:    63 KACVDPAPVIDGRRANCNLAAFGVQRSKPSSPIHGHV------GGRGMKVTSPFKTHFGT 116

Query:   144 ----YQQPLPYNYQQGMVYPS-YGYATYGPEYVYP-QGIYNPY----QQYVPIYGVPGTV 193
                    PLP+++   + Y + +G+++Y  +Y YP Q  YN Y     Q+ P+YG     
Sbjct:   117 AATAIPSPLPFSHYT-LPYTNPFGFSSYSMDYNYPTQSYYNVYGGATAQH-PMYGSGPMT 174

Query:   194 NTAVYPYGQLGQTIPGSHAYTPVQGYG---MPGHQIMQFGGPNLNAITTSPLPTVQAPYP 250
               A  P       +  +    PV GY     P H +  +  P  N    +  P   AP P
Sbjct:   175 GVAAAPAAGFYPYLQFAEGNGPVTGYAPLHYPNH-MFHYSAPGGNYPHHNGSPVSLAPSP 233

Query:   251 TV 252
              +
Sbjct:   234 VI 235

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005576 "extracellular region" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

TAIR|locus:2102435 ARP1 "ABA-regulated RNA-binding protein 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 346 (126.9 bits), Expect = 1.6e-31, P = 1.6e-31
 Identities = 97/236 (41%), Positives = 121/236 (51%)

Query:    22 LNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFR 81
             +N  FGDT  TKVFVGGLAW+T  E M  +F ++G+ILEAV+I+DK T RSKGYGFVTF+
Sbjct:     7 VNGCFGDTKLTKVFVGGLAWDTHKEAMYDHFIKYGDILEAVIISDKLTRRSKGYGFVTFK 66

Query:    82 EPEAARRACADPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSGSTQATRGPYIGS 141
             + +AA RAC D TP I+GRRANCNLASLG        GRLR +   +   Q   GP  G+
Sbjct:    67 DAKAATRACEDSTPIINGRRANCNLASLG--------GRLRKSPTMTSPQQ---GPKNGN 115

Query:   142 FGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQGIYNPYQQYVPIYGVPG-TVNTAV--- 197
                  P   N+ Q   YPS G+     +    Q +  P+  Y   Y  P  T N  V   
Sbjct:   116 RA-TPPHVGNHSQ-WYYPS-GFTNQQHQQQNHQAV--PFYGYPSAYVAPNMTFNQKVGYV 170

Query:   198 ---YPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGGPNLNAITTSPLPTVQAPYP 250
                Y  G   Q  P   +    Q Y    H  M +GG  +     SP+      YP
Sbjct:   171 GGTYMNGYYAQMQPQPQSQPQPQYY----HHHM-YGGGRVMVGAASPMVPFYTVYP 221

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0009507 "chloroplast" evidence=ISM

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

GO:0005634 "nucleus" evidence=IDA

GO:0009414 "response to water deprivation" evidence=IMP

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

GO:0009737 "response to abscisic acid stimulus" evidence=IEP

GO:0010029 "regulation of seed germination" evidence=IMP

ZFIN|ZDB-GENE-030131-5923 rbm38 "RNA binding motif protein 38" [Danio rerio (taxid:7955)]

 Score = 333 (122.3 bits), Expect = 3.8e-30, P = 3.8e-30
 Identities = 88/226 (38%), Positives = 119/226 (52%)

Query:    28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
             DTT+TK+FVGGL + T   ++R+YFE FG+I EAVVITD+ TG+S+GYGFVT  +  AA 
Sbjct:    21 DTTFTKIFVGGLPYHTTDASLRKYFETFGDIDEAVVITDRQTGKSRGYGFVTMMDKSAAE 80

Query:    88 RACADPTPFIDGRRANCNLASLG-RPRPQVLYGRLRPATLFSGSTQATRGPYIG-SFGYQ 145
             RAC DP P IDGR+AN NLA LG +PR         P T +S   Q      I   +G  
Sbjct:    81 RACKDPNPIIDGRKANVNLAYLGAKPRS--------PLTGYSTGVQQVHPTLIQRQYGLS 132

Query:   146 QPLPYNY---QQGMVYPSYGYATYGPEYV-----YPQGIYNPYQQYVPIYGVPGTVNTAV 197
             QP  Y     Q  ++ P+   +T    Y+     Y Q   + ++QY P    PG ++  +
Sbjct:   133 QPYVYPQAVLQPSLLLPTQVSSTSSSPYLDFSTAYAQYAASAFEQY-PYAASPGFLSY-M 190

Query:   198 YPYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGGPNLNAITTSPLP 243
             YP G  G   P S   TP+      G +      P+  ++ TS  P
Sbjct:   191 YPPGTAG---PSSAISTPIPNPLSTGEEPHPL--PSSRSLHTSSTP 231

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

ZFIN|ZDB-GENE-040628-1 rbm24a "RNA binding motif protein 24a" [Danio rerio (taxid:7955)]

 Score = 325 (119.5 bits), Expect = 2.7e-29, P = 2.7e-29
 Identities = 84/214 (39%), Positives = 107/214 (50%)

Query:    28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
             DTTYTK+FVGGL + T   ++R+YFE FGEI EAVVITD+ TG+S+GYGFVT  +  AA 
Sbjct:     7 DTTYTKIFVGGLPYHTTDSSLRKYFEVFGEIEEAVVITDRQTGKSRGYGFVTMADRSAAD 66

Query:    88 RACADPTPFIDGRRANCNLASLG-RPR---PQVLYG--RLRPATLFSGSTQATRGPYIGS 141
             RAC DP P IDGR+AN NLA LG +PR   P   +G  ++ PA  F          Y+  
Sbjct:    67 RACKDPNPIIDGRKANVNLAYLGAKPRVMQPGFTFGVPQIHPA--FIQRPYGIPTHYVYP 124

Query:   142 FGYQQP---LPYNYQQGMVYPSYGYATYGPEYVYPQGIYNPYQQYVPIYGVPGTVNTAVY 198
               + QP   +P+      + P+   AT    Y+   G    Y QY              Y
Sbjct:   125 QAFMQPSVVIPH------IQPTATSATASSPYIDYTGA--AYAQYASAATAAAAAAYEQY 176

Query:   199 PYGQLGQTIPGSHAYTPVQGYGMPGHQIMQFGGP 232
             PY       P +  Y    GYG    Q +    P
Sbjct:   177 PYA----ASPAATGYVAAAGYGYAMQQPLATAAP 206

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003730 "mRNA 3'-UTR binding" evidence=ISS

GO:0043488 "regulation of mRNA stability" evidence=ISS

GO:0010830 "regulation of myotube differentiation" evidence=ISS

GO:0003228 "atrial cardiac muscle tissue development" evidence=IMP

GO:0072358 "cardiovascular system development" evidence=IGI

GO:0001947 "heart looping" evidence=IMP

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0030154 "cell differentiation" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

Your Input:
	GSVIVG00002935001	SubName- Full=Chromosome chr18 scaffold_137, whole genome shotgun sequence; (258 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00001957001	SubName- Full=Chromosome chr5 scaffold_124, whole genome shotgun sequence; (169 aa)			•						0.498
	GSVIVG00024380001	SubName- Full=Chromosome chr6 scaffold_3, whole genome shotgun sequence; (69 aa)			•						0.480
	GSVIVG00012366001	SubName- Full=Chromosome chr4 scaffold_373, whole genome shotgun sequence; (227 aa)			•						0.445
	GSVIVG00018411001	SubName- Full=Chromosome chr13 scaffold_17, whole genome shotgun sequence; (301 aa)			•						0.442
	GSVIVG00011496001	SubName- Full=Chromosome chr10 scaffold_312, whole genome shotgun sequence; (226 aa)			•						0.408

---

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	258
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-43
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	4e-27
smart00360	73	smart00360, RRM, RNA recognition motif	1e-23
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	3e-22
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	9e-21
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-20
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	5e-20
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	3e-19
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	6e-19
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	1e-18
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	1e-18
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-18
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	2e-18
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	4e-18
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-18
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	7e-18
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-17
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	3e-17
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	8e-17
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	1e-16
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	1e-16
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	3e-16
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	5e-16
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	6e-16
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	6e-16
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	6e-16
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	7e-16
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	2e-15
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	2e-15
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-15
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	2e-15
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	9e-15
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-14
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-14
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	2e-14
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	2e-14
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	4e-14
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	6e-14
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	7e-14
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	1e-13
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-13
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-13
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	2e-13
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-13
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	4e-13
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	9e-13
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-12
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	2e-12
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	2e-12
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	3e-12
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	4e-12
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	5e-12
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	8e-12
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-11
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	1e-11
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-11
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	3e-11
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	3e-11
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	4e-11
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	4e-11
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	7e-11
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	1e-10
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	1e-10
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	1e-10
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	2e-10
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-10
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	3e-10
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	5e-10
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	5e-10
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	6e-10
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	7e-10
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	8e-10
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-09
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-09
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-09
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	2e-09
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-09
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	3e-09
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	3e-09
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	4e-09
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-09
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	9e-09
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	1e-08
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	1e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-08
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	2e-08
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	2e-08
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	3e-08
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	3e-08
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	3e-08
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	3e-08
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	3e-08
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	3e-08
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	3e-08
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	5e-08
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	5e-08
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	5e-08
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	6e-08
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	6e-08
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	8e-08
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	9e-08
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	1e-07
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	1e-07
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-07
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	2e-07
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-07
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-07
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-07
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-07
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	3e-07
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	3e-07
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	3e-07
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	3e-07
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	4e-07
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	4e-07
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	4e-07
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	4e-07
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	5e-07
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	6e-07
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	7e-07
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	7e-07
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-06
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-06
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	2e-06
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	2e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-06
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	2e-06
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	2e-06
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	3e-06
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-06
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	4e-06
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	5e-06
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	8e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-05
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	1e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-05
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	1e-05
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	2e-05
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-05
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	2e-05
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	2e-05
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	2e-05
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	2e-05
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	2e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-05
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	3e-05
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	3e-05
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	3e-05
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	3e-05
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-05
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	4e-05
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	4e-05
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	4e-05
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	4e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-05
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	5e-05
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	5e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	6e-05
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	7e-05
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	7e-05
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	7e-05
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	8e-05
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	8e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	9e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-04
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	1e-04
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	1e-04
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	1e-04
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	1e-04
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	1e-04
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	1e-04
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	1e-04
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	3e-04
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	3e-04
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	3e-04
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	3e-04
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	3e-04
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	4e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	4e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	4e-04
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	4e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	4e-04
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	4e-04
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	5e-04
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	5e-04
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	5e-04
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	5e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	5e-04
cd12535	86	cd12535, RRM_FUS_TAF15, RNA recognition motif in v	5e-04
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	5e-04
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	6e-04
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	6e-04
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	6e-04
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	8e-04
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	8e-04
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	8e-04
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	8e-04
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	0.001
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	0.001
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	0.001
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	0.001
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	0.001
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	0.001
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	0.001
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	0.001
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.002
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	0.002
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	0.002
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	0.002
cd12303	86	cd12303, RRM_spSet1p_like, RNA recognition motif i	0.002
cd12591	80	cd12591, RRM2_p54nrb, RNA recognition motif 2 in v	0.002
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	0.002
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	0.002
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	0.002
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	0.002
cd12356	79	cd12356, RRM_PPARGC1B, RNA recognition motif in pe	0.002
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	0.003
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	0.003
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	0.003
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	0.003
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	0.003
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	0.003
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	0.003
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	0.003
cd12623	91	cd12623, RRM_PPARGC1A, RNA recognition motif in pe	0.003
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	0.003
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.004
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	0.004
cd12537	85	cd12537, RRM1_RBM23, RNA recognition motif 1 in ve	0.004
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	0.004

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

 Score =  141 bits (358), Expect = 2e-43
 Identities = 50/76 (65%), Positives = 63/76 (82%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           TK+FVGGL + T  +++R+YF QFGEI EAVVITD+ TG+S+GYGFVTF++ E+A RAC 
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 92  DPTPFIDGRRANCNLA 107
           DP P IDGR+AN NLA
Sbjct: 61  DPNPIIDGRKANVNLA 76

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

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

 Score = 99.2 bits (248), Expect = 4e-27
 Identities = 29/67 (43%), Positives = 47/67 (70%)

Query: 35  FVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT 94
           F+GGL+W+T  E++R YF ++GE+++ V++ D  TGRS+G+GFVTF +P +  +  A   
Sbjct: 2   FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKP 61

Query: 95  PFIDGRR 101
             +DGR 
Sbjct: 62  HVLDGRE 68

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

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

 Score = 90.3 bits (225), Expect = 1e-23
 Identities = 27/70 (38%), Positives = 39/70 (55%), Gaps = 1/70 (1%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC-A 91
            +FVG L  +T  E +R  F +FG++    ++ DK TG+SKG+ FV F   E A +A  A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 92  DPTPFIDGRR 101
                +DGR 
Sbjct: 61  LNGKELDGRP 70

Length = 73

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

 Score = 86.7 bits (215), Expect = 3e-22
 Identities = 32/76 (42%), Positives = 48/76 (63%), Gaps = 1/76 (1%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC-A 91
            +FVG L+W    E ++  FE+FG ++ A VITD+ TGRS+G+G+V F  PE A++A  A
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 92  DPTPFIDGRRANCNLA 107
                +DGR  N + +
Sbjct: 61  MDGKELDGRPINVDFS 76

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

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

 Score = 83.3 bits (206), Expect = 9e-21
 Identities = 34/68 (50%), Positives = 48/68 (70%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVGGL+WET  ET+RRYF Q+GE+++ V++ DK T RS+G+GFV F++P       A 
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60

Query: 93  PTPFIDGR 100
               +DGR
Sbjct: 61  GPHTLDGR 68

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

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

 Score = 82.0 bits (203), Expect = 2e-20
 Identities = 27/68 (39%), Positives = 42/68 (61%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVGGL  +   E  + YF QFG++++A ++ D +TGRS+G+GFVTF    A  R  + 
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 93  PTPFIDGR 100
               + G+
Sbjct: 61  GMLELGGK 68

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

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

 Score = 81.3 bits (201), Expect = 5e-20
 Identities = 31/73 (42%), Positives = 49/73 (67%)

Query: 35  FVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT 94
           F+GGL+W+T +E +R YF +FGEI E +V+ D  T RS+G+GFVTF +P +  +  A   
Sbjct: 2   FIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGP 61

Query: 95  PFIDGRRANCNLA 107
             +DG++ +  +A
Sbjct: 62  HELDGKKIDPKVA 74

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

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

 Score = 79.0 bits (195), Expect = 3e-19
 Identities = 27/75 (36%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
            + V GL W+T  + ++ YF  FGE+L   V  D  TG+SKG+GFV F + E   +  + 
Sbjct: 1   DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60

Query: 93  PTPFIDGRRANCNLA 107
               IDGR  +  + 
Sbjct: 61  -RHMIDGRWCDVKIP 74

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

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

 Score = 78.1 bits (193), Expect = 6e-19
 Identities = 29/69 (42%), Positives = 41/69 (59%), Gaps = 2/69 (2%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC-AD 92
           +FVG L  +T  E +R  F +FGEI    ++ DK+ G+SKG+ FV F  PE A +A  A 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKD-GKSKGFAFVEFESPEDAEKALEAL 59

Query: 93  PTPFIDGRR 101
               +DGR+
Sbjct: 60  NGKELDGRK 68

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

 Score = 77.8 bits (192), Expect = 1e-18
 Identities = 30/68 (44%), Positives = 44/68 (64%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+F+GGL++ET  ++++ YF Q+GEI + VV+ D NT RS+G+GFVTF        A   
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 93  PTPFIDGR 100
               +DGR
Sbjct: 61  RPHKVDGR 68

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

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 77.3 bits (190), Expect = 1e-18
 Identities = 26/68 (38%), Positives = 44/68 (64%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVGGL+W+T  + ++ YF +FGE+ +  +  D NTGRS+G+GF+ F++  +  +    
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

Query: 93  PTPFIDGR 100
               +DGR
Sbjct: 61  KEHRLDGR 68

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

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

 Score = 77.3 bits (191), Expect = 2e-18
 Identities = 31/77 (40%), Positives = 41/77 (53%), Gaps = 3/77 (3%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA- 91
            ++VG L +    E ++  F QFGE+  A VITD+ TGRS+G+GFV     E A  A   
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 92  -DPTPFIDGRRANCNLA 107
            + T F  GR    N A
Sbjct: 61  LNGTDF-GGRTLTVNEA 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|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 76.8 bits (189), Expect = 2e-18
 Identities = 25/57 (43%), Positives = 43/57 (75%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          K+F+GGL+++T  +++ + F ++G+I E VV+ D+ T RS+G+GFVTF  P+ A+ A
Sbjct: 2  KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDA 58

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

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

 Score = 75.9 bits (187), Expect = 4e-18
 Identities = 26/72 (36%), Positives = 44/72 (61%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVGGL+  T  + +++YF QFG++ +A+++ DK T R +G+GFVTF   +   + C  
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60

Query: 93  PTPFIDGRRANC 104
               I+ +   C
Sbjct: 61  HFHEINNKMVEC 72

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 75.7 bits (187), Expect = 5e-18
 Identities = 23/56 (41%), Positives = 33/56 (58%), Gaps = 1/56 (1%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +FVG L  +T  E ++  F +FG I    ++ D  TGRSKG+ FV F + E A +A
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKA 55

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. 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|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 75.4 bits (186), Expect = 7e-18
 Identities = 25/70 (35%), Positives = 39/70 (55%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVGGL  +   E +R YF Q+G +    ++TDK TG+ +G+ FVTF + +   +    
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

Query: 93  PTPFIDGRRA 102
               I+G R 
Sbjct: 61  KYHTINGHRV 70

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

>gnl|CDD|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 = 74.6 bits (184), Expect = 2e-17
 Identities = 23/58 (39%), Positives = 34/58 (58%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           K+FV GL+  T  + +   F +FG + E +++ D  TG S+G+GFVTF   E A  A
Sbjct: 2  NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAA 59

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

 Score = 73.8 bits (181), Expect = 3e-17
 Identities = 26/52 (50%), Positives = 41/52 (78%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEA 85
          +F+GGL WET  +++R YF QFGE+ +  V+ D  TGRS+G+GF+TF++P++
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKS 52

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

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

 Score = 72.7 bits (179), Expect = 8e-17
 Identities = 28/71 (39%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           ++FVGG+  +T  E +R +F +FG + +  +ITD+  G SKGYGFVTF   E A +  A 
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILAM 62

Query: 93  PTPFIDGRRAN 103
                 G++ N
Sbjct: 63  GNLNFRGKKLN 73

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

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

 Score = 72.3 bits (178), Expect = 1e-16
 Identities = 27/72 (37%), Positives = 38/72 (52%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVG L W   S+ ++ YF QFG++    V  DK TG SKGYGFV+F   +    A   
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 93  PTPFIDGRRANC 104
               ++G +   
Sbjct: 61  QKHILEGNKLQV 72

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

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

 Score = 72.5 bits (178), Expect = 1e-16
 Identities = 29/67 (43%), Positives = 42/67 (62%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
          K+FVGGL  +T    +RR+F ++G++ E VV+ D NT RS+G+GF+TF   + A  A   
Sbjct: 4  KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA 63

Query: 93 PTPFIDG 99
              IDG
Sbjct: 64 QPHSIDG 70

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

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

 Score = 71.2 bits (174), Expect = 3e-16
 Identities = 26/58 (44%), Positives = 41/58 (70%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
          K+FVGGL+  T  E +++YFEQFG++ +A+++ DK T R +G+GFVTF   +   + C
Sbjct: 1  KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC 58

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 70.4 bits (173), Expect = 5e-16
 Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
           +FVG L+W  + + +  +F++ GE+++  +  D + GRSKG+G V F   E A++A    
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALEKS 60

Query: 94  TPFIDGRRANCNLA 107
              + GR    +LA
Sbjct: 61  GEELLGREIRVDLA 74

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|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 70.3 bits (172), Expect = 6e-16
 Identities = 25/67 (37%), Positives = 43/67 (64%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
           +FVGGL+W+T  + ++ YF +FGE+++  +  D  TGRS+G+GFV F++  +  +     
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 94  TPFIDGR 100
              +DGR
Sbjct: 61  EHKLDGR 67

This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

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

 Score = 70.5 bits (172), Expect = 6e-16
 Identities = 31/75 (41%), Positives = 50/75 (66%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+F+GGL+W+T  +++R YF +FGEI E +V+ D  T RS+G+GFVTF +P +  +  A 
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60

Query: 93  PTPFIDGRRANCNLA 107
           P   +D +  +  +A
Sbjct: 61  PHHELDSKTIDPKVA 75

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

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

 Score = 70.5 bits (173), Expect = 6e-16
 Identities = 25/77 (32%), Positives = 40/77 (51%)

Query: 31  YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
             K+FVGGL        +R+YF QFG + E VV+ D    R +G+GF+TF   ++  +  
Sbjct: 2   TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVV 61

Query: 91  ADPTPFIDGRRANCNLA 107
            +    I+G++     A
Sbjct: 62  NEHFHDINGKKVEVKRA 78

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

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

 Score = 75.4 bits (184), Expect = 7e-16
 Identities = 26/109 (23%), Positives = 47/109 (43%), Gaps = 2/109 (1%)

Query: 31  YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
              +FVG L ++   E +R  F++FG +    ++ D+ TG+S+G+ FV F   E+A +A 
Sbjct: 115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAI 174

Query: 91  -ADPTPFIDGRRANCNLA-SLGRPRPQVLYGRLRPATLFSGSTQATRGP 137
                  ++GR      A    +PR ++               +A    
Sbjct: 175 EELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLE 223

Length = 306

>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 69.3 bits (169), Expect = 2e-15
 Identities = 30/79 (37%), Positives = 47/79 (59%)

Query: 29  TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
           T   K+FVGGL+  T  E +++YFEQFG++ +A+++ DK T R +G+GFVTF   +   +
Sbjct: 1   TRTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEK 60

Query: 89  ACADPTPFIDGRRANCNLA 107
            C      I+ +   C  A
Sbjct: 61  VCEIHFHEINNKMVECKKA 79

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

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

 Score = 68.9 bits (169), Expect = 2e-15
 Identities = 26/69 (37%), Positives = 40/69 (57%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVGGL+ ET  E +R YF +FG I+E  +  DK T + +G+ F+TF   E  ++    
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60

Query: 93  PTPFIDGRR 101
               I G++
Sbjct: 61  QFHVIGGKK 69

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

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

 Score = 68.9 bits (169), Expect = 2e-15
 Identities = 29/56 (51%), Positives = 38/56 (67%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +FVG L+ E  +ET+R  F  FGEI +A V+ D  TG+SKGYGFV+F + E A  A
Sbjct: 2  IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENA 57

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

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 68.9 bits (168), Expect = 2e-15
 Identities = 25/68 (36%), Positives = 43/68 (63%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+F+GGL+W+T  + +  Y  +FGE+L+  + TD  TGRS+G+GFV F++  +  +    
Sbjct: 1   KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60

Query: 93  PTPFIDGR 100
               +DG+
Sbjct: 61  KEHKLDGK 68

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

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

 Score = 69.3 bits (169), Expect = 9e-15
 Identities = 37/97 (38%), Positives = 57/97 (58%), Gaps = 3/97 (3%)

Query: 15  SSSGFQYLNSPFGDTTY--TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRS 72
           SS+G   + S  G      TK+F+GGL+W T   ++R  F  FG++++A VI D+ TGRS
Sbjct: 16  SSNGNVPVTSMLGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRS 75

Query: 73  KGYGFVTFREPEAARRACAD-PTPFIDGRRANCNLAS 108
           +G+GFV F +  AA  A ++     ++GR    N A+
Sbjct: 76  RGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAN 112

Length = 144

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

 Score = 67.2 bits (165), Expect = 1e-14
 Identities = 23/59 (38%), Positives = 37/59 (62%), Gaps = 1/59 (1%)

Query: 31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +T V+V  L  +   E ++  F ++G+I  A V+ D + G+SKG+GFV F   EAA++A
Sbjct: 1  FTNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKA 58

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

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

 Score = 66.5 bits (163), Expect = 2e-14
 Identities = 28/80 (35%), Positives = 41/80 (51%), Gaps = 6/80 (7%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
           VF+  L ++   E ++  F QFGE+  A ++ DK TG SKG  FV F+  E+A++     
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 94  TPF------IDGRRANCNLA 107
                    +DGRR    LA
Sbjct: 63  DNAEDSGLSLDGRRLIVTLA 82

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

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 66.2 bits (161), Expect = 2e-14
 Identities = 24/67 (35%), Positives = 44/67 (65%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
           +F+GGL+W+T  + ++ YF +FGE+++  +  D  TGRS+G+GFV F+E E+  +     
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 94  TPFIDGR 100
              ++G+
Sbjct: 61  EHKLNGK 67

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 66.2 bits (161), Expect = 2e-14
 Identities = 30/75 (40%), Positives = 46/75 (61%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+F+GGL+W+T  E +R YF QFGE+ E +V+ D  T RS+G+GFVTF +     +  A 
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 93  PTPFIDGRRANCNLA 107
               +D +  +  +A
Sbjct: 62  SRHELDSKTIDPKVA 76

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

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

 Score = 65.5 bits (159), Expect = 4e-14
 Identities = 30/68 (44%), Positives = 45/68 (66%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+F+GGL++ET  E++R +FEQ+G + + VV+ D NT RS+G+GFVT+   E    A   
Sbjct: 4   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63

Query: 93  PTPFIDGR 100
               +DGR
Sbjct: 64  RPHKVDGR 71

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

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

 Score = 65.0 bits (159), Expect = 6e-14
 Identities = 24/55 (43%), Positives = 33/55 (60%)

Query: 35 FVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +VG L +    + +R  FE FGEI    +  D  TGRSKGYGF+ F + E A++A
Sbjct: 2  YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKA 56

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

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

 Score = 64.6 bits (158), Expect = 7e-14
 Identities = 29/69 (42%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC-A 91
           ++FV  L + T  E +R  FE FGEI E  +  DK T RSKG+ FV+F  PE A +A   
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 92  DPTPFIDGR 100
                  GR
Sbjct: 61  LDGSIFQGR 69

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

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 64.4 bits (156), Expect = 1e-13
 Identities = 30/70 (42%), Positives = 46/70 (65%)

Query: 31  YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
           + K+F+GGL++ET  E++R Y+EQ+G++ + VV+ D  + RS+G+GFVTF        A 
Sbjct: 2   FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAM 61

Query: 91  ADPTPFIDGR 100
           A     IDGR
Sbjct: 62  AARPHTIDGR 71

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

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

 Score = 64.2 bits (156), Expect = 1e-13
 Identities = 27/69 (39%), Positives = 41/69 (59%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVGGL  +     +  +F QFG + +A VI DK TG+ +G+GFV F+  ++A +A   
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60

Query: 93  PTPFIDGRR 101
               I+G R
Sbjct: 61  KFHPINGHR 69

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

>gnl|CDD|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 = 63.8 bits (156), Expect = 2e-13
 Identities = 20/57 (35%), Positives = 33/57 (57%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
          VFVG + ++   E +   F + G ++   ++TD++TG+ KGYGF  F + E A  A 
Sbjct: 1  VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAI 57

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

 Score = 64.0 bits (155), Expect = 2e-13
 Identities = 29/69 (42%), Positives = 46/69 (66%), Gaps = 2/69 (2%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA-CA 91
           K+F+GGL++ET  +++R +FE++G + + VV+ D  T RS+G+GFVT+   E    A  A
Sbjct: 4   KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSA 63

Query: 92  DPTPFIDGR 100
            P   +DGR
Sbjct: 64  RPHK-VDGR 71

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

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

 Score = 63.3 bits (155), Expect = 2e-13
 Identities = 26/57 (45%), Positives = 35/57 (61%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          K+FVG L      E +R  FE++G I E  +I DK+TG+SKG  FV F   E A++A
Sbjct: 1  KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKA 57

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

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

 Score = 63.0 bits (154), Expect = 4e-13
 Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 5/74 (6%)

Query: 31  YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF---REPEAAR 87
           +  +FV  L ++T    +RR FE++G I    ++ DK TG+ +GY F+ F   R+ +AA 
Sbjct: 1   FKTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAY 60

Query: 88  RACADPTPFIDGRR 101
           +        IDGRR
Sbjct: 61  KYADGKK--IDGRR 72

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

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

 Score = 61.8 bits (151), Expect = 9e-13
 Identities = 24/69 (34%), Positives = 42/69 (60%), Gaps = 2/69 (2%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAV-VITDKNTGRSKGYGFVTFREPEAARRACAD 92
           VFVG L ++ + E +R++FE  G++ EAV ++ D+ TG  KG+G+V F+  ++   A   
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDV-EAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL 60

Query: 93  PTPFIDGRR 101
               + GR+
Sbjct: 61  NGIKLKGRK 69

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

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

 Score = 61.0 bits (148), Expect = 2e-12
 Identities = 26/58 (44%), Positives = 33/58 (56%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
          +FV  LA+    E +  +F     I  AVV+TD  TG S+GYGFVTF   E A+ A A
Sbjct: 2  LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALA 59

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

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

 Score = 60.6 bits (147), Expect = 2e-12
 Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
           +FVG L+ E    T+   F  F    +A V+ D  +GRS+GYGFV+FR  + A  A  + 
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 94  T-PFIDGRRANCN 105
              ++  R   CN
Sbjct: 62  NGKWLGSRPIRCN 74

This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 75

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 60.8 bits (147), Expect = 2e-12
 Identities = 21/56 (37%), Positives = 39/56 (69%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
          K+FVGG+  +T+   +R YFEQ+G+I    ++TD+ +G+ +G+ FVTF + ++  +
Sbjct: 2  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 57

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

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

 Score = 60.3 bits (147), Expect = 3e-12
 Identities = 28/69 (40%), Positives = 38/69 (55%), Gaps = 3/69 (4%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
           VF  GL+  T    +R  F ++G I +  V+ D+ TGRS+G+GFV F   E A+ A    
Sbjct: 4   VF--GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 94  TPF-IDGRR 101
               IDGRR
Sbjct: 62  NGMEIDGRR 70

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

>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 60.1 bits (145), Expect = 4e-12
 Identities = 25/70 (35%), Positives = 43/70 (61%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVGG+  +T+   +R YFE++G+I    +ITD+ +G+ +G+GFVTF + +   +    
Sbjct: 2   KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQ 61

Query: 93  PTPFIDGRRA 102
               I+G  A
Sbjct: 62  KYHTINGHNA 71

This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 59.9 bits (146), Expect = 5e-12
 Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD- 92
           +FV  L ++T  E +  +F + G I    V+ DK + + +G+G+VTF   E A+RA  + 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 93  PTPFIDGRRANCNLA 107
                 GR+ +   A
Sbjct: 62  KKTKFGGRKIHVEFA 76

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

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

 Score = 59.4 bits (144), Expect = 8e-12
 Identities = 23/56 (41%), Positives = 38/56 (67%), Gaps = 1/56 (1%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
          ++FVGG+ ++T    +R++F Q+G + E  ++ D+  G SKGYGFVTF   E A++
Sbjct: 4  RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQK 58

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

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

 Score = 58.7 bits (143), Expect = 1e-11
 Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 3/69 (4%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD- 92
           ++V  L      E +R +F  +G++    ++ +K+  R +G+ FV F  PE A  A    
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 93  PTPFIDGRR 101
               +DGR 
Sbjct: 59  NGLVLDGRT 67

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

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

 Score = 58.8 bits (143), Expect = 1e-11
 Identities = 23/52 (44%), Positives = 33/52 (63%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPE 84
          ++FVG L  E   E + R F ++    +A V+ DK TG+SKGYGFV+F +P 
Sbjct: 8  RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPN 59

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

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

 Score = 58.0 bits (141), Expect = 2e-11
 Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 5/64 (7%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR-----SKGYGFVTFREPEAA 86
          T +FV  L ++T  ET++++FE+ G +    +   K+        S GYGFV F+  EAA
Sbjct: 1  TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 87 RRAC 90
          ++A 
Sbjct: 61 QKAL 64

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

 Score = 57.3 bits (139), Expect = 3e-11
 Identities = 25/58 (43%), Positives = 34/58 (58%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          T V++ GL   T  E + +  + FG+I+    I DK T + KGYGFV F  PEAA +A
Sbjct: 1  TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKA 58

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

 Score = 57.6 bits (140), Expect = 3e-11
 Identities = 19/40 (47%), Positives = 25/40 (62%)

Query: 48 MRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
          +R+YF QFG +    +   K TG+SKGY FV F  PE A+
Sbjct: 16 LRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAK 55

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

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

 Score = 57.1 bits (138), Expect = 4e-11
 Identities = 21/60 (35%), Positives = 35/60 (58%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
          +FVG L++ET  + +R +F + G I    ++T +++G+ KG+ FV F E E A  A    
Sbjct: 1  LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 57.2 bits (139), Expect = 4e-11
 Identities = 25/57 (43%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
          +F+  L     ++ +   F  FG IL   V TD+N G SKGYGFV F   EAA RA 
Sbjct: 5  IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDEN-GGSKGYGFVHFETEEAAVRAI 60

This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 77

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

 Score = 56.9 bits (138), Expect = 7e-11
 Identities = 21/55 (38%), Positives = 25/55 (45%)

Query: 35 FVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          FV  L   T  E +   F +FG+I    VI DK TG S  Y F+ F   E    A
Sbjct: 7  FVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61

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

>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 56.1 bits (135), Expect = 1e-10
 Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 2/74 (2%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVGG+  +T+   +R YFE++G+I    V+ D+ +G+ +G+ FVTF + +   +    
Sbjct: 2   KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQ 61

Query: 93  PTPFIDGRRANCNL 106
               I+G   NC +
Sbjct: 62  KYHTINGH--NCEV 73

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 56.1 bits (135), Expect = 1e-10
 Identities = 31/77 (40%), Positives = 45/77 (58%), Gaps = 8/77 (10%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPE---AARRAC 90
           +FV GL+ +T  ET++  F+  G I  A ++TD++TG SKG+GFV F   E   AA+ A 
Sbjct: 3   LFVKGLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 91  ADPTPFIDGRRANCNLA 107
            D    IDG +   + A
Sbjct: 60  EDGE--IDGNKVTLDFA 74

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

>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 55.7 bits (135), Expect = 1e-10
 Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
            KVFVG L  +   E +R+YF QFGE+ +  +         + + FVTF +PE A+  C 
Sbjct: 1   RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFVTFADPEVAQSLCG 55

Query: 92  DPTPFIDGRRANCNLA 107
           +    I G   + + A
Sbjct: 56  E-DHIIKGVSVHVSNA 70

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

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

 Score = 55.4 bits (133), Expect = 2e-10
 Identities = 22/56 (39%), Positives = 34/56 (60%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
          K+FVGGL  E   E +R YF +FGEI    +  D  T + +G+ F+TF+E +  ++
Sbjct: 6  KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKK 61

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 80

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

 Score = 54.9 bits (133), Expect = 3e-10
 Identities = 21/56 (37%), Positives = 31/56 (55%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          ++VGGLA E   + +   F  FG+I +  +  D  T + +G+ FV F EPE A  A
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAA 56

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

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 55.1 bits (133), Expect = 3e-10
 Identities = 25/63 (39%), Positives = 36/63 (57%)

Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
           D    K+FVG +    + + +R  FEQFG+I E  V+ DK TG  KG  F+T+   E+A
Sbjct: 1  KDDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESA 60

Query: 87 RRA 89
           +A
Sbjct: 61 LKA 63

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 54.3 bits (131), Expect = 5e-10
 Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           ++FVG L  +   + ++ +F++FG +LE  + +    GR   +GFV F +PEA ++  A+
Sbjct: 5   QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64

Query: 93  -PTPFIDGRRAN 103
            P  F    R N
Sbjct: 65  KPIYFRGDHRLN 76

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

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

 Score = 58.8 bits (142), Expect = 5e-10
 Identities = 23/57 (40%), Positives = 36/57 (63%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           K++VG L +    + +R+ FE FG+I +  +  D  TGRSKG+GF+ F + E A+ A
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEA 244

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

 Score = 53.8 bits (130), Expect = 6e-10
 Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 3/68 (4%)

Query: 36  VGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA--CADP 93
           V  L + T  + +RR FE++GE+ +  +  D+ T  S+G+ FV F +   A  A    D 
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 94  TPFIDGRR 101
               DGR 
Sbjct: 63  KEL-DGRE 69

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

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

 Score = 53.8 bits (130), Expect = 7e-10
 Identities = 24/57 (42%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
          +FV  L +    + ++  F + G +L A V TD N GRSKG+G V F  PE A+RA 
Sbjct: 1  IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTD-NDGRSKGFGTVLFESPEDAQRAI 56

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

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

 Score = 53.4 bits (129), Expect = 8e-10
 Identities = 19/39 (48%), Positives = 27/39 (69%)

Query: 51 YFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           F  FG ++ A V  DKNTG+SK +GFV++  PE+A+ A
Sbjct: 18 LFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAA 56

This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. . Length = 73

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

 Score = 53.1 bits (128), Expect = 2e-09
 Identities = 19/47 (40%), Positives = 28/47 (59%), Gaps = 1/47 (2%)

Query: 43 TQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          TQ E +R  FE  G I    ++ D+ TG+S GYGFV + +   A++A
Sbjct: 13 TQEE-LRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKA 58

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

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

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 23/79 (29%), Positives = 44/79 (55%), Gaps = 7/79 (8%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVI---TDKNTGRS-KGYGFVTFREPEAARR 88
           +++V  L ++   + +R  F +FGE+ E++ I    D+  GR   G+ FVTF++  +A  
Sbjct: 2   EIYVRNLDFKLDEDDLRGIFSKFGEV-ESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 89  AC-ADPTPFIDGRRANCNL 106
           A   + T  + GR+ + +L
Sbjct: 61  ALQLNGTE-LGGRKISVSL 78

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

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

 Score = 52.6 bits (127), Expect = 2e-09
 Identities = 23/44 (52%), Positives = 28/44 (63%), Gaps = 1/44 (2%)

Query: 46 ETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          E +R  F  FG I  A V+TD+  GRSKG+GFV F  PE A +A
Sbjct: 16 ERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKA 58

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

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

 Score = 52.4 bits (126), Expect = 2e-09
 Identities = 25/69 (36%), Positives = 36/69 (52%), Gaps = 3/69 (4%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA-D 92
           V++G LAW+   + +R +F+   EI    + TDK TG  KG+G V F + E+   A   D
Sbjct: 2   VYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALKLD 60

Query: 93  PTPFIDGRR 101
            T    GR 
Sbjct: 61  GTVLC-GRP 68

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

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

 Score = 52.5 bits (127), Expect = 2e-09
 Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 4/63 (6%)

Query: 39  LAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFID 98
           L+ +   + +R  F  FG I    +  DK TG+S+G+ FVTF   E A RA       ++
Sbjct: 7   LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIE----KLN 62

Query: 99  GRR 101
           G  
Sbjct: 63  GFG 65

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

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

 Score = 56.7 bits (137), Expect = 2e-09
 Identities = 43/204 (21%), Positives = 59/204 (28%), Gaps = 37/204 (18%)

Query: 45  SETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD-------PTPFI 97
            E +R  F + GEI  A V+ D+  G S+G+GFV F  PE A RA  +         P  
Sbjct: 299 DEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLY 357

Query: 98  -------DGRRANCNLASLGRPRPQVLYGRLRP-------ATLFSGS--TQATRGPYIGS 141
                  + RRA            Q  + +L+P        +   G+       G     
Sbjct: 358 VALAQRKEQRRA----------HLQDQFMQLQPRMRQLPMGSPMGGAMGQPPYYGQGPQQ 407

Query: 142 FGYQQPLPYNYQQGMVYPSYGYATYGPE-YVYPQGIYNPYQQYVPIYGVPGTVNTAVYPY 200
               QPL +     M  P        P        +  P +        P        P 
Sbjct: 408 QFNGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQNAAQKPPMQPVMYPPN 467

Query: 201 GQLGQTIPG--SHAYTPVQGYGMP 222
            Q             T  QG    
Sbjct: 468 YQSLPLSQDLPQPQSTASQGGQNK 491

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

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

 Score = 52.3 bits (125), Expect = 3e-09
 Identities = 22/56 (39%), Positives = 35/56 (62%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
          K+FVGGL+ +T  E +R YF  FGE+    +  D  T + +G+ F+TF+E E  ++
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK 56

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

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

 Score = 52.1 bits (125), Expect = 3e-09
 Identities = 23/56 (41%), Positives = 33/56 (58%), Gaps = 1/56 (1%)

Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFRE 82
          G      VFVGG+        +R +F ++G + E  +ITD+ TG SKGYGFV+F +
Sbjct: 1  GKIMPNTVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYD 55

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

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

 Score = 52.0 bits (125), Expect = 4e-09
 Identities = 23/47 (48%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 43 TQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          TQ E +R  F   GEI    +I DK TG+S GYGFV + +PE A +A
Sbjct: 14 TQDE-IRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKA 59

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

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

 Score = 51.6 bits (124), Expect = 4e-09
 Identities = 23/66 (34%), Positives = 38/66 (57%), Gaps = 2/66 (3%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA- 91
          ++FV  L +  + + + + F +FGE+ E  V  DK +G+SKG+ +V F +PE A +A   
Sbjct: 4  RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 92 -DPTPF 96
           D   F
Sbjct: 64 LDGKVF 69

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

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

 Score = 55.6 bits (134), Expect = 7e-09
 Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
              +T ++V  L      + +R  F +FGEI  A V+ D + GRS+G+ FV F + E A 
Sbjct: 175 LKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGS-GRSRGFAFVNFEKHEDAA 233

Query: 88  RA 89
           +A
Sbjct: 234 KA 235

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

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

 Score = 50.8 bits (122), Expect = 9e-09
 Identities = 27/68 (39%), Positives = 41/68 (60%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
           V+VGG+ + +  + +R YF   GEI E  ++T  +TGR +G  F+TF+  EAA+RA A  
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALALD 60

Query: 94  TPFIDGRR 101
              + GR 
Sbjct: 61  GEDMGGRF 68

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

 Score = 50.9 bits (121), Expect = 1e-08
 Identities = 30/76 (39%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD- 92
           VFVG L+ E  +E ++  F  FG+I +A V+ D  TG+SKGYGFV+F     A  A    
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 93  PTPFIDGRRANCNLAS 108
              ++ GR+   N A+
Sbjct: 64  GGQWLGGRQIRTNWAT 79

This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

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

 Score = 50.2 bits (120), Expect = 1e-08
 Identities = 21/56 (37%), Positives = 30/56 (53%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +++G L      + +++YF QFG +    V   K TG SK YGF+ F  PE A  A
Sbjct: 2  IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIA 57

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

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

 Score = 49.9 bits (120), Expect = 1e-08
 Identities = 24/58 (41%), Positives = 27/58 (46%), Gaps = 6/58 (10%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          T V+VG L      E ++R F  FG I E  V  D      KGY FV F   EAA  A
Sbjct: 1  TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATA 52

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

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

 Score = 49.7 bits (119), Expect = 2e-08
 Identities = 24/62 (38%), Positives = 33/62 (53%), Gaps = 3/62 (4%)

Query: 48  MRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD-PTPFIDGRRANCNL 106
           +R+ F QFG IL+  +I   N   SKG+GFVTF     A RA        ++GR+   N 
Sbjct: 17  LRQMFGQFGPILDVEIIF--NERGSKGFGFVTFANSADADRAREKLHGTVVEGRKIEVNN 74

Query: 107 AS 108
           A+
Sbjct: 75  AT 76

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

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

 Score = 49.1 bits (118), Expect = 2e-08
 Identities = 23/57 (40%), Positives = 29/57 (50%), Gaps = 8/57 (14%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          K+FVG L   T SE +R  FE++G + E  V+        K YGFV   E E A  A
Sbjct: 1  KLFVGNLPDATTSEELRALFEKYGTVTECDVV--------KNYGFVHMEEEEDAEDA 49

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

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

 Score = 50.3 bits (120), Expect = 3e-08
 Identities = 19/60 (31%), Positives = 33/60 (55%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
            +FV  L ++   E++  +F +FG +  A+ + DK+TGR+KG GFV F++         
Sbjct: 2  FTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLK 61

This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 107

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

 Score = 49.8 bits (119), Expect = 3e-08
 Identities = 25/59 (42%), Positives = 33/59 (55%), Gaps = 6/59 (10%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
          K+FVG L+ +     +R  F  FG I E  V+ D+N G+S+G  FVTF     A R CA
Sbjct: 3  KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQN-GQSRGCAFVTF-----ASRQCA 55

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

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

 Score = 49.2 bits (117), Expect = 3e-08
 Identities = 22/56 (39%), Positives = 33/56 (58%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
          KVFVGGL+ +T  E ++ YF  FGEI    +  D  T   +G+ FVT+ + E  ++
Sbjct: 1  KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQK 56

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

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

 Score = 49.3 bits (118), Expect = 3e-08
 Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 3/70 (4%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA- 91
           ++F+  LA+    E + + F ++G + E  +  DK T + KG+ FVT+  PE A +A A 
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 92  -DPTPFIDGR 100
            D T F  GR
Sbjct: 64  LDGTVF-QGR 72

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

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

 Score = 49.6 bits (119), Expect = 3e-08
 Identities = 24/59 (40%), Positives = 34/59 (57%)

Query: 31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          Y  +FVG L+ +T  ET+R  F ++G+I    ++ D  TG SKGY FV +     A RA
Sbjct: 3  YLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRA 61

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

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

 Score = 49.1 bits (118), Expect = 3e-08
 Identities = 23/78 (29%), Positives = 43/78 (55%), Gaps = 4/78 (5%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           +++ V  L      + +R +FE  GE+ +  V+  ++ G+S+ +GFV F+  E A++A  
Sbjct: 1   SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSEEDAQQAVK 59

Query: 92  --DPTPFIDGRRANCNLA 107
             + T FID  + +  LA
Sbjct: 60  YFNKT-FIDTSKISVELA 76

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

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

 Score = 49.1 bits (118), Expect = 3e-08
 Identities = 17/58 (29%), Positives = 32/58 (55%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
          VFV  L+ + +   +  +F + G++ +  +I D+N+ RSKG  +V F + E+   A  
Sbjct: 2  VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG 59

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

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

 Score = 48.9 bits (116), Expect = 5e-08
 Identities = 29/76 (38%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD- 92
           VFVG L+ E  ++ ++  F  FG I +A V+ D  TG+SKGYGFV+F     A  A    
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 93  PTPFIDGRRANCNLAS 108
              ++ GR+   N A+
Sbjct: 64  GGQWLGGRQIRTNWAT 79

This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

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

 Score = 49.1 bits (118), Expect = 5e-08
 Identities = 21/58 (36%), Positives = 33/58 (56%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          T VFVG +      + +R+  E+ G++L    + D +TG+ K +GF  F +PE A RA
Sbjct: 1  TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRA 58

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

 Score = 48.5 bits (116), Expect = 5e-08
 Identities = 20/44 (45%), Positives = 29/44 (65%)

Query: 46 ETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          E +R  F++FG+I    ++ DKNTG SKG+G+V F +P  A  A
Sbjct: 15 EDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVA 58

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

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

 Score = 48.8 bits (116), Expect = 6e-08
 Identities = 21/57 (36%), Positives = 31/57 (54%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          K+FVG +      + +R  FE+ G +LE  +I DK TG  +G  FV +   + A RA
Sbjct: 1  KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRA 57

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

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

 Score = 48.3 bits (115), Expect = 6e-08
 Identities = 19/56 (33%), Positives = 33/56 (58%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          VFVG + +E   E ++  F + G ++   ++ D+ TG+ KGYGF  +++ E A  A
Sbjct: 1  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSA 56

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

 Score = 48.1 bits (115), Expect = 8e-08
 Identities = 16/58 (27%), Positives = 31/58 (53%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
          +FVG + + T  E ++ +F+  G I    ++ DK TG+ KG+ ++ F +  +   A  
Sbjct: 2  IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL 59

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

 Score = 48.1 bits (115), Expect = 9e-08
 Identities = 18/58 (31%), Positives = 31/58 (53%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
          V+V  L      E ++  F ++G ++   +   K+TG  KG+ F+ F  PE A++AC 
Sbjct: 2  VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACK 59

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

 Score = 47.7 bits (114), Expect = 1e-07
 Identities = 25/70 (35%), Positives = 38/70 (54%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
           +FVG L ++T +E +  +F+  G      ++TDK TG+SKG  FV F   EA  +A    
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 94  TPFIDGRRAN 103
              + GR+ N
Sbjct: 63  HTLLKGRKIN 72

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

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 47.7 bits (114), Expect = 1e-07
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 6/72 (8%)

Query: 34  VFVGGLAWETQSETMRRYFEQFG--EILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           ++VG L W T  E +     + G  ++        K  G+SKG+ +V F    AA  A  
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAA-AAVK 59

Query: 92  DPTPFIDGRRAN 103
           +    ++GR  N
Sbjct: 60  E---KLEGREFN 68

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

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

 Score = 47.7 bits (114), Expect = 1e-07
 Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +FVG L+ +   E +   F + G+ILE  +I   N   +  + F+ F   +AA RA
Sbjct: 6  IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARA 59

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

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

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 19/59 (32%), Positives = 31/59 (52%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
          K+F+GGL      + ++   E FG++    ++ D  TG SKGY F  + +P    +A A
Sbjct: 2  KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIA 60

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

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 20/54 (37%), Positives = 28/54 (51%)

Query: 36 VGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +G L        +   F + GE+    +I +K TG+S GYGFV F   EAA +A
Sbjct: 4  MGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQA 57

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 3/68 (4%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA-D 92
           VFV  L +    + +R+ F + GEI +  ++ +   G+SKGY +V F   E+ + A   D
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALKLD 60

Query: 93  PTPFIDGR 100
               I GR
Sbjct: 61  REL-IKGR 67

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

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

 Score = 47.0 bits (112), Expect = 2e-07
 Identities = 21/56 (37%), Positives = 36/56 (64%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +FVG L+++   +++   F ++GEI    + TD ++GR KG+G+V F   EAA+ A
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAA 56

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

 Score = 46.9 bits (112), Expect = 2e-07
 Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 34 VFVGGLAWETQSETMRRYFEQ-FGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +FVG LA +     ++  F   +  +  A V+ D  TGRSKGYGFV F + +   RA
Sbjct: 4  IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRA 60

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

>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 29/80 (36%), Positives = 42/80 (52%), Gaps = 12/80 (15%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA-- 91
           ++VG +  +T    +R+ F+ FGEI E + +  ++ G +  YGFVT+R    A RA    
Sbjct: 5   IYVGKIPIDTTRSELRQRFQPFGEI-EEITLHFRDDGDN--YGFVTYRYACDAFRAIEHG 61

Query: 92  --DPT-PFID----GRRANC 104
             DPT P  D    GRR  C
Sbjct: 62  NDDPTEPKYDLCFGGRRQFC 81

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

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

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 19/55 (34%), Positives = 35/55 (63%), Gaps = 2/55 (3%)

Query: 26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 80
          + D+ Y  +++GGL +E     +   F Q+GEI++  ++ DK TG+SKG+ F+ +
Sbjct: 6  YKDSAY--IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAY 58

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

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 46.7 bits (110), Expect = 3e-07
 Identities = 23/60 (38%), Positives = 36/60 (60%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
          T +++ GL   T  + + +  + +G+I+    I DKNT + KGYGFV F  P AA++A A
Sbjct: 5  TNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVA 64

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

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

 Score = 46.4 bits (111), Expect = 3e-07
 Identities = 16/57 (28%), Positives = 29/57 (50%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
          +FVGGL+       +   F +FG + +  +I  K+ G  +G+ ++  R  EA  + C
Sbjct: 2  LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKC 58

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

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

 Score = 46.5 bits (111), Expect = 4e-07
 Identities = 19/55 (34%), Positives = 27/55 (49%)

Query: 35 FVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           VG L  E   E  R     FG +    ++  ++TG SKGYGFV +    +A +A
Sbjct: 3  CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKA 57

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

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

 Score = 46.0 bits (110), Expect = 4e-07
 Identities = 18/59 (30%), Positives = 26/59 (44%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
          V + GL +    E +R +F       + + I   + GR  G  +V F  PE ARRA   
Sbjct: 2  VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRK 60

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

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 46.1 bits (110), Expect = 4e-07
 Identities = 23/50 (46%), Positives = 30/50 (60%), Gaps = 4/50 (8%)

Query: 46 ETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF-REPEA--ARRACAD 92
          E + + F QFGE+  AVVI D   GRS G G V F R+P A  A + C++
Sbjct: 14 ELLEQAFSQFGEVERAVVIVDDR-GRSTGEGIVEFSRKPGAQAAIKRCSE 62

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

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

 Score = 46.4 bits (111), Expect = 4e-07
 Identities = 19/55 (34%), Positives = 25/55 (45%)

Query: 35 FVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +VG L  +     +   F   G +L   V  D  T RS GY +V F+ P  A RA
Sbjct: 3  YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERA 57

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

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

 Score = 45.9 bits (109), Expect = 5e-07
 Identities = 21/57 (36%), Positives = 34/57 (59%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +V+VG +++E   +T+R+ F  FG I    +  D  T + KG+ FV +  PEAA+ A
Sbjct: 2  RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLA 58

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

 Score = 46.1 bits (110), Expect = 6e-07
 Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVIT-DKNTGRSKGYGFVTFREPEAARRA 89
          +F+G L  E   + +   F  FG IL+   I  D +TG SKG+ F+++   EA+  A
Sbjct: 4  LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAA 60

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

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

 Score = 45.7 bits (109), Expect = 7e-07
 Identities = 18/60 (30%), Positives = 34/60 (56%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           +++V  +  +   + ++  FE FG+I    +  D  TG+ KGYGF+ +  P++A+ A A
Sbjct: 1  NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

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

 Score = 45.2 bits (107), Expect = 7e-07
 Identities = 22/57 (38%), Positives = 30/57 (52%), Gaps = 8/57 (14%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          K+FVG L  E   + +R  FEQ+G++LE  +I        K YGFV   +  AA  A
Sbjct: 2  KLFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEA 50

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

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

 Score = 48.7 bits (116), Expect = 1e-06
 Identities = 17/59 (28%), Positives = 30/59 (50%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           ++++G L      + ++   E FG++    +I D  TG SKGY F  +++P     A A
Sbjct: 297 RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIA 355

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

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          TK+ V  + +E   + +R  F  FG++ ++V +  K  G  +G+ FV F   + A+ A
Sbjct: 1  TKLIVRNVPFEATKKELRELFSPFGQV-KSVRLPKKFDGSHRGFAFVEFVTKQEAQNA 57

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

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 44.8 bits (105), Expect = 2e-06
 Identities = 21/60 (35%), Positives = 35/60 (58%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
          T +++ GL   T  + + +  + +G+I+    I DK T + KGYGFV F  P AA++A +
Sbjct: 8  TNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVS 67

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 44.3 bits (105), Expect = 2e-06
 Identities = 22/68 (32%), Positives = 31/68 (45%), Gaps = 5/68 (7%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
           VFV G    T  E +  YF  FG ++   VI DK+ G    Y  V F   E   +  ++P
Sbjct: 5   VFVSGFKRGTSEEQLMDYFSAFGPVMN--VIMDKDKGV---YAIVEFDSKEGVDKVLSEP 59

Query: 94  TPFIDGRR 101
              ++G R
Sbjct: 60  QHTLNGHR 67

This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS). . Length = 74

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

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 19/76 (25%), Positives = 39/76 (51%), Gaps = 3/76 (3%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA-- 91
           V+V  L +   +  + + F ++G++++  ++ DK T +SKG  F+ F + E A +     
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 92  DPTPFIDGRRANCNLA 107
           +      GR   C++A
Sbjct: 64  NNKELF-GRTLKCSIA 78

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

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

 Score = 44.1 bits (105), Expect = 2e-06
 Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 8/77 (10%)

Query: 38  GLAWETQSETMRRYFEQFGEI-LEAV-VITDKNTGRSKGYGFVTFREPEAARRA-----C 90
           GL   T  E + +       + ++ V +I DK TG S+G+ FV F   E A +       
Sbjct: 9   GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNN 68

Query: 91  ADPTPFIDGRRANCNLA 107
            DP   IDGR    + A
Sbjct: 69  LDPF-VIDGRVVRVSYA 84

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

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 44.1 bits (104), Expect = 2e-06
 Identities = 19/56 (33%), Positives = 29/56 (51%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          VFVG L +E   E + R F + G I    ++ D  T   KG+ +V F++  A  +A
Sbjct: 2  VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKA 57

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 43.7 bits (103), Expect = 3e-06
 Identities = 23/76 (30%), Positives = 33/76 (43%), Gaps = 9/76 (11%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
            K+FVG ++    S+ +R  FE+FG ++E   +        K Y FV     E A  A  
Sbjct: 1   WKIFVGNVSATCTSDELRGLFEEFGRVVECDKV--------KDYAFVHMEREEEALAAIE 52

Query: 92  DPT-PFIDGRRANCNL 106
                 + GRR N  L
Sbjct: 53  ALNGKEVKGRRINVEL 68

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

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

 Score = 43.8 bits (104), Expect = 3e-06
 Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 4/71 (5%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           ++ V  L ++     +++ F  FG + E V I  K  G+ KG+ FV F     A +A   
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWE-VTIPRKPDGKKKGFAFVQFTSKADAEKAIKG 59

Query: 93  --PTPFIDGRR 101
                 I GR 
Sbjct: 60  VNGKK-IKGRP 69

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

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

 Score = 43.6 bits (103), Expect = 4e-06
 Identities = 15/57 (26%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          K+FV GL +    E + + F++ G +    ++T+++ G+ KG  +V +    +A +A
Sbjct: 4  KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRS-GKPKGLAYVEYENESSASQA 59

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

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 43.2 bits (101), Expect = 5e-06
 Identities = 21/58 (36%), Positives = 34/58 (58%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          T +++ GL   T  + + +  + +G+I+    I DK T + KGYGFV F  P AA++A
Sbjct: 2  TNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 59

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

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

 Score = 42.6 bits (101), Expect = 8e-06
 Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          T++ V  L ++   E +   F + GE+ +  +  D+ +GRS+G   V F + E A RA
Sbjct: 1  TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERA 57

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

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

 Score = 46.0 bits (109), Expect = 1e-05
 Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
             +FV  L     ++ +   F +FG IL   V TD+N G+S+GYGFV F + E+A+ A
Sbjct: 89  GNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDEN-GKSRGYGFVHFEKEESAKAA 145

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

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

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 46 ETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF-REPEAAR 87
          + +R  F  FGEI +  V+ DK T  SKG  +V F +   AAR
Sbjct: 17 DDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAAR 59

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

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

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 8/56 (14%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          ++V  L   T  E +R  F ++GE+     I D        Y FV F E + A +A
Sbjct: 4  LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKA 51

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

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

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 36  VGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP 95
           V GL+  T    +R  F ++G +    V+ D+ TGRS+G+ FV F   + ++ A      
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 96  F-IDGRR 101
             +DGRR
Sbjct: 64  MELDGRR 70

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

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 2/58 (3%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
          ++FV  L ++   + ++  F Q G ++ A +  +   G+SKG G V F  PE+A +AC
Sbjct: 1  QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKME--NGKSKGCGTVRFDSPESAEKAC 56

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

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

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 17/58 (29%), Positives = 32/58 (55%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          T ++V  +A  T+ + +RR F ++G I++  +  D  T R +G+ +V F +   A  A
Sbjct: 1  TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDA 58

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

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

 Score = 41.6 bits (97), Expect = 2e-05
 Identities = 25/83 (30%), Positives = 35/83 (42%), Gaps = 4/83 (4%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           T + V  L      + +R  F   GE+  A +I DK  G S GYGFV +   + A RA  
Sbjct: 2   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61

Query: 92  DPTPFIDGRRANCNLASLGRPRP 114
                ++G R       +   RP
Sbjct: 62  T----LNGLRLQSKTIKVSYARP 80

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

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

 Score = 41.6 bits (97), Expect = 2e-05
 Identities = 21/62 (33%), Positives = 33/62 (53%)

Query: 28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
          + + T + V  L      E ++  F   GEI    ++ DK TG+S GYGFV + +P+ A 
Sbjct: 1  EDSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAE 60

Query: 88 RA 89
          +A
Sbjct: 61 KA 62

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

>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 41.5 bits (97), Expect = 2e-05
 Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 2/58 (3%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
          ++FV  L ++   + ++  F + G +L A +  +   G+SKG G V F  PE A RAC
Sbjct: 1  QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVRFESPEVAERAC 56

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

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

 Score = 41.3 bits (97), Expect = 2e-05
 Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 2/59 (3%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR--SKGYGFVTFREPEAARRA 89
          K+FVG +      + +R  FEQ+G + +  V+ D++     SKG  FVTF   +AA  A
Sbjct: 3  KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 61

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

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

 Score = 41.2 bits (97), Expect = 2e-05
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 12/69 (17%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           +V++G L +  +   + R+F+ +G I E   I  KN     G+GFV F +P  A  A  +
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRIRE---INLKN-----GFGFVEFEDPRDADDAVYE 52

Query: 93  PTPFIDGRR 101
               ++G+ 
Sbjct: 53  ----LNGKE 57

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

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

 Score = 40.6 bits (96), Expect = 2e-05
 Identities = 15/61 (24%), Positives = 25/61 (40%), Gaps = 8/61 (13%)

Query: 49  RRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNL 106
            + F  FG + + + +  K      G+ FV F   EAA +A    +   F  GR    + 
Sbjct: 2   YKLFSPFGNVEK-IKLLKKK----PGFAFVEFSTEEAAEKAVQYLNGVLF-GGRPLRVDY 55

Query: 107 A 107
           +
Sbjct: 56  S 56

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

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

 Score = 41.2 bits (97), Expect = 3e-05
 Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 48 MRRYFEQFGEILEAV-VITDKNTGRSKGYGFVTFREPEAARRA 89
          ++R F   GE + +V +I +K TG   GY FV F +   A R 
Sbjct: 16 IKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERC 58

This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 84

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

 Score = 41.3 bits (96), Expect = 3e-05
 Identities = 22/58 (37%), Positives = 30/58 (51%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          T + V  L      E  R  F   GEI    ++ DK TG+S GYGFV + +P+ A +A
Sbjct: 3  TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

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

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

 Score = 41.1 bits (96), Expect = 3e-05
 Identities = 17/58 (29%), Positives = 31/58 (53%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
            ++V GL      + + + F Q+G I+ + ++ D+ TG S+G GF+ F +   A  A
Sbjct: 1  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEA 58

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

>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 43 TQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          TQ E +   F  +G I+ + ++ D  TG S+G GF+ F +   A RA
Sbjct: 13 TQQE-LEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERA 58

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

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

 Score = 44.3 bits (104), Expect = 3e-05
 Identities = 23/57 (40%), Positives = 37/57 (64%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           +V+VG +++E + +T+RR F+ FG I    +  D  TG+ KG+ FV +  PEAA+ A
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLA 165

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|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 40.9 bits (96), Expect = 4e-05
 Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          K+FVG L+ +   + +RR FE FG I E  ++   + G SKG  FV F     A+ A
Sbjct: 3  KLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPD-GNSKGCAFVKFSSHAEAQAA 58

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

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

 Score = 40.6 bits (95), Expect = 4e-05
 Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 8/59 (13%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
          K+FVG +  +T  E +R  FE +G +L   V+        + + FV  R   AA RA  
Sbjct: 2  KIFVGNVDEDTSQEELRALFEAYGAVLSCAVM--------RQFAFVHLRGEAAADRAIE 52

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

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

 Score = 40.4 bits (95), Expect = 4e-05
 Identities = 24/58 (41%), Positives = 27/58 (46%), Gaps = 6/58 (10%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          T VFVGGL      + +R  F  FGEI+  V I        KG GFV F    AA  A
Sbjct: 2  TTVFVGGLDPAVTEDELRSLFGPFGEIV-YVKIPP-----GKGCGFVQFVHRAAAEAA 53

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

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

 Score = 40.4 bits (95), Expect = 4e-05
 Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +FV  L ++   + ++  F+  G+++ A +  DK  G+S+G G V F  P  A +A
Sbjct: 1  IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQA 55

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

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

 Score = 43.8 bits (103), Expect = 4e-05
 Identities = 23/60 (38%), Positives = 31/60 (51%)

Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          + T + V  L      E +R  F   GEI    ++ DK TG+S GYGFV +  PE A +A
Sbjct: 2  SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKA 61

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

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

 Score = 40.4 bits (95), Expect = 5e-05
 Identities = 17/46 (36%), Positives = 23/46 (50%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVT 79
          +FV  L  +     + + F  FG +    VI D  T + KGYGFVT
Sbjct: 4  IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVT 49

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

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

 Score = 40.8 bits (95), Expect = 5e-05
 Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 36  VGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP 95
           V GL+  T    +R  F ++G I +  ++ D+ + RS+G+ FV F   + A+ A      
Sbjct: 14  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 73

Query: 96  F-IDGRR 101
             +DGRR
Sbjct: 74  MELDGRR 80

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

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

 Score = 40.0 bits (94), Expect = 6e-05
 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 9/60 (15%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFV---TFREPEAARRA 89
          ++FVG L  +   E  +  F ++GE+ E V +      + KG+GF+   T    E A+  
Sbjct: 3  RLFVGNLPNDITEEEFKELFSKYGEVSE-VFLN-----KEKGFGFIRLDTRTNAEKAKAE 56

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

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

 Score = 40.1 bits (94), Expect = 7e-05
 Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 10/84 (11%)

Query: 34  VFVGGLAWETQSE-----TMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
           VFV  L   ++S+      +  +F ++G ++   V+ D    R + Y FV F   + A+ 
Sbjct: 5   VFVASLP-ASKSDDELEAAVTEHFSKYGTLVFVKVLRDW---RQRPYAFVQFTNDDDAKN 60

Query: 89  ACADP-TPFIDGRRANCNLASLGR 111
           A A      +DGR   C  A + R
Sbjct: 61  ALAKGQGTILDGRHIRCERAKVNR 84

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

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

 Score = 39.9 bits (94), Expect = 7e-05
 Identities = 26/75 (34%), Positives = 36/75 (48%), Gaps = 10/75 (13%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           T ++VGGL      + +R +F QFGEI    V+  +         FVTF   EAA +A A
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQ------CAFVTFTTREAAEKA-A 54

Query: 92  DPTP---FIDGRRAN 103
           +       I+GRR  
Sbjct: 55  ERLFNKLIINGRRLK 69

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

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

 Score = 40.0 bits (94), Expect = 7e-05
 Identities = 19/58 (32%), Positives = 25/58 (43%), Gaps = 1/58 (1%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
          +FVG L      E +   F Q G  LE V I     G+ K + FVTF+   +   A  
Sbjct: 4  LFVGNLDARVTEEILYELFLQAGP-LEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQ 60

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

 Score = 39.6 bits (92), Expect = 8e-05
 Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
          +FVG L    + E +   F Q G + +  +  DK  G+ K +GFV F+  E+   A A
Sbjct: 4  LFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAIA 60

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)

 Score = 40.0 bits (93), Expect = 8e-05
 Identities = 26/60 (43%), Positives = 33/60 (55%), Gaps = 4/60 (6%)

Query: 36 VGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA---CAD 92
          V  L+    +E + + F QFG +  AVVI D + GR  G GFV F    AAR+A   CAD
Sbjct: 4  VKNLSPVVSNELLEQAFSQFGPVERAVVIVD-DRGRPTGKGFVEFAAKPAARKALERCAD 62

This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

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

 Score = 43.0 bits (101), Expect = 9e-05
 Identities = 19/58 (32%), Positives = 33/58 (56%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           VFV  LA + +   +  +F + G++ +   I D+N+ RSKG  +V F + E+  +A A
Sbjct: 92  VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA 149

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

 Score = 42.6 bits (100), Expect = 1e-04
 Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 1/83 (1%)

Query: 8   GPGSGSSSSSGF-QYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITD 66
            P +    ++G          D     +FV  L+ +T    + + F  FG +    +I D
Sbjct: 245 SPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRD 304

Query: 67  KNTGRSKGYGFVTFREPEAARRA 89
             T + KGYGFV+    + A  A
Sbjct: 305 LTTNQCKGYGFVSMTNYDEAAMA 327

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

>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 20/58 (34%), Positives = 35/58 (60%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          T+VFVG +  +   + +   FE+ G I +  ++ D  +G+++GY F+TF   EAA+ A
Sbjct: 2  TEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEA 59

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. . Length = 79

>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 10/54 (18%)

Query: 58  ILEAVVITDK------NTGRSKGYGFVTFREPEAA----RRACADPTPFIDGRR 101
           I +  ++ D         G+SKGYGFV F   E A    R    +P  F   +R
Sbjct: 36  IKQVKIMRDLKRVDPNGKGKSKGYGFVEFTNHEHALKALRALNNNPEIFGPDKR 89

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

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

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 3/56 (5%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFV---TFREPEAA 86
          +FV G+  E Q E +   F +FGEI    +  D+ TG  KGY  +   T +E +AA
Sbjct: 9  IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAA 64

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

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 39.2 bits (91), Expect = 1e-04
 Identities = 21/58 (36%), Positives = 34/58 (58%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          T++FVG +  +   + +   FE+ G I +  ++ D  TG ++GY FVTF   EAA+ A
Sbjct: 2  TEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEA 59

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

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

 Score = 39.3 bits (92), Expect = 1e-04
 Identities = 17/61 (27%), Positives = 30/61 (49%)

Query: 29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
          T + K F   L  +    ++  +F   GEI    + TD+ TG SKG+ ++ F+  +   +
Sbjct: 1  TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 89 A 89
          A
Sbjct: 61 A 61

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 39.2 bits (91), Expect = 1e-04
 Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 8/60 (13%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
          +V++G L+++ +   + R+F+ +G+ILE   +  KN     GYGFV F +   A  A  +
Sbjct: 1  RVYIGRLSYQARERDVERFFKGYGKILE---VDLKN-----GYGFVEFDDLRDADDAVYE 52

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

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

 Score = 39.2 bits (91), Expect = 1e-04
 Identities = 26/84 (30%), Positives = 43/84 (51%), Gaps = 1/84 (1%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           + +FV  +A +T+SE +RR F ++G I++  V  D  T R +G+ +V F +   A  A  
Sbjct: 1   SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 92  D-PTPFIDGRRANCNLASLGRPRP 114
           +    +I GR+     A   R  P
Sbjct: 61  NLDRKWICGRQIEIQFAQGDRKTP 84

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

>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 22/51 (43%), Positives = 28/51 (54%), Gaps = 4/51 (7%)

Query: 45 SETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA---CAD 92
          +E +   F QFG +  AVVI D + GRS G G V F    AAR+A   C +
Sbjct: 13 NELLEEAFSQFGPVERAVVIVD-DRGRSTGKGIVEFASKPAARKAFERCTE 62

This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 80

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

 Score = 38.3 bits (89), Expect = 3e-04
 Identities = 19/56 (33%), Positives = 31/56 (55%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +F+  L  E     + + F  FG ++ A V  D+ T +SK +GFV+F  P +A+ A
Sbjct: 7  LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAA 62

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

>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 10/71 (14%)

Query: 33  KVFVGGLAWETQS-ETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC- 90
           ++F+G L  +  S E + R F  +GE+ + V+   KN      YGFV F  PE+   A  
Sbjct: 1   RLFIGNLPTKRVSKEDLFRIFSTYGELAQIVL---KN-----AYGFVQFDSPESCANAIN 52

Query: 91  ADPTPFIDGRR 101
            +    I GR+
Sbjct: 53  CEQGKMIRGRK 63

This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues. . Length = 71

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

 Score = 38.2 bits (88), Expect = 3e-04
 Identities = 16/55 (29%), Positives = 34/55 (61%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
          ++V GL+  T++  ++  F ++G+++ A V+T+  +  ++ YGFVT    E A +
Sbjct: 4  LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATK 58

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

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 38.1 bits (88), Expect = 3e-04
 Identities = 18/56 (32%), Positives = 31/56 (55%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          ++V GL      + M + F Q+G I+ + ++ D+ TG S+G GF+ F +   A  A
Sbjct: 4  LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEA 59

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 38.2 bits (88), Expect = 4e-04
 Identities = 23/68 (33%), Positives = 32/68 (47%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
           +FV  LA +     + + F  FG +    VI D NT + KG+GFVT    + A  A A  
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 94  TPFIDGRR 101
             +  G R
Sbjct: 66  NGYRLGDR 73

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 38.0 bits (88), Expect = 4e-04
 Identities = 18/58 (31%), Positives = 34/58 (58%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          T ++V  L  +   + +R+ FE +G I++  ++ DK+TG  +G  FV + + E A+ A
Sbjct: 1  TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAA 58

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

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

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 11/61 (18%)

Query: 33 KVFVGGLAWE--TQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
          +VFVG L  +  ++ +     F ++G+IL   +         KGYGFV F   E AR A 
Sbjct: 2  RVFVGNLNTDKVSKEDLEEI-FSKYGKILGISL--------HKGYGFVQFDNEEDARAAV 52

Query: 91 A 91
          A
Sbjct: 53 A 53

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

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

 Score = 37.9 bits (88), Expect = 4e-04
 Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 34 VFVGGLAWETQSETMRRYFE-QFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +FVG L+ E     +   F+ +F     A ++TD  TG S+GYGFV F +    +RA
Sbjct: 4  IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRA 60

This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 80

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

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 9/69 (13%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           KV+VG L        +   FE++G  L +V +         G+ FV F +P  A  A   
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGP-LRSVWVARNPP----GFAFVEFEDPRDAEDAVRA 55

Query: 93  PTPFIDGRR 101
               +DGRR
Sbjct: 56  ----LDGRR 60

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

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

 Score = 37.7 bits (88), Expect = 4e-04
 Identities = 14/54 (25%), Positives = 33/54 (61%)

Query: 36 VGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          V GL+  T++  +++ F ++G+++ A ++T+  +  ++ +GFVT    E A + 
Sbjct: 4  VSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKC 57

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

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

 Score = 37.8 bits (88), Expect = 5e-04
 Identities = 17/44 (38%), Positives = 24/44 (54%)

Query: 46 ETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          E  R  F   G +    ++ DK TG S G+GFV ++  E A+RA
Sbjct: 15 EEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRA 58

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

 Score = 37.7 bits (87), Expect = 5e-04
 Identities = 20/58 (34%), Positives = 28/58 (48%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
          +F+  L  +     + + F  FG +    VI D NT + KG+GFVT    E A  A A
Sbjct: 4  IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIA 61

This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 37.7 bits (87), Expect = 5e-04
 Identities = 19/58 (32%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          + VFV  L ++   + ++  F   G ++ A ++ DK+ G+S+G G VTF +P  A +A
Sbjct: 1  STVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKD-GKSRGIGTVTFEQPIEAVQA 57

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 37.5 bits (87), Expect = 5e-04
 Identities = 18/68 (26%), Positives = 34/68 (50%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
           V+VG + +   +E +  +F   G +    ++ DK +G  KG+ ++ F + E+ R A A  
Sbjct: 2   VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALD 61

Query: 94  TPFIDGRR 101
                GR+
Sbjct: 62  ESLFRGRQ 69

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 37.6 bits (87), Expect = 5e-04
 Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 8/67 (11%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
          +++FVG L  +   E MR+ FE++G+  E  +  D      KG+GF+       A  A A
Sbjct: 2  SRLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIAKA 55

Query: 92 --DPTPF 96
            D  P 
Sbjct: 56 ELDNMPL 62

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused in Ewing's sarcoma protein (FUS), TATA-binding protein-associated factor 15 (TAF15) and similar proteins

 Score = 37.6 bits (87), Expect = 5e-04
 Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 12/80 (15%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAV--------VITDKNTGRSKGYGFVTFREPEA 85
           +FV GL  +   E++  YF+Q G I            + TD+ TG+ KG   V+F +P +
Sbjct: 5   IFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 64

Query: 86  ARRACADPTPFIDGRRANCN 105
           A+ A      + DG+  + N
Sbjct: 65  AKAA----IDWFDGKEFSGN 80

This subgroup corresponds to the RRM of FUS and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed 75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS (Translocated in liposarcoma), is a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multi-functional protein and has been implicated in pre-mRNA splicing, chromosome stability, cell spreading, and transcription. FUS was originally identified in human myxoid and round cell liposarcomas as an oncogenic fusion with the stress-induced DNA-binding transcription factor CHOP (CCAAT enhancer-binding homologous protein) and later as hnRNP P2, a component of hnRNP H complex assembled on pre-mRNA. It can form ternary complexes with hnRNP A1 and hnRNP C1/C2. Additional research indicates that FUS binds preferentially to GGUG-containing RNAs. In the presence of Mg2+, it can bind both single- and double-stranded DNA (ssDNA/dsDNA) and promote ATP-independent annealing of complementary ssDNA and D-loop formation in superhelical dsDNA. FUS has been shown to be recruited by single stranded noncoding RNAs to the regulatory regions of target genes such as cyclin D1, where it represses transcription by disrupting complex formation. TAF15 (TAFII68), also termed TATA-binding protein-associated factor 2N (TAF2N), or RNA-binding protein 56 (RBP56), originally identified as a TAF in the general transcription initiation TFIID complex, is a novel RNA/ssDNA-binding protein with homology to the proto-oncoproteins FUS and EWS (also termed EWSR1), belonging to the FET family as well. TAF15 likely functions in RNA polymerase II (RNAP II) transcription by interacting with TFIID and subunits of RNAP II itself. TAF15 is also associated with U1 snRNA, chromatin and RNA, in a complex distinct from the Sm-containing U1 snRNP that functions in splicing. Like other members in the FET family, both FUS and TAF15 contain an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. . Length = 86

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

 Score = 37.7 bits (87), Expect = 5e-04
 Identities = 19/56 (33%), Positives = 31/56 (55%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +F+  L  E     + + F  FG ++ A V  DK T  SK +GFV++  P++A+ A
Sbjct: 7  LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAA 62

This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 79

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

 Score = 37.8 bits (87), Expect = 6e-04
 Identities = 21/58 (36%), Positives = 29/58 (50%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          T + V  L      E  +  F   GEI    ++ DK TG+S GYGFV + +P  A +A
Sbjct: 4  TNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKA 61

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

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

 Score = 37.1 bits (86), Expect = 6e-04
 Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 1/56 (1%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          ++VG L      + +++ F+  G +    +I DKN  +   YGFV + +   A  A
Sbjct: 1  LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNN-KGVNYGFVEYHQSHDAEIA 55

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

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

 Score = 37.5 bits (87), Expect = 6e-04
 Identities = 18/70 (25%), Positives = 36/70 (51%), Gaps = 3/70 (4%)

Query: 33  KVFVGGLAWETQS-ETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           K+ +  L W  +    +++ F ++G++ EA +   +  G+  G+ FVT ++ + A  A  
Sbjct: 2   KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRG-GKLCGFAFVTMKKRKNAEIALE 60

Query: 92  DPTPF-IDGR 100
           +     IDGR
Sbjct: 61  NTNGLEIDGR 70

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

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

 Score = 37.4 bits (86), Expect = 8e-04
 Identities = 22/68 (32%), Positives = 33/68 (48%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
           +FV  L+ ++    + + F  FG +    VI D NT + KG+GFVT    + A  A A  
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 94  TPFIDGRR 101
             +  G R
Sbjct: 66  NGYRLGDR 73

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 37.3 bits (86), Expect = 8e-04
 Identities = 19/56 (33%), Positives = 31/56 (55%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +F+  L  E   + + + F  FG ++ A V  DK T  SK +GFV++  P +A+ A
Sbjct: 10 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 65

This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 92

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 36.8 bits (85), Expect = 8e-04
 Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 7/55 (12%)

Query: 36 VGGLAWETQSETMRRYFEQFGEILEAVVI-TDKNTGRSKGYGFVTFREPEAARRA 89
          V  L++    ++++  FE+      A  I   +N GR KGY FV F   E A+ A
Sbjct: 6  VNNLSYSASEDSLQEVFEK------ATSIRIPQNNGRPKGYAFVEFESAEDAKEA 54

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 36.7 bits (86), Expect = 8e-04
 Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 7/59 (11%)

Query: 35 FVGGLAWETQSETMRR----YFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          ++  L  + + + ++R     F QFG +L+ V      T + +G  FV F++ E+A  A
Sbjct: 3  YINNLNEKIKKDELKRSLYALFSQFGPVLDIVA---SKTLKMRGQAFVVFKDVESATNA 58

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 2/60 (3%)

Query: 34 VFVGGLAWETQSETMRRYF-EQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
          +FVG L  +     +  +F +++     A V+ D+N G S+GYGFV F +    +RA  +
Sbjct: 4  LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQN-GNSRGYGFVRFSDESEQKRALTE 62

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

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          ++F+G L  +   + +    E+ G+I E  ++ D N G ++GY FVTF   + A+ A
Sbjct: 3  EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFN-GNNRGYAFVTFSNKQEAKNA 58

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 5/50 (10%)

Query: 46 ETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP 95
          + +R+ F ++G++   VV++ K     KG   V F   +AA  A  +   
Sbjct: 19 DELRKIFSKYGDV-SDVVVSSK----KKGSAIVEFASKKAAEAAVENECG 63

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

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

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 22/68 (32%), Positives = 31/68 (45%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
           +FV  L+ E     + + F  FG +    VI D  T + KG+GFVT    + A  A A  
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 94  TPFIDGRR 101
             +  G R
Sbjct: 64  NGYRLGDR 71

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 3/60 (5%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSK--GYGFVTFREPEAARRA 89
          +K+ V  + +E   + +R  F  FGE+ + V +  K TG     G+GFV F   + A+RA
Sbjct: 1  SKILVRNIPFEATVKELRELFSTFGEL-KTVRLPKKMTGTGSHRGFGFVDFITKQDAKRA 59

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 14/56 (25%), Positives = 26/56 (46%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          + VG L      + ++  F  +G + +  +  D+     +GY +V F  PE A +A
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKA 56

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

 Score = 36.6 bits (84), Expect = 0.001
 Identities = 16/58 (27%), Positives = 32/58 (55%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
          ++V GL+  T++  ++  F ++G++L A V+T+  +  +K YG VT        R  +
Sbjct: 2  LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCIS 59

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

>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 36.6 bits (84), Expect = 0.001
 Identities = 17/56 (30%), Positives = 31/56 (55%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          ++V GL      + + + F Q+G I+ + ++ D+ TG S+G GF+ F +   A  A
Sbjct: 5  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 60

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 38.6 bits (90), Expect = 0.002
 Identities = 21/56 (37%), Positives = 29/56 (51%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          ++VG L  +     +   F+ FG +L   V  D  T RS GYG+V F+ P  A RA
Sbjct: 3  LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERA 58

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

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

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA-D 92
          V+VG + + + +E +  +F   G I    ++ DK +G  KGY ++ F   ++   A A D
Sbjct: 2  VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVALD 61

Query: 93 PTPF 96
           + F
Sbjct: 62 ESSF 65

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

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

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 21/56 (37%), Positives = 28/56 (50%), Gaps = 6/56 (10%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          V+ GG+      + MR+ F  FG+I+E  V  D      KGY FV F   E+A  A
Sbjct: 3  VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD------KGYSFVRFNSHESAAHA 52

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

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

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 35 FVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          FVG L      E +RR FE++G + + V I     G+   Y FV F   + A RA
Sbjct: 6  FVGNLEITITEEELRRAFERYGVVED-VDIKRPPRGQGNAYAFVKFLNLDMAHRA 59

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

>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 8/64 (12%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREP--------EA 85
          + + GL+  T  + +R +F  FGEI E+ +  D  TG+S G   VTFR          EA
Sbjct: 1  ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEA 60

Query: 86 ARRA 89
          A+ A
Sbjct: 61 AKAA 64

This subfamily corresponds to the RRM of spSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, or Set1 complex component, is encoded by SET1 from the fission yeast S. pombe. It is essential for the H3 lysine-4 methylation. in vivo, and plays an important role in telomere maintenance and DNA repair in an ATM kinase Rad3-dependent pathway. spSet1p is the homology counterpart of Saccharomyces cerevisiae Set1p (scSet1p). However, it is more closely related to Set1 found in mammalian. Moreover, unlike scSet1p, spSet1p is not required for heterochromatin assembly in fission yeast. spSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 86

>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 4/51 (7%)

Query: 45 SETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA---CAD 92
          +E +   F  FG++  AVVI D + GR  G G V F    +AR+A   C+D
Sbjct: 13 NELLEEAFSMFGQVERAVVIVD-DRGRPTGKGIVEFAGKPSARKALDRCSD 62

This subgroup corresponds to the RRM2 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. It binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 35.7 bits (82), Expect = 0.002
 Identities = 15/38 (39%), Positives = 24/38 (63%)

Query: 55 FGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
          FG +    ++  + TG SKGYGFV + + ++A RA +D
Sbjct: 23 FGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSD 60

This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          TK+ V  L +    + ++  F +FG + +A V  D++ GRS G   V F     A +A
Sbjct: 1  TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRS-GRSLGTADVVFERRADALKA 57

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

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

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 1/40 (2%)

Query: 52 FEQFGEILEAVV-ITDKNTGRSKGYGFVTFREPEAARRAC 90
          F +FG      + +    TG++KGY FV F  PE A+ A 
Sbjct: 28 FSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAV 67

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

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

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 11/72 (15%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           TK+ VG ++    ++ +R  FE++G ++E  ++ D        Y FV     E A  A  
Sbjct: 1   TKLHVGNISSSCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIR 52

Query: 92  --DPTPFIDGRR 101
             D T F  G+R
Sbjct: 53  GLDNTEF-QGKR 63

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

>gnl|CDD|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator 1-beta (PGC-1-beta) and similar proteins

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 3/53 (5%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
          +++  L+    S  +++ FE FGEI E  V+      R + YGF+T+R  E A
Sbjct: 5  IYIRNLSSSMSSTELKKRFEVFGEIEECKVLIKS---RGEKYGFITYRHSEHA 54

This subfamily corresponds to the RRM of PGC-1beta, also termed PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or PGC-1-related estrogen receptor alpha coactivator, which is one of the members of PGC-1 transcriptional coactivators family, including PGC-1alpha and PGC-1-related coactivator (PRC). PGC-1beta plays a nonredundant role in controlling mitochondrial oxidative energy metabolism and affects both, insulin sensitivity and mitochondrial biogenesis, and functions in a number of oxidative tissues. It is involved in maintaining baseline mitochondrial function and cardiac contractile function following pressure overload hypertrophy by preserving glucose metabolism and preventing oxidative stress. PGC-1beta induces hypertriglyceridemia in response to dietary fats through activating hepatic lipogenesis and lipoprotein secretion. It can stimulate apolipoprotein C3 (APOC3) expression, further mediating hypolipidemic effect of nicotinic acid. PGC-1beta also drives nuclear respiratory factor 1 (NRF-1) target gene expression and NRF-1 and estrogen related receptor alpha (ERRalpha)-dependent mitochondrial biogenesis. The modulation of the expression of PGC-1beta can trigger ERRalpha-induced adipogenesis. PGC-1beta is also a potent regulator inducing angiogenesis in skeletal muscle. The transcriptional activity of PGC-1beta can be increased through binding to host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. PGC-1beta is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, two glutamic/aspartic acid-rich acidic domains, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha, PGC-1beta lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 79

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

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 7/49 (14%)

Query: 45 SETM-RRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
          +E + ++ F  FG I+      + +  + K  GFVTF + E+A RA A+
Sbjct: 15 TEEILKKAFSPFGNII------NISMEKEKNCGFVTFEKMESADRAIAE 57

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

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

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +F+G L        +RR F+++G I+E VVI     G+   Y F+ F+  + A RA
Sbjct: 11 LFIGNLDHNVSEVELRRAFDKYG-IIEEVVIKRPARGQGGAYAFLKFQNLDMAHRA 65

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

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

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 1/56 (1%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +F+G L        +RR F++FG I E V I     G++  YGF+ F   + A RA
Sbjct: 10 LFLGNLDITVTETDLRRAFDRFGVITE-VDIKRPGRGQTSTYGFLKFENLDMAHRA 64

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

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

 Score = 35.4 bits (81), Expect = 0.003
 Identities = 21/56 (37%), Positives = 28/56 (50%), Gaps = 8/56 (14%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +FV  LA     E + + F +FG+ LE V        + K Y FV F E +AA RA
Sbjct: 4  LFVRNLATTVTEEILEKSFSEFGK-LERV-------KKLKDYAFVHFEERDAAVRA 51

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

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

 Score = 35.1 bits (81), Expect = 0.003
 Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 7/76 (9%)

Query: 35  FVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT 94
           F+G L   T    +R  FE+FGEI++   I  K  G +  Y F+ + +  +  +A     
Sbjct: 6   FIGNLEKTTTYSDLREAFERFGEIID---IDIKKQGGNPAYAFIQYADIASVVKAMRK-- 60

Query: 95  PFIDGRRANCNLASLG 110
             +DG     N   LG
Sbjct: 61  --MDGEYLGNNRVKLG 74

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 35.5 bits (81), Expect = 0.003
 Identities = 17/56 (30%), Positives = 31/56 (55%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          ++V GL      + + + F Q+G I+ + ++ D+ TG S+G GF+ F +   A  A
Sbjct: 8  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 63

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

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

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 8/57 (14%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +V++G L++  + + ++R+F  +G++LE   I  KN     GYGFV F +   A  A
Sbjct: 1  RVYIGRLSYHVREKDIQRFFGGYGKLLE---IDLKN-----GYGFVEFEDSRDADDA 49

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

>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 6/57 (10%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
          ++VGGL   T    + R F++FG I    +  D      + Y ++ +   EAA+ A 
Sbjct: 1  LWVGGLGPWTSLAELEREFDRFGAIRR--IDYDPG----RNYAYIEYESIEAAQAAK 51

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

>gnl|CDD|241067 cd12623, RRM_PPARGC1A, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1alpha, or PPARGC-1-alpha) and similar proteins

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 3/48 (6%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFR 81
          ++VG +  +T    +R  FE FGEI E  V   ++ G S  YGF+T+R
Sbjct: 5  IYVGKIRPDTTRTELRDRFEVFGEIEECTV-NLRDDGDS--YGFITYR 49

This subgroup corresponds to the RRM of PGC-1alpha, also termed PPARGC-1-alpha, or ligand effect modulator 6, a member of a family of transcription coactivators that plays a central role in the regulation of cellular energy metabolism. As an inducible transcription coactivator, PGC-1alpha can interact with a broad range of transcription factors involved in a wide variety of biological responses, such as adaptive thermogenesis, skeletal muscle fiber type switching, glucose/fatty acid metabolism, and heart development. PGC-1alpha stimulates mitochondrial biogenesis and promotes oxidative metabolism. It participates in the regulation of both carbohydrate and lipid metabolism and plays a role in disorders such as obesity, diabetes, and cardiomyopathy. PGC-1alpha is a multi-domain protein containing an N-terminal activation domain region, a central region involved in the interaction with at least a nuclear receptor, and a C-terminal domain region. The N-terminal domain region consists of three leucine-rich motifs (L1, NR box 2 and 3), among which the two last are required for interaction with nuclear receptors, potential nuclear localization signals (NLS), and a proline-rich region overlapping a putative repression domain. The C-terminus of PGC-1alpha is composed of two arginine/serine-rich regions (SR domains), a putative dimerization domain, and an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). PGC-1alpha could interact favorably with single-stranded RNA. . Length = 91

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +VFVG +  +   + +   FE  G I E  ++ D + G+++GY FV + +   A+RA
Sbjct: 3  EVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFD-GKNRGYAFVMYTQKHEAKRA 58

This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 37.6 bits (87), Expect = 0.004
 Identities = 19/56 (33%), Positives = 31/56 (55%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           ++V GL        +   F  FG+I+ + +++D  TG SKG GF+ F + + A RA
Sbjct: 92  LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRA 147

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

>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins

 Score = 35.3 bits (81), Expect = 0.004
 Identities = 16/56 (28%), Positives = 29/56 (51%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
          ++FVG L  +     ++ +F  FG ++E  + T    G+   +GFV F + E  +R
Sbjct: 7  QLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQR 62

This subgroup corresponds to the RRM of G3BP2, also termed GAP SH3 domain-binding protein 2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing five PXXP motifs, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). It binds to the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity, through its N-terminal NTF2-like domain. The acidic domain is sufficient for the interaction of G3BP2 with the IkappaBalpha cytoplasmic retention sequence. Furthermore, G3BP2 might influence stability or translational efficiency of particular mRNAs by binding to RNA-containing structures within the cytoplasm through its RNA-binding domain. Length = 83

>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

 Score = 35.4 bits (81), Expect = 0.004
 Identities = 16/52 (30%), Positives = 29/52 (55%)

Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEA 85
          VF   LA   +   +  +F   G++ +  +I+D+N+ RSKG  +V F E ++
Sbjct: 4  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 55

This subgroup corresponds to the RRM1 of RBM23, also termed RNA-binding region-containing protein 4, or splicing factor SF2, which may function as a pre-mRNA splicing factor. It shows high sequence homology to RNA-binding protein 39 (RBM39 or HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In contrast to RBM39, RBM23 contains only two RRMs. . Length = 85

>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 34.9 bits (80), Expect = 0.004
 Identities = 14/56 (25%), Positives = 31/56 (55%), Gaps = 3/56 (5%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
          ++FVG L  +     ++ +F+Q+G ++E  +    + G+   +GFV F + E  ++
Sbjct: 5  QLFVGNLPHDVDKSELKEFFQQYGNVVELRI---NSGGKLPNFGFVVFDDSEPVQK 57

This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. Length = 80

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	258
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.91
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.83
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.74
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.72
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.71
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.71
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.69
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.64
KOG0122	270	consensus Translation initiation factor 3, subunit	99.63
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.62
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.62
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.59
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.58
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.58
PLN03120	260	nucleic acid binding protein; Provisional	99.58
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.58
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.57
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.56
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.56
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.56
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.55
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.54
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.53
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.53
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.52
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.52
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.52
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.51
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.5
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.49
PLN03121	243	nucleic acid binding protein; Provisional	99.48
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.48
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.48
smart00362	72	RRM_2 RNA recognition motif.	99.47
PLN03213	759	repressor of silencing 3; Provisional	99.46
smart00360	71	RRM RNA recognition motif.	99.46
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.45
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.45
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.45
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.43
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.42
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.41
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.4
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.39
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.38
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.37
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.37
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.36
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.35
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.34
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.34
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.33
smart00361	70	RRM_1 RNA recognition motif.	99.27
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.26
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.26
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.25
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.24
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.21
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.19
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.18
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.17
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.17
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.16
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.15
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.15
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.1
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.09
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.08
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.03
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.02
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.99
KOG0226	290	consensus RNA-binding proteins [General function p	98.97
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.95
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.91
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.87
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.85
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.84
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.78
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.67
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.64
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.63
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.59
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.56
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.49
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.48
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.45
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.3
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.27
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.25
KOG0151	877	consensus Predicted splicing regulator, contains R	98.21
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.2
KOG4210	285	consensus Nuclear localization sequence binding pr	98.06
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.0
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.89
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.89
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.81
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.77
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.76
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.68
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.67
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.66
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.6
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.6
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.54
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.45
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	97.34
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.33
KOG2314	698	consensus Translation initiation factor 3, subunit	97.14
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.09
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.06
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.01
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	96.92
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.82
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.72
KOG3152	278	consensus TBP-binding protein, activator of basal	96.69
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.61
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	96.58
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.48
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	96.44
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.41
KOG1548	382	consensus Transcription elongation factor TAT-SF1	96.41
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.34
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.34
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.28
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	96.18
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	95.83
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	95.73
KOG1996	378	consensus mRNA splicing factor [RNA processing and	95.67
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.46
KOG2591	684	consensus c-Mpl binding protein, contains La domai	94.92
KOG4210	285	consensus Nuclear localization sequence binding pr	94.62
KOG2135	526	consensus Proteins containing the RNA recognition	94.61
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	94.56
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	94.07
KOG2068	327	consensus MOT2 transcription factor [Transcription	93.58
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	93.46
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	93.06
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	92.92
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	91.86
KOG4660	549	consensus Protein Mei2, essential for commitment t	89.15
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	89.11
KOG4483	528	consensus Uncharacterized conserved protein [Funct	87.64
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	86.28
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	83.21
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	82.13

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.91  E-value=9.5e-24  Score=178.27  Aligned_cols=93  Identities=83%  Similarity=1.411  Sum_probs=86.8

Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCce
Q 025068           22 LNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRR  101 (258)
Q Consensus        22 ~~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~  101 (258)
                      ...+..|.+.+|||||+|+|++.+|+|+++|++||+|++..||.|+.|+++|||+||+|+|.|+|++||+..+.+|+||+
T Consensus         3 ~~~~~~DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~   82 (247)
T KOG0149|consen    3 HNNPFGDTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRK   82 (247)
T ss_pred             CCCCCCCceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccc
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeccC-CCCCC
Q 025068          102 ANCNLASL-GRPRP  114 (258)
Q Consensus       102 i~V~~a~~-~~~~~  114 (258)
                      .+|++|.. .++|.
T Consensus        83 aNcnlA~lg~~pR~   96 (247)
T KOG0149|consen   83 ANCNLASLGGKPRP   96 (247)
T ss_pred             cccchhhhcCccCC
Confidence            99999986 44444

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

Probab=99.83  E-value=2.6e-19  Score=144.76  Aligned_cols=83  Identities=39%  Similarity=0.719  Sum_probs=77.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+||+++++|++|+++|++||.|++|+|++|+.|+++||||||+|++.++|++||+.++ ++|+|+.|+|++
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            3456799999999999999999999999999999999999999999999999999999999999865 779999999999


Q ss_pred             ccCC
Q 025068          107 ASLG  110 (258)
Q Consensus       107 a~~~  110 (258)
                      +..+
T Consensus       111 a~~~  114 (144)
T PLN03134        111 ANDR  114 (144)
T ss_pred             CCcC
Confidence            9654

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.74  E-value=1.6e-17  Score=152.13  Aligned_cols=84  Identities=23%  Similarity=0.318  Sum_probs=78.3

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEE
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANC  104 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V  104 (258)
                      .++...++|||+||++++||++|+++|++||.|++|+|++|+.|+++||||||+|.++++|++||++++ .+|.+++|+|
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V  181 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKV  181 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeee
Confidence            456678899999999999999999999999999999999999999999999999999999999999866 6799999999


Q ss_pred             EeccC
Q 025068          105 NLASL  109 (258)
Q Consensus       105 ~~a~~  109 (258)
                      .+++.
T Consensus       182 ~~a~p  186 (346)
T TIGR01659       182 SYARP  186 (346)
T ss_pred             ecccc
Confidence            99864

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.72  E-value=4.9e-17  Score=148.63  Aligned_cols=85  Identities=24%  Similarity=0.325  Sum_probs=78.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      .....+|||+||+.++++++|+++|++||.|++|+|++|+.|+++||||||+|.+.++|.+||+.++ ..|+||.|+|.+
T Consensus       266 ~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~  345 (352)
T TIGR01661       266 DGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSF  345 (352)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3445589999999999999999999999999999999999999999999999999999999999976 569999999999


Q ss_pred             ccCCCC
Q 025068          107 ASLGRP  112 (258)
Q Consensus       107 a~~~~~  112 (258)
                      +..+..
T Consensus       346 ~~~~~~  351 (352)
T TIGR01661       346 KTNKAY  351 (352)
T ss_pred             ccCCCC
Confidence            976643

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

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

Probab=99.71  E-value=1.8e-16  Score=153.92  Aligned_cols=87  Identities=31%  Similarity=0.512  Sum_probs=78.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+||++++|+++|+++|++||.|++|+|+.| .++++||||||+|.+.++|++||++++ ..|+||+|+|.+
T Consensus       282 ~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~  360 (562)
T TIGR01628       282 KAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVAL  360 (562)
T ss_pred             ccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEe
Confidence            345678999999999999999999999999999999999 479999999999999999999999866 669999999999


Q ss_pred             ccCCCCCCC
Q 025068          107 ASLGRPRPQ  115 (258)
Q Consensus       107 a~~~~~~~~  115 (258)
                      |.+++.+..
T Consensus       361 a~~k~~~~~  369 (562)
T TIGR01628       361 AQRKEQRRA  369 (562)
T ss_pred             ccCcHHHHH
Confidence            987765543

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.71  E-value=2.2e-16  Score=144.68  Aligned_cols=83  Identities=24%  Similarity=0.421  Sum_probs=74.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCC--ceEEEE
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDG--RRANCN  105 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G--~~i~V~  105 (258)
                      ...++|||+||+.+++|++|+++|++||+|++|+|++|+.++++||||||+|.+.++|++||+.++ .+|++  ++|+|+
T Consensus       191 ~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~  270 (346)
T TIGR01659       191 IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVR  270 (346)
T ss_pred             cccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEE
Confidence            456789999999999999999999999999999999999999999999999999999999999976 44655  689999


Q ss_pred             eccCCC
Q 025068          106 LASLGR  111 (258)
Q Consensus       106 ~a~~~~  111 (258)
                      ++....
T Consensus       271 ~a~~~~  276 (346)
T TIGR01659       271 LAEEHG  276 (346)
T ss_pred             ECCccc
Confidence            986543

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.69  E-value=1.2e-16  Score=146.06  Aligned_cols=81  Identities=30%  Similarity=0.459  Sum_probs=75.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      ..++|||+|||.+++|++|+++|++||+|++|+|++|+.+++++|||||+|.+.++|++||+.++ ..|.|+.|+|+++.
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            36799999999999999999999999999999999999999999999999999999999999866 56999999999986


Q ss_pred             CC
Q 025068          109 LG  110 (258)
Q Consensus       109 ~~  110 (258)
                      .+
T Consensus        82 ~~   83 (352)
T TIGR01661        82 PS   83 (352)
T ss_pred             cc
Confidence            44

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

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.64  E-value=4.3e-16  Score=137.34  Aligned_cols=82  Identities=30%  Similarity=0.579  Sum_probs=75.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      ...+.++|+|+|||+...|-||+.+|++||.|.+|+||.+.  .-||||+||+|++.++|++|-++++ ..|.||+|+|+
T Consensus        92 s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn  169 (376)
T KOG0125|consen   92 SKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVN  169 (376)
T ss_pred             CCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEe
Confidence            45578899999999999999999999999999999999984  7799999999999999999999977 56999999999


Q ss_pred             eccCC
Q 025068          106 LASLG  110 (258)
Q Consensus       106 ~a~~~  110 (258)
                      .|+.+
T Consensus       170 ~ATar  174 (376)
T KOG0125|consen  170 NATAR  174 (376)
T ss_pred             ccchh
Confidence            99755

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.63  E-value=2.1e-15  Score=128.43  Aligned_cols=83  Identities=29%  Similarity=0.423  Sum_probs=77.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCc-cCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~-i~G~~i~V~~  106 (258)
                      ..+.++|-|.||+.+++|++|+++|.+||.|.+|.|.+|+.||.+||||||+|.++++|.+||+.++.. .+.-.|+|+|
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEw  265 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEW  265 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEe
Confidence            346788999999999999999999999999999999999999999999999999999999999998755 8889999999


Q ss_pred             ccCC
Q 025068          107 ASLG  110 (258)
Q Consensus       107 a~~~  110 (258)
                      ++++
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            9653

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.62  E-value=5.3e-15  Score=127.57  Aligned_cols=77  Identities=35%  Similarity=0.555  Sum_probs=71.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      .++|+||||||+.-++|++||+.|+.||.|.+|+|.++      +||+||.|++.|.|.+||.++| .+|.|..++|.|.
T Consensus       162 p~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWG  235 (321)
T KOG0148|consen  162 PDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWG  235 (321)
T ss_pred             CCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEecc
Confidence            56899999999999999999999999999999999988      5799999999999999999965 7899999999998


Q ss_pred             cCCC
Q 025068          108 SLGR  111 (258)
Q Consensus       108 ~~~~  111 (258)
                      +...
T Consensus       236 Ke~~  239 (321)
T KOG0148|consen  236 KEGD  239 (321)
T ss_pred             ccCC
Confidence            6543

>PF00076 RRM_1: RNA recognition motif

Probab=99.62  E-value=1.6e-15  Score=106.11  Aligned_cols=69  Identities=36%  Similarity=0.681  Sum_probs=64.1

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCccCCceEE
Q 025068           34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPFIDGRRAN  103 (258)
Q Consensus        34 lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~i~G~~i~  103 (258)
                      |||+|||.++++++|+++|++||.|+.+++..+ .+++.+++|||+|++.++|++||+.+ +..|+|+.|+
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 47999999999999999999999975 4679999875

(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 ....

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.59  E-value=2.3e-15  Score=129.80  Aligned_cols=82  Identities=40%  Similarity=0.599  Sum_probs=77.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCC-ccCCceEEEEeccC
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP-FIDGRRANCNLASL  109 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~-~i~G~~i~V~~a~~  109 (258)
                      -..|||+.|..+|+-++||+.|.+||+|.+++|++|..|+++|||+||.|.+.++|++||..|+. -|++|.|+-+||.+
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            45799999999999999999999999999999999999999999999999999999999999884 59999999999987


Q ss_pred             CCC
Q 025068          110 GRP  112 (258)
Q Consensus       110 ~~~  112 (258)
                      |..
T Consensus       142 Kp~  144 (321)
T KOG0148|consen  142 KPS  144 (321)
T ss_pred             Ccc
Confidence            763

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.58  E-value=5.3e-14  Score=135.86  Aligned_cols=74  Identities=24%  Similarity=0.388  Sum_probs=67.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcC--CCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQF--GEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~f--G~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ..++|||+||+++++|++|+++|++|  |+|++|++++        +||||+|++.++|++||+.++ .+|+|+.|+|++
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~  303 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--------DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTL  303 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45789999999999999999999999  9999998764        499999999999999999866 679999999999


Q ss_pred             ccCCC
Q 025068          107 ASLGR  111 (258)
Q Consensus       107 a~~~~  111 (258)
                      +++..
T Consensus       304 Akp~~  308 (578)
T TIGR01648       304 AKPVD  308 (578)
T ss_pred             ccCCC
Confidence            97643

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.

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.58  E-value=4.9e-15  Score=123.39  Aligned_cols=88  Identities=30%  Similarity=0.551  Sum_probs=80.7

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEE
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRAN  103 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~  103 (258)
                      |.+-+...+|-|-||...++.++|+.+|++||.|-+|.|.+|+.|+.++|||||.|.+..+|+.|++.|+ .+|+|+.|.
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelr   86 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELR   86 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceee
Confidence            5566677899999999999999999999999999999999999999999999999999999999999976 679999999


Q ss_pred             EEeccCCCC
Q 025068          104 CNLASLGRP  112 (258)
Q Consensus       104 V~~a~~~~~  112 (258)
                      |..|.-...
T Consensus        87 Vq~arygr~   95 (256)
T KOG4207|consen   87 VQMARYGRP   95 (256)
T ss_pred             ehhhhcCCC
Confidence            999874433

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.58  E-value=1e-14  Score=126.99  Aligned_cols=76  Identities=17%  Similarity=0.257  Sum_probs=70.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEeccC
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASL  109 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~~  109 (258)
                      .++|||+||+++++|++|+++|+.||+|++|+|++|+.   .+|||||+|++.++|++||..++..|.|+.|+|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccC
Confidence            57999999999999999999999999999999999853   57899999999999999997666889999999999863

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

Probab=99.58  E-value=8.2e-15  Score=141.82  Aligned_cols=82  Identities=18%  Similarity=0.373  Sum_probs=76.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...++|||+||+.++++++|+++|++||.|++|+|++|+.++++||||||+|++.++|.+||+.+| .+|+|+.|+|.++
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            356799999999999999999999999999999999999999999999999999999999999977 5699999999998


Q ss_pred             cCC
Q 025068          108 SLG  110 (258)
Q Consensus       108 ~~~  110 (258)
                      ..+
T Consensus       282 i~p  284 (612)
T TIGR01645       282 VTP  284 (612)
T ss_pred             CCC
Confidence            743

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.57  E-value=6.6e-15  Score=103.78  Aligned_cols=69  Identities=35%  Similarity=0.645  Sum_probs=63.3

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEE
Q 025068           34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRAN  103 (258)
Q Consensus        34 lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~  103 (258)
                      |||+|||+++++++|+++|+.+|.|.++++.+++. ++.+++|||+|.+.++|++|++.++ ..|+|+.|+
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            79999999999999999999999999999999987 8999999999999999999999976 679999875

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 ....

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.56  E-value=8.3e-14  Score=127.25  Aligned_cols=78  Identities=27%  Similarity=0.420  Sum_probs=71.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      .+.+.|||+||+.++|||.|+++|++||.|++|+.++|        ||||+|.++++|.+|++.++ ++|+|..|.|.+|
T Consensus       257 s~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLA  328 (506)
T KOG0117|consen  257 SKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLA  328 (506)
T ss_pred             hheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEec
Confidence            46789999999999999999999999999999998877        99999999999999999976 7799999999999


Q ss_pred             cCCCCCC
Q 025068          108 SLGRPRP  114 (258)
Q Consensus       108 ~~~~~~~  114 (258)
                      ++...++
T Consensus       329 KP~~k~k  335 (506)
T KOG0117|consen  329 KPVDKKK  335 (506)
T ss_pred             CChhhhc
Confidence            8654443

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.56  E-value=8.3e-15  Score=133.24  Aligned_cols=88  Identities=30%  Similarity=0.464  Sum_probs=77.9

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC--CccCC--ce
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT--PFIDG--RR  101 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~--~~i~G--~~  101 (258)
                      .+|.+.-+|||+-||..++|+|||++|++||.|.+|.|++||.|+.+||||||+|.+.++|.+||..++  ++|-|  ..
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            345667799999999999999999999999999999999999999999999999999999999999854  44554  67


Q ss_pred             EEEEeccCCCCC
Q 025068          102 ANCNLASLGRPR  113 (258)
Q Consensus       102 i~V~~a~~~~~~  113 (258)
                      |.|++|+.++.|
T Consensus       109 vqvk~Ad~E~er  120 (510)
T KOG0144|consen  109 VQVKYADGERER  120 (510)
T ss_pred             eeecccchhhhc
Confidence            899999866555

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

Probab=99.56  E-value=1.1e-14  Score=140.88  Aligned_cols=80  Identities=33%  Similarity=0.591  Sum_probs=74.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...++|||+||+.+++|++|+++|++||.|++|+|++|+.|+++||||||+|++.++|++||+.++ ..|+|+.|+|...
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            356899999999999999999999999999999999999999999999999999999999999866 6699999999865


Q ss_pred             c
Q 025068          108 S  108 (258)
Q Consensus       108 ~  108 (258)
                      .
T Consensus       185 ~  185 (612)
T TIGR01645       185 S  185 (612)
T ss_pred             c
Confidence            4

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.55  E-value=1.4e-14  Score=126.35  Aligned_cols=80  Identities=34%  Similarity=0.619  Sum_probs=75.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcC-CCCccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD-PTPFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~-~~~~i~G~~i~V~~a  107 (258)
                      ...++|||+.|+.+++|++|++.|++||.|+.|.||+|+.||++||||||+|+++.+..+|-++ .+..|+|+.|.|.+.
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            4678999999999999999999999999999999999999999999999999999999999998 456799999999876


Q ss_pred             c
Q 025068          108 S  108 (258)
Q Consensus       108 ~  108 (258)
                      .
T Consensus       179 R  179 (335)
T KOG0113|consen  179 R  179 (335)
T ss_pred             c
Confidence            3

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

Probab=99.54  E-value=2e-14  Score=139.71  Aligned_cols=77  Identities=29%  Similarity=0.487  Sum_probs=72.8

Q ss_pred             EEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccC
Q 025068           33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASL  109 (258)
Q Consensus        33 ~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~  109 (258)
                      +|||+||+.++||++|+++|++||.|++|+|++|+.|++++|||||+|.+.++|++||+.++ ..|.|+.|+|.++..
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~   79 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            79999999999999999999999999999999999999999999999999999999999977 559999999998753

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.53  E-value=2.1e-14  Score=116.89  Aligned_cols=75  Identities=28%  Similarity=0.449  Sum_probs=68.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      -.++|||+||+.++++.||+.+|.+||.|.+|.|-+++     .|||||+|++..+|+.|+..|+ ..|+|..|.|+++.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            47899999999999999999999999999999887654     6899999999999999999976 67999999999985


Q ss_pred             C
Q 025068          109 L  109 (258)
Q Consensus       109 ~  109 (258)
                      -
T Consensus        84 G   84 (195)
T KOG0107|consen   84 G   84 (195)
T ss_pred             C
Confidence            3

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.53  E-value=3.8e-14  Score=134.20  Aligned_cols=83  Identities=25%  Similarity=0.393  Sum_probs=76.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      +...++|||+||+.++++++|+++|++||.|++|+|++|+.++++||||||+|.+.++|++||..++..|.|+.|.|..+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~  165 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSS  165 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeec
Confidence            34578999999999999999999999999999999999999999999999999999999999987778899999999987


Q ss_pred             cCC
Q 025068          108 SLG  110 (258)
Q Consensus       108 ~~~  110 (258)
                      ...
T Consensus       166 ~~~  168 (457)
T TIGR01622       166 QAE  168 (457)
T ss_pred             chh
Confidence            543

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.52  E-value=3.7e-14  Score=136.90  Aligned_cols=77  Identities=30%  Similarity=0.441  Sum_probs=68.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-Ccc-CCceEEEEec
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFI-DGRRANCNLA  107 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i-~G~~i~V~~a  107 (258)
                      ..++|||+|||++++|++|+++|++||.|.+|+|++| .++++||||||+|.+.++|++||+.++ .+| .++.|.|..+
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 689999999999999999999999976 445 4666655433

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.

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.52  E-value=1.1e-14  Score=122.45  Aligned_cols=85  Identities=29%  Similarity=0.475  Sum_probs=78.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      .+-++||||+|.++++|.-|...|..||+|++|++..|-.++++|||+||+|...|+|.+||..++ .+|.||.|+|++|
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            346799999999999999999999999999999999999999999999999999999999999987 7799999999999


Q ss_pred             cCCCCC
Q 025068          108 SLGRPR  113 (258)
Q Consensus       108 ~~~~~~  113 (258)
                      .+.+.+
T Consensus        88 kP~kik   93 (298)
T KOG0111|consen   88 KPEKIK   93 (298)
T ss_pred             CCcccc
Confidence            866543

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.52  E-value=3.5e-14  Score=129.70  Aligned_cols=80  Identities=28%  Similarity=0.442  Sum_probs=73.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-Ccc-CCceEEEEe
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFI-DGRRANCNL  106 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i-~G~~i~V~~  106 (258)
                      ..-|.||||.||.++.|++|..+|++.|+|-+++|+.|+.+|.+||||||+|.+.++|++||+.+| ++| .||.|.|..
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            456899999999999999999999999999999999999999999999999999999999999955 665 589998876


Q ss_pred             cc
Q 025068          107 AS  108 (258)
Q Consensus       107 a~  108 (258)
                      +.
T Consensus       161 Sv  162 (506)
T KOG0117|consen  161 SV  162 (506)
T ss_pred             ee
Confidence            64

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.51  E-value=1e-14  Score=132.65  Aligned_cols=87  Identities=24%  Similarity=0.357  Sum_probs=77.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCC--cc--CCceEEEE
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP--FI--DGRRANCN  105 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~--~i--~G~~i~V~  105 (258)
                      ++++|||+.|+..++|++++++|++||.|++|.|++|.. +.+||||||+|+++|.|..||+.+|.  ++  +..+|.|+
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~-~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD-GLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheeccc-ccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            378999999999999999999999999999999999985 99999999999999999999999773  34  45789999


Q ss_pred             eccCCCCCCCCc
Q 025068          106 LASLGRPRPQVL  117 (258)
Q Consensus       106 ~a~~~~~~~~~~  117 (258)
                      +|+.++++..++
T Consensus       202 FADtqkdk~~~~  213 (510)
T KOG0144|consen  202 FADTQKDKDGKR  213 (510)
T ss_pred             ecccCCCchHHH
Confidence            999887775443

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.50  E-value=1.4e-13  Score=131.98  Aligned_cols=83  Identities=23%  Similarity=0.454  Sum_probs=76.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...++|||+||+.++++++|+++|+.||.|+.+.|++++.+|+++|||||+|.+.++|++||+.++ ..|.|+.|.|.++
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            345799999999999999999999999999999999999899999999999999999999999876 6699999999999


Q ss_pred             cCCC
Q 025068          108 SLGR  111 (258)
Q Consensus       108 ~~~~  111 (258)
                      ....
T Consensus       373 ~~~~  376 (509)
T TIGR01642       373 CVGA  376 (509)
T ss_pred             ccCC
Confidence            6543

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.49  E-value=1.6e-13  Score=129.85  Aligned_cols=78  Identities=33%  Similarity=0.627  Sum_probs=74.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      .++|||+||+.++++++|+++|++||.|+.|.|++++.+++++|||||+|.+.++|++||+.++ ..|.|+.|+|.++.
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            6899999999999999999999999999999999999989999999999999999999999866 56999999999987

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.48  E-value=2e-13  Score=117.36  Aligned_cols=76  Identities=18%  Similarity=0.174  Sum_probs=69.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~  108 (258)
                      ...+|||+||++++||++|+++|+.||+|++|+|++|   ++.+++|||+|+++++++.||...+.+|.++.|.|....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D---~et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS---GEYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC---CCcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCc
Confidence            3468999999999999999999999999999999998   455689999999999999999888899999999998764

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.48  E-value=2.5e-13  Score=116.77  Aligned_cols=83  Identities=28%  Similarity=0.450  Sum_probs=77.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCC-ccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP-FIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~-~i~G~~i~V~~  106 (258)
                      ++..++|.|.-||.++|+||||.+|...|+|++|++++|+.+|.+.||+||.|.++++|++||..++. .+..|.|+|++
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            45567899999999999999999999999999999999999999999999999999999999999774 59999999999


Q ss_pred             ccCC
Q 025068          107 ASLG  110 (258)
Q Consensus       107 a~~~  110 (258)
                      |++.
T Consensus       118 ARPS  121 (360)
T KOG0145|consen  118 ARPS  121 (360)
T ss_pred             ccCC
Confidence            9654

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.48  E-value=8.3e-14  Score=108.04  Aligned_cols=80  Identities=21%  Similarity=0.339  Sum_probs=74.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      .++++|||+||+..++||+|.++|+++|+|+.|.+-.|+.+....|||||+|.+.++|+.|+.-++ ..++.+.|.|.+.
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            468999999999999999999999999999999999999988999999999999999999999966 5699999999987


Q ss_pred             c
Q 025068          108 S  108 (258)
Q Consensus       108 ~  108 (258)
                      .
T Consensus       114 ~  114 (153)
T KOG0121|consen  114 A  114 (153)
T ss_pred             c
Confidence            3

>smart00362 RRM_2 RNA recognition motif

Probab=99.47  E-value=2.7e-13  Score=93.74  Aligned_cols=71  Identities=31%  Similarity=0.566  Sum_probs=65.2

Q ss_pred             EEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        33 ~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      +|||+||+.++++++|+++|++||.|.++++..++  +.++++|||+|.+.++|++|++.++ ..+.|++|.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999999886  7788999999999999999999866 67999998874

>PLN03213 repressor of silencing 3; Provisional

Probab=99.46  E-value=2e-13  Score=126.22  Aligned_cols=78  Identities=14%  Similarity=0.288  Sum_probs=69.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCH--HHHHHHhcCCC-CccCCceEEE
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREP--EAARRACADPT-PFIDGRRANC  104 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~--~~A~~Ai~~~~-~~i~G~~i~V  104 (258)
                      .....+||||||.+++++++|+.+|+.||.|.+|.|+++  ||  ||||||+|.+.  +++.+||+.++ .+++|+.|+|
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE--TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKV   82 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT--KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRL   82 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc--cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEE
Confidence            345679999999999999999999999999999999954  67  99999999987  68999999976 6699999999


Q ss_pred             EeccC
Q 025068          105 NLASL  109 (258)
Q Consensus       105 ~~a~~  109 (258)
                      +.|+.
T Consensus        83 NKAKP   87 (759)
T PLN03213         83 EKAKE   87 (759)
T ss_pred             eeccH
Confidence            99964

>smart00360 RRM RNA recognition motif

Probab=99.46  E-value=3.3e-13  Score=92.91  Aligned_cols=70  Identities=36%  Similarity=0.620  Sum_probs=64.8

Q ss_pred             EcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           36 VGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        36 VgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      |+||+.++++++|+++|+.||.|.++.+..++.+++++++|||+|.+.++|++|++.++ ..++++.|+|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            57999999999999999999999999999998889999999999999999999999876 66899998874

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.45  E-value=1.1e-13  Score=124.30  Aligned_cols=104  Identities=39%  Similarity=0.696  Sum_probs=87.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEeccC
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASL  109 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~~  109 (258)
                      +.++|||++|+|++++|.|++.|+.||+|.+|.|++|+.+++++||+||+|.+.+.+.++|....+.|+|+.|.++.|.+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~   84 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVS   84 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccC
Confidence            68999999999999999999999999999999999999999999999999999999999999988999999999999976


Q ss_pred             CCCCCCCccCCCCCCCCCCCCCCCC
Q 025068          110 GRPRPQVLYGRLRPATLFSGSTQAT  134 (258)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~g~~~~~  134 (258)
                      ++......+ .....+.++|+.+..
T Consensus        85 r~~~~~~~~-~~~tkkiFvGG~~~~  108 (311)
T KOG4205|consen   85 REDQTKVGR-HLRTKKIFVGGLPPD  108 (311)
T ss_pred             ccccccccc-ccceeEEEecCcCCC
Confidence            654332221 113445556655443

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.45  E-value=2.2e-14  Score=117.39  Aligned_cols=83  Identities=28%  Similarity=0.491  Sum_probs=75.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      .++.-|||||||.+.||.+|.-+|++||+|++|.+++|+.||+||||||++|+|..+..-||..+| ..|.||.|+|...
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            456689999999999999999999999999999999999999999999999999999999998876 4599999999876


Q ss_pred             cCCC
Q 025068          108 SLGR  111 (258)
Q Consensus       108 ~~~~  111 (258)
                      ..-+
T Consensus       113 ~~Yk  116 (219)
T KOG0126|consen  113 SNYK  116 (219)
T ss_pred             cccc
Confidence            5433

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.45  E-value=3.5e-13  Score=115.84  Aligned_cols=78  Identities=29%  Similarity=0.628  Sum_probs=74.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      .++|||+||+.++++++|+++|.+||.|..+.|..|+.+++++|||||+|.+.++|.+||+.++ ..|.|++|.|.++.
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            6899999999999999999999999999999999998899999999999999999999999977 67999999999975

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.43  E-value=2.5e-13  Score=126.93  Aligned_cols=81  Identities=32%  Similarity=0.592  Sum_probs=77.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccCC
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASLG  110 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~~  110 (258)
                      ++||||||+.+++|++|.++|+..|.|.+++++.|+.||+.|||+|++|.+.+++++|++.++ .++.|++|+|+++...
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            899999999999999999999999999999999999999999999999999999999999977 7799999999999755


Q ss_pred             CC
Q 025068          111 RP  112 (258)
Q Consensus       111 ~~  112 (258)
                      +.
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            44

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.42  E-value=6.5e-13  Score=103.99  Aligned_cols=90  Identities=23%  Similarity=0.357  Sum_probs=81.3

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceE
Q 025068           24 SPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRA  102 (258)
Q Consensus        24 ~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i  102 (258)
                      .|.....--.|||.++..+++|++|.+.|..||+|+.+.+..|+.||-.|||++|+|++.++|++||..+| ..|.|..|
T Consensus        65 gPqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v  144 (170)
T KOG0130|consen   65 GPQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNV  144 (170)
T ss_pred             CCccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCce
Confidence            34444556689999999999999999999999999999999999999999999999999999999999977 67999999


Q ss_pred             EEEeccCCCCC
Q 025068          103 NCNLASLGRPR  113 (258)
Q Consensus       103 ~V~~a~~~~~~  113 (258)
                      .|.|+..+.+.
T Consensus       145 ~VDw~Fv~gp~  155 (170)
T KOG0130|consen  145 SVDWCFVKGPE  155 (170)
T ss_pred             eEEEEEecCCc
Confidence            99999866553

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.41  E-value=3.4e-13  Score=117.55  Aligned_cols=71  Identities=30%  Similarity=0.560  Sum_probs=66.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCC-ccCCceEEEEeccCC
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP-FIDGRRANCNLASLG  110 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~-~i~G~~i~V~~a~~~  110 (258)
                      .+|||+|||.++++.+|+.+|++||+|++|+||++        ||||+.++.+.++.||..+++ +|+|+.|+|+.++.|
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            47999999999999999999999999999999988        999999999999999998775 599999999998766

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.40  E-value=2.5e-13  Score=117.18  Aligned_cols=87  Identities=28%  Similarity=0.393  Sum_probs=80.1

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCc-cCCceEE
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRRAN  103 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~-i~G~~i~  103 (258)
                      ..+..+-|+|||-.||.+..+.||..+|-.||.|.+.||..|+.|..+|+|+||.|+++.+++.||..+|.. |+-|+|+
T Consensus       279 qreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLK  358 (371)
T KOG0146|consen  279 QREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLK  358 (371)
T ss_pred             hhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhh
Confidence            345667899999999999999999999999999999999999999999999999999999999999998855 9999999


Q ss_pred             EEeccCCC
Q 025068          104 CNLASLGR  111 (258)
Q Consensus       104 V~~a~~~~  111 (258)
                      |.+.++|+
T Consensus       359 VQLKRPkd  366 (371)
T KOG0146|consen  359 VQLKRPKD  366 (371)
T ss_pred             hhhcCccc
Confidence            99986554

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

Probab=99.39  E-value=1.8e-12  Score=123.93  Aligned_cols=78  Identities=14%  Similarity=0.204  Sum_probs=70.2

Q ss_pred             CCCCcEEEEcCCCC-CCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           28 DTTYTKVFVGGLAW-ETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        28 ~~~~~~lfVgnLp~-~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      ....++|||+||++ ++++++|+++|+.||.|++|+|++++     +|+|||+|.+.++|++||+.++ ..|.|+.|+|+
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            34668999999998 69999999999999999999999874     6899999999999999999866 66999999999


Q ss_pred             eccCC
Q 025068          106 LASLG  110 (258)
Q Consensus       106 ~a~~~  110 (258)
                      +++.+
T Consensus       347 ~s~~~  351 (481)
T TIGR01649       347 PSKQQ  351 (481)
T ss_pred             Ecccc
Confidence            98654

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).

>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=99.38  E-value=3.5e-12  Score=88.58  Aligned_cols=73  Identities=32%  Similarity=0.603  Sum_probs=66.3

Q ss_pred             EEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCc-cCCceEEEEe
Q 025068           33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRRANCNL  106 (258)
Q Consensus        33 ~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~-i~G~~i~V~~  106 (258)
                      +|+|+||+.++++++|+++|+.+|.|..+.+..++.+ +.++++||+|.+.++|..|++.++.. +++++|.|++
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            4899999999999999999999999999999988754 77899999999999999999997754 9999998864

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.37  E-value=9e-13  Score=107.99  Aligned_cols=81  Identities=28%  Similarity=0.385  Sum_probs=75.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCC-ccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP-FIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~-~i~G~~i~V~~  106 (258)
                      .....+|||+||+..++++.|.++|-+.|.|.++++.+|+.+...+|||||+|.++|+|+-||+.++. .+-||+|+|+.
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~k   85 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNK   85 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEe
Confidence            34567999999999999999999999999999999999999999999999999999999999999884 49999999999


Q ss_pred             cc
Q 025068          107 AS  108 (258)
Q Consensus       107 a~  108 (258)
                      +.
T Consensus        86 as   87 (203)
T KOG0131|consen   86 AS   87 (203)
T ss_pred             cc
Confidence            96

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.37  E-value=1.7e-11  Score=110.12  Aligned_cols=86  Identities=31%  Similarity=0.585  Sum_probs=80.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEeccC
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASL  109 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~~  109 (258)
                      +.++|||++|+.++++++|++.|++||.|.++.++.|+.+.+.+||+||+|.+++.+++++...-++|+++.+.|+.|.+
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~~f~~~~gk~vevkrA~p  175 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQKFHDFNGKKVEVKRAIP  175 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecccceeeecCceeeEeeccc
Confidence            46799999999999999999999999999999999999999999999999999999999999988999999999999987


Q ss_pred             CCCCCC
Q 025068          110 GRPRPQ  115 (258)
Q Consensus       110 ~~~~~~  115 (258)
                      +.....
T Consensus       176 k~~~~~  181 (311)
T KOG4205|consen  176 KEVMQS  181 (311)
T ss_pred             hhhccc
Confidence            765543

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

Probab=99.36  E-value=2.8e-12  Score=122.68  Aligned_cols=75  Identities=19%  Similarity=0.260  Sum_probs=67.3

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC--C-CccCCceEEEEec
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP--T-PFIDGRRANCNLA  107 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~--~-~~i~G~~i~V~~a  107 (258)
                      +++|||+||+++++|++|+++|++||.|++|+|+++      |++|||+|++.++|++||+.+  + ..|+|+.|+|.++
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s   75 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYS   75 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEec
Confidence            578999999999999999999999999999999864      579999999999999999863  3 5699999999999


Q ss_pred             cCCC
Q 025068          108 SLGR  111 (258)
Q Consensus       108 ~~~~  111 (258)
                      ..++
T Consensus        76 ~~~~   79 (481)
T TIGR01649        76 TSQE   79 (481)
T ss_pred             CCcc
Confidence            7543

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).

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.35  E-value=5.6e-12  Score=94.52  Aligned_cols=88  Identities=19%  Similarity=0.308  Sum_probs=74.9

Q ss_pred             CCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCC-ccC
Q 025068           20 QYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP-FID   98 (258)
Q Consensus        20 ~~~~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~-~i~   98 (258)
                      ...+...+.+.++-|||.|||.++|.|++.++|.+||.|..|+|-..+.   .+|-|||.|++..+|.+||..+.. .++
T Consensus         7 ~~~~~rlppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~   83 (124)
T KOG0114|consen    7 KKQNIRLPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVD   83 (124)
T ss_pred             ccCCCCCChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccC
Confidence            3444555666788999999999999999999999999999999976644   588999999999999999999774 499


Q ss_pred             CceEEEEeccCC
Q 025068           99 GRRANCNLASLG  110 (258)
Q Consensus        99 G~~i~V~~a~~~  110 (258)
                      ++.|.|-+-...
T Consensus        84 ~ryl~vlyyq~~   95 (124)
T KOG0114|consen   84 NRYLVVLYYQPE   95 (124)
T ss_pred             CceEEEEecCHH
Confidence            999999876543

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.34  E-value=7.2e-12  Score=103.05  Aligned_cols=80  Identities=23%  Similarity=0.382  Sum_probs=69.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~i~G~~i~V~~a  107 (258)
                      ...++|||+|||.+|.|.+|+++|.|||.|.+|++...   -...+||||+|++..+|+.||..- +..++|.+|+|+++
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            35789999999999999999999999999999987443   234579999999999999999984 46699999999999


Q ss_pred             cCCC
Q 025068          108 SLGR  111 (258)
Q Consensus       108 ~~~~  111 (258)
                      ...+
T Consensus        81 rggr   84 (241)
T KOG0105|consen   81 RGGR   84 (241)
T ss_pred             cCCC
Confidence            6544

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.34  E-value=5.8e-12  Score=108.46  Aligned_cols=92  Identities=25%  Similarity=0.322  Sum_probs=81.4

Q ss_pred             CCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCC-cc
Q 025068           19 FQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP-FI   97 (258)
Q Consensus        19 ~~~~~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~-~i   97 (258)
                      ......|......-.|||-||..+++|.-|..+|..||.|..|+|++|..|.+.|||+||+..+-++|..||..++. .+
T Consensus       266 l~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~l  345 (360)
T KOG0145|consen  266 LAGVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRL  345 (360)
T ss_pred             eeeeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccc
Confidence            33344555566677899999999999999999999999999999999999999999999999999999999999875 59


Q ss_pred             CCceEEEEeccCC
Q 025068           98 DGRRANCNLASLG  110 (258)
Q Consensus        98 ~G~~i~V~~a~~~  110 (258)
                      .+|.|.|++...+
T Consensus       346 g~rvLQVsFKtnk  358 (360)
T KOG0145|consen  346 GDRVLQVSFKTNK  358 (360)
T ss_pred             cceEEEEEEecCC
Confidence            9999999987644

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.33  E-value=5e-12  Score=118.16  Aligned_cols=87  Identities=33%  Similarity=0.523  Sum_probs=77.3

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC----C---Ccc
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP----T---PFI   97 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~----~---~~i   97 (258)
                      +.++...++|||.||+++++|++|.+.|++||+|..+.|+.++.|+.++|.|||.|.+.+++.+||+.-    .   ..|
T Consensus       286 ~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll  365 (678)
T KOG0127|consen  286 RENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLL  365 (678)
T ss_pred             cccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEE
Confidence            444455689999999999999999999999999999999999999999999999999999999999874    1   238


Q ss_pred             CCceEEEEeccCCC
Q 025068           98 DGRRANCNLASLGR  111 (258)
Q Consensus        98 ~G~~i~V~~a~~~~  111 (258)
                      +||.|+|.+|..++
T Consensus       366 ~GR~Lkv~~Av~Rk  379 (678)
T KOG0127|consen  366 DGRLLKVTLAVTRK  379 (678)
T ss_pred             eccEEeeeeccchH
Confidence            99999999997553

>smart00361 RRM_1 RNA recognition motif

Probab=99.27  E-value=1.3e-11  Score=87.45  Aligned_cols=61  Identities=30%  Similarity=0.513  Sum_probs=53.8

Q ss_pred             HHHHHHHHh----cCCCEEEEE-EeecCCC--CCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           45 SETMRRYFE----QFGEILEAV-VITDKNT--GRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        45 e~~L~~~F~----~fG~I~~v~-v~~d~~t--g~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      +++|+++|+    +||.|.+|. |+.++.+  +++|||+||+|.+.++|.+||..++ ..++|+.|+|.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            678888888    999999995 7777766  8999999999999999999999966 67999999873

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.26  E-value=6.8e-12  Score=102.86  Aligned_cols=84  Identities=24%  Similarity=0.436  Sum_probs=76.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEE-EEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEA-VVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v-~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      ..+|||+||+++++|..|.++|++||.|.+. +|++|..||.++||+||.|.+.|.+.+||+.++ ..++.++|.|.++.
T Consensus        96 ganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~  175 (203)
T KOG0131|consen   96 GANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAF  175 (203)
T ss_pred             cccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEE
Confidence            3689999999999999999999999998764 899999999999999999999999999999976 66999999999998


Q ss_pred             CCCCCC
Q 025068          109 LGRPRP  114 (258)
Q Consensus       109 ~~~~~~  114 (258)
                      ++..+.
T Consensus       176 k~~~kg  181 (203)
T KOG0131|consen  176 KKDTKG  181 (203)
T ss_pred             ecCCCc
Confidence            765544

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.26  E-value=1.4e-11  Score=113.79  Aligned_cols=80  Identities=33%  Similarity=0.550  Sum_probs=72.5

Q ss_pred             EEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccCCC
Q 025068           33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASLGR  111 (258)
Q Consensus        33 ~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~~~  111 (258)
                      .|||.||+.++|.++|.++|+.||+|++|+|.+|.+ | +||| ||+|+++++|++||+.+| ..+.++.|.|.....++
T Consensus        78 ~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~  154 (369)
T KOG0123|consen   78 LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKE  154 (369)
T ss_pred             eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchh
Confidence            399999999999999999999999999999999984 5 9999 999999999999999976 45899999999998766


Q ss_pred             CCCC
Q 025068          112 PRPQ  115 (258)
Q Consensus       112 ~~~~  115 (258)
                      .|..
T Consensus       155 er~~  158 (369)
T KOG0123|consen  155 EREA  158 (369)
T ss_pred             hhcc
Confidence            5543

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.25  E-value=1e-11  Score=110.94  Aligned_cols=81  Identities=30%  Similarity=0.478  Sum_probs=75.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....+.|||..|.+-+++++|+-+|+.||.|.+|.||+|+.||.+..||||+|++.+++++|.-.|. ..|+.++|+|.+
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            3456799999999999999999999999999999999999999999999999999999999999965 569999999998


Q ss_pred             cc
Q 025068          107 AS  108 (258)
Q Consensus       107 a~  108 (258)
                      +.
T Consensus       316 SQ  317 (479)
T KOG0415|consen  316 SQ  317 (479)
T ss_pred             hh
Confidence            75

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.24  E-value=1.9e-11  Score=114.29  Aligned_cols=81  Identities=25%  Similarity=0.447  Sum_probs=73.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccC
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASL  109 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~  109 (258)
                      --+|+|.||||.+.+++|+.+|+.||.|.+|.|.+.+. ++.+|||||.|.+..+|.+||+.+| ++|+||.|-|.||..
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~d-gklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKD-GKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVD  195 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCC-CCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecc
Confidence            45899999999999999999999999999999998876 6666999999999999999999966 779999999999976


Q ss_pred             CCC
Q 025068          110 GRP  112 (258)
Q Consensus       110 ~~~  112 (258)
                      +..
T Consensus       196 Kd~  198 (678)
T KOG0127|consen  196 KDT  198 (678)
T ss_pred             ccc
Confidence            643

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.21  E-value=1.2e-11  Score=106.93  Aligned_cols=85  Identities=28%  Similarity=0.433  Sum_probs=75.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC--CccC--CceEEEE
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT--PFID--GRRANCN  105 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~--~~i~--G~~i~V~  105 (258)
                      ++++||||.|.+.-+|||++.+|..||.|++|.|++..+ |.+||++||.|.+..+|+.||..++  .++-  ...|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~d-g~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPD-GNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCC-CCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            578999999999999999999999999999999999985 9999999999999999999999976  2343  4679999


Q ss_pred             eccCCCCCCC
Q 025068          106 LASLGRPRPQ  115 (258)
Q Consensus       106 ~a~~~~~~~~  115 (258)
                      +++..+.|..
T Consensus        97 ~ADTdkER~l  106 (371)
T KOG0146|consen   97 FADTDKERTL  106 (371)
T ss_pred             eccchHHHHH
Confidence            9987766543

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=99.19  E-value=1.4e-10  Score=107.93  Aligned_cols=80  Identities=25%  Similarity=0.381  Sum_probs=69.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEeccC
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASL  109 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~~  109 (258)
                      ....|||+|||.++++++|+++|..||.|++..|......++..+||||+|.+.++++.||+.....|++++|.|+....
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEeccc
Confidence            34559999999999999999999999999988776654335556999999999999999999986679999999998744

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.18  E-value=2.2e-11  Score=114.04  Aligned_cols=78  Identities=33%  Similarity=0.603  Sum_probs=72.6

Q ss_pred             EEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccCC
Q 025068           33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASLG  110 (258)
Q Consensus        33 ~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~~  110 (258)
                      +|||+||.++++|++|+.+|+.||.|+.|.+.+|..||.+|||+||+|.+.++|.+|++.+| -+|-|+.|+|...+.+
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            39999999999999999999999999999999999899999999999999999999999976 5699999999877543

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=99.17  E-value=1.4e-10  Score=109.09  Aligned_cols=80  Identities=23%  Similarity=0.419  Sum_probs=74.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      -.++|||.+|...+...+|+.+|++||+|+-.+|+++..+--.+||+||++.+.++|.+||+.++ .+|.|+.|.|+.++
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            35789999999999999999999999999999999998888889999999999999999999988 56999999999886


Q ss_pred             C
Q 025068          109 L  109 (258)
Q Consensus       109 ~  109 (258)
                      .
T Consensus       484 N  484 (940)
T KOG4661|consen  484 N  484 (940)
T ss_pred             c
Confidence            4

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.17  E-value=9.2e-11  Score=104.58  Aligned_cols=81  Identities=32%  Similarity=0.480  Sum_probs=73.6

Q ss_pred             CCCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcC-CCC-ccCCc
Q 025068           23 NSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD-PTP-FIDGR  100 (258)
Q Consensus        23 ~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~-~~~-~i~G~  100 (258)
                      ..|.+|...++|||++|.+.++|.+|+++|.+||+|+++.++..+      ++|||+|.+.++|++|.++ .+. .|+|+
T Consensus       220 lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G~  293 (377)
T KOG0153|consen  220 LEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVINGF  293 (377)
T ss_pred             cCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecce
Confidence            678889999999999999999999999999999999999987764      4999999999999999998 454 49999


Q ss_pred             eEEEEeccC
Q 025068          101 RANCNLASL  109 (258)
Q Consensus       101 ~i~V~~a~~  109 (258)
                      +|+|.|...
T Consensus       294 Rl~i~Wg~~  302 (377)
T KOG0153|consen  294 RLKIKWGRP  302 (377)
T ss_pred             EEEEEeCCC
Confidence            999999966

>PF13893 RRM_5: RNA recognition motif

Probab=99.16  E-value=8e-11  Score=79.52  Aligned_cols=55  Identities=27%  Similarity=0.549  Sum_probs=48.3

Q ss_pred             HHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           48 MRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        48 L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      |+++|++||+|+++.+..++     +++|||+|.+.++|++|++.++ ..++|++|+|++|
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            78999999999999997764     5899999999999999999865 5699999999985

(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 ....

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.15  E-value=2.2e-11  Score=109.17  Aligned_cols=77  Identities=32%  Similarity=0.605  Sum_probs=73.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      .|+||||.|.+++.||.||..|..||.|+++.+-+|+.|+++|||+||+|+-+|.|+-|++.+| .+++||.|+|...
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCC
Confidence            5899999999999999999999999999999999999999999999999999999999999987 5699999999854

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.15  E-value=1.2e-10  Score=106.66  Aligned_cols=79  Identities=18%  Similarity=0.405  Sum_probs=72.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHh-cCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFE-QFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~-~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ...+.+||.|||.++.+.+|+++|. +.|+|+.|.++.|. +|++||+|.|+|+++|.++||++.++ +++.||.|+|+.
T Consensus        42 ~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKE  120 (608)
T KOG4212|consen   42 ARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKE  120 (608)
T ss_pred             cccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEec
Confidence            3456799999999999999999995 68999999999998 59999999999999999999999988 569999999987


Q ss_pred             cc
Q 025068          107 AS  108 (258)
Q Consensus       107 a~  108 (258)
                      ..
T Consensus       121 d~  122 (608)
T KOG4212|consen  121 DH  122 (608)
T ss_pred             cC
Confidence            64

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.10  E-value=1e-10  Score=102.20  Aligned_cols=76  Identities=26%  Similarity=0.471  Sum_probs=69.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|+|+||.+.++.+||++.|++||.|.+|+|++|        |+||+|+-.++|..||..++ .+|.|++++|.+
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            446779999999999999999999999999999999987        99999999999999999855 779999999999


Q ss_pred             ccCCC
Q 025068          107 ASLGR  111 (258)
Q Consensus       107 a~~~~  111 (258)
                      ++++.
T Consensus       147 stsrl  151 (346)
T KOG0109|consen  147 STSRL  151 (346)
T ss_pred             ecccc
Confidence            97653

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.09  E-value=3.8e-10  Score=108.23  Aligned_cols=78  Identities=18%  Similarity=0.279  Sum_probs=62.5

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcC------------CCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcC
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQF------------GEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD   92 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~f------------G~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~   92 (258)
                      +..+...++|||+||+.++|+++|+++|.++            +.|..+.+      .+.+|||||+|.+.++|++||+.
T Consensus       169 ~~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~l  242 (509)
T TIGR01642       169 QQATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMAL  242 (509)
T ss_pred             ccCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhcC
Confidence            3455677899999999999999999999975            23333333      45678999999999999999975


Q ss_pred             CCCccCCceEEEEecc
Q 025068           93 PTPFIDGRRANCNLAS  108 (258)
Q Consensus        93 ~~~~i~G~~i~V~~a~  108 (258)
                      ++..|.|+.|+|....
T Consensus       243 ~g~~~~g~~l~v~r~~  258 (509)
T TIGR01642       243 DSIIYSNVFLKIRRPH  258 (509)
T ss_pred             CCeEeeCceeEecCcc
Confidence            5567999999997553

Members of this subfamily are found in plants, metazoa and fungi.

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.08  E-value=4.1e-10  Score=94.15  Aligned_cols=87  Identities=24%  Similarity=0.382  Sum_probs=76.2

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcC-CCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCc-cCCce
Q 025068           24 SPFGDTTYTKVFVGGLAWETQSETMRRYFEQF-GEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRR  101 (258)
Q Consensus        24 ~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~f-G~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~-i~G~~  101 (258)
                      ...+......++|..|+.-+.+.+|..+|.+| |.|+++++-+++.||.|||||||+|++.|.|+-|-+.||.. +.++.
T Consensus        42 ~~p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~l  121 (214)
T KOG4208|consen   42 EKPEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHL  121 (214)
T ss_pred             cCCccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhhe
Confidence            34455667789999999999999999999998 78888888899999999999999999999999999998754 88999


Q ss_pred             EEEEeccCC
Q 025068          102 ANCNLASLG  110 (258)
Q Consensus       102 i~V~~a~~~  110 (258)
                      |.|..-.+.
T Consensus       122 L~c~vmppe  130 (214)
T KOG4208|consen  122 LECHVMPPE  130 (214)
T ss_pred             eeeEEeCch
Confidence            999887544

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.03  E-value=9.2e-10  Score=93.26  Aligned_cols=81  Identities=26%  Similarity=0.447  Sum_probs=71.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHH----HHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCc-cCCceEE
Q 025068           29 TTYTKVFVGGLAWETQSETMRR----YFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRRAN  103 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~----~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~-i~G~~i~  103 (258)
                      ..+.+|||.||++.+..++|++    +|+.||+|.+|...+   |.+.||-|||.|++.+.|..|+..++.. +-||.++
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mr   83 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMR   83 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhh
Confidence            3455999999999999999998    999999999987755   5889999999999999999999997755 8999999


Q ss_pred             EEeccCCCC
Q 025068          104 CNLASLGRP  112 (258)
Q Consensus       104 V~~a~~~~~  112 (258)
                      |.+|..+..
T Consensus        84 iqyA~s~sd   92 (221)
T KOG4206|consen   84 IQYAKSDSD   92 (221)
T ss_pred             eecccCccc
Confidence            999976643

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.02  E-value=5.2e-10  Score=108.40  Aligned_cols=78  Identities=21%  Similarity=0.404  Sum_probs=70.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccC
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASL  109 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~  109 (258)
                      +++||||.|+.+++|.+|+.+|+.||+|.+|.++..      ++||||+....++|.+|+.++. ..|..+.|+|.||..
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            579999999999999999999999999999998765      5699999999999999999965 669999999999987


Q ss_pred             CCCCC
Q 025068          110 GRPRP  114 (258)
Q Consensus       110 ~~~~~  114 (258)
                      +-.+.
T Consensus       495 ~G~ks  499 (894)
T KOG0132|consen  495 KGPKS  499 (894)
T ss_pred             CCcch
Confidence            66554

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=98.99  E-value=5.8e-10  Score=100.21  Aligned_cols=82  Identities=18%  Similarity=0.385  Sum_probs=75.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCC-ccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP-FIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~-~i~G~~i~V~~  106 (258)
                      ....++|||..+..+.+|+||+.+|+.||+|+.|++-++..++.+|||+|++|.+......||..+|- .++|.-|+|-.
T Consensus       207 Ak~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk  286 (544)
T KOG0124|consen  207 AKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGK  286 (544)
T ss_pred             HHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccc
Confidence            35678999999999999999999999999999999999998899999999999999999999999984 59999999987


Q ss_pred             ccC
Q 025068          107 ASL  109 (258)
Q Consensus       107 a~~  109 (258)
                      +..
T Consensus       287 ~vT  289 (544)
T KOG0124|consen  287 CVT  289 (544)
T ss_pred             ccC
Confidence            753

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.97  E-value=4.5e-10  Score=96.56  Aligned_cols=85  Identities=33%  Similarity=0.549  Sum_probs=76.7

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEE
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRAN  103 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~  103 (258)
                      .+.++++.+||+|.|..+++++.|-..|.+|-.-...+|++|+.|+++|||+||.|.+..++.+|+.+++ +.|+.+.|+
T Consensus       184 ~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpik  263 (290)
T KOG0226|consen  184 AEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIK  263 (290)
T ss_pred             ccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhH
Confidence            3456778899999999999999999999999988899999999999999999999999999999999976 669999998


Q ss_pred             EEeccC
Q 025068          104 CNLASL  109 (258)
Q Consensus       104 V~~a~~  109 (258)
                      +....-
T Consensus       264 lRkS~w  269 (290)
T KOG0226|consen  264 LRKSEW  269 (290)
T ss_pred             hhhhhH
Confidence            876543

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.95  E-value=7.3e-10  Score=102.45  Aligned_cols=88  Identities=32%  Similarity=0.541  Sum_probs=78.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      ......+|||.||+..++++.|+++|+.+|+|++++|+.+. .++++||+||+|++.++|.+|+..++ ..+.++.|.|.
T Consensus       266 ~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~~-~g~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~va  344 (369)
T KOG0123|consen  266 VSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVDE-NGKSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVA  344 (369)
T ss_pred             ccccccccccccCccccchhHHHHHHhcccceeeEEEEecc-CCCccceEEEEcCCHHHHHHHHHhhChhhhcCCchhhh
Confidence            35567799999999999999999999999999999999997 59999999999999999999999966 66999999999


Q ss_pred             eccCCCCCCC
Q 025068          106 LASLGRPRPQ  115 (258)
Q Consensus       106 ~a~~~~~~~~  115 (258)
                      ++..+..++.
T Consensus       345 v~qr~~~r~~  354 (369)
T KOG0123|consen  345 VAQRKEDRRA  354 (369)
T ss_pred             HHhhhccchh
Confidence            9975554443

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=98.91  E-value=3.2e-09  Score=97.36  Aligned_cols=81  Identities=28%  Similarity=0.450  Sum_probs=71.1

Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCc
Q 025068           22 LNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGR  100 (258)
Q Consensus        22 ~~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~  100 (258)
                      ..+.-...+.|+|||.|||.+.|+..|++-|..||.|+.++|+.   +|++||  .|.|.++++|++||..++ ..|+|+
T Consensus       527 g~a~gaarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr  601 (608)
T KOG4212|consen  527 GNAVGAARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGR  601 (608)
T ss_pred             cccccccccccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCc
Confidence            34445567889999999999999999999999999999999865   488887  899999999999999977 569999


Q ss_pred             eEEEEec
Q 025068          101 RANCNLA  107 (258)
Q Consensus       101 ~i~V~~a  107 (258)
                      .|+|.+.
T Consensus       602 ~I~V~y~  608 (608)
T KOG4212|consen  602 NIKVTYF  608 (608)
T ss_pred             eeeeeeC
Confidence            9999863

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.87  E-value=5.8e-09  Score=100.48  Aligned_cols=81  Identities=30%  Similarity=0.538  Sum_probs=70.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCC---CcccEEEEEEcCHHHHHHHhcCCC-CccCCceEE
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTG---RSKGYGFVTFREPEAARRACADPT-PFIDGRRAN  103 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg---~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~  103 (258)
                      ..+.++|||.||+++++.++|+.+|.+.|.|.++.|.+.++..   .|.|||||+|.+.++|++|++.++ +.|+|+.|.
T Consensus       512 ~~~~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~  591 (725)
T KOG0110|consen  512 EETETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLE  591 (725)
T ss_pred             cccchhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEE
Confidence            3444559999999999999999999999999999888776422   255999999999999999999987 679999999


Q ss_pred             EEecc
Q 025068          104 CNLAS  108 (258)
Q Consensus       104 V~~a~  108 (258)
                      |+++.
T Consensus       592 lk~S~  596 (725)
T KOG0110|consen  592 LKISE  596 (725)
T ss_pred             EEecc
Confidence            99996

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.85  E-value=2e-09  Score=103.59  Aligned_cols=84  Identities=25%  Similarity=0.449  Sum_probs=75.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCc-cCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~-i~G~~i~V~~  106 (258)
                      +...++|+|.|||+..+..+++++|..||.|.+|+|.+....+.++|||||+|-+.++|.+|+..+..+ +-||+|.++|
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            334779999999999999999999999999999999888666778999999999999999999997644 9999999999


Q ss_pred             ccCCC
Q 025068          107 ASLGR  111 (258)
Q Consensus       107 a~~~~  111 (258)
                      |....
T Consensus       690 A~~d~  694 (725)
T KOG0110|consen  690 AKSDN  694 (725)
T ss_pred             hccch
Confidence            96543

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.84  E-value=1e-08  Score=89.13  Aligned_cols=84  Identities=30%  Similarity=0.429  Sum_probs=75.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      .+...++|.|.||+..|++++|+++|+.||.++.+.|-.|+ .|++.|.|-|.|+..++|.+||+..+ ..++|+.|+++
T Consensus        79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~  157 (243)
T KOG0533|consen   79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIE  157 (243)
T ss_pred             cCCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeE
Confidence            45566899999999999999999999999999999999998 59999999999999999999999965 44999999999


Q ss_pred             eccCCC
Q 025068          106 LASLGR  111 (258)
Q Consensus       106 ~a~~~~  111 (258)
                      +.....
T Consensus       158 ~i~~~~  163 (243)
T KOG0533|consen  158 IISSPS  163 (243)
T ss_pred             EecCcc
Confidence            876443

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.78  E-value=2e-08  Score=87.12  Aligned_cols=85  Identities=24%  Similarity=0.308  Sum_probs=77.6

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEE
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCN  105 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~  105 (258)
                      ..+.+.+.+||+|++..++.++++..|+.||.|..+.|..|+.++.+|||+||+|.+.+.+++++..+...|.++.|+|.
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVT  175 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceee
Confidence            34678899999999999999999999999999999999999999999999999999999999999955577999999999


Q ss_pred             eccCC
Q 025068          106 LASLG  110 (258)
Q Consensus       106 ~a~~~  110 (258)
                      +....
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            87544

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.67  E-value=2.9e-07  Score=78.15  Aligned_cols=86  Identities=22%  Similarity=0.283  Sum_probs=67.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEe-ecCCCCCcccEEEEEEcCHHHHHHHhcCCCCc-cC---CceE
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVI-TDKNTGRSKGYGFVTFREPEAARRACADPTPF-ID---GRRA  102 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~-~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~-i~---G~~i  102 (258)
                      ....++|||.+||.|+...||..+|..|---+.+.|. +++.....+-+|||+|.+..+|.+|+..+|.+ |+   +..|
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            3458999999999999999999999998766655443 33332345679999999999999999997744 54   7889


Q ss_pred             EEEeccCCCCC
Q 025068          103 NCNLASLGRPR  113 (258)
Q Consensus       103 ~V~~a~~~~~~  113 (258)
                      +|++|+...++
T Consensus       111 hiElAKSNtK~  121 (284)
T KOG1457|consen  111 HIELAKSNTKR  121 (284)
T ss_pred             EeeehhcCccc
Confidence            99999755433

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.64  E-value=1.6e-07  Score=87.46  Aligned_cols=82  Identities=21%  Similarity=0.327  Sum_probs=69.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEe
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNL  106 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~  106 (258)
                      +..+...|-+.+|||++|++||.++|+.++ |+++++.++  +|+..|-|||+|.++|++++|++++...+..|-|.|-.
T Consensus         6 e~~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~   82 (510)
T KOG4211|consen    6 EGSTAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR--NGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFT   82 (510)
T ss_pred             CCCcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEecc--CCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEc
Confidence            344566788899999999999999999984 677666554  79999999999999999999999987778999999988


Q ss_pred             ccCCC
Q 025068          107 ASLGR  111 (258)
Q Consensus       107 a~~~~  111 (258)
                      +..++
T Consensus        83 ~~~~e   87 (510)
T KOG4211|consen   83 AGGAE   87 (510)
T ss_pred             cCCcc
Confidence            75444

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.63  E-value=1.2e-07  Score=84.92  Aligned_cols=80  Identities=19%  Similarity=0.311  Sum_probs=72.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEE--------EEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccC
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEIL--------EAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFID   98 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~--------~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~   98 (258)
                      ...+++|||.|||.++|.+++.++|+++|.|.        .|+|-++.. |+.||=|+++|...++++-||..++ ..|.
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCccccc
Confidence            45667899999999999999999999999886        478888875 9999999999999999999999976 5699


Q ss_pred             CceEEEEecc
Q 025068           99 GRRANCNLAS  108 (258)
Q Consensus        99 G~~i~V~~a~  108 (258)
                      |+.|+|+.|+
T Consensus       210 g~~~rVerAk  219 (382)
T KOG1548|consen  210 GKKLRVERAK  219 (382)
T ss_pred             CcEEEEehhh
Confidence            9999999885

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.59  E-value=1.8e-06  Score=77.61  Aligned_cols=74  Identities=19%  Similarity=0.401  Sum_probs=62.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCC--CEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEE
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFG--EILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANC  104 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG--~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V  104 (258)
                      .-.+|||||-|.+|+++|.+.+..-|  .|.++|+..++.+|++||||+|...+...+++.++.+. ++|.|..-.|
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            34689999999999999999887766  56788888999999999999999999999999988876 5688765433

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.56  E-value=2.3e-08  Score=84.55  Aligned_cols=77  Identities=13%  Similarity=0.192  Sum_probs=68.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      ..++|||+||...++|+.|.++|..-|.|.+|.|..+++ ++.| ||||.|+++..+.-|++.++ ..+.+..|.|.+-.
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            467899999999999999999999999999999988875 7777 99999999999999999977 44888888777654

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.49  E-value=3.6e-07  Score=82.27  Aligned_cols=89  Identities=26%  Similarity=0.274  Sum_probs=77.8

Q ss_pred             CCCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEE--------EEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC
Q 025068           23 NSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEIL--------EAVVITDKNTGRSKGYGFVTFREPEAARRACADPT   94 (258)
Q Consensus        23 ~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~--------~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~   94 (258)
                      .+..+.....+|||.+|+..+++++|.++|.+++.|.        .|+|-+|+.|++.||-|.|+|+|...|+.||+-..
T Consensus        58 ~~~~~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~a  137 (351)
T KOG1995|consen   58 SSMADKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFA  137 (351)
T ss_pred             CccccccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhc
Confidence            3444566778999999999999999999999999886        46788899999999999999999999999999854


Q ss_pred             -CccCCceEEEEeccCCC
Q 025068           95 -PFIDGRRANCNLASLGR  111 (258)
Q Consensus        95 -~~i~G~~i~V~~a~~~~  111 (258)
                       +.+.+..|+|.+|..+.
T Consensus       138 gkdf~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  138 GKDFCGNTIKVSLAERRT  155 (351)
T ss_pred             cccccCCCchhhhhhhcc
Confidence             77999999999996544

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.48  E-value=8.7e-08  Score=90.36  Aligned_cols=71  Identities=30%  Similarity=0.377  Sum_probs=63.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEE
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRAN  103 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~  103 (258)
                      +...++|+|-|||..|++++|+++|+.||+|++|+.     |-..+|..||+|-|..+|++|+++++ .+|.|++|+
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            567789999999999999999999999999999654     45567899999999999999999977 669999988

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.45  E-value=1.7e-07  Score=80.01  Aligned_cols=70  Identities=29%  Similarity=0.572  Sum_probs=62.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccC
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASL  109 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~  109 (258)
                      .+|||++|++.+.+++|+++|.+||.|.+|.+.        .||+||+|.+..+|..||..++ ++|.+.++.|+++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            479999999999999999999999999998763        3589999999999999999966 668888888888853

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=98.30  E-value=2e-07  Score=87.84  Aligned_cols=87  Identities=23%  Similarity=0.350  Sum_probs=78.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEe
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNL  106 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~  106 (258)
                      ++.+.++||+--|...+++.+|.++|+.+|.|.+|.||.|+.++++||.++|+|.|.+.+..||...+..+.|..|.|..
T Consensus       175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~  254 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQL  254 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEecc
Confidence            44566789999999999999999999999999999999999999999999999999999999998888889999999998


Q ss_pred             ccCCCCC
Q 025068          107 ASLGRPR  113 (258)
Q Consensus       107 a~~~~~~  113 (258)
                      ....+.+
T Consensus       255 sEaeknr  261 (549)
T KOG0147|consen  255 SEAEKNR  261 (549)
T ss_pred             cHHHHHH
Confidence            7655444

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.27  E-value=6.3e-06  Score=62.03  Aligned_cols=77  Identities=19%  Similarity=0.220  Sum_probs=63.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhc--CCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCc---c-CCceEEE
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQ--FGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPF---I-DGRRANC  104 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~--fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~---i-~G~~i~V  104 (258)
                      ++|-|+|||...|.++|.+++..  .|....+-+.-|..+..+.|||||.|.+.+.|.+-.+.. +..   + ..|.+.|
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            68999999999999999999965  466677888889888999999999999999999988773 332   2 3667788


Q ss_pred             Eecc
Q 025068          105 NLAS  108 (258)
Q Consensus       105 ~~a~  108 (258)
                      .+|.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            8874

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.25  E-value=1.3e-06  Score=82.84  Aligned_cols=85  Identities=24%  Similarity=0.482  Sum_probs=77.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCc-cCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~-i~G~~i~V~~  106 (258)
                      -...+++||++|+..+++++++++++.||.+....++.|..+|.+|||||.+|.+......||+.++.+ +.++.|.|..
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            345679999999999999999999999999999999999999999999999999999999999998755 8889999998


Q ss_pred             ccCCCC
Q 025068          107 ASLGRP  112 (258)
Q Consensus       107 a~~~~~  112 (258)
                      |.....
T Consensus       366 A~~g~~  371 (500)
T KOG0120|consen  366 AIVGAS  371 (500)
T ss_pred             hhccch
Confidence            875543

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.21  E-value=3.6e-06  Score=81.57  Aligned_cols=82  Identities=22%  Similarity=0.370  Sum_probs=71.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCC---CCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKN---TGRSKGYGFVTFREPEAARRACADPT-PFIDGRRA  102 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~---tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i  102 (258)
                      +|...++|||+||+..++|+.|-..|..||.|..++|+..+.   ..+.+-++||.|-+..+|++|++.++ ..|.+..+
T Consensus       170 gDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~  249 (877)
T KOG0151|consen  170 GDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEM  249 (877)
T ss_pred             CCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeee
Confidence            356788999999999999999999999999999999998762   23455799999999999999999976 56899999


Q ss_pred             EEEecc
Q 025068          103 NCNLAS  108 (258)
Q Consensus       103 ~V~~a~  108 (258)
                      ++.|++
T Consensus       250 K~gWgk  255 (877)
T KOG0151|consen  250 KLGWGK  255 (877)
T ss_pred             eecccc
Confidence            999883

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.20  E-value=3.7e-06  Score=78.57  Aligned_cols=80  Identities=23%  Similarity=0.297  Sum_probs=66.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEE-EEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILE-AVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~-v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      .....|-+.+||+.++|+||.+||+..-.+.. +.++.++ .+++.|-|||.|++.|.|++||..+...|.-|-|.|-.+
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRS  179 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHHHHHhhccceEEeehh
Confidence            45678999999999999999999998765555 4556665 478999999999999999999999777788888888766


Q ss_pred             cC
Q 025068          108 SL  109 (258)
Q Consensus       108 ~~  109 (258)
                      ..
T Consensus       180 s~  181 (510)
T KOG4211|consen  180 SR  181 (510)
T ss_pred             HH
Confidence            53

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.06  E-value=5.4e-06  Score=74.25  Aligned_cols=78  Identities=28%  Similarity=0.460  Sum_probs=70.1

Q ss_pred             CcEEE-EcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEecc
Q 025068           31 YTKVF-VGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLAS  108 (258)
Q Consensus        31 ~~~lf-VgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~  108 (258)
                      ..++| |++|+.++++++|+..|..+|.|..+++..++.++..+||++|+|.+.+...+++......+.++.+.+....
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  262 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALNDQTRSIGGRPLRLEEDE  262 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhcccCcccCcccccccCC
Confidence            34455 9999999999999999999999999999999999999999999999999999999873466999999998874

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.00  E-value=5e-05  Score=69.75  Aligned_cols=76  Identities=13%  Similarity=0.261  Sum_probs=67.1

Q ss_pred             CcEEEEcCCCCC-CcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           31 YTKVFVGGLAWE-TQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        31 ~~~lfVgnLp~~-~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      ++.|.|.||..+ +|.+.|..+|.-||+|.+|+|+.++.     --|+|.+.|...|+-|++.++ +.+.||+|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            688999999665 99999999999999999999999863     479999999999999999976 67999999999986


Q ss_pred             CCC
Q 025068          109 LGR  111 (258)
Q Consensus       109 ~~~  111 (258)
                      -..
T Consensus       372 H~~  374 (492)
T KOG1190|consen  372 HTN  374 (492)
T ss_pred             Ccc
Confidence            443

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=97.89  E-value=1.4e-05  Score=68.33  Aligned_cols=78  Identities=23%  Similarity=0.315  Sum_probs=65.5

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceE
Q 025068           24 SPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRA  102 (258)
Q Consensus        24 ~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i  102 (258)
                      -.....+.+.|+|.+|..++.+.+|++.|+.+|.++...+        .++++||+|++.+++.+||+.++ ..+.++.|
T Consensus        92 ~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l  163 (216)
T KOG0106|consen   92 YRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRI  163 (216)
T ss_pred             cCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCcee
Confidence            3345678899999999999999999999999999955443        34589999999999999999976 66999999


Q ss_pred             EEEeccC
Q 025068          103 NCNLASL  109 (258)
Q Consensus       103 ~V~~a~~  109 (258)
                      .|.....
T Consensus       164 ~~~~~~~  170 (216)
T KOG0106|consen  164 SVEKNSR  170 (216)
T ss_pred             eecccCc
Confidence            9965543

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.89  E-value=1.8e-05  Score=60.59  Aligned_cols=69  Identities=28%  Similarity=0.419  Sum_probs=43.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC------CccCCceEEEE
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT------PFIDGRRANCN  105 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~------~~i~G~~i~V~  105 (258)
                      +.|.|.++...++.++|+++|+.||.|..|++.+...      .|+|.|.+.+.|++|++.+.      ..|.+..+.++
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~------~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT------EGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S------EEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC------EEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            4688999999999999999999999999998866533      79999999999999997532      23667766665


Q ss_pred             e
Q 025068          106 L  106 (258)
Q Consensus       106 ~  106 (258)
                      .
T Consensus        76 v   76 (105)
T PF08777_consen   76 V   76 (105)
T ss_dssp             -
T ss_pred             E
Confidence            4

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>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=97.81  E-value=7.3e-05  Score=54.41  Aligned_cols=67  Identities=19%  Similarity=0.339  Sum_probs=46.0

Q ss_pred             cEEEEcCCCCCCcHHH----HHHHHhcCC-CEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCc-cCCceEEEE
Q 025068           32 TKVFVGGLAWETQSET----MRRYFEQFG-EILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRRANCN  105 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~----L~~~F~~fG-~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~-i~G~~i~V~  105 (258)
                      ..|+|.|||.+.+...    |+.++..+| .|.+|          +.+-|+|.|.+.|.|.+|.+.++.+ +.|++|.|+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v----------~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV----------SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE----------eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            4699999999988776    555666665 55554          1357999999999999999997655 999999999


Q ss_pred             ecc
Q 025068          106 LAS  108 (258)
Q Consensus       106 ~a~  108 (258)
                      +..
T Consensus        73 ~~~   75 (90)
T PF11608_consen   73 FSP   75 (90)
T ss_dssp             SS-
T ss_pred             EcC
Confidence            874

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=97.77  E-value=2.1e-05  Score=66.99  Aligned_cols=63  Identities=14%  Similarity=0.264  Sum_probs=50.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT   94 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~   94 (258)
                      .....+|||.||..+++||+|+.+|+.|--...++|.. + .|  -+.+||+|++.+.|..|+..+.
T Consensus       207 ~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~-~-~g--~~vaf~~~~~~~~at~am~~lq  269 (284)
T KOG1457|consen  207 ARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA-R-GG--MPVAFADFEEIEQATDAMNHLQ  269 (284)
T ss_pred             chhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec-C-CC--cceEeecHHHHHHHHHHHHHhh
Confidence            34456899999999999999999999998766666532 2 23  3589999999999999998754

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.76  E-value=0.00012  Score=71.31  Aligned_cols=79  Identities=19%  Similarity=0.305  Sum_probs=64.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....+.|-|.|+|++++-+||.+||..|-.+-.-.+++-.+.|+..|-|.|.|++.++|.+|...++ +.|..++|+|.+
T Consensus       864 ~pGp~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  864 SPGPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CCCCeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            3445689999999999999999999999766543333433459999999999999999999999976 559999988865

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.68  E-value=0.00014  Score=48.63  Aligned_cols=52  Identities=21%  Similarity=0.390  Sum_probs=41.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHh
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC   90 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai   90 (258)
                      +.|-|.+.+.+..+ ++.+.|..||+|+++.+..+      +-+.+|+|.++.+|++||
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            46778888877654 45668999999999887522      338999999999999986

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.67  E-value=0.00015  Score=68.36  Aligned_cols=65  Identities=28%  Similarity=0.490  Sum_probs=50.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCC---CCCccc---EEEEEEcCHHHHHHHhcCC
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKN---TGRSKG---YGFVTFREPEAARRACADP   93 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~---tg~skG---~aFV~F~~~~~A~~Ai~~~   93 (258)
                      ..-.++||||+||++++|++|...|..||.+. |++.....   --..||   |+|+.|+++..+.+.|.+.
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            34568999999999999999999999999865 44442111   123567   9999999999888877664

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=97.66  E-value=7e-05  Score=68.80  Aligned_cols=75  Identities=19%  Similarity=0.336  Sum_probs=62.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-C--CccCCceEEE
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-T--PFIDGRRANC  104 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~--~~i~G~~i~V  104 (258)
                      .+.++.|.++|||++++|+||.+++..||+|+.+.+++.++      -||++|.|++.|..-+..- .  ..+.++.|.|
T Consensus        25 ~~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGkn------QAflem~d~~sAvtmv~~y~~~~p~lr~~~~yi   98 (492)
T KOG1190|consen   25 AEPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKN------QAFLEMADEESAVTMVNYYTSVTPVLRGQPIYI   98 (492)
T ss_pred             cCCcceeEeccCCccccHHHHHHhcccccceeeeeeeccch------hhhhhhcchhhhhheeecccccCccccCcceee
Confidence            34678999999999999999999999999999998877653      7999999999887755442 2  3478899998


Q ss_pred             Eecc
Q 025068          105 NLAS  108 (258)
Q Consensus       105 ~~a~  108 (258)
                      .++.
T Consensus        99 q~sn  102 (492)
T KOG1190|consen   99 QYSN  102 (492)
T ss_pred             hhhh
Confidence            8764

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.60  E-value=0.0002  Score=67.61  Aligned_cols=64  Identities=33%  Similarity=0.416  Sum_probs=59.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHh-cCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcC
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFE-QFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD   92 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~-~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~   92 (258)
                      +..++||||+||.-++.++|-.+|+ -||.|+-+-|-+|.+-+-.||-|-|+|++..+-.+||+.
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            4567999999999999999999999 699999999999977788999999999999999999987

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.60  E-value=0.00013  Score=65.62  Aligned_cols=80  Identities=25%  Similarity=0.392  Sum_probs=61.0

Q ss_pred             CcEEEEcCCCCCCcHHH------HHHHHhcCCCEEEEEEeecCCCCCc-ccEE--EEEEcCHHHHHHHhcCC-CCccCCc
Q 025068           31 YTKVFVGGLAWETQSET------MRRYFEQFGEILEAVVITDKNTGRS-KGYG--FVTFREPEAARRACADP-TPFIDGR  100 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~------L~~~F~~fG~I~~v~v~~d~~tg~s-kG~a--FV~F~~~~~A~~Ai~~~-~~~i~G~  100 (258)
                      -.-+||-+|+..+..|+      -.++|.+||.|..|.|-+....-.+ .+.+  +|+|.+.|+|.+||.+. +..++||
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            45689999999877776      3688999999999877554311111 2223  99999999999999995 4679999


Q ss_pred             eEEEEeccCC
Q 025068          101 RANCNLASLG  110 (258)
Q Consensus       101 ~i~V~~a~~~  110 (258)
                      .|++.+...+
T Consensus       194 ~lkatYGTTK  203 (480)
T COG5175         194 VLKATYGTTK  203 (480)
T ss_pred             eEeeecCchH
Confidence            9999887654

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.54  E-value=0.00012  Score=67.61  Aligned_cols=72  Identities=21%  Similarity=0.270  Sum_probs=59.4

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeec---CCC--CC--------cccEEEEEEcCHHHHHHHhc
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITD---KNT--GR--------SKGYGFVTFREPEAARRACA   91 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d---~~t--g~--------skG~aFV~F~~~~~A~~Ai~   91 (258)
                      ..++...++|.+-|||.+-.-+.|.++|+.+|.|+.|+|...   ...  +.        .+-+|||+|++.+.|.+|.+
T Consensus       225 ~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e  304 (484)
T KOG1855|consen  225 DEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARE  304 (484)
T ss_pred             cccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHH
Confidence            344568899999999999999999999999999999998776   221  11        25689999999999999999


Q ss_pred             CCCCc
Q 025068           92 DPTPF   96 (258)
Q Consensus        92 ~~~~~   96 (258)
                      .++.+
T Consensus       305 ~~~~e  309 (484)
T KOG1855|consen  305 LLNPE  309 (484)
T ss_pred             hhchh
Confidence            87643

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.45  E-value=0.00064  Score=51.48  Aligned_cols=78  Identities=24%  Similarity=0.304  Sum_probs=51.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEE-EeecC------CCCCcccEEEEEEcCHHHHHHHhcCCCCccCCce
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAV-VITDK------NTGRSKGYGFVTFREPEAARRACADPTPFIDGRR  101 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~-v~~d~------~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~  101 (258)
                      ...+-|.|=+.|.+ ..+.|.+.|++||+|.+.. +.++.      ..-....+-.|+|+++.+|.+||.+++..|.|..
T Consensus         4 ~~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~   82 (100)
T PF05172_consen    4 DSETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSL   82 (100)
T ss_dssp             GGCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCE
T ss_pred             cCCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcE
Confidence            34566888899988 4567788899999998774 11110      0011234889999999999999999998888764


Q ss_pred             E-EEEec
Q 025068          102 A-NCNLA  107 (258)
Q Consensus       102 i-~V~~a  107 (258)
                      + -|.+.
T Consensus        83 mvGV~~~   89 (100)
T PF05172_consen   83 MVGVKPC   89 (100)
T ss_dssp             EEEEEE-
T ss_pred             EEEEEEc
Confidence            4 46665

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.

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=97.34  E-value=0.00087  Score=57.25  Aligned_cols=74  Identities=24%  Similarity=0.301  Sum_probs=60.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccC-CceEEEEe
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFID-GRRANCNL  106 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~-G~~i~V~~  106 (258)
                      .....||+-|||.+++.+.|..+|+.|.--++++++..+     ++.|||+|.+...+..|...+. ..|- ...+.|..
T Consensus       144 ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~  218 (221)
T KOG4206|consen  144 PPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITF  218 (221)
T ss_pred             CCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEecc
Confidence            456789999999999999999999999999999887754     5799999999998888888754 2233 66666666


Q ss_pred             c
Q 025068          107 A  107 (258)
Q Consensus       107 a  107 (258)
                      +
T Consensus       219 a  219 (221)
T KOG4206|consen  219 A  219 (221)
T ss_pred             c
Confidence            5

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=97.33  E-value=0.002  Score=58.91  Aligned_cols=82  Identities=20%  Similarity=0.258  Sum_probs=69.8

Q ss_pred             CCCCCCCCCCcEEEEcCCCCC-CcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCC
Q 025068           22 LNSPFGDTTYTKVFVGGLAWE-TQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDG   99 (258)
Q Consensus        22 ~~~p~~~~~~~~lfVgnLp~~-~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G   99 (258)
                      ...|......+.+.|-+|+.. +.-+.|-.+|..||.|++|++++.+     .|-|.|+..|..++++||..++ ..+-|
T Consensus       278 ~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG  352 (494)
T KOG1456|consen  278 YASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFG  352 (494)
T ss_pred             CCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCcccc
Confidence            344456677889999999875 6778899999999999999999876     3679999999999999999976 55889


Q ss_pred             ceEEEEecc
Q 025068          100 RRANCNLAS  108 (258)
Q Consensus       100 ~~i~V~~a~  108 (258)
                      .+|.|..++
T Consensus       353 ~kl~v~~Sk  361 (494)
T KOG1456|consen  353 GKLNVCVSK  361 (494)
T ss_pred             ceEEEeecc
Confidence            999988874

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.14  E-value=0.0012  Score=62.96  Aligned_cols=78  Identities=22%  Similarity=0.296  Sum_probs=59.5

Q ss_pred             CCCcEEEEcCCCCCC------cHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccC-Cc
Q 025068           29 TTYTKVFVGGLAWET------QSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFID-GR  100 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~------te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~-G~  100 (258)
                      .-...|+|.|+|.--      -..-|.++|+++|+|..+.+.-+.. |..+||.|++|.+..+|+.|++.++ +.|+ .+
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 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNH  134 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhcccceecccc
Confidence            345678888887632      1234778899999999999988876 5599999999999999999999965 4444 56


Q ss_pred             eEEEEec
Q 025068          101 RANCNLA  107 (258)
Q Consensus       101 ~i~V~~a  107 (258)
                      ++.|..-
T Consensus       135 tf~v~~f  141 (698)
T KOG2314|consen  135 TFFVRLF  141 (698)
T ss_pred             eEEeehh
Confidence            6666543

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=97.09  E-value=0.003  Score=43.48  Aligned_cols=58  Identities=22%  Similarity=0.354  Sum_probs=47.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcC---CCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQF---GEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP   93 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~f---G~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~   93 (258)
                      +....+|+|.+++ +.+.++|+.+|..|   ....+|+++.|.       -|-|.|.+.+.|.+||..+
T Consensus         2 ~~rpeavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    2 TIRPEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             cceeceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            3456789999995 47778999999998   235688999886       5789999999999999763

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=97.06  E-value=0.0013  Score=60.13  Aligned_cols=79  Identities=23%  Similarity=0.326  Sum_probs=64.3

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCC-EEE--EEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCc-cCCceEEEEe
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGE-ILE--AVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRRANCNL  106 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~-I~~--v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~-i~G~~i~V~~  106 (258)
                      ...|-+.+||.+.+.|+|.++|..|.. |..  |.++.+. .|+..|-|||.|.+.|+|..|....++. .+.|-|+|--
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp  358 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFP  358 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEee
Confidence            446889999999999999999999874 333  6777775 4899999999999999999999887655 4588888877


Q ss_pred             ccCC
Q 025068          107 ASLG  110 (258)
Q Consensus       107 a~~~  110 (258)
                      +...
T Consensus       359 ~S~e  362 (508)
T KOG1365|consen  359 CSVE  362 (508)
T ss_pred             ccHH
Confidence            6543

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.01  E-value=0.00043  Score=68.79  Aligned_cols=78  Identities=15%  Similarity=0.243  Sum_probs=68.3

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccC
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASL  109 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~  109 (258)
                      -.+|||.|+++..|+++|+.+++++|.++++.++..+. |+.||.+||.|.++.++.+++.... ..+.-+.+.|..+.+
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~-gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRA-GKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhc-cccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            45799999999999999999999999999999888884 9999999999999999999998865 346667777777654

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=96.92  E-value=0.005  Score=56.34  Aligned_cols=86  Identities=20%  Similarity=0.247  Sum_probs=68.1

Q ss_pred             CCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcC--CC-Cc
Q 025068           20 QYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD--PT-PF   96 (258)
Q Consensus        20 ~~~~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~--~~-~~   96 (258)
                      +-..+|.....+-.|.|.+|-..++|.+|.+.++.||.|.-+.++-.+.      -+.|+|+|.+.|+.++..  .+ ..
T Consensus        20 e~~~dphk~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~r------~alvefedi~~akn~Vnfaa~n~i~   93 (494)
T KOG1456|consen   20 EDNADPHKPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHKR------QALVEFEDIEGAKNCVNFAADNQIY   93 (494)
T ss_pred             ccCCCCCCCCCCceEEEeccccccchhHHHHHHhcCCceEEEEeccccc------eeeeeeccccchhhheehhccCccc
Confidence            3344555555667899999999999999999999999999887665533      799999999999999875  33 34


Q ss_pred             cCCceEEEEeccCCC
Q 025068           97 IDGRRANCNLASLGR  111 (258)
Q Consensus        97 i~G~~i~V~~a~~~~  111 (258)
                      |.|....++++++++
T Consensus        94 i~gq~Al~NyStsq~  108 (494)
T KOG1456|consen   94 IAGQQALFNYSTSQC  108 (494)
T ss_pred             ccCchhhcccchhhh
Confidence            888888888775443

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=96.82  E-value=0.0013  Score=60.13  Aligned_cols=75  Identities=23%  Similarity=0.264  Sum_probs=56.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcC----CCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEE
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQF----GEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCN  105 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~f----G~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~  105 (258)
                      +.-.|-+.+||++.++.++.++|..-    +..+.|.+++.. .|+..|-|||.|..+++|+.||.++...|+.|-|++-
T Consensus       160 ~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElF  238 (508)
T KOG1365|consen  160 NQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELF  238 (508)
T ss_pred             cceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHH
Confidence            34456677999999999999999632    244566666655 4899999999999999999999886555655555443

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=96.72  E-value=0.00018  Score=71.35  Aligned_cols=71  Identities=28%  Similarity=0.392  Sum_probs=61.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGR  100 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~  100 (258)
                      +.+++||.||+..+.+++|+..|..++.|..+.|.-.+++++.||.|+|+|.+.+++.+||+.....+.||
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK  736 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGK  736 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhh
Confidence            44688999999999999999999999999988777556678999999999999999999999876554443

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.69  E-value=0.00099  Score=57.94  Aligned_cols=72  Identities=18%  Similarity=0.322  Sum_probs=58.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCC--------CCcc----cEEEEEEcCHHHHHHHhcCCC-Cc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNT--------GRSK----GYGFVTFREPEAARRACADPT-PF   96 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~t--------g~sk----G~aFV~F~~~~~A~~Ai~~~~-~~   96 (258)
                      ..-.||+++||+.++...|+++|+.||.|-+|.+-....+        +.++    --|.|+|.+...|.++.+.+| ..
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            5578999999999999999999999999999988766544        2222    236799999999999888866 45


Q ss_pred             cCCce
Q 025068           97 IDGRR  101 (258)
Q Consensus        97 i~G~~  101 (258)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            87764

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.61  E-value=0.00043  Score=69.10  Aligned_cols=80  Identities=19%  Similarity=0.308  Sum_probs=62.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      +...+++||++||+..+++.+|+..|..+|.|++|+|-+.+. +.---|+||.|.+.+.+-+|+.++. ..|..-.+++.
T Consensus       368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~g  446 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIG  446 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCcccchhhcCCccccCccccc
Confidence            345678999999999999999999999999999999877643 3334599999999999999988865 34444444444


Q ss_pred             ec
Q 025068          106 LA  107 (258)
Q Consensus       106 ~a  107 (258)
                      +.
T Consensus       447 lG  448 (975)
T KOG0112|consen  447 LG  448 (975)
T ss_pred             cc
Confidence            44

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=96.58  E-value=0.043  Score=45.87  Aligned_cols=78  Identities=21%  Similarity=0.254  Sum_probs=62.6

Q ss_pred             CCCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-Cc--cCC
Q 025068           23 NSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PF--IDG   99 (258)
Q Consensus        23 ~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~--i~G   99 (258)
                      ..+.......+|.|.+||.+-++.+|+++..+-|+|+..+|.+|       |.+.|+|...|+.+-||..+. ..  -.|
T Consensus       107 rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~seG  179 (241)
T KOG0105|consen  107 RGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFRSEG  179 (241)
T ss_pred             cCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhccccccCcC
Confidence            34555566778999999999999999999999999999999887       388999999999999998854 32  345


Q ss_pred             ceEEEEec
Q 025068          100 RRANCNLA  107 (258)
Q Consensus       100 ~~i~V~~a  107 (258)
                      ....+..-
T Consensus       180 e~~yirv~  187 (241)
T KOG0105|consen  180 ETAYIRVR  187 (241)
T ss_pred             cEeeEEec
Confidence            55555443

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.48  E-value=0.0082  Score=48.32  Aligned_cols=56  Identities=25%  Similarity=0.360  Sum_probs=45.1

Q ss_pred             HHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEeccCC
Q 025068           47 TMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLG  110 (258)
Q Consensus        47 ~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~~~  110 (258)
                      +|.+.|..||++.=++++.+        --.|+|.+-+.|.+|+...+..|+|+.|+|++.++.
T Consensus        52 ~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALSLDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHHGCCSEETTEEEEEEE----
T ss_pred             HHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHccCCcEECCEEEEEEeCCcc
Confidence            57777889999888887765        358999999999999999999999999999987644

; PDB: 1UFW_A 2DNR_A.

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=96.44  E-value=0.0079  Score=57.54  Aligned_cols=61  Identities=20%  Similarity=0.259  Sum_probs=47.9

Q ss_pred             HHHHHhcCCCEEEEEEeecCCCC---CcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           48 MRRYFEQFGEILEAVVITDKNTG---RSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        48 L~~~F~~fG~I~~v~v~~d~~tg---~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      ++.-+++||.|..|+|.++-...   -..|-.||+|.+.+++++|.+++. ..+.++.|.+++-.
T Consensus       426 vr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  426 VRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             HHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            44445689999999998872222   234678999999999999999976 56999999888763

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=96.41  E-value=0.0018  Score=60.03  Aligned_cols=77  Identities=17%  Similarity=0.293  Sum_probs=58.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC--CccCCceEEEEeccC
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT--PFIDGRRANCNLASL  109 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~--~~i~G~~i~V~~a~~  109 (258)
                      ++||++||...++.++|+.+|..--.-..-.++.      ..||+||...+...|.+||+.++  .++.|+++.|.....
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            4799999999999999999997641111111111      24799999999999999999976  348999999998876


Q ss_pred             CCCCC
Q 025068          110 GRPRP  114 (258)
Q Consensus       110 ~~~~~  114 (258)
                      ++.+.
T Consensus        76 kkqrs   80 (584)
T KOG2193|consen   76 KKQRS   80 (584)
T ss_pred             HHHHh
Confidence            65543

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=96.41  E-value=0.0092  Score=54.06  Aligned_cols=78  Identities=22%  Similarity=0.363  Sum_probs=59.5

Q ss_pred             CCCCCcEEEEcCCC----CCCc-------HHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-
Q 025068           27 GDTTYTKVFVGGLA----WETQ-------SETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-   94 (258)
Q Consensus        27 ~~~~~~~lfVgnLp----~~~t-------e~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-   94 (258)
                      -....++|.|.||=    .+.+       +++|++-.++||.|.+|.|--    ....|.+-|.|.+.++|..||+.|+ 
T Consensus       261 k~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d----~hPdGvvtV~f~n~eeA~~ciq~m~G  336 (382)
T KOG1548|consen  261 KARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYD----RHPDGVVTVSFRNNEEADQCIQTMDG  336 (382)
T ss_pred             cccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEec----cCCCceeEEEeCChHHHHHHHHHhcC
Confidence            34557889999872    1233       345667788999999987643    2357899999999999999999977 


Q ss_pred             CccCCceEEEEecc
Q 025068           95 PFIDGRRANCNLAS  108 (258)
Q Consensus        95 ~~i~G~~i~V~~a~  108 (258)
                      ..|+||.|.-++-.
T Consensus       337 R~fdgRql~A~i~D  350 (382)
T KOG1548|consen  337 RWFDGRQLTASIWD  350 (382)
T ss_pred             eeecceEEEEEEeC
Confidence            55999999877653

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.34  E-value=0.0013  Score=57.16  Aligned_cols=56  Identities=29%  Similarity=0.419  Sum_probs=46.5

Q ss_pred             cCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccCC
Q 025068           54 QFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASLG  110 (258)
Q Consensus        54 ~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~~  110 (258)
                      +||+|++++|-.+. .-..+|-++|.|...++|++|++.++ ..+.|++|.+++..-.
T Consensus        92 kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT  148 (260)
T KOG2202|consen   92 KYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVT  148 (260)
T ss_pred             Hhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcC
Confidence            89999999776654 24567889999999999999999966 6699999999887533

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.34  E-value=0.005  Score=60.27  Aligned_cols=85  Identities=19%  Similarity=0.104  Sum_probs=68.9

Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEE-EEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCC
Q 025068           22 LNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE-AVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDG   99 (258)
Q Consensus        22 ~~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~-v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G   99 (258)
                      +..++.......|||..||..+++.++.++|.+--.|++ |.|-+.+ +++.++.|||+|..++++.+|+.... +.++-
T Consensus       425 q~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~  503 (944)
T KOG4307|consen  425 QNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGH  503 (944)
T ss_pred             CCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCc
Confidence            446677777889999999999999999999999888887 5555554 68889999999999888888887755 44777


Q ss_pred             ceEEEEec
Q 025068          100 RRANCNLA  107 (258)
Q Consensus       100 ~~i~V~~a  107 (258)
                      +.|+|...
T Consensus       504 r~irv~si  511 (944)
T KOG4307|consen  504 RIIRVDSI  511 (944)
T ss_pred             eEEEeech
Confidence            77887644

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.28  E-value=0.015  Score=42.42  Aligned_cols=54  Identities=19%  Similarity=0.290  Sum_probs=40.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP   93 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~   93 (258)
                      .+..+|. .|.++...||.++|+.||.|. |.++.|.       -|||...+.+.|..++...
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~~~~~v~~~~   62 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRDQAKVVMNTL   62 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCHHHHHHHHHH
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHHHHHHHHHHh
Confidence            3455555 999999999999999999976 6677664       7999999999999887764

; 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.

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=96.18  E-value=0.0069  Score=55.68  Aligned_cols=77  Identities=13%  Similarity=0.132  Sum_probs=61.7

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCC---CCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNT---GRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~t---g~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      ...|-|.||...++.+++..+|.-.|+|.++.|.-+...   ....-.|||.|.|...+..|-...|.+|-++.|.|...
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~   86 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPY   86 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEec
Confidence            448999999999999999999999999999988664321   23445899999999999988877777766677666654

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=95.83  E-value=0.0068  Score=58.41  Aligned_cols=81  Identities=12%  Similarity=0.146  Sum_probs=63.8

Q ss_pred             CCCCCCCCCcEEEEcCCCCCCcHHHHHHHHh-cCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCc----c
Q 025068           23 NSPFGDTTYTKVFVGGLAWETQSETMRRYFE-QFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF----I   97 (258)
Q Consensus        23 ~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~-~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~----i   97 (258)
                      .+|......+.|+|.||-.-+|.-+|++++. ..|.|++. || |    +-|..|||.|.+.++|.+.+..++..    -
T Consensus       436 pSPsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-Wm-D----kIKShCyV~yss~eEA~atr~AlhnV~WP~s  509 (718)
T KOG2416|consen  436 PSPSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WM-D----KIKSHCYVSYSSVEEAAATREALHNVQWPPS  509 (718)
T ss_pred             CCCCCCCccceEeeecccccchHHHHHHHHhhccCchHHH-HH-H----HhhcceeEecccHHHHHHHHHHHhccccCCC
Confidence            4555667788999999999999999999998 46666666 32 2    23568999999999999999886632    5


Q ss_pred             CCceEEEEeccC
Q 025068           98 DGRRANCNLASL  109 (258)
Q Consensus        98 ~G~~i~V~~a~~  109 (258)
                      +.|.|.+.++..
T Consensus       510 NPK~L~adf~~~  521 (718)
T KOG2416|consen  510 NPKHLIADFVRA  521 (718)
T ss_pred             CCceeEeeecch
Confidence            678898888753

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=95.73  E-value=0.0086  Score=52.23  Aligned_cols=62  Identities=26%  Similarity=0.424  Sum_probs=54.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT   94 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~   94 (258)
                      ..|+|.||..-++.|.|++-|+.||.|+...++.|- .++..+-++|.|...-.+.+|+..+.
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 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHHHHHHhc
Confidence            689999999999999999999999999987777775 38888899999999999998888753

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=95.67  E-value=0.031  Score=49.79  Aligned_cols=63  Identities=17%  Similarity=0.304  Sum_probs=48.7

Q ss_pred             HHHHHHHHhcCCCEEEEEEeecCCCCCcc-cEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           45 SETMRRYFEQFGEILEAVVITDKNTGRSK-GYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        45 e~~L~~~F~~fG~I~~v~v~~d~~tg~sk-G~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ++++++.+++||.|..|.|..++..-... ---||+|+..++|.+|+..++ ..|+|+.+...+-
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFY  364 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheec
Confidence            45788889999999999887775433332 246999999999999999977 5699988765443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.46  E-value=0.06  Score=43.22  Aligned_cols=75  Identities=20%  Similarity=0.294  Sum_probs=56.2

Q ss_pred             CCCCCcEEEEcCCCCCCc-HHH---HHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceE
Q 025068           27 GDTTYTKVFVGGLAWETQ-SET---MRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRA  102 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~t-e~~---L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i  102 (258)
                      .+....+|.|.=|..++. .+|   +...++.||.|.+|.+     .|+  --|.|.|+|..+|-+|+.+.....-|..+
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~-----cGr--qsavVvF~d~~SAC~Av~Af~s~~pgtm~  154 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTL-----CGR--QSAVVVFKDITSACKAVSAFQSRAPGTMF  154 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeee-----cCC--ceEEEEehhhHHHHHHHHhhcCCCCCceE
Confidence            355667888876666543 233   4455678999999855     233  37999999999999999997777889999


Q ss_pred             EEEecc
Q 025068          103 NCNLAS  108 (258)
Q Consensus       103 ~V~~a~  108 (258)
                      .|+|-.
T Consensus       155 qCsWqq  160 (166)
T PF15023_consen  155 QCSWQQ  160 (166)
T ss_pred             Eeeccc
Confidence            999864

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=94.92  E-value=0.034  Score=53.38  Aligned_cols=73  Identities=12%  Similarity=0.194  Sum_probs=58.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhc--CCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC---CccCCceE
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQ--FGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT---PFIDGRRA  102 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~--fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~---~~i~G~~i  102 (258)
                      ..+.|.|.|..|+..+-+|+++.+|+.  +-.+.+|.+-.+.       -=||+|++..+|++|.+.+.   ++|-||.|
T Consensus       172 ~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpI  244 (684)
T KOG2591|consen  172 NHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPI  244 (684)
T ss_pred             CcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcch
Confidence            356788999999999999999999964  6778888776553       24899999999999988754   56889988


Q ss_pred             EEEec
Q 025068          103 NCNLA  107 (258)
Q Consensus       103 ~V~~a  107 (258)
                      ...+.
T Consensus       245 mARIK  249 (684)
T KOG2591|consen  245 MARIK  249 (684)
T ss_pred             hhhhh
Confidence            65543

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=94.62  E-value=0.025  Score=50.75  Aligned_cols=83  Identities=18%  Similarity=0.178  Sum_probs=70.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...+++|++++.+++.+.++..++.+.|.+..+.+........+++++.|.|...+.+..||.... ..+.++.+...+.
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            357899999999999999999999999988888877777778999999999999999999999865 4677777766666


Q ss_pred             cCCC
Q 025068          108 SLGR  111 (258)
Q Consensus       108 ~~~~  111 (258)
                      ....
T Consensus       166 ~~~~  169 (285)
T KOG4210|consen  166 TRRG  169 (285)
T ss_pred             cccc
Confidence            5443

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=94.61  E-value=0.021  Score=53.81  Aligned_cols=74  Identities=19%  Similarity=0.162  Sum_probs=57.5

Q ss_pred             CCcEEEEcCCCCC-CcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWE-TQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~-~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~  108 (258)
                      +.+.|-+.-.+.. -+-++|...|.+||+|..|.|-...      -.|.|+|.+..+|-+|-......|+++.|+|.|-.
T Consensus       371 dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~------~~a~vTF~t~aeag~a~~s~~avlnnr~iKl~whn  444 (526)
T KOG2135|consen  371 DHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSS------LHAVVTFKTRAEAGEAYASHGAVLNNRFIKLFWHN  444 (526)
T ss_pred             ccchhhhhccCCCCchHhhhhhhhhhcCccccccccCch------hhheeeeeccccccchhccccceecCceeEEEEec
Confidence            3444545444544 3567899999999999999885553      27899999999998777777778999999999986


Q ss_pred             C
Q 025068          109 L  109 (258)
Q Consensus       109 ~  109 (258)
                      .
T Consensus       445 p  445 (526)
T KOG2135|consen  445 P  445 (526)
T ss_pred             C
Confidence            5

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=94.56  E-value=0.044  Score=55.29  Aligned_cols=78  Identities=29%  Similarity=0.424  Sum_probs=63.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCc-cCC--ceEEE
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF-IDG--RRANC  104 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~-i~G--~~i~V  104 (258)
                      ....+.++|++|..++....|...|..||.|..|.+-.    |  .-|++|.+++.+.++.|+..+... |++  ++|.|
T Consensus       452 st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h----g--q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rv  525 (975)
T KOG0112|consen  452 STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH----G--QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRV  525 (975)
T ss_pred             cccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc----C--CcceeeecccCccchhhHHHHhcCcCCCCCccccc
Confidence            44567899999999999999999999999999987632    2  349999999999999999996533 553  77999


Q ss_pred             EeccCCC
Q 025068          105 NLASLGR  111 (258)
Q Consensus       105 ~~a~~~~  111 (258)
                      .++...-
T Consensus       526 dla~~~~  532 (975)
T KOG0112|consen  526 DLASPPG  532 (975)
T ss_pred             ccccCCC
Confidence            9986443

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=94.07  E-value=0.22  Score=44.61  Aligned_cols=74  Identities=18%  Similarity=0.200  Sum_probs=52.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceE-EEEeccC
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRA-NCNLASL  109 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i-~V~~a~~  109 (258)
                      +.=|-|-+++..- -..|..+|++||+|++..-.      ..-.+-.|.|.++.+|+|||..++.+|+|..+ -|+....
T Consensus       197 D~WVTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALskng~ii~g~vmiGVkpCtD  269 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALSKNGTIIDGDVMIGVKPCTD  269 (350)
T ss_pred             cceEEEeccCccc-hhHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhhhcCeeeccceEEeeeecCC
Confidence            3445555676653 35677889999999876433      22238899999999999999999888887654 5665544


Q ss_pred             CC
Q 025068          110 GR  111 (258)
Q Consensus       110 ~~  111 (258)
                      +.
T Consensus       270 ks  271 (350)
T KOG4285|consen  270 KS  271 (350)
T ss_pred             HH
Confidence            43

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=93.58  E-value=0.024  Score=51.25  Aligned_cols=81  Identities=27%  Similarity=0.403  Sum_probs=58.3

Q ss_pred             CCcEEEEcCCCCCCcHHHH---HHHHhcCCCEEEEEEeecCC--CCC-cccEEEEEEcCHHHHHHHhcCCC-CccCCceE
Q 025068           30 TYTKVFVGGLAWETQSETM---RRYFEQFGEILEAVVITDKN--TGR-SKGYGFVTFREPEAARRACADPT-PFIDGRRA  102 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L---~~~F~~fG~I~~v~v~~d~~--tg~-skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i  102 (258)
                      ..+.+||-+|+..+.++.+   .+.|.+||.|..|.+-++..  .+. .-.-++|+|+..|+|..||...+ ..++|+.|
T Consensus        76 qknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~l  155 (327)
T KOG2068|consen   76 QKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRAL  155 (327)
T ss_pred             hhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhh
Confidence            4456888889887655544   35778889999988777652  111 12347999999999999999965 45788887


Q ss_pred             EEEeccCC
Q 025068          103 NCNLASLG  110 (258)
Q Consensus       103 ~V~~a~~~  110 (258)
                      +..+...+
T Consensus       156 ka~~gttk  163 (327)
T KOG2068|consen  156 KASLGTTK  163 (327)
T ss_pred             HHhhCCCc
Confidence            77776544

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=93.46  E-value=0.24  Score=35.12  Aligned_cols=66  Identities=17%  Similarity=0.231  Sum_probs=37.9

Q ss_pred             EEEEc-CCCCCCcHHHHHHHHhcCCC-----EEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           33 KVFVG-GLAWETQSETMRRYFEQFGE-----ILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        33 ~lfVg-nLp~~~te~~L~~~F~~fG~-----I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      +|||. +--+.++..+|..++..-+.     |-+++|..+        |+||+-.. +.|+++++.++ ..+.|++|+|+
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve   72 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVE   72 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-T-T-HHHHHHHHTT--SSS----EE
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEE
Confidence            45554 33456888999999987654     456776544        88998865 46778888855 66999999998


Q ss_pred             ec
Q 025068          106 LA  107 (258)
Q Consensus       106 ~a  107 (258)
                      .|
T Consensus        73 ~A   74 (74)
T PF03880_consen   73 RA   74 (74)
T ss_dssp             E-
T ss_pred             EC
Confidence            75

; PDB: 2G0C_A 3MOJ_B.

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=93.06  E-value=0.31  Score=41.00  Aligned_cols=60  Identities=17%  Similarity=0.200  Sum_probs=43.4

Q ss_pred             cHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC--C-ccCCceEEEEeccC
Q 025068           44 QSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT--P-FIDGRRANCNLASL  109 (258)
Q Consensus        44 te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~--~-~i~G~~i~V~~a~~  109 (258)
                      ..+.|+++|..++.+....+++.-      +-..|.|.+.++|.+|...++  . .+.|+.|+|-++..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            457899999999999988777653      367899999999999999976  4 49999999988843

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.

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=92.92  E-value=0.11  Score=50.96  Aligned_cols=70  Identities=21%  Similarity=0.213  Sum_probs=59.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      .....+|||+||...+.++-++.++..+|.|..++.+.         |+|..|.+.....+|+..+. ..++++.+.++.
T Consensus        37 ~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   37 LPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             CCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            34566899999999999999999999999998876543         99999999999999998876 448888776655

>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=91.86  E-value=1.8  Score=33.30  Aligned_cols=62  Identities=18%  Similarity=0.186  Sum_probs=44.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCC-CEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFG-EILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT   94 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG-~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~   94 (258)
                      ...+.+...+.-++.++|..+.+.+- .|+.++|++|.  ...+-.++++|.+.++|++-.+..|
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fN   75 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFN   75 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhC
Confidence            33444555566677777876666654 57788999984  3456688999999999999988844

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=89.15  E-value=0.57  Score=45.16  Aligned_cols=80  Identities=18%  Similarity=0.177  Sum_probs=52.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhc----------------------------CCCEEEEEEeecCCCCCcccEEEEEE
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQ----------------------------FGEILEAVVITDKNTGRSKGYGFVTF   80 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~----------------------------fG~I~~v~v~~d~~tg~skG~aFV~F   80 (258)
                      ....++-|+||+..-...+|.++...                            .|.-..+.+..|-.+....|||||.|
T Consensus       359 ~~Rtt~~i~ni~n~~~~~dl~~Ildge~~rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm  438 (549)
T KOG4660|consen  359 DRRTTVMIKNIPNKYGQLDLLRILDGECPRTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINM  438 (549)
T ss_pred             cchhhhhhhccccchhHHHHHHHHhCcCchhhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEee
Confidence            34455666777766666666555532                            33344555666666677889999999


Q ss_pred             cCHHHHHHHhcC-CCC--c-cCC-ceEEEEecc
Q 025068           81 REPEAARRACAD-PTP--F-IDG-RRANCNLAS  108 (258)
Q Consensus        81 ~~~~~A~~Ai~~-~~~--~-i~G-~~i~V~~a~  108 (258)
                      .+.+++.++.++ +++  + |.+ |.+.+.+|.
T Consensus       439 ~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYAr  471 (549)
T KOG4660|consen  439 TSPEAIIRFYKAFNGKKWEKFNSEKIASITYAR  471 (549)
T ss_pred             cCHHHHHHHHHHHcCCchhhhcceeeeeeehhh
Confidence            999999988887 332  2 554 444666664

>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=89.11  E-value=0.3  Score=40.70  Aligned_cols=81  Identities=15%  Similarity=0.124  Sum_probs=45.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhc-CCCE---EEEEE-eecCCCCC-cccEEEEEEcCHHHHHHHhcCCC-Cc-cCCc
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQ-FGEI---LEAVV-ITDKNTGR-SKGYGFVTFREPEAARRACADPT-PF-IDGR  100 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~-fG~I---~~v~v-~~d~~tg~-skG~aFV~F~~~~~A~~Ai~~~~-~~-i~G~  100 (258)
                      ....+|.|++||.++||+++.+.++. ++..   ..+.- ..+..... .-.-|+|.|.+.+++..-+...+ +. ++.+
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            34569999999999999999987766 5554   23321 11221222 23568999999999888887744 33 3322


Q ss_pred             ----eEEEEeccC
Q 025068          101 ----RANCNLASL  109 (258)
Q Consensus       101 ----~i~V~~a~~  109 (258)
                          ...|++|.-
T Consensus        85 g~~~~~~VE~Apy   97 (176)
T PF03467_consen   85 GNEYPAVVEFAPY   97 (176)
T ss_dssp             S-EEEEEEEE-SS
T ss_pred             CCCcceeEEEcch
Confidence                345666653

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.

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.64  E-value=1.6  Score=40.70  Aligned_cols=68  Identities=13%  Similarity=0.138  Sum_probs=54.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCE-EEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCce
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEI-LEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRR  101 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I-~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~  101 (258)
                      +.+-.+.|-|-+++.....++|...|+.|+.- .+|+++.|.       .+|-.|++...|..||...+..|.=|.
T Consensus       387 e~dlpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt-------halaVFss~~~AaeaLt~kh~~lKiRp  455 (528)
T KOG4483|consen  387 ESDLPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT-------HALAVFSSVNRAAEALTLKHDWLKIRP  455 (528)
T ss_pred             cccccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc-------eeEEeecchHHHHHHhhccCceEEeee
Confidence            44566789999999999999999999998753 477888775       799999999999999987544444333

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=86.28  E-value=0.45  Score=48.06  Aligned_cols=70  Identities=20%  Similarity=0.236  Sum_probs=58.1

Q ss_pred             EEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-Cc--cCCceEEEEecc
Q 025068           33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PF--IDGRRANCNLAS  108 (258)
Q Consensus        33 ~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~--i~G~~i~V~~a~  108 (258)
                      +..+.|.+-..+...|..+|++||+|.+...++|-+      .+.|+|.+.+.|..|++.+. ++  +.|-+.+|.+|+
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N------~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak  372 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN------MALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAK  372 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccccc------chhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecc
Confidence            445667777888899999999999999998888865      89999999999999999864 44  567778888884

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=83.21  E-value=6.5  Score=35.24  Aligned_cols=49  Identities=10%  Similarity=0.137  Sum_probs=36.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCE-EEEEEeecCCCCCcccEEEEEEcCHH
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEI-LEAVVITDKNTGRSKGYGFVTFREPE   84 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I-~~v~v~~d~~tg~skG~aFV~F~~~~   84 (258)
                      ..+-|+|+||+.++.-.+|+..+.+-+.+ .++.+      ..++|-||++|.+..
T Consensus       329 ~~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~isw------kg~~~k~flh~~~~~  378 (396)
T KOG4410|consen  329 AKTDIKLTNLSRDIRVKDLKSELRKRECTPMSISW------KGHFGKCFLHFGNRK  378 (396)
T ss_pred             cccceeeccCccccchHHHHHHHHhcCCCceeEee------ecCCcceeEecCCcc
Confidence            34569999999999999999999887643 23333      224567899997643

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=82.13  E-value=5.6  Score=27.69  Aligned_cols=53  Identities=13%  Similarity=0.343  Sum_probs=37.8

Q ss_pred             CCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEE
Q 025068           42 ETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRAN  103 (258)
Q Consensus        42 ~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~  103 (258)
                      .++-++|+..+.+|.-   .+|+.|+     .|| ||.|.+.++|++|....+ ..+..-+|.
T Consensus        11 ~~~v~d~K~~Lr~y~~---~~I~~d~-----tGf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~   64 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW---DRIRDDR-----TGF-YIVFNDSKEAERCFRAEDGTLFFTYRMQ   64 (66)
T ss_pred             CccHHHHHHHHhcCCc---ceEEecC-----CEE-EEEECChHHHHHHHHhcCCCEEEEEEEE
Confidence            5678899999999963   2344454     233 899999999999998855 335544443

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	258
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		4e-27
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		4e-14
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		2e-12
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		5e-12
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		6e-12
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		5e-11
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		9e-11
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		9e-11
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		9e-11
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		9e-11
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-10
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		1e-10
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		1e-10
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		1e-10
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		1e-10
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-10
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		8e-10
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		4e-09
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		3e-08
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		7e-08
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-07
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		2e-07
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		3e-07
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		5e-07
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		9e-07
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		1e-06
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		1e-06
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		2e-06
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		3e-06
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		3e-06
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		5e-06
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		8e-06
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		1e-05
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		1e-05
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		1e-05
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		2e-05
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-05
2dgq_A	108	Solution Structure Of The N-Terminal Rna Binding Do		3e-05
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		4e-05
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		6e-05
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		6e-05
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		8e-05
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		9e-05
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		9e-05
2dnq_A	90	Solution Structure Of Rna Binding Domain 1 In Rna-B		1e-04
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		1e-04
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		1e-04
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		1e-04
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		2e-04
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		2e-04
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		3e-04
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		3e-04
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		4e-04
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		4e-04
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		4e-04
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		4e-04
1x4h_A	111	Solution Structure Of Rrm Domain In Rna-Binding Pro		5e-04
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		7e-04
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		8e-04
2dnp_A	90	Solution Structure Of Rna Binding Domain 2 In Rna-B		9e-04

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score =  118 bits (295), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 55/87 (63%), Positives = 68/87 (78%), Gaps = 1/87 (1%)
Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
           DTT+TK+FVGGL + T   ++R+YFE FG+I EAVVITD+ TG+S+GYGFVT  +  AA 
Sbjct: 14  DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73
Query: 88  RACADPTPFIDGRRANCNLASLG-RPR 113
           RAC DP P IDGR+AN NLA LG +PR
Sbjct: 74  RACKDPNPIIDGRKANVNLAYLGAKPR 100

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 75.1 bits (183), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 31/71 (43%), Positives = 46/71 (64%)
Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVGGL W T  ET+R YF Q+GE+++ V++ DK T +S+G+GFV F++P       A 
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 93  PTPFIDGRRAN 103
               +DGR  +
Sbjct: 78  RPHTLDGRNID 88

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 69.3 bits (168), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 48/79 (60%)
Query: 22  LNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFR 81
           +N+   +    K FVGGL+W+T  + ++ YF +FGE+++  +  D NTGRS+G+GF+ F+
Sbjct: 2   INASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK 61
Query: 82  EPEAARRACADPTPFIDGR 100
           +  +  +        +DGR
Sbjct: 62  DAASVEKVLDQKEHRLDGR 80

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 67.8 bits (164), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 30/75 (40%), Positives = 46/75 (61%)
Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+F+GGL+W+T  E +R YF QFGE+ E +V+ D  T RS+G+GFVTF +     +  A 
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 93  PTPFIDGRRANCNLA 107
               +D +  +  +A
Sbjct: 62  SRHELDSKTIDPKVA 76

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 67.8 bits (164), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 32/87 (36%), Positives = 52/87 (59%)
Query: 29  TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
           ++  K+F+GGL+W+T  E +R YF QFGE+ E +V+ D  T RS+G+GFVTF +     +
Sbjct: 23  SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK 82
Query: 89  ACADPTPFIDGRRANCNLASLGRPRPQ 115
             A     +D +  +  +A   R +P+
Sbjct: 83  VLAQSRHELDSKTIDPKVAFPRRAQPK 109

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 64.7 bits (156), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 50/76 (65%), Gaps = 1/76 (1%)
Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA-CA 91
           K+FVGGL+++T  +++ + F ++G+I E VV+ D+ T RS+G+GFVTF   + A+ A  A
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 92  DPTPFIDGRRANCNLA 107
                +DGR+   + A
Sbjct: 74  MNGKSVDGRQIRVDQA 89

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 58.2 bits (139), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 2/77 (2%)
Query: 30  TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           T  K+FVGG+  +T+   +R YFEQ+G+I    ++TD+ +G+ +G+ FVTF + ++  + 
Sbjct: 103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 162
Query: 90  CADPTPFIDGRRANCNL 106
                  ++G   NC +
Sbjct: 163 VIQKYHTVNGH--NCEV 177

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 58.2 bits (139), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 2/77 (2%)
Query: 30  TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           T  K+FVGG+  +T+   +R YFEQ+G+I    ++TD+ +G+ +G+ FVTF + ++  + 
Sbjct: 103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 162
Query: 90  CADPTPFIDGRRANCNL 106
                  ++G   NC +
Sbjct: 163 VIQKYHTVNGH--NCEV 177

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 58.2 bits (139), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 2/77 (2%)
Query: 30  TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           T  K+FVGG+  +T+   +R YFEQ+G+I    ++TD+ +G+ +G+ FVTF + ++  + 
Sbjct: 102 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 161
Query: 90  CADPTPFIDGRRANCNL 106
                  ++G   NC +
Sbjct: 162 VIQKYHTVNGH--NCEV 176

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 58.2 bits (139), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 2/77 (2%)
Query: 30  TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           T  K+FVGG+  +T+   +R YFEQ+G+I    ++TD+ +G+ +G+ FVTF + ++  + 
Sbjct: 104 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 163
Query: 90  CADPTPFIDGRRANCNL 106
                  ++G   NC +
Sbjct: 164 VIQKYHTVNGH--NCEV 178

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 58.2 bits (139), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 2/77 (2%)
Query: 30  TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           T  K+FVGG+  +T+   +R YFEQ+G+I    ++TD+ +G+ +G+ FVTF + ++  + 
Sbjct: 101 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 160
Query: 90  CADPTPFIDGRRANCNL 106
                  ++G   NC +
Sbjct: 161 VIQKYHTVNGH--NCEV 175

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 58.2 bits (139), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 2/77 (2%)
Query: 30  TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           T  K+FVGG+  +T+   +R YFEQ+G+I    ++TD+ +G+ +G+ FVTF + ++  + 
Sbjct: 96  TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 155
Query: 90  CADPTPFIDGRRANCNL 106
                  ++G   NC +
Sbjct: 156 VIQKYHTVNGH--NCEV 170

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 63.5 bits (153), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 44/74 (59%)
Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
           +FVGGL+  T  E ++ YFEQFG++ +A+++ DK T R +G+GFVTF   +   + C   
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 94  TPFIDGRRANCNLA 107
              I+ +   C  A
Sbjct: 62  FHEINNKMVECKKA 75

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 63.2 bits (152), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 46/70 (65%)
Query: 31  YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
           + K+F+GGL++ET  E++R Y+EQ+G++ + VV+ D  + RS+G+GFVTF        A 
Sbjct: 27  FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
Query: 91  ADPTPFIDGR 100
           A     IDGR
Sbjct: 87  AARPHSIDGR 96

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 63.2 bits (152), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 23/55 (41%), Positives = 40/55 (72%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
          +F+GGL+W+T  + ++ YF +FGE+++  +  D  TGRS+G+GFV F+E E+  +
Sbjct: 2  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDK 56

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 62.4 bits (150), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 29/70 (41%), Positives = 42/70 (60%)
Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
          G +  + ++VG L +    + +R  FE FG+I   V++ D +TGRSKGYGF+TF + E A
Sbjct: 1  GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 87 RRACADPTPF 96
          RRA      F
Sbjct: 61 RRALEQLNGF 70

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 60.5 bits (145), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           + + V GL W+T  + ++ YF  FGE+L   V  D  TG SKG+GFV F E E   +  +
Sbjct: 16  SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75
Query: 92  DPTPFIDGRRANCNL 106
                IDGR  +C L
Sbjct: 76  -QRHMIDGRWCDCKL 89

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 58.2 bits (139), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 26/66 (39%), Positives = 43/66 (65%), Gaps = 2/66 (3%)
Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVGG+  + + +    +F Q+G I++A ++ DK+TG+S+G+GFVT+   +A  R C  
Sbjct: 89  KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ- 147
Query: 93  PTPFID 98
              FID
Sbjct: 148 -NKFID 152

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 55.5 bits (132), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 37/64 (57%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
          +++VG L +    + +R  FE FG I    ++ D  TGRSKGYGF+TF + E A++A   
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 93 PTPF 96
             F
Sbjct: 88 LNGF 91

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 54.3 bits (129), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 33/86 (38%), Positives = 46/86 (53%), Gaps = 1/86 (1%)
Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD- 92
           VFVG L+ E  +E ++  F  FG I +A V+ D  TG+SKGYGFV+F     A  A    
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 93  PTPFIDGRRANCNLASLGRPRPQVLY 118
              ++ GR+   N A+   P P+  Y
Sbjct: 78  GGQWLGGRQIRTNWATRKPPAPKSTY 103

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 32/88 (36%), Positives = 47/88 (53%), Gaps = 1/88 (1%)
Query: 29  TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
           + +  VFVG L+ E  +E ++  F  FG+I +A V+ D  TG+SKGYGFV+F     A  
Sbjct: 13  SNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAEN 72
Query: 89  ACAD-PTPFIDGRRANCNLASLGRPRPQ 115
           A       ++ GR+   N A+   P P 
Sbjct: 73  AIVHMGGQWLGGRQIRTNWATRKPPAPS 100

>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of Hnrnp D (Auf1) With Telomere Dna Length = 79

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 22/56 (39%), Positives = 35/56 (62%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
          K+FVGGL+ +T  E +R YF  FGE+    +  D  T + +G+ F+TF+E E  ++
Sbjct: 3  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK 58

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 37/60 (61%), Gaps = 1/60 (1%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
          K+F+GGL  ET  + ++  F + G I E ++I D+ T +S+G+ F+TF  P  A+ A  D
Sbjct: 9  KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKD 67

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 51.2 bits (121), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 1/82 (1%)
Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC- 90
           T + V  L + T  +T+RR FE++G + +  +  D+ T  S+G+ FV F +   A  A  
Sbjct: 48  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 91  ADPTPFIDGRRANCNLASLGRP 112
           A     +DGR     +A  GRP
Sbjct: 108 AMDGAVLDGRELRVQMARYGRP 129

>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1) Length = 75

Iteration: 1
 Score = 50.4 bits (119), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 21/55 (38%), Positives = 34/55 (61%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
          +FVGGL+ +T  E +R YF  FGE+    +  D  T + +G+ F+TF+E E  ++
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK 56

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/77 (38%), Positives = 43/77 (55%), Gaps = 8/77 (10%)
Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPE---AARRAC 90
           +FV GL+ +T  ET++   E F   + A ++TD+ TG SKG+GFV F   E   AA+ A 
Sbjct: 18  LFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 91  ADPTPFIDGRRANCNLA 107
            D    IDG +   + A
Sbjct: 75  EDGE--IDGNKVTLDWA 89

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 40/77 (51%)
Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
            K+FVGG+        +R YF++FG + E V+I D    R +G+GF+TF + ++  +A  
Sbjct: 11  NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 92  DPTPFIDGRRANCNLAS 108
                I G++     A 
Sbjct: 71  MHFHDIMGKKVEVKRAE 87

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 1/82 (1%)
Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC- 90
           T + V  L + T  +T+RR FE++G + +  +  D+ T  S+G+ FV F +   A  A  
Sbjct: 71  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 91  ADPTPFIDGRRANCNLASLGRP 112
           A     +DGR     +A  GRP
Sbjct: 131 AMDGAVLDGRELRVQMARYGRP 152

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/70 (35%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 48  MRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRRANCNL 106
           +R+ FE++G I    ++ D+ T +S+GYGFV F+   +A++A A    F I  +R    L
Sbjct: 59  LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL 118
Query: 107 ASLGRPRPQV 116
           A+ G  RP +
Sbjct: 119 AASGHQRPGI 128

>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 4 Rna-Binding Protein Length = 106

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 38/67 (56%)
Query: 23 NSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFRE 82
          +S   D    K+F+G +      + ++  FE+FG+I E  V+ D+ TG  KG  F+T+ E
Sbjct: 5  SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCE 64
Query: 83 PEAARRA 89
           E+A +A
Sbjct: 65 RESALKA 71

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/63 (39%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
           D T+  +FVG L      ET+R  F+ F   L   V+ D  TG S+GYGFV+F   + A+
Sbjct: 85  DDTFN-LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQ 143
Query: 88  RAC 90
            A 
Sbjct: 144 NAM 146

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 47.4 bits (111), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 80
          P G      VFVGG+        +R +F ++G + E  +ITD+ TG SKGYGFV+F
Sbjct: 3  PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA-- 91
          ++VG L +   SE ++  F QFG++    +I D+ T + KG+GFV  +E E+   A A  
Sbjct: 4  IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 92 DPTPFI 97
          D T F+
Sbjct: 63 DNTDFM 68

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 23/56 (41%), Positives = 31/56 (55%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +FVG L      ET+R  F+ F   L   V+ D  TG S+GYGFV+F   + A+ A
Sbjct: 4  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 59

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 80
          VFVGG+        +R +F ++G + E  +ITD+ TG SKGYGFV+F
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 58

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 80
          P G      VFVGG+        +R +F ++G + E  +ITD+ TG SKGYGFV+F
Sbjct: 3  PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57

>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 = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 17/67 (25%), Positives = 37/67 (55%)
Query: 30  TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
            + +++V  +  +   + ++  FE FG+I  A +  D  TG+ KGYGF+ + + ++++ A
Sbjct: 124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDA 183
Query: 90  CADPTPF 96
            +    F
Sbjct: 184 VSSMNLF 190

>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 6 Rna-Binding Protein Length = 108

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 35/65 (53%)
Query: 25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPE 84
          P  D    K+FVG +      + ++  FE+FG I E  V+ D+ TG  KG  F+T+   +
Sbjct: 9  PMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARD 68
Query: 85 AARRA 89
          +A +A
Sbjct: 69 SALKA 73

>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 = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 36/65 (55%)
Query: 25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPE 84
          P  D +   VFVG + +E   E ++  F + G ++   ++ D+ TG+ KGYGF  +++ E
Sbjct: 2  PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 85 AARRA 89
           A  A
Sbjct: 62 TALSA 66

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           +F+  L     ++ +   F  FG IL   V+ D+N   SKGYGFV F   EAA RA
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 159

>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 = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 16/67 (23%), Positives = 36/67 (53%)
Query: 30  TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
            + +++V  +  +   + ++  FE FG+I    +  D  TG+ KGYGF+ + + ++++ A
Sbjct: 108 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDA 167
Query: 90  CADPTPF 96
            +    F
Sbjct: 168 VSSXNLF 174

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 43.9 bits (102), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 16/67 (23%), Positives = 36/67 (53%)
Query: 30  TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
            + +++V  +  +   + ++  FE FG+I    +  D  TG+ KGYGF+ + + ++++ A
Sbjct: 109 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDA 168
Query: 90  CADPTPF 96
            +    F
Sbjct: 169 VSSMNLF 175

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 43.9 bits (102), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           +F+  L     ++ +   F  FG IL   V+ D+N   SKGYGFV F   EAA RA
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 154

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 43.9 bits (102), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 22/63 (34%), Positives = 34/63 (53%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
          + V  L+ +T+   ++  F  FG I    +  DK TG+SKG+ F++F   E A RA A  
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 94 TPF 96
          + F
Sbjct: 78 SGF 80

>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding Protein 30 Length = 90

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 8/63 (12%)
Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
          G +   K+F+G L  E   + +R  FEQ+G++LE  +I        K YGFV   +  AA
Sbjct: 4  GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAA 55
Query: 87 RRA 89
            A
Sbjct: 56 EDA 58

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +F+  L     ++ +   F  FG IL   V+ D+N   SKGYGFV F   EAA RA
Sbjct: 8  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 61

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 15/54 (27%), Positives = 34/54 (62%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
          V+V  L +   +  + R F ++G++++  ++ DK+T +SKG  F+ F + ++A+
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +F+  L     ++ +   F  FG IL   V+ D+N   SKGYGFV F   EAA RA
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 67

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/63 (33%), Positives = 36/63 (57%)
Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
          G +  + +++ GL   T  + + +  + +G+I+    I DK T + KGYGFV F  P AA
Sbjct: 1  GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 87 RRA 89
          ++A
Sbjct: 61 QKA 63

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 30  TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           ++  VFVG L+ E  +  +   F  FG I +A V+ D  TG+SKGYGFV+F     A  A
Sbjct: 5   SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64
Query: 90  CAD-PTPFIDGRRANCNLAS 108
                  ++ GR+   N A+
Sbjct: 65  IQQMGGQWLGGRQIRTNWAT 84

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 38  GLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF- 96
           GL+  T    +R  F ++G I +  ++ D+ + RS+G+ FV F   + A+ A        
Sbjct: 53  GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 112
Query: 97  IDGRRANCNLASLGRP 112
           +DGRR   + +   RP
Sbjct: 113 LDGRRIRVDFSITKRP 128

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 36  VGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP 95
           V GL+  T    +R  F ++G I +  ++ D+ + RS+G+ FV F   + A+ A      
Sbjct: 17  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 96  F-IDGRRANCNLASLGRP 112
             +DGRR   + +   RP
Sbjct: 77  MELDGRRIRVDFSITKRP 94

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/98 (29%), Positives = 43/98 (43%), Gaps = 6/98 (6%)
Query: 30  TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           + T + V  L      E  R  F   GEI    ++ DK TG+S GYGFV + +P+ A +A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 90  CADPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLF 127
                  ++G R       +   RP      +R A L+
Sbjct: 61  INT----LNGLRLQTKTIKVSYARPS--SASIRDANLY 92

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
          ++V  L      E +R+ F  FG I  A V+ +   GRSKG+GFV F  PE A +A  +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE 74

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 27/82 (32%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 27  GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
           G TT   ++VGGLA E   + +   F  FG+I +  +  D  T + +G+ FV F   E A
Sbjct: 1   GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60
Query: 87  RRACADPTPF-IDGRRANCNLA 107
             A  +     + GR    NLA
Sbjct: 61  AAAIDNMNESELFGRTIRVNLA 82

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 36  VGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP 95
           V GL+  T    +R  F ++G I +  ++ D+ + RS+G+ FV F   + A+ A      
Sbjct: 20  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 96  F-IDGRRANCNLASLGRP 112
             +DGRR   + +   RP
Sbjct: 80  MELDGRRIRVDFSITKRP 97

>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28 Length = 111

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 26/88 (29%), Positives = 44/88 (50%), Gaps = 8/88 (9%)
Query: 28  DTTYTK-VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
           D T  K VF+  L+++++ E +    +QFG++    V+   +T  SKG  F  F   EAA
Sbjct: 11  DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70
Query: 87  RRACADPT-------PFIDGRRANCNLA 107
           ++  A  +         +DGR+   +LA
Sbjct: 71  QKCLAAASLEAEGGGLKLDGRQLKVDLA 98

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 40.8 bits (94), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 4/68 (5%)
Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           ++FV  L++ +  E + + F  +G + E     D  T + KG+ FVTF  PE A +A A+
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 93  PTPFIDGR 100
               +DG+
Sbjct: 70  ----VDGQ 73

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEA-VVITDKNTGRSKGYGFVTFREPEA 85
          G +  + +F+G L  E   + +   F  FG IL+   ++ D +TG SKGY F+ F   +A
Sbjct: 1  GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 86 ARRA 89
          +  A
Sbjct: 61 SDAA 64

>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding Protein 14 Length = 90

Iteration: 1
 Score = 40.4 bits (93), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 9/83 (10%)
Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVG ++    S+ +R  FE+ G ++E  V+ D        Y FV   +   A+ A A 
Sbjct: 11  KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQ 62
Query: 93  PT-PFIDGRRANCNLASLGRPRP 114
                + G+R N  L++ G+ + 
Sbjct: 63  LNGKEVKGKRINVELSTKGQKKS 85

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	258
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	4e-47
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	6e-43
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-42
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	8e-42
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-41
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	4e-41
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-40
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-40
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	8e-39
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	5e-35
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-34
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-30
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-34
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	4e-30
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	4e-30
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	9e-30
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-29
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-28
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-28
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-27
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	9e-27
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	4e-26
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	8e-26
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	8e-19
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-25
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-25
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-25
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	3e-25
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	5e-25
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-25
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-18
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	6e-25
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	8e-25
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	8e-25
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-24
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-24
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-24
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-24
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	5e-24
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-24
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-23
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	7e-24
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	8e-24
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-23
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-23
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-23
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-23
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	4e-23
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	5e-23
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-23
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	9e-19
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	7e-23
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	8e-23
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	9e-23
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-17
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-12
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-22
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-22
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-22
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-22
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-22
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-22
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	9e-18
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	5e-22
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	5e-22
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-19
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	6e-22
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	9e-22
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-19
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-21
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-21
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-21
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-21
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-21
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-21
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-21
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-21
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-16
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	3e-21
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	4e-21
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	7e-21
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	8e-21
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	8e-21
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	9e-21
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-20
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-20
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-20
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	7e-20
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	8e-20
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-19
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-19
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-19
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-19
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	3e-19
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-19
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-15
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	5e-19
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	5e-19
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	5e-19
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	7e-19
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	9e-19
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-18
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-18
1x5o_A	114	RNA binding motif, single-stranded interacting pro	5e-18
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	7e-18
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	7e-18
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	9e-18
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-17
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-17
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-17
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-16
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	6e-17
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	7e-17
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	7e-17
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	9e-17
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-16
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-16
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-16
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-16
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-16
2div_A	99	TRNA selenocysteine associated protein; structural	3e-16
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	5e-16
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	9e-16
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	9e-16
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-15
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	8e-15
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-15
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-15
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	3e-15
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-15
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-15
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	5e-15
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	5e-15
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	6e-15
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	7e-15
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-14
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-14
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-14
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-14
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-14
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-14
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-14
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	7e-14
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-13
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-13
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	6e-13
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-12
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-12
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-12
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-12
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-12
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-12
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-12
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	6e-12
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-11
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-11
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-11
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-04
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	7e-11
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-10
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-10
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	1e-10
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	2e-10
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	5e-10
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	5e-10
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-10
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	6e-10
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	9e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-09
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-09
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-09
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-09
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	3e-09
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-05
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-08
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-08
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-08
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-07
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-07
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-07
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	8e-06
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	4e-05

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score =  151 bits (384), Expect = 4e-47
 Identities = 61/105 (58%), Positives = 76/105 (72%), Gaps = 4/105 (3%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG   ++    DTT+TK+FVGGL + T   ++R+YFE FG+I EAVVITD+ TG+
Sbjct: 1   GSSGSSG---MHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGK 57

Query: 72  SKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLG-RPRPQ 115
           S+GYGFVT  +  AA RAC DP P IDGR+AN NLA LG +PR  
Sbjct: 58  SRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSL 102

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score =  140 bits (355), Expect = 6e-43
 Identities = 39/104 (37%), Positives = 57/104 (54%), Gaps = 4/104 (3%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG     +  G     K+FVGGL W T  ET+R YF Q+GE+++ V++ DK T +
Sbjct: 1   GSSGSSG----MNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQ 56

Query: 72  SKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQ 115
           S+G+GFV F++P       A     +DGR  +    +    +P 
Sbjct: 57  SRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRGMQPS 100

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score =  139 bits (352), Expect = 1e-42
 Identities = 28/86 (32%), Positives = 51/86 (59%)

Query: 22  LNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFR 81
           +N+   +    K+FVGGL+W+T  + ++ YF +FGE+++  +  D NTGRS+G+GF+ F+
Sbjct: 2   INASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFK 61

Query: 82  EPEAARRACADPTPFIDGRRANCNLA 107
           +  +  +        +DGR  +   A
Sbjct: 62  DAASVEKVLDQKEHRLDGRVIDPKKA 87

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score =  137 bits (348), Expect = 8e-42
 Identities = 36/104 (34%), Positives = 50/104 (48%), Gaps = 6/104 (5%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG             + + V GL W+T  + ++ YF  FGE+L   V  D  TG 
Sbjct: 1   GSSGSSG-----VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGH 55

Query: 72  SKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQ 115
           SKG+GFV F E E   +  +     IDGR  +C L +  + +  
Sbjct: 56  SKGFGFVRFTEYETQVKVMSQR-HMIDGRWCDCKLPNSKQSQDS 98

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score =  137 bits (347), Expect = 1e-41
 Identities = 32/93 (34%), Positives = 52/93 (55%)

Query: 23  NSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFRE 82
                 ++  K+F+GGL+W+T  E +R YF QFGE+ E +V+ D  T RS+G+GFVTF +
Sbjct: 17  RGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 76

Query: 83  PEAARRACADPTPFIDGRRANCNLASLGRPRPQ 115
                +  A     +D +  +  +A   R +P+
Sbjct: 77  QAGVDKVLAQSRHELDSKTIDPKVAFPRRAQPK 109

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score =  136 bits (344), Expect = 4e-41
 Identities = 33/109 (30%), Positives = 51/109 (46%), Gaps = 3/109 (2%)

Query: 7   PGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITD 66
            G      +               + K+F+GGL++ET  E++R Y+EQ+G++ + VV+ D
Sbjct: 3   SGSSGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRD 62

Query: 67  KNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQ 115
             + RS+G+GFVTF        A A     IDGR      A     R +
Sbjct: 63  PASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAV---AREE 108

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score =  133 bits (338), Expect = 1e-40
 Identities = 30/75 (40%), Positives = 46/75 (61%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+F+GGL+W+T  E +R YF QFGE+ E +V+ D  T RS+G+GFVTF +     +  A 
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 93  PTPFIDGRRANCNLA 107
               +D +  +  +A
Sbjct: 62  SRHELDSKTIDPKVA 76

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score =  133 bits (338), Expect = 1e-40
 Identities = 29/75 (38%), Positives = 45/75 (60%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVGGL+  T  E ++ YFEQFG++ +A+++ DK T R +G+GFVTF   +   + C  
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 93  PTPFIDGRRANCNLA 107
               I+ +   C  A
Sbjct: 61  HFHEINNKMVECKKA 75

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score =  129 bits (326), Expect = 8e-39
 Identities = 23/75 (30%), Positives = 39/75 (52%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVGGL+ +T  E +R YF  FGE+    +  D  T + +G+ F+TF+E E  ++    
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 93  PTPFIDGRRANCNLA 107
               +   +    +A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score =  119 bits (302), Expect = 5e-35
 Identities = 27/93 (29%), Positives = 45/93 (48%), Gaps = 3/93 (3%)

Query: 23  NSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFRE 82
           +S    +   K+FVGG+        +R YF++FG + E V+I D    R +G+GF+TF +
Sbjct: 2   SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFED 61

Query: 83  PEAARRACADPTPFIDGRRANCNLASLGRPRPQ 115
            ++  +A       I G++     A    PR  
Sbjct: 62  EQSVDQAVNMHFHDIMGKKVEVKRA---EPRDS 91

>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 =  122 bits (308), Expect = 1e-34
 Identities = 36/97 (37%), Positives = 52/97 (53%), Gaps = 1/97 (1%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+F+GGL++ET  E++R +FEQ+G + + VV+ D NT RS+G+GFVT+   E    A   
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74

Query: 93  PTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSG 129
               +DGR      A   R   Q     L    +F G
Sbjct: 75  RPHKVDGRVVEPKRAV-SREDSQRPGAHLTVKKIFVG 110

>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 =  111 bits (279), Expect = 2e-30
 Identities = 25/93 (26%), Positives = 47/93 (50%), Gaps = 3/93 (3%)

Query: 23  NSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFRE 82
             P    T  K+FVGG+  +T+   +R YFEQ+G+I    ++TD+ +G+ +G+ FVTF +
Sbjct: 96  QRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 155

Query: 83  PEAARRACADPTPFIDGRRANCNLASLGRPRPQ 115
            ++  +        ++G       A     + +
Sbjct: 156 HDSVDKIVIQKYHTVNGHNCEVRKAL---SKQE 185

>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 =  120 bits (303), Expect = 3e-34
 Identities = 28/97 (28%), Positives = 52/97 (53%), Gaps = 8/97 (8%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+F+GGL W+T  + +R YF ++G + +  ++ D  TGRS+G+GF++F +P +       
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64

Query: 93  PTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSG 129
               +DG+  +   A    PR +    + +   +F G
Sbjct: 65  QH-ILDGKVIDPKRAI---PRDE----QDKTGKIFVG 93

>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 =  109 bits (275), Expect = 4e-30
 Identities = 25/75 (33%), Positives = 44/75 (58%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVGG+  + + +    +F Q+G I++A ++ DK+TG+S+G+GFVT+   +A  R C +
Sbjct: 89  KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN 148

Query: 93  PTPFIDGRRANCNLA 107
                  R+     A
Sbjct: 149 KFIDFKDRKIEIKRA 163

>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 =  107 bits (270), Expect = 4e-30
 Identities = 30/102 (29%), Positives = 46/102 (45%), Gaps = 10/102 (9%)

Query: 23  NSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFRE 82
           + P G      VFVGG+        +R +F ++G + E  +ITD+ TG SKGYGFV+F  
Sbjct: 1   SLPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYN 59

Query: 83  PEAARRACADPTPFIDGRRANCNLA--------SLGRPRPQV 116
               ++       F  G++     A           +PRP +
Sbjct: 60  DVDVQKIVESQINF-HGKKLKLGPAIRKQNLSTYHVQPRPLI 100

>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 =  107 bits (269), Expect = 9e-30
 Identities = 27/125 (21%), Positives = 50/125 (40%), Gaps = 16/125 (12%)

Query: 31  YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
             K+F+GGL  ET  + ++  F + G I E ++I D+ T +S+G+ F+TF  P  A+ A 
Sbjct: 7   PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAA 65

Query: 91  ADPTP-FIDGRRANCNLASLGRPRPQVLYGRLRPATLFSGSTQATRGPYIGSFGYQQPLP 149
            D     + G+      A   +          +          +      GS  +     
Sbjct: 66  KDMNGKSLHGKAIKVEQA---KKPSF------QSGGRRRPPASSRNRSPSGSLEH----- 111

Query: 150 YNYQQ 154
           +++  
Sbjct: 112 HHHHH 116

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score =  105 bits (265), Expect = 1e-29
 Identities = 21/93 (22%), Positives = 42/93 (45%), Gaps = 9/93 (9%)

Query: 23  NSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFRE 82
            S       +KVFVG    +  +E ++++F Q+GE+++  +         + + FVTF +
Sbjct: 3   GSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFAD 57

Query: 83  PEAARRACADPTPFIDGRRANCNLASLGRPRPQ 115
            + A+  C +    I G   + + A    P+  
Sbjct: 58  DKVAQSLCGEDL-IIKGISVHISNA---EPKHN 86

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score =  103 bits (259), Expect = 1e-28
 Identities = 19/89 (21%), Positives = 40/89 (44%), Gaps = 9/89 (10%)

Query: 27  GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
           G +  + VFVG    +   + +R +F Q+G++++  +         + + FVTF + + A
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIA 55

Query: 87  RRACADPTPFIDGRRANCNLASLGRPRPQ 115
           +  C +    I G   + + A    P+  
Sbjct: 56  QSLCGED-LIIKGISVHISNA---EPKHN 80

>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 =  102 bits (258), Expect = 2e-28
 Identities = 27/85 (31%), Positives = 37/85 (43%), Gaps = 4/85 (4%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             +FVG L      ET+R  F+ F   L   V+ D  TG S+GYGFV+F   + A+ A  
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 92  DPT-PFIDGRRANCNLASLGRPRPQ 115
                 ++GR    N A        
Sbjct: 62  SMQGQDLNGRPLRINWA---AKLEH 83

>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 =  101 bits (253), Expect = 1e-27
 Identities = 32/111 (28%), Positives = 51/111 (45%), Gaps = 15/111 (13%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG      P   T    VF+  L+++++ E +    +QFG++    V+   +T  
Sbjct: 1   GSSGSSG-----LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEH 55

Query: 72  SKGYGFVTFREPEAARRACADPTPF-------IDGRRANCNLASLGRPRPQ 115
           SKG  F  F   EAA++  A  +         +DGR+   +LA     R +
Sbjct: 56  SKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLA---VTRDE 103

>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 = 98.9 bits (247), Expect = 9e-27
 Identities = 35/105 (33%), Positives = 56/105 (53%), Gaps = 12/105 (11%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG          +   K+FVGGL+++T  +++ + F ++G+I E VV+ D+ T R
Sbjct: 1   GSSGSSGM--------ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQR 52

Query: 72  SKGYGFVTFREPEAARRACADPTPF-IDGRRANCNLASLGRPRPQ 115
           S+G+GFVTF   + A+ A        +DGR+   + A        
Sbjct: 53  SRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA---GKSSD 94

>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 = 97.3 bits (243), Expect = 4e-26
 Identities = 30/100 (30%), Positives = 47/100 (47%), Gaps = 6/100 (6%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG +    P        + V GL+  T    +R  F ++G I +  ++ D+ + R
Sbjct: 1   GSSGSSGNRANPDPN-----CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRR 55

Query: 72  SKGYGFVTFREPEAARRACADPTPF-IDGRRANCNLASLG 110
           S+G+ FV F   + A+ A        +DGRR   +  S G
Sbjct: 56  SRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPSSG 95

>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 = 98.8 bits (247), Expect = 8e-26
 Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 1/80 (1%)

Query: 30  TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
              K+F+GGL      + ++     FG +    ++ D  TG SKGY F  + +     +A
Sbjct: 93  GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 152

Query: 90  CADPTPF-IDGRRANCNLAS 108
            A      +  ++     AS
Sbjct: 153 IAGLNGMQLGDKKLLVQRAS 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 = 80.0 bits (198), Expect = 8e-19
 Identities = 14/74 (18%), Positives = 28/74 (37%), Gaps = 7/74 (9%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAV-----VITDKNTGRSKGYGFVTFREPEAAR 87
           +++VG + +    E M  +F     +          +      + K + F+ FR  +   
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 88  RACA-DPTPFIDGR 100
           +A A D   F  G+
Sbjct: 66  QAMAFDGIIF-QGQ 78

>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 = 95.4 bits (238), Expect = 2e-25
 Identities = 24/100 (24%), Positives = 48/100 (48%), Gaps = 10/100 (10%)

Query: 10  GSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNT 69
            SGSS  SG    +        + V+V  L +   +  + R F ++G++++  ++ DK+T
Sbjct: 2   SSGSSGMSGGLAPSK-------STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDT 54

Query: 70  GRSKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLA 107
            +SKG  F+ F + ++A+      +      GR    ++A
Sbjct: 55  RKSKGVAFILFLDKDSAQNCTRAINNKQL-FGRVIKASIA 93

>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 = 94.9 bits (237), Expect = 2e-25
 Identities = 24/85 (28%), Positives = 42/85 (49%), Gaps = 1/85 (1%)

Query: 27  GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
           G +  + +++ GL   T  + + +  + +G+I+    I DK T + KGYGFV F  P AA
Sbjct: 1   GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60

Query: 87  RRACADPTPF-IDGRRANCNLASLG 110
           ++A        +  + A  +  S G
Sbjct: 61  QKAVTALKASGVQAQMAKQSGPSSG 85

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 96.5 bits (240), Expect = 3e-25
 Identities = 23/115 (20%), Positives = 43/115 (37%), Gaps = 10/115 (8%)

Query: 4   QSIPGPGSGSSSSSGFQYLNSPFGDTTY-------TKVFVGGLAWETQSETMRRYFEQFG 56
           QS+  P       S      +P    TY         V+VG  +W T  + + +     G
Sbjct: 21  QSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIG 80

Query: 57  --EILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD-PTPFIDGRRANCNLAS 108
             +++E     ++  G+SKGY  V      +  +     P   ++G + +   A+
Sbjct: 81  VYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPAT 135

>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 = 95.5 bits (238), Expect = 3e-25
 Identities = 40/121 (33%), Positives = 54/121 (44%), Gaps = 9/121 (7%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG          + +  VFVG L+ E  +E ++  F  FG I +A V+ D  TG+
Sbjct: 1   GSSGSSG-----QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGK 55

Query: 72  SKGYGFVTFREPEAARRACADPTPF-IDGRRANCNLASLGRPRPQVLYGRLRPATLFSGS 130
           SKGYGFV+F     A  A        + GR+   N A     +P          T  SG 
Sbjct: 56  SKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA---TRKPPAPKSTYESNTKQSGP 112

Query: 131 T 131
           +
Sbjct: 113 S 113

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 95.6 bits (238), Expect = 5e-25
 Identities = 30/111 (27%), Positives = 44/111 (39%), Gaps = 3/111 (2%)

Query: 7   PGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITD 66
              G          Y   P      T + V  L + T  +T+RR FE++G + +  +  D
Sbjct: 23  SMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRD 82

Query: 67  KNTGRSKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPRPQ 115
           + T  S+G+ FV F +   A  A    D     DGR     +A  GRP   
Sbjct: 83  RYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL-DGRELRVQMARYGRPPDS 132

>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 = 97.0 bits (242), Expect = 5e-25
 Identities = 25/110 (22%), Positives = 44/110 (40%), Gaps = 1/110 (0%)

Query: 2   AYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEA 61
            +   P PG   + S     + S     +  K+F+GGL      + ++     FG +   
Sbjct: 85  PHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAF 144

Query: 62  VVITDKNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRRANCNLASLG 110
            ++ D  TG SKGY F  + +     +A A      +  ++     AS+G
Sbjct: 145 NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG 194

>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 = 79.3 bits (196), Expect = 3e-18
 Identities = 18/117 (15%), Positives = 36/117 (30%), Gaps = 9/117 (7%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAV-----VITDKNTGRSKGYGFVTFREPEAAR 87
           +++VG + +    E M  +F     +          +      + K + F+ FR  +   
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 88  RACA-DPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSGSTQATRGP--YIGS 141
           +A A D   F  G+          +P P +             +         +IG 
Sbjct: 66  QAMAFDGIIF-QGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGG 121

>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 = 93.8 bits (234), Expect = 6e-25
 Identities = 30/83 (36%), Positives = 41/83 (49%), Gaps = 4/83 (4%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
            VFVG L+ E  +  +   F  FG I +A V+ D  TG+SKGYGFV+F     A  A   
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 93  PT-PFIDGRRANCNLASLGRPRP 114
               ++ GR+   N A     +P
Sbjct: 68  MGGQWLGGRQIRTNWA---TRKP 87

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 94.8 bits (236), Expect = 8e-25
 Identities = 25/109 (22%), Positives = 47/109 (43%), Gaps = 1/109 (0%)

Query: 5   SIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVI 64
            +     G     G +++ +         + V GL+  T    +R  F ++G I +  ++
Sbjct: 20  HMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIV 79

Query: 65  TDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASLGRP 112
            D+ + RS+G+ FV F   + A+ A        +DGRR   + +   RP
Sbjct: 80  YDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRP 128

>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 = 95.7 bits (238), Expect = 8e-25
 Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 3/86 (3%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           T + V  L + T  +T+RR FE++G + +  +  D+ T  S+G+ FV F +   A  A  
Sbjct: 71  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130

Query: 92  --DPTPFIDGRRANCNLASLGRPRPQ 115
             D     DGR     +A  GRP   
Sbjct: 131 AMDGAVL-DGRELRVQMARYGRPPDS 155

>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 = 91.8 bits (229), Expect = 2e-24
 Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 3/78 (3%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             ++VGGLA E   + +   F  FG+I +  +  D  T + +G+ FV F   E A  A  
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67

Query: 92  --DPTPFIDGRRANCNLA 107
             + +    GR    NLA
Sbjct: 68  NMNESEL-FGRTIRVNLA 84

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 92.0 bits (229), Expect = 4e-24
 Identities = 15/83 (18%), Positives = 31/83 (37%), Gaps = 7/83 (8%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFG--EILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
             + +  +A  T  +++      +    +    +I DK T +++G+ FV       A + 
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 90  C-----ADPTPFIDGRRANCNLA 107
                   P   IDG+    + A
Sbjct: 70  LQILQSLHPPLKIDGKTIGVDFA 92

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 93.3 bits (232), Expect = 4e-24
 Identities = 27/107 (25%), Positives = 40/107 (37%), Gaps = 4/107 (3%)

Query: 4   QSIPGPGSGSSSSSGFQYLNSPFGDT-TYTKVFVGGLAWETQSETMRRYFEQFGEILEAV 62
                  +      G        G   T   ++VGGLA E   + +   F  FG+I +  
Sbjct: 35  AYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQ 94

Query: 63  VITDKNTGRSKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLA 107
           +  D  T + +G+ FV F   E A  A    + +    GR    NLA
Sbjct: 95  IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL-FGRTIRVNLA 140

>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 = 92.0 bits (229), Expect = 4e-24
 Identities = 28/78 (35%), Positives = 43/78 (55%), Gaps = 7/78 (8%)

Query: 12 GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
          GSS SSG +       D    K+F+G +      + ++  FE+FG+I E  V+ D+ TG 
Sbjct: 1  GSSGSSGMK-------DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGM 53

Query: 72 SKGYGFVTFREPEAARRA 89
           KG  F+T+ E E+A +A
Sbjct: 54 HKGCAFLTYCERESALKA 71

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 91.9 bits (229), Expect = 5e-24
 Identities = 35/120 (29%), Positives = 50/120 (41%), Gaps = 20/120 (16%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG          TT   ++VGGLA E   + +   F  FG+I +  +  D  T +
Sbjct: 1   GSSGSSGMA--------TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEK 52

Query: 72  SKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSG 129
            +G+ FV F   E A  A    + +    GR    NLA   +P         + +   SG
Sbjct: 53  HRGFAFVEFELAEDAAAAIDNMNESEL-FGRTIRVNLA---KPMRI------KESGPSSG 102

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 94.7 bits (236), Expect = 6e-24
 Identities = 21/86 (24%), Positives = 43/86 (50%), Gaps = 2/86 (2%)

Query: 31  YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
           + +++V  +  +   + ++  FE FG+I  A +  D  TG+ KGYGF+ + + ++++ A 
Sbjct: 125 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV 184

Query: 91  ADPTPF-IDGRRANCNLASLGRPRPQ 115
           +    F + G+      A    P P 
Sbjct: 185 SSMNLFDLGGQYLRVGKAV-TPPMPL 209

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 93.1 bits (232), Expect = 3e-23
 Identities = 26/102 (25%), Positives = 42/102 (41%), Gaps = 1/102 (0%)

Query: 27  GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
                ++V+VG + +E   +T+R+ F  FG I    +  D  T + KG+ FV +  PEAA
Sbjct: 24  ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAA 83

Query: 87  RRACADPTP-FIDGRRANCNLASLGRPRPQVLYGRLRPATLF 127
           + A        + GR       S       ++      A  F
Sbjct: 84  QLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF 125

>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 = 91.1 bits (227), Expect = 7e-24
 Identities = 30/86 (34%), Positives = 43/86 (50%), Gaps = 6/86 (6%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           + ++VG L +    + +R  FE FG+I   V++ D +TGRSKGYGF+TF + E ARRA  
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65

Query: 92  --DPTPFIDGRRANCNLASLGRPRPQ 115
             +      GR            R  
Sbjct: 66  QLNGFEL-AGRPMRVGHV---TERLD 87

>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 = 91.6 bits (228), Expect = 8e-24
 Identities = 28/84 (33%), Positives = 41/84 (48%), Gaps = 4/84 (4%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
            +++VG L +    + +R  FE FG I    ++ D  TGRSKGYGF+TF + E A++A  
Sbjct: 27  MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86

Query: 92  DPTPF-IDGRRANCNLASLGRPRP 114
               F + GR            R 
Sbjct: 87  QLNGFELAGRPMKVGHV---TERT 107

>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 = 90.8 bits (226), Expect = 1e-23
 Identities = 33/106 (31%), Positives = 48/106 (45%), Gaps = 13/106 (12%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG     S        ++ V  + +  +   +R+ F QFG+IL+  +I ++    
Sbjct: 1   GSSGSSGNSESKSTP-----KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RG 53

Query: 72  SKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPRPQ 115
           SKG+GFVTF     A RA      T   +GR+   N A     R  
Sbjct: 54  SKGFGFVTFENSADADRAREKLHGTVV-EGRKIEVNNA---TARVM 95

>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 = 90.4 bits (225), Expect = 2e-23
 Identities = 29/105 (27%), Positives = 46/105 (43%), Gaps = 10/105 (9%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG               + V  L + T  +++RR FE++G + +  +  + +T  
Sbjct: 1   GSSGSSGPDVDGM-------ITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKA 53

Query: 72  SKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPRP 114
            +G+ FV F +   A+ A A  D     DGR     +A  GR   
Sbjct: 54  PRGFAFVRFHDRRDAQDAEAAMDGAEL-DGRELRVQVARYGRRDL 97

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 90.8 bits (226), Expect = 2e-23
 Identities = 26/110 (23%), Positives = 44/110 (40%), Gaps = 7/110 (6%)

Query: 12  GSSSSSGFQYLNSPFGDTTY-----TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITD 66
           GSS SSG   +  P  + +        VF   LA   +   +  +F   G++ +  +I+D
Sbjct: 1   GSSGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISD 60

Query: 67  KNTGRSKGYGFVTFREPEAARRACA-DPTPFIDGRRANCNLASLGRPRPQ 115
           +N+ RSKG  +V F E ++   A          G       +   + R  
Sbjct: 61  RNSRRSKGIAYVEFCEIQSVPLAIGLTGQRL-LGVPIIVQASQAEKNRLS 109

>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 = 89.6 bits (223), Expect = 2e-23
 Identities = 16/86 (18%), Positives = 33/86 (38%), Gaps = 3/86 (3%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFG--EILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
            +++G L W T  E +       G  +ILE     ++  G+SKG+  V      ++++  
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 91  AD-PTPFIDGRRANCNLASLGRPRPQ 115
              P   + G+      ++       
Sbjct: 63  DLLPKRELHGQNPVVTPSNKLEHHHH 88

>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 = 89.6 bits (223), Expect = 4e-23
 Identities = 34/119 (28%), Positives = 50/119 (42%), Gaps = 17/119 (14%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG +             ++V  L      E +R+ F  FG I  A V+ +   GR
Sbjct: 1   GSSGSSGDRITRYQV-----VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGR 53

Query: 72  SKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSG 129
           SKG+GFV F  PE A +A  +     +  +     LA   + + +      R +   SG
Sbjct: 54  SKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA---QRKEE------RQSGPSSG 103

>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 = 88.9 bits (221), Expect = 5e-23
 Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 4/80 (5%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTG---RSKGYGFVTFREPEAARR 88
           + +F+  L + T  ET++  F + G I    +   KN      S G+GFV +++PE A++
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 89  ACADPTPF-IDGRRANCNLA 107
           A        +DG +    ++
Sbjct: 66  ALKQLQGHTVDGHKLEVRIS 85

>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 = 91.1 bits (227), Expect = 6e-23
 Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 2/60 (3%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTG--RSKGYGFVTFREPEAARRA 89
           K+FVG +      + +R  FEQ+G + E  V+ D++    +SKG  FVTF   +AA  A
Sbjct: 4  IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63

>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 = 80.0 bits (198), Expect = 9e-19
 Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
            K+F+G ++ +     +R  F  FG+I E  ++     G S+G  FVTF     A+ A
Sbjct: 96  RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTA 152

>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 = 88.8 bits (221), Expect = 7e-23
 Identities = 25/86 (29%), Positives = 42/86 (48%), Gaps = 3/86 (3%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
            ++FV  L++ +  E + + F  +G + E     D  T + KG+ FVTF  PE A +A A
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 92  --DPTPFIDGRRANCNLASLGRPRPQ 115
             D   F  GR  +   +++ +   Q
Sbjct: 69  EVDGQVF-QGRMLHVLPSTIKKEASQ 93

>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 = 88.5 bits (220), Expect = 8e-23
 Identities = 36/105 (34%), Positives = 53/105 (50%), Gaps = 12/105 (11%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG    + P        +FV GL+ +T  ET++   E F   + A ++TD+ TG 
Sbjct: 1   GSSGSSGPNARSQP-----SKTLFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGS 52

Query: 72  SKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASLGRPRPQ 115
           SKG+GFV F   E A+ A        IDG +   + A   +P+ +
Sbjct: 53  SKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA---KPKGE 94

>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 = 93.1 bits (232), Expect = 9e-23
 Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 1/93 (1%)

Query: 29  TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
            T   + V  L      +        FG +    ++  + TG+SKGYGF  + + ++A R
Sbjct: 93  PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152

Query: 89  ACADPTPF-IDGRRANCNLASLGRPRPQVLYGR 120
           A +D     +  R    +    G+  P +L+ R
Sbjct: 153 AKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSR 185

>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 = 78.1 bits (193), Expect = 3e-17
 Identities = 14/90 (15%), Positives = 27/90 (30%), Gaps = 5/90 (5%)

Query: 31  YTKVFVGGLAWE-TQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
              + V  L       + + R            +   +  G+ KG+  + +   E A  A
Sbjct: 184 SRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEA 242

Query: 90  CA--DPTPFIDGRRANCNLASLGRPRPQVL 117
               D    + G     +  + G P   +L
Sbjct: 243 QQQADGLS-LGGSHLRVSFCAPGPPGRSML 271

>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 = 63.1 bits (154), Expect = 6e-12
 Identities = 11/58 (18%), Positives = 20/58 (34%), Gaps = 7/58 (12%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           K+ + GL  +  ++ +      +        +      + KG  FVT    E A  A
Sbjct: 23 RKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAA 73

>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 = 88.0 bits (219), Expect = 1e-22
 Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 5/84 (5%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             ++VG + +   +E +  +F   G +    ++ DK +G  KG+ ++ F + E+ R + A
Sbjct: 7   RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66

Query: 92  -DPTPFIDGRRANCNLASLGRPRP 114
            D + F  GR+         R   
Sbjct: 67  LDESLF-RGRQIKVIPK---RTNR 86

>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 = 88.5 bits (220), Expect = 1e-22
 Identities = 32/124 (25%), Positives = 49/124 (39%), Gaps = 15/124 (12%)

Query: 12  GSSSSSGFQYLNSPFGDTTY-----TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITD 66
           GSS SSG    +     +         +F+  L  E   + + + F  FG ++ A V  D
Sbjct: 1   GSSGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID 60

Query: 67  KNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRRANCNLASLGRPRPQVLYGRLRPAT 125
           K T  SK +GFV++  P +A+ A      F I  +R    L    R +          + 
Sbjct: 61  KQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK---RSKND------SKSG 111

Query: 126 LFSG 129
             SG
Sbjct: 112 PSSG 115

>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 = 88.0 bits (219), Expect = 1e-22
 Identities = 31/106 (29%), Positives = 44/106 (41%), Gaps = 11/106 (10%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG               + V  L+ +T+   ++  F  FG I    +  DK TG+
Sbjct: 1   GSSGSSG-----PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQ 55

Query: 72  SKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPRPQ 115
           SKG+ F++F   E A RA A      + D    N   A   +P   
Sbjct: 56  SKGFAFISFHRREDAARAIAGVSGFGY-DHLILNVEWA---KPSTN 97

>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 = 89.0 bits (221), Expect = 2e-22
 Identities = 25/116 (21%), Positives = 42/116 (36%), Gaps = 4/116 (3%)

Query: 1   MAYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE 60
              Q+                            + V  +        +R+ FE++G I  
Sbjct: 12  PYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIES 71

Query: 61  AVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRRANCNLASLGRPRPQ 115
             ++ D+ T +S+GYGFV F+   +A++A A    F I  +R    LA       Q
Sbjct: 72  VKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA---ASGHQ 124

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 86.9 bits (216), Expect = 3e-22
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 4/85 (4%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             V++G + ++   E +       G ++   ++ D  TGRSKGY F+ FR+ E++  A  
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 92  DPTPF-IDGRRANCNLASLGRPRPQ 115
           +   + +  R   C  +        
Sbjct: 63  NLNGYQLGSRFLKCGYS---SNSDI 84

>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 = 88.8 bits (221), Expect = 4e-22
 Identities = 14/88 (15%), Positives = 29/88 (32%), Gaps = 1/88 (1%)

Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
            TT   +F+G L        ++    +     +  V+  + TG ++ +G+V F   E   
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLE 68

Query: 88  RACADPTPFIDGRRANCNLASLGRPRPQ 115
           +A       + G             +  
Sbjct: 69  KALELTGLKVFGNEIKLEKPKGRDSKKV 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 = 77.3 bits (191), Expect = 9e-18
 Identities = 15/78 (19%), Positives = 28/78 (35%), Gaps = 6/78 (7%)

Query: 31  YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
              +    L++    + ++  FE   EI           G+SKG  ++ F+    A +  
Sbjct: 99  ARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEKNL 153

Query: 91  ADPTPF-IDGRRANCNLA 107
            +     IDGR  +    
Sbjct: 154 EEKQGAEIDGRSVSLYYT 171

>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 = 86.1 bits (214), Expect = 5e-22
 Identities = 28/85 (32%), Positives = 42/85 (49%), Gaps = 7/85 (8%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA- 91
            ++VG L +   SE ++  F QFG++    +I D+ T + KG+GFV  +E E+   A A 
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 92  -DPTPFIDGRRANCNLASLGRPRPQ 115
            D T F  GR      A    P+  
Sbjct: 62  LDNTDF-MGRTIRVTEA---NPKKS 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 = 88.4 bits (220), Expect = 5e-22
 Identities = 20/86 (23%), Positives = 32/86 (37%), Gaps = 3/86 (3%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           T + V  L  +     +   F   G I    ++ D  TG S GY FV F     ++RA  
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63

Query: 92  --DPTPFIDGRRANCNLASLGRPRPQ 115
             +    +  +R   + A  G    +
Sbjct: 64  VLNGIT-VRNKRLKVSYARPGGESIK 88

>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 = 82.2 bits (204), Expect = 1e-19
 Identities = 17/58 (29%), Positives = 31/58 (53%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           T ++V  L      + +   F ++G I++  ++ DK TGR +G  FV + + E A+ A
Sbjct: 90  TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 147

>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 = 86.1 bits (214), Expect = 6e-22
 Identities = 25/105 (23%), Positives = 44/105 (41%), Gaps = 11/105 (10%)

Query: 27  GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE-AVVITDKNTGRSKGYGFVTFREPEA 85
           G +  + +F+G L  E   + +   F  FG IL+   ++ D +TG SKGY F+ F   +A
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60

Query: 86  ARRACADPT-PFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSG 129
           +  A       ++  R    + A     +        + +   SG
Sbjct: 61  SDAAIEAMNGQYLCNRPITVSYA---FKKDS------KGSGPSSG 96

>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 = 88.0 bits (219), Expect = 9e-22
 Identities = 22/58 (37%), Positives = 30/58 (51%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          T + V  L      E  R  F   GEI    ++ DK TG+S GYGFV + +P+ A +A
Sbjct: 3  TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 81.9 bits (203), Expect = 2e-19
 Identities = 17/60 (28%), Positives = 31/60 (51%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             ++V GL      + + + F Q+G I+ + ++ D+ TG S+G GF+ F +   A  A  
Sbjct: 89  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148

>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 = 85.4 bits (212), Expect = 1e-21
 Identities = 32/100 (32%), Positives = 45/100 (45%), Gaps = 6/100 (6%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG      P  +     VFVG L    + E +   F Q G + +  +  D+  G+
Sbjct: 1   GSSGSSGMF----PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGK 55

Query: 72  SKGYGFVTFREPEAARRACADPTPF-IDGRRANCNLASLG 110
            K +GFV F+ PE+   A A      + GR  N +  S G
Sbjct: 56  PKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPSSG 95

>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 = 85.8 bits (213), Expect = 1e-21
 Identities = 15/87 (17%), Positives = 29/87 (33%), Gaps = 4/87 (4%)

Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
            TT   +F+G L        ++    +       + + D  TG ++ +G+V F   E   
Sbjct: 14  STTPFNLFIGNLNPNKSVAELKVAISELFAK-NDLAVVDVRTGTNRKFGYVDFESAEDLE 72

Query: 88  RACADPTPFIDGRRANCNLASLGRPRP 114
           +A       + G           + R 
Sbjct: 73  KALELTGLKVFGNEIKLEKP---KGRD 96

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 85.4 bits (212), Expect = 2e-21
 Identities = 24/106 (22%), Positives = 42/106 (39%), Gaps = 12/106 (11%)

Query: 12  GSSSSSG-FQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTG 70
           GSS SSG F+Y  S        K+F+ GL +    E +    +  G + +  ++T++  G
Sbjct: 1   GSSGSSGVFRYSTSLEK----HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AG 55

Query: 71  RSKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPRP 114
           + KG  +V +     A +A    D             ++      P
Sbjct: 56  KPKGLAYVEYENESQASQAVMKMDGMTI-KENIIKVAIS---NSGP 97

>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 = 84.5 bits (210), Expect = 2e-21
 Identities = 20/87 (22%), Positives = 32/87 (36%), Gaps = 7/87 (8%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKN-TGRSKGYGFVTFREPEAARRAC 90
           TKV +G L      + +   F  +G+I    +  ++     SKGY +V F  P+ A +A 
Sbjct: 5   TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64

Query: 91  A--DPTPFIDGRRANCNLASLGRPRPQ 115
              D     DG+               
Sbjct: 65  KHMDGGQI-DGQEITATAV---LAPWP 87

>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 = 85.5 bits (212), Expect = 2e-21
 Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 5/83 (6%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA- 91
            V+VG + + + ++ +  +F   G I    ++ DK +G  KGY ++ F E  +   A A 
Sbjct: 38  SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAM 97

Query: 92  DPTPFIDGRRANCNLASLGRPRP 114
           D T F  GR          R   
Sbjct: 98  DETVF-RGRTIKVLPK---RTNM 116

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 84.6 bits (210), Expect = 2e-21
 Identities = 14/85 (16%), Positives = 29/85 (34%), Gaps = 9/85 (10%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             +    L++    + ++  FE   E     +      G+SKG  ++ F+    A +   
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKGIAYIEFKSEADAEKNLE 71

Query: 92  DPTPF-IDGRRANCNLASLGRPRPQ 115
           +     IDGR  +         +  
Sbjct: 72  EKQGAEIDGRSVSLYYT---GEKGG 93

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 85.1 bits (211), Expect = 2e-21
 Identities = 26/85 (30%), Positives = 41/85 (48%), Gaps = 8/85 (9%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
            ++ V  + +  +   +R+ F QFG+IL+  +I ++    SKG+GFVTF     A RA  
Sbjct: 30  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRARE 87

Query: 92  --DPTPFIDGRRANCNLASLGRPRP 114
               T   +GR+   N A     R 
Sbjct: 88  KLHGTVV-EGRKIEVNNA---TARV 108

>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 = 89.0 bits (221), Expect = 2e-21
 Identities = 27/129 (20%), Positives = 46/129 (35%), Gaps = 7/129 (5%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             + V  L+    +E + + F QFG + +AVV+ D + GR+ G GFV F     AR+A  
Sbjct: 97  AALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALE 155

Query: 92  --DPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSGSTQATRGPYIGSFGYQQPLP 149
                 F+        +      +     G           TQ           + QP  
Sbjct: 156 RCGDGAFLLTTTPRPVIVEP-MEQFDDEDGLPEKLMQK---TQQYHKEREQPPRFAQPGT 211

Query: 150 YNYQQGMVY 158
           + ++    +
Sbjct: 212 FEFEYASRW 220

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 75.5 bits (186), Expect = 2e-16
 Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 9/82 (10%)

Query: 29  TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
           T   ++FVG L  +   E  +R FE++GE  E  +       R +G+GF+       A  
Sbjct: 20  TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN------RDRGFGFIRLESRTLAEI 73

Query: 89  ACA--DPTPFIDGRRANCNLAS 108
           A A  D T  +  R      A+
Sbjct: 74  AKAELDGTI-LKSRPLRIRFAT 94

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 88.2 bits (218), Expect = 3e-21
 Identities = 29/187 (15%), Positives = 56/187 (29%), Gaps = 12/187 (6%)

Query: 7   PGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFG--EILEAVVI 64
             P  G     G               +++G L W T  E +       G  +ILE    
Sbjct: 44  LPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFF 103

Query: 65  TDKNTGRSKGYGFVTFREPEAARRACAD-PTPFIDGRRANCNLAS-------LGRPRPQV 116
            ++  G+SKG+  V      ++++     P   + G+       +         + R   
Sbjct: 104 ENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTT 163

Query: 117 LYGRLRPATLFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVYPSYGYATYGPEYVYPQGI 176
             G++           ++R  +      +   P     G  +P       GP   +P G 
Sbjct: 164 QSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPG-PAGPGGPPPPFPAG- 221

Query: 177 YNPYQQY 183
              +  +
Sbjct: 222 QTHHHHH 228

>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 = 84.3 bits (209), Expect = 4e-21
 Identities = 27/105 (25%), Positives = 41/105 (39%), Gaps = 13/105 (12%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG    +          + +  L++    ET++  FE+       + +     G+
Sbjct: 1   GSSGSSGNSTWSGES-----KTLVLSNLSYSATEETLQEVFEKATF----IKVPQNQNGK 51

Query: 72  SKGYGFVTFREPEAARRACADPTPF-IDGRRANCNLASLGRPRPQ 115
           SKGY F+ F   E A+ A        I+GR     L     PR  
Sbjct: 52  SKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQ---GPRGS 93

>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 = 83.8 bits (208), Expect = 7e-21
 Identities = 28/100 (28%), Positives = 39/100 (39%), Gaps = 3/100 (3%)

Query: 27  GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
           G      +F+  L     ++ +   F  FG IL   V+ D     SKGYGFV F   EAA
Sbjct: 1   GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAA 58

Query: 87  RRACADPT-PFIDGRRANCNLASLGRPRPQVLYGRLRPAT 125
            RA        ++ R+         + R   L  R +  T
Sbjct: 59  ERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFT 98

>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 = 83.5 bits (207), Expect = 8e-21
 Identities = 31/105 (29%), Positives = 42/105 (40%), Gaps = 8/105 (7%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG               V+VGGL  +     +   F Q G ++   +  D+ TG+
Sbjct: 1   GSSGSSG-----PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQ 55

Query: 72  SKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPRP 114
            +GYGFV F   E A  A    D    + G+    N AS      
Sbjct: 56  HQGYGFVEFLSEEDADYAIKIMDMIK-LYGKPIRVNKASAHNKNL 99

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 83.1 bits (206), Expect = 8e-21
 Identities = 18/81 (22%), Positives = 27/81 (33%), Gaps = 5/81 (6%)

Query: 27  GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
           G +    VFV G      S  +  YF  FG +    V+ DK+ G    +  V   +  A 
Sbjct: 4   GSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVAS--VVMDKDKGV---FAIVEMGDVGAR 58

Query: 87  RRACADPTPFIDGRRANCNLA 107
               +     + G R      
Sbjct: 59  EAVLSQSQHSLGGHRLRVRPR 79

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 83.6 bits (207), Expect = 9e-21
 Identities = 20/109 (18%), Positives = 37/109 (33%), Gaps = 7/109 (6%)

Query: 27  GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
           G     +V    L    +   ++    ++GE+ E  ++    T +  G   V F     A
Sbjct: 2   GQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGA 61

Query: 87  RRACA--DPTPFIDGRRANCNLASLGRPR----PQVLYGRLRPATLFSG 129
           +        T    G   +  L   G+ R      ++ G   P T+ +G
Sbjct: 62  KETVKNLHLTSV-MGNIIHAQLDIKGQQRMKYYELIVNGSYTPQTVPTG 109

>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 = 83.1 bits (206), Expect = 1e-20
 Identities = 25/93 (26%), Positives = 46/93 (49%), Gaps = 3/93 (3%)

Query: 25  PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPE 84
           P  D +   VFVG + +E   E ++  F + G ++   ++ D+ TG+ KGYGF  +++ E
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 85  AARRACA--DPTPFIDGRRANCNLASLGRPRPQ 115
            A  A    +   F  GR    + A+  + + +
Sbjct: 62  TALSAMRNLNGREF-SGRALRVDNAASEKNKEE 93

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 84.1 bits (208), Expect = 2e-20
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 9/88 (10%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC- 90
             +FV  +  E Q + ++  F  +GEI    +  D+ TG SKGY  V +   + A  A  
Sbjct: 73  WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 132

Query: 91  ----ADPTPFIDGRRANCNLASLGRPRP 114
               A+    I G+    +   +  P+ 
Sbjct: 133 ALNGAE----IMGQTIQVDWCFVKGPKR 156

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 81.9 bits (203), Expect = 2e-20
 Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 2/60 (3%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           ++FV  L ++   + ++  F + G +L A +  +   G+SKG G V F  PE A RAC 
Sbjct: 9  CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACR 66

>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 = 81.2 bits (201), Expect = 7e-20
 Identities = 31/109 (28%), Positives = 44/109 (40%), Gaps = 13/109 (11%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDK-NTG 70
           GSS SSG      P   TT +K+ V  + ++     +R  F  FGE+    +      TG
Sbjct: 1   GSSGSSG----QVPKKQTT-SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTG 55

Query: 71  RSKGYGFVTFREPEAARRAC---ADPTPFIDGRRANCNLASLGRPRPQV 116
             +G+GFV F   + A++A       T    GRR     A        V
Sbjct: 56  AHRGFGFVDFITKQDAKKAFNALCHSTHL-YGRRLVLEWA---DSEVTV 100

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 80.8 bits (200), Expect = 8e-20
 Identities = 22/100 (22%), Positives = 36/100 (36%), Gaps = 15/100 (15%)

Query: 23  NSPFGDTTY---TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVT 79
               G         +FV G+  E   E +   F ++GEI    +  D+ TG  KGY  V 
Sbjct: 12  GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 71

Query: 80  FREPEAARRAC-----ADPTPFIDGRRANCNLASLGRPRP 114
           +   + A+ A       D    + G+  + +       R 
Sbjct: 72  YETYKEAQAAMEGLNGQD----LMGQPISVDWC---FVRG 104

>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 = 80.9 bits (200), Expect = 1e-19
 Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 9/88 (10%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC- 90
             +FV G+  E   E +   F ++GEI    +  D+ TG  KGY  V +   + A+ A  
Sbjct: 23  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82

Query: 91  ----ADPTPFIDGRRANCNLASLGRPRP 114
                D    + G+  + +   +  P  
Sbjct: 83  GLNGQD----LMGQPISVDWCFVRGPPK 106

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 80.5 bits (199), Expect = 2e-19
 Identities = 26/107 (24%), Positives = 45/107 (42%), Gaps = 5/107 (4%)

Query: 2   AYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEA 61
                    S +++++  + +  P G      +F+  L  E     +   F  FG ++ A
Sbjct: 15  TSPLASVALSAAAAAAAGKQIEGPEG----CNLFIYHLPQEFTDTDLASTFLPFGNVISA 70

Query: 62  VVITDKNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRRANCNLA 107
            V  DK T  SK +GFV+F  P++A+ A      F +  +R    L 
Sbjct: 71  KVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117

>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 = 80.0 bits (198), Expect = 2e-19
 Identities = 28/122 (22%), Positives = 50/122 (40%), Gaps = 13/122 (10%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG     +       + VFV  L ++   + ++  F   G ++ A ++ DK+ G+
Sbjct: 1   GSSGSSG-----ALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GK 54

Query: 72  SKGYGFVTFREPEAARRACADPTPF----IDGRRANCNLASLGRPRPQVLYGRLRPATLF 127
           S+G G VTF +   A +A +    F    +  R  +  +     P+           +  
Sbjct: 55  SRGIGTVTFEQSIEAVQAISM---FNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGP 111

Query: 128 SG 129
           S 
Sbjct: 112 SS 113

>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 = 79.6 bits (197), Expect = 2e-19
 Identities = 27/106 (25%), Positives = 43/106 (40%), Gaps = 14/106 (13%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG +   +       +++FVG L  +   E MR+ FE++G+  E  +       +
Sbjct: 1   GSSGSSGGEKTFTQR-----SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------K 49

Query: 72  SKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPRPQ 115
            KG+GF+       A  A    D  P   G++     A        
Sbjct: 50  DKGFGFIRLETRTLAEIAKVELDNMPL-RGKQLRVRFACHSASLTS 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 = 79.2 bits (196), Expect = 3e-19
 Identities = 24/93 (25%), Positives = 37/93 (39%), Gaps = 8/93 (8%)

Query: 20  QYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVT 79
                  G  T  K+ V  L +      ++  F +FG + +A V  D+ +GRS G   V 
Sbjct: 18  SGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVH 76

Query: 80  FREPEAARRACADPTPF----IDGRRANCNLAS 108
           F     A +A      +    +DGR  N  L +
Sbjct: 77  FERKADALKAMKQ---YNGVPLDGRPMNIQLVT 106

>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 = 81.0 bits (201), Expect = 3e-19
 Identities = 23/57 (40%), Positives = 31/57 (54%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
            +FVG L      ET+R  F+ F   L   V+ D  TG S+GYGFV+F   + A+ A
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 145

>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 = 70.2 bits (173), Expect = 3e-15
 Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 4/77 (5%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA-- 91
           ++VG L      + +++YF+  G I    ++ DK   ++  Y FV + +   A  A    
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61

Query: 92  DPTPFIDGRRANCNLAS 108
           +    I+      N A 
Sbjct: 62  NGKQ-IENNIVKINWAF 77

>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 = 78.9 bits (195), Expect = 5e-19
 Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 12/87 (13%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC-- 90
            +FV  +  E Q + ++  F  +GEI    +  D+ TG SKGY  V +   + A  A   
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 91  ---ADPTPFIDGRRANCNLASLGRPRP 114
              A+    I G+    +       + 
Sbjct: 88  LNGAE----IMGQTIQVDWC---FVKG 107

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 78.6 bits (194), Expect = 5e-19
 Identities = 14/74 (18%), Positives = 28/74 (37%), Gaps = 1/74 (1%)

Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
           D     V++ G   +   + ++ + E  G++L   +    +    KG  FV F   E+A+
Sbjct: 8   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAK 66

Query: 88  RACADPTPFIDGRR 101
           +    P        
Sbjct: 67  KFVETPGQKYKETD 80

>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 = 78.5 bits (194), Expect = 5e-19
 Identities = 28/78 (35%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 12 GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
          GSS SSG +            K+FVG L  +   E + R F+ FG I E  V+   + G 
Sbjct: 1  GSSGSSGSESRGGRD-----RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GS 54

Query: 72 SKGYGFVTFREPEAARRA 89
          SKG  FV F     A+ A
Sbjct: 55 SKGCAFVKFSSHTEAQAA 72

>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 = 79.0 bits (195), Expect = 7e-19
 Identities = 24/95 (25%), Positives = 37/95 (38%), Gaps = 4/95 (4%)

Query: 23  NSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFRE 82
               G  T  K+ V  L +      ++  F +FG + +A V  D+ +GRS G   V F  
Sbjct: 27  GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFER 85

Query: 83  PEAARRACA--DPTPFIDGRRANCNLASLGRPRPQ 115
              A +A       P +DGR  +  L +       
Sbjct: 86  RADALKAMKQYKGVP-LDGRPMDIQLVASQIDLEH 119

>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 = 78.5 bits (194), Expect = 9e-19
 Identities = 24/111 (21%), Positives = 40/111 (36%), Gaps = 8/111 (7%)

Query: 12  GSSSSSGFQYLNSPF------GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVIT 65
           GSS SSG +    P       G+     +++  L+       +   F +F E     +  
Sbjct: 1   GSSGSSGEEIRKIPMFSSYNPGEPN-KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQF 59

Query: 66  DKNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRRANCNLASLGRPRPQ 115
              TGR +G  F+TF   E A +A      + + G+          + R  
Sbjct: 60  RMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRSS 110

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 77.4 bits (191), Expect = 2e-18
 Identities = 26/94 (27%), Positives = 38/94 (40%), Gaps = 14/94 (14%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAV--------VITDKNTGRSKGYGFVTFREP 83
             +FV GL      E++  YF+Q G I            + TD+ TG+ KG   V+F +P
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 84  EAARRACA--DPTPFIDGRRANCNLASLGRPRPQ 115
            +A+ A    D   F  G     + A     R  
Sbjct: 68  PSAKAAIDWFDGKEF-SGNPIKVSFA---TRRAD 97

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 78.3 bits (193), Expect = 3e-18
 Identities = 23/93 (24%), Positives = 41/93 (44%), Gaps = 5/93 (5%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             ++VG L++ T  E +   F + G+I + ++  DK    + G+ FV +     A  A  
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99

Query: 92  --DPTPFIDGRRANCNLASLGRPRPQVLYGRLR 122
             + T  +D R    +  +  +   Q  YGR R
Sbjct: 100 YINGTR-LDDRIIRTDWDAGFKEGRQ--YGRGR 129

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 76.5 bits (189), Expect = 5e-18
 Identities = 14/74 (18%), Positives = 30/74 (40%), Gaps = 1/74 (1%)

Query: 16 SSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGY 75
          +SG Q   +   +   T +++  L      + +    + FG+++   ++ D  +G S+G 
Sbjct: 10 ASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGV 68

Query: 76 GFVTFREPEAARRA 89
          GF      E     
Sbjct: 69 GFARMESTEKCEAV 82

>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 = 75.3 bits (186), Expect = 7e-18
 Identities = 29/105 (27%), Positives = 46/105 (43%), Gaps = 22/105 (20%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG              K+FVG ++    S+ +R  FE+ G ++E  V+       
Sbjct: 1   GSSGSSG-----------NTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV------- 42

Query: 72  SKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPRP 114
            K Y FV   +   A+ A A  +      G+R N  L++ G+ + 
Sbjct: 43  -KDYAFVHMEKEADAKAAIAQLNGKEV-KGKRINVELSTKGQKKS 85

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 78.0 bits (192), Expect = 7e-18
 Identities = 24/118 (20%), Positives = 38/118 (32%), Gaps = 8/118 (6%)

Query: 2   AYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEA 61
            Y                       G  T  K+ V  L +      ++  F +FG + +A
Sbjct: 59  PYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKA 118

Query: 62  VVITDKNTGRSKGYGFVTFREPEAARRACADPTPF----IDGRRANCNLASLGRPRPQ 115
            V  D+ +GRS G   V F     A +A      +    +DGR  +  L +       
Sbjct: 119 AVDYDR-SGRSLGTADVHFERRADALKAMKQ---YKGVPLDGRPMDIQLVASQIDLEH 172

>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 = 75.4 bits (186), Expect = 9e-18
 Identities = 25/87 (28%), Positives = 38/87 (43%), Gaps = 11/87 (12%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAV--------VITDKNTGRSKGYGFVTFREP 83
             +FV GL      E++  YF+Q G I            + TD+ TG+ KG   V+F +P
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 84  EAARRACA--DPTPFIDGRRANCNLAS 108
            +A+ A    D   F  G     + A+
Sbjct: 74  PSAKAAIDWFDGKEF-SGNPIKVSFAT 99

>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 = 74.7 bits (184), Expect = 2e-17
 Identities = 28/107 (26%), Positives = 45/107 (42%), Gaps = 7/107 (6%)

Query: 10  GSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNT 69
            SGSS  SG   +  P G+    +++VG L  + +++ +   F ++G I +  +   KN 
Sbjct: 2   SSGSSGMSGGGVIRGPAGNND-CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNR 57

Query: 70  GRSKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPRP 114
                + FV F +P  A  A    D   + DG R        GR   
Sbjct: 58  RGGPPFAFVEFEDPRDAEDAVYGRDGYDY-DGYRLRVEFPRSGRGTG 103

>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 = 78.5 bits (194), Expect = 2e-17
 Identities = 5/58 (8%), Positives = 18/58 (31%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
             +++           +R   +    +  ++ +       S+ + ++     E AR  
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYC 175

>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 = 77.7 bits (192), Expect = 5e-17
 Identities = 19/85 (22%), Positives = 34/85 (40%), Gaps = 5/85 (5%)

Query: 32  TKVFVGGLAWETQSE-TMRRYFEQFGEILEAVVITD-KNTGRSKGYGFVTFREPEAARRA 89
            ++ +  L+ E   E  +R  FE FG I +  +    K    +    F+ F   ++A RA
Sbjct: 211 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 270

Query: 90  CADPTPFIDGRRANCNLASLGRPRP 114
                  +  R  + +LA     +P
Sbjct: 271 LQMNRSLLGNREISVSLAD---KKP 292

>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 = 74.3 bits (183), Expect = 7e-16
 Identities = 12/58 (20%), Positives = 21/58 (36%), Gaps = 2/58 (3%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          T V V  L        + +YF+  G I+   V       ++  +  + F   + A  A
Sbjct: 42 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAA 97

>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 = 73.1 bits (180), Expect = 6e-17
 Identities = 19/106 (17%), Positives = 34/106 (32%), Gaps = 23/106 (21%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG              K+++G L+    ++ +R+ F                   
Sbjct: 1   GSSGSSGM------------NKLYIGNLSPAVTADDLRQLFGDRKLP------LAGQVLL 42

Query: 72  SKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPRPQ 115
             GY FV + +   A RA         + G+    + +     +  
Sbjct: 43  KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYS---VSKKL 85

>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 = 72.6 bits (179), Expect = 7e-17
 Identities = 29/106 (27%), Positives = 42/106 (39%), Gaps = 26/106 (24%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG              K+F+G L  E   + +R  FEQ+G++LE  +I       
Sbjct: 1   GSSGSSG------------MVKLFIGNLPREATEQEIRSLFEQYGKVLECDII------- 41

Query: 72  SKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPRPQ 115
            K YGFV   +  AA  A           G   N   +   + + +
Sbjct: 42  -KNYGFVHIEDKTAAEDAIRNLHHYKL-HGVNINVEAS---KNKSK 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 = 73.2 bits (180), Expect = 7e-17
 Identities = 22/118 (18%), Positives = 41/118 (34%), Gaps = 12/118 (10%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG         ++      +  + +      + ++ E       AV +   N G+
Sbjct: 1   GSSGSSG-----EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQ 55

Query: 72  SKGYGFVTFREPEAARRACADPTPFIDGRRANCNLAS-------LGRPRPQVLYGRLR 122
             G   V F+  + AR++       ++GR A  ++ +          P  Q   G   
Sbjct: 56  GLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGPSS 113

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 72.7 bits (179), Expect = 9e-17
 Identities = 26/104 (25%), Positives = 43/104 (41%), Gaps = 9/104 (8%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG +    P         +VG L + T    +   F+    I    ++ DK+T +
Sbjct: 1   GSSGSSGKELPTEP-----PYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDK 54

Query: 72  SKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPRPQ 115
            KG+ +V F E ++ + A       +  R    ++A     R Q
Sbjct: 55  FKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIA---EGRKQ 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 = 72.7 bits (179), Expect = 1e-16
 Identities = 32/109 (29%), Positives = 42/109 (38%), Gaps = 15/109 (13%)

Query: 12  GSSSSSGFQYLNS-----PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITD 66
           GSS SSG                    V+ GG+A     + MR+ F  FG+I+E  V  +
Sbjct: 1   GSSGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE 60

Query: 67  KNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRRANCNLASLGRPRP 114
                 KGY FV F   E+A  A        I+G    C     G+  P
Sbjct: 61  ------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKC---YWGKESP 100

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 71.5 bits (176), Expect = 1e-16
 Identities = 25/84 (29%), Positives = 35/84 (41%), Gaps = 8/84 (9%)

Query: 24  SPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREP 83
           S   D T T ++VGGL        +R +F QFGEI    V+        +   F+ F   
Sbjct: 5   SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATR 58

Query: 84  EAARRACADPT--PFIDGRRANCN 105
           +AA  A         ++GRR N  
Sbjct: 59  QAAEVAAEKSFNKLIVNGRRLNVK 82

>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 = 71.5 bits (176), Expect = 2e-16
 Identities = 30/105 (28%), Positives = 46/105 (43%), Gaps = 22/105 (20%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG             TK+ VG ++    ++ +R  FE++G ++E  ++       
Sbjct: 1   GSSGSSG----------KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV------- 43

Query: 72  SKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPRP 114
            K Y FV     E A  A    D T F  G+R +  L++  R R 
Sbjct: 44  -KDYAFVHMERAEDAVEAIRGLDNTEF-QGKRMHVQLST-SRLRT 85

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 71.7 bits (176), Expect = 2e-16
 Identities = 27/97 (27%), Positives = 37/97 (38%), Gaps = 5/97 (5%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG    NSP        V + GL +    E + ++F     +   + +     GR
Sbjct: 1   GSSGSSG----NSPDTANDGF-VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGR 55

Query: 72  SKGYGFVTFREPEAARRACADPTPFIDGRRANCNLAS 108
           S G  FV F   E A +A       I  R      +S
Sbjct: 56  STGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS 92

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 71.7 bits (176), Expect = 2e-16
 Identities = 31/113 (27%), Positives = 49/113 (43%), Gaps = 19/113 (16%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAV--------V 63
           GSS SSG      P  D+  + ++V GL      + +  +F+Q G +            +
Sbjct: 1   GSSGSSG-----DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHI 55

Query: 64  ITDKNTGRSKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPRP 114
             DK TG+ KG   V++ +P  A+ A    D   F  G +   +LA   R +P
Sbjct: 56  YLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF-QGSKLKVSLA---RKKP 104

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 71.2 bits (175), Expect = 3e-16
 Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAV-VITDKNTGRSKGYGFVTFREPEAARRA 89
            +++G L        + R F   GE + +V +I ++ TG   GY FV F +   A + 
Sbjct: 10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKC 68

>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 = 70.8 bits (174), Expect = 5e-16
 Identities = 26/119 (21%), Positives = 42/119 (35%), Gaps = 26/119 (21%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG               +FV  LA     E + + F QFG++     +       
Sbjct: 1   GSSGSSG---------MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL------- 44

Query: 72  SKGYGFVTFREPEAARRACA-----DPTPFIDGRRANCNLASLGRPRPQVLYGRLRPAT 125
            K Y F+ F E + A +A       D    ++G       A     + +    + + A+
Sbjct: 45  -KDYAFIHFDERDGAVKAMEEMNGKD----LEGENIEIVFAKPPDQKRKERKAQRQAAS 98

>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 = 70.0 bits (172), Expect = 9e-16
 Identities = 25/106 (23%), Positives = 36/106 (33%), Gaps = 17/106 (16%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG +   S         ++V  L   T  E + + F          V       +
Sbjct: 1   GSSGSSGDEDTMSSV-----KILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KK 49

Query: 72  SKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPRPQ 115
            + Y FV F   E A  A    +    +DG      LA   +P  +
Sbjct: 50  IRDYAFVHFSNREDAVEAMKALNGKV-LDGSPIEVTLA---KPVDK 91

>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 = 70.6 bits (173), Expect = 9e-16
 Identities = 21/93 (22%), Positives = 41/93 (44%)

Query: 9   PGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKN 68
            GS   S SG +   S         V++ GL +E +++ +  +F++   + +++ I    
Sbjct: 3   SGSSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGP 62

Query: 69  TGRSKGYGFVTFREPEAARRACADPTPFIDGRR 101
            G++ G GFV FR     + A      ++  R 
Sbjct: 63  NGKATGEGFVEFRNEADYKAALCRHKQYMGNRF 95

>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 = 72.7 bits (179), Expect = 1e-15
 Identities = 21/69 (30%), Positives = 29/69 (42%)

Query: 21 YLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 80
           +N          ++VG L  +     +   F   G IL   V  D  T RS GY +V F
Sbjct: 5  SMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNF 64

Query: 81 REPEAARRA 89
          ++P  A RA
Sbjct: 65 QQPADAERA 73

>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 = 70.4 bits (173), Expect = 8e-15
 Identities = 22/62 (35%), Positives = 29/62 (46%), Gaps = 2/62 (3%)

Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
            +    +F+  L     ++ +   F  FG IL   V+ D     SKGYGFV F   EAA 
Sbjct: 100 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAE 157

Query: 88  RA 89
           RA
Sbjct: 158 RA 159

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 69.6 bits (171), Expect = 1e-15
 Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 4/87 (4%)

Query: 34  VFVGGLAWETQSETMRRYF-EQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA- 91
           +FVG L  +     +  +F + +       V+ D+ TG SKGYGFV F +    +RA   
Sbjct: 12  LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTE 70

Query: 92  -DPTPFIDGRRANCNLASLGRPRPQVL 117
                 +  +    ++A     R + +
Sbjct: 71  CQGAVGLGSKPVRLSVAIPKASRVKPV 97

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 69.2 bits (170), Expect = 2e-15
 Identities = 20/91 (21%), Positives = 35/91 (38%), Gaps = 11/91 (12%)

Query: 27  GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
           G+ + T++FV     + Q   +   F  FG + E  ++         G+ FV F E E+A
Sbjct: 27  GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESA 78

Query: 87  RRACA--DPTPFIDGRRANCNLASLGRPRPQ 115
            +A        F   +      + L   R +
Sbjct: 79  AKAIEEVHGKSF-ANQPLEVVYSKLPAKRYR 108

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 69.2 bits (169), Expect = 3e-15
 Identities = 19/94 (20%), Positives = 33/94 (35%), Gaps = 12/94 (12%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDK--NTGRSKGYGFVTFREPEAARRAC 90
           KVFVGGL  +   + +   F +FG ++       +  +    KGY F+ F+E  + +   
Sbjct: 10  KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69

Query: 91  ADPTPF-------IDGRRANCNLASLGRPRPQVL 117
                        +             + RP  L
Sbjct: 70  DACLEEDGKLYLCVSSPTIKDKPV---QIRPWNL 100

>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 = 69.1 bits (169), Expect = 3e-15
 Identities = 20/101 (19%), Positives = 34/101 (33%), Gaps = 3/101 (2%)

Query: 4   QSIPGPGSGSSSSSGFQYLNSPFG---DTTYTKVFVGGLAWETQSETMRRYFEQFGEILE 60
             +   GS  +S +G Q +              V + GL +    E + ++F     +  
Sbjct: 12  SGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPN 71

Query: 61  AVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRR 101
            + +     G+  G  FV F   E A +A       I  R 
Sbjct: 72  GITLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRY 112

>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 = 68.4 bits (168), Expect = 4e-15
 Identities = 14/84 (16%), Positives = 34/84 (40%), Gaps = 5/84 (5%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKN-TGRSKGYGFVTFREPEAARRACA 91
             F+G L ++   E+++ +F     I    +  + +   R KG+G+  F + ++   A +
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 92  DPTPFIDGRRANCNLASLGRPRPQ 115
                +  +R   ++A        
Sbjct: 76  LNEESLGNKRIRVDVA---DQAQD 96

>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 = 68.0 bits (167), Expect = 5e-15
 Identities = 15/82 (18%), Positives = 34/82 (41%), Gaps = 5/82 (6%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNT-GRSKGYGFVTFREPEAARRACA 91
             F+G L ++   E+++ +F     I    +  + +   R KG+G+  F + ++   A +
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79

Query: 92  DPTPFIDGRRANCNLASLGRPR 113
                +  RR   ++A      
Sbjct: 80  LNEESLGNRRIRVDVA---DQA 98

>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 = 68.0 bits (167), Expect = 5e-15
 Identities = 22/78 (28%), Positives = 31/78 (39%), Gaps = 7/78 (8%)

Query: 12 GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
          GSS SSG         D     ++VG L+ +     + + F Q G      +IT+  +  
Sbjct: 1  GSSGSSG-----MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSND 55

Query: 72 SKGYGFVTFREPEAARRA 89
             Y FV F E   A  A
Sbjct: 56 P--YCFVEFYEHRDAAAA 71

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 69.1 bits (169), Expect = 6e-15
 Identities = 22/84 (26%), Positives = 31/84 (36%), Gaps = 9/84 (10%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
            KV+VG L        + R F  +G +    V  +       G+ FV F +P  A  A  
Sbjct: 74  CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVR 128

Query: 92  --DPTPFIDGRRANCNLASLGRPR 113
             D      G R    L++ G  R
Sbjct: 129 ELDGRTL-CGCRVRVELSN-GEKR 150

>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 = 67.3 bits (165), Expect = 7e-15
 Identities = 20/81 (24%), Positives = 30/81 (37%), Gaps = 5/81 (6%)

Query: 12 GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
          GSS SSG     S  G    T + V  + +    + +  +F  +  I  +V +     G 
Sbjct: 1  GSSGSSG-----SSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGM 55

Query: 72 SKGYGFVTFREPEAARRACAD 92
            G   V F   + A  A  D
Sbjct: 56 PTGEAMVAFESRDEATAAVID 76

>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 = 66.9 bits (164), Expect = 1e-14
 Identities = 19/81 (23%), Positives = 30/81 (37%), Gaps = 5/81 (6%)

Query: 12 GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
          GSS SSG     +  G    T + V  + +    + +  +F  +  I  +V +     G 
Sbjct: 1  GSSGSSG-----ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGM 55

Query: 72 SKGYGFVTFREPEAARRACAD 92
            G   V F   + A  A  D
Sbjct: 56 PTGEAMVAFESRDEATAAVID 76

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 66.9 bits (164), Expect = 1e-14
 Identities = 17/90 (18%), Positives = 27/90 (30%), Gaps = 10/90 (11%)

Query: 25  PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPE 84
                  T  ++G +        +   F+ FG IL+     +      KG  F+ +   E
Sbjct: 21  RSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHE 74

Query: 85  AARRACADPTPF-IDGRRANCNLASLGRPR 113
            A         F   GR         G+ R
Sbjct: 75  QAAVCIVALANFPFQGRNLRT---GWGKER 101

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 66.9 bits (164), Expect = 1e-14
 Identities = 25/105 (23%), Positives = 41/105 (39%), Gaps = 17/105 (16%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG               ++V G   +     +R  F  FG I       D +   
Sbjct: 1   GSSGSSG-----ERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNI------IDLSMDP 47

Query: 72  SKGYGFVTFREPEAARRACADPTPF-IDGRRANCNLASLGRPRPQ 115
            +   FVT+ + E+A +A A+     ++  +   N+A   R +P 
Sbjct: 48  PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA---RKQPM 89

>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 = 66.7 bits (163), Expect = 2e-14
 Identities = 15/81 (18%), Positives = 35/81 (43%), Gaps = 5/81 (6%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVI--TDKNTGRSKGYGFVTFREPEA---A 86
            ++F+GG+    + E +     +  E +  V++  +  +  +++G+ FV +    A   A
Sbjct: 9   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68

Query: 87  RRACADPTPFIDGRRANCNLA 107
           RR        + G +   + A
Sbjct: 69  RRKLMPGRIQLWGHQIAVDWA 89

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 70.6 bits (172), Expect = 3e-14
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 31  YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
           +  +FV  + ++T    +RR FE +G I    ++  K +G+ +GY F+ +        A 
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161

Query: 91  ADPT-PFIDGRRANCNLA 107
                  IDGRR   ++ 
Sbjct: 162 KHADGKKIDGRRVLVDVE 179

>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 = 66.2 bits (162), Expect = 3e-14
 Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 4/85 (4%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             +++  L ++  +E M   F ++G I +  V    NT  ++G  +V + +   A+ A  
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKNAVD 65

Query: 92  DPTPF-IDGRRANCNLASLGRPRPQ 115
             + F +  R       +  R   +
Sbjct: 66  HLSGFNVSNRYLVVLYYNANRAFQK 90

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 65.0 bits (159), Expect = 7e-14
 Identities = 24/107 (22%), Positives = 34/107 (31%), Gaps = 12/107 (11%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA- 91
           KV+VG L        + R F  +G +    +  +       G+ FV F +P  A  A   
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56

Query: 92  -DPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSGSTQATRGP 137
            D      G R    L++    R        RP            GP
Sbjct: 57  LDGKVI-CGSRVRVELSTGMPRRS----RFDRPPARRKLLEVLFNGP 98

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 63.9 bits (156), Expect = 2e-13
 Identities = 19/93 (20%), Positives = 38/93 (40%), Gaps = 13/93 (13%)

Query: 24  SPFGDTTYTKVFVGGLAWETQSET-MRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFRE 82
            P G    +++F+G L  +  S+  + R F  +G I++  +           +GF+ F  
Sbjct: 15  VPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDN 66

Query: 83  PEAARRACA--DPTPFIDGRRANCNLASLGRPR 113
           P++ R A           G++    ++S    R
Sbjct: 67  PQSVRDAIEXESQEMN-FGKKLILEVSS-SNAR 97

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 63.6 bits (155), Expect = 2e-13
 Identities = 15/73 (20%), Positives = 28/73 (38%), Gaps = 8/73 (10%)

Query: 25 PFGDTTYTKVFVGGL------AWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFV 78
          P G   Y  + V G             + +   F + G+++      D+ TG++KG+ FV
Sbjct: 2  PLGSDQY--IVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFV 59

Query: 79 TFREPEAARRACA 91
                 A++   
Sbjct: 60 ECGSMNDAKKIIK 72

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 62.2 bits (152), Expect = 6e-13
 Identities = 20/92 (21%), Positives = 40/92 (43%), Gaps = 13/92 (14%)

Query: 32  TKVFVGGLAWETQSET-MRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
           +++F+G L  +  S+  + R F  +G I++  +           +GF+ F  P++ R A 
Sbjct: 11  SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 62

Query: 91  A--DPTPFIDGRRANCNLASLGRPRPQVLYGR 120
                     G++    ++S    RPQ  +G 
Sbjct: 63  ECESQEMN-FGKKLILEVSS-SNARPQFDHGD 92

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 62.0 bits (151), Expect = 1e-12
 Identities = 26/112 (23%), Positives = 41/112 (36%), Gaps = 19/112 (16%)

Query: 12  GSSSSSGFQYLNSPFGDTTY-------TKVFVGGLAWETQSET-MRRYFEQFGEILEAVV 63
           GSS SSG          T         ++VF+G L      ++ +   F ++G +    V
Sbjct: 1   GSSGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV 60

Query: 64  ITDKNTGRSKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPR 113
                    KGY FV +     AR A    +      G+  + N+A   +P 
Sbjct: 61  --------HKGYAFVQYSNERHARAAVLGENGRVL-AGQTLDINMAGEPKPD 103

>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 = 61.8 bits (150), Expect = 1e-12
 Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 7/81 (8%)

Query: 34  VFVGGLAWETQSETMRR---YFEQFGEILEAVVITDKNTGRSK---GYGFVTFREPEAAR 87
           VFV GL+       + +   YF +FG+I + V+    +   S+      +VT+   E A 
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 88  RACADPTPF-IDGRRANCNLA 107
           RA        +DGR    +L 
Sbjct: 78  RAIQCVNNVVVDGRTLKASLG 98

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 61.3 bits (149), Expect = 2e-12
 Identities = 15/78 (19%), Positives = 28/78 (35%), Gaps = 11/78 (14%)

Query: 32  TKVFVGGLAWETQS------ETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEA 85
           + + V  +              + + F +FG+I        +  G++KGY F+ +  P  
Sbjct: 16  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAH 73

Query: 86  ARRACA--DPTPFIDGRR 101
           A  A    D     D + 
Sbjct: 74  AVDAVKNADGYKL-DKQH 90

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 60.7 bits (148), Expect = 3e-12
 Identities = 14/61 (22%), Positives = 32/61 (52%), Gaps = 7/61 (11%)

Query: 34 VFVGGLAWETQSETMRR----YFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          +++  L  + + + +++     F +FG+IL+ +V     + + +G  FV F+E  +A  A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFKEVSSATNA 67

Query: 90 C 90
           
Sbjct: 68 L 68

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 61.8 bits (150), Expect = 3e-12
 Identities = 14/63 (22%), Positives = 26/63 (41%), Gaps = 5/63 (7%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVV-----ITDKNTGRSKGYGFVTFREPEAA 86
            +++V  LA   Q + ++  F ++ +           I     GR KG  F+     +AA
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105

Query: 87  RRA 89
            +A
Sbjct: 106 AKA 108

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 60.2 bits (146), Expect = 4e-12
 Identities = 17/78 (21%), Positives = 28/78 (35%), Gaps = 8/78 (10%)

Query: 12 GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
          GSS SSG     S        K+ +  +    Q E +     Q+G +     +   +   
Sbjct: 1  GSSGSSG-----SVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET- 54

Query: 72 SKGYGFVTFREPEAARRA 89
                VT+   + AR+A
Sbjct: 55 --AVVNVTYSSKDQARQA 70

>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 = 59.6 bits (145), Expect = 6e-12
 Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 6/59 (10%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
          T+++VGGL   T    + R F++FG I     +          + ++ +   +AA+ AC
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAAC 70

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 60.3 bits (146), Expect = 6e-12
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 7/63 (11%)

Query: 32 TKVFVGGLAWETQSETMRR----YFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
            V +  +  E   E ++          G+IL+   I    +  + G  ++ F   E+A+
Sbjct: 30 QVVLITNINPEVPKEKLQALLYALASSQGDILD---IVVDLSDDNSGKAYIVFATQESAQ 86

Query: 88 RAC 90
             
Sbjct: 87 AFV 89

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 59.5 bits (144), Expect = 1e-11
 Identities = 22/92 (23%), Positives = 31/92 (33%), Gaps = 5/92 (5%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFG--EILEAVVITDKNT 69
           GSS SSG      P G   Y  V + GL W    E ++ +       + +  V       
Sbjct: 1   GSSGSSGMM--LGPEGGEGYV-VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE 57

Query: 70  GRSKGYGFVTFREPEAARRACADPTPFIDGRR 101
           GR  G  FV     +  + A       +  R 
Sbjct: 58  GRQSGEAFVELESEDDVKLALKKDRESMGHRY 89

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 59.5 bits (144), Expect = 1e-11
 Identities = 22/94 (23%), Positives = 32/94 (34%), Gaps = 3/94 (3%)

Query: 11  SGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEI---LEAVVITDK 67
           SGSS       +           V + GL +   +E +  +F Q   I    E ++    
Sbjct: 3   SGSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY 62

Query: 68  NTGRSKGYGFVTFREPEAARRACADPTPFIDGRR 101
             GR  G  FV F   E A+ A       +  R 
Sbjct: 63  PDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRY 96

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 58.2 bits (141), Expect = 1e-11
 Identities = 13/65 (20%), Positives = 25/65 (38%), Gaps = 8/65 (12%)

Query: 32 TKVFVGGLAWETQS------ETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEA 85
          + + V  +              + + F +FG+I        +  G++KGY F+ +  P  
Sbjct: 2  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAH 59

Query: 86 ARRAC 90
          A  A 
Sbjct: 60 AVDAV 64

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 58.6 bits (142), Expect = 1e-11
 Identities = 26/90 (28%), Positives = 31/90 (34%), Gaps = 7/90 (7%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG     S F  TT   V + GL +      +  +F         V I     GR
Sbjct: 1   GSSGSSG-----SSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN--PMRVHIEIGPDGR 53

Query: 72  SKGYGFVTFREPEAARRACADPTPFIDGRR 101
             G   V F   E A  A A     +  R 
Sbjct: 54  VTGEADVEFATHEDAVAAMAKDKANMQHRY 83

>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 = 60.7 bits (146), Expect = 5e-11
 Identities = 32/226 (14%), Positives = 60/226 (26%), Gaps = 10/226 (4%)

Query: 34  VFVGGLAWETQSETMRR----YFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           +++  L  + + + +++     F QFG+IL+ +V     + + +G  FV F+E  +A  A
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIFKEVSSATNA 68

Query: 90  CADPTPF-IDGRRANCNLASLGRPRPQVLYGRLRPATLFSGSTQATRGPYIGSFGYQQPL 148
                 F    +      A         + G            +        +    Q  
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGG 128

Query: 149 PYNYQQGMVYPSYGYATYGPEYVYPQGIYNPYQQYVPIYGVPGTVNTAVY--PYGQLGQT 206
                 G V           +             Y+P  G+      A    P G +   
Sbjct: 129 GATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQ 188

Query: 207 IPGSHAYTPVQGYGMPGHQIMQFGGPNLNAITTSPLPTVQAPYPTV 252
                   P Q         + F            L  +   +P  
Sbjct: 189 QLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGF 234

>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 = 41.0 bits (95), Expect = 2e-04
 Identities = 13/57 (22%), Positives = 18/57 (31%), Gaps = 5/57 (8%)

Query: 35  FVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           F+  L  ET    +   F QF    E  ++  +         FV F     A  A  
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARD 262

>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 = 56.3 bits (136), Expect = 7e-11
 Identities = 13/78 (16%), Positives = 25/78 (32%), Gaps = 10/78 (12%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           + + V  L  ++  + +    + +        +      R+K   FVT    E A+ A  
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 92  --DPTPFIDGRRANCNLA 107
                 F  G+     L 
Sbjct: 59  MFHQYSF-RGKDLIVQLQ 75

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 56.3 bits (136), Expect = 1e-10
 Identities = 23/90 (25%), Positives = 34/90 (37%), Gaps = 6/90 (6%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG      P        V V G+ +      +R +F      ++AV +   + GR
Sbjct: 1   GSSGSSG---KPLPINPDDLY-VSVHGMPFSAMENDVRDFFHGLR--VDAVHLLKDHVGR 54

Query: 72  SKGYGFVTFREPEAARRACADPTPFIDGRR 101
           + G G V F  P+    A       +  R 
Sbjct: 55  NNGNGLVKFLSPQDTFEALKRNRMLMIQRY 84

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 55.8 bits (135), Expect = 1e-10
 Identities = 22/90 (24%), Positives = 33/90 (36%), Gaps = 12/90 (13%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG          TT   V + G  +    + +  +      +  A+ I     G 
Sbjct: 1   GSSGSSG----------TTCHTVKLRGAPFNVTEKNVMEFLAPLKPV--AIRIVRNAHGN 48

Query: 72  SKGYGFVTFREPEAARRACADPTPFIDGRR 101
             GY FV F   E  ++A      ++ GR 
Sbjct: 49  KTGYIFVDFSNEEEVKQALKCNREYMGGRY 78

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 56.8 bits (137), Expect = 1e-10
 Identities = 19/93 (20%), Positives = 27/93 (29%), Gaps = 2/93 (2%)

Query: 9   PGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKN 68
              G     G          TT   V + GL ++     +  +F     +   V I    
Sbjct: 24  MTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV--RVHIEIGP 81

Query: 69  TGRSKGYGFVTFREPEAARRACADPTPFIDGRR 101
            GR  G   V F   E A  A +     +  R 
Sbjct: 82  DGRVTGEADVEFATHEEAVAAMSKDRANMQHRY 114

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 55.7 bits (134), Expect = 2e-10
 Identities = 21/75 (28%), Positives = 29/75 (38%), Gaps = 3/75 (4%)

Query: 27  GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
           G +    V V GL      E +  YFE         V++ +   R    G +TFREP  A
Sbjct: 4   GSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ---RLGCGGVLTFREPADA 60

Query: 87  RRACADPTPFIDGRR 101
            R  A     + G +
Sbjct: 61  ERVLAQADHELHGAQ 75

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 54.5 bits (131), Expect = 5e-10
 Identities = 10/76 (13%), Positives = 23/76 (30%), Gaps = 3/76 (3%)

Query: 27  GDTTYTKVFVGGLAWETQSETMRRYFEQFG--EILEAVVITDKNTGRSKGYGFVTFREPE 84
            D  +  +   GL W    E +  +F           +       G+ +G   +     +
Sbjct: 8   VDDVFL-IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQ 66

Query: 85  AARRACADPTPFIDGR 100
             ++A      ++  R
Sbjct: 67  DVQKALEKHRMYMGQR 82

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 54.0 bits (130), Expect = 5e-10
 Identities = 10/62 (16%), Positives = 23/62 (37%), Gaps = 5/62 (8%)

Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVV-----ITDKNTGRSKGYGFVTFREPEAAR 87
          +++VG + +    E M  +F     +          +      + K + F+ FR  +   
Sbjct: 8  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 88 RA 89
          +A
Sbjct: 68 QA 69

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 54.5 bits (131), Expect = 6e-10
 Identities = 17/108 (15%), Positives = 33/108 (30%), Gaps = 14/108 (12%)

Query: 9   PGSGSSSSSGFQYLNSPFGDTTYTK-----VFVGGLAWETQSETMRRYFEQFGEILEAVV 63
                  SSG     S  GD+         + +  L  +     +      FG++   ++
Sbjct: 4   SHHHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM 63

Query: 64  ITDKNTGRSKGYGFVTFREPEAARRA---CADPTPFIDGRRANCNLAS 108
           +      + K   F+     EAA          TP + G+      ++
Sbjct: 64  L------KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN 105

>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 = 56.4 bits (135), Expect = 6e-10
 Identities = 13/82 (15%), Positives = 29/82 (35%), Gaps = 1/82 (1%)

Query: 19  FQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFV 78
            +  +    D     V++ G   +   + ++ + E  G++   + +        KG  FV
Sbjct: 97  PEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQV-LNIQMRRTLHKAFKGSIFV 155

Query: 79  TFREPEAARRACADPTPFIDGR 100
            F   E+A++    P       
Sbjct: 156 VFDSIESAKKFVETPGQKYKET 177

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 54.1 bits (130), Expect = 9e-10
 Identities = 15/117 (12%), Positives = 26/117 (22%), Gaps = 9/117 (7%)

Query: 1   MAYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE 60
           M         S      G      P       ++ +  L      + ++    +      
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMSKLPAKRY---RITMKNLPEGCSWQDLKDLARENSLE-- 55

Query: 61  AVVITDKNTGRSKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPRPQ 115
               +  NT    G G + F   E    A    +   F  G            P  +
Sbjct: 56  -TTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEF-RGSVITVERDDNPPPIRR 110

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 53.6 bits (129), Expect = 1e-09
 Identities = 19/78 (24%), Positives = 28/78 (35%), Gaps = 9/78 (11%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA---C 90
           V + GL        +    ++FG I   VV+        K    V F +   A  A    
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNAVNYA 77

Query: 91  ADPTPFIDGRRANCNLAS 108
           AD   +I G  A  N ++
Sbjct: 78  ADNQIYIAGHPAFVNYST 95

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 53.3 bits (128), Expect = 1e-09
 Identities = 25/101 (24%), Positives = 40/101 (39%), Gaps = 16/101 (15%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKV-FVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTG 70
           GSS SSG  +  S       + V  V GL        +    E+FG I   +++      
Sbjct: 1   GSSGSSGSHHKVSV------SPVVHVRGLCESVVEADLVEALEKFGTICYVMMM------ 48

Query: 71  RSKGYGFVTFREPEAARRA---CADPTPFIDGRRANCNLAS 108
             K    V F   ++A+      AD   +I G++A  N ++
Sbjct: 49  PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYST 89

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 53.0 bits (127), Expect = 2e-09
 Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 13/85 (15%)

Query: 12 GSSSSSGFQY-------LNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVI 64
          GSS SSG ++       + +    T    V  GGL        +    E+ G +   ++ 
Sbjct: 1  GSSGSSGAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP 60

Query: 65 TDKNTGRSKGYGFVTFREPEAARRA 89
           +      K Y F  +R  E ++RA
Sbjct: 61 PN------KPYSFARYRTTEESKRA 79

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 53.5 bits (128), Expect = 2e-09
 Identities = 18/105 (17%), Positives = 30/105 (28%), Gaps = 7/105 (6%)

Query: 4   QSIPGPGSGSSSSSGFQYLN-----SPFGDTTYTKVFVGGLAWETQSETMRRYFEQFG-- 56
             +   GS  +S +G Q +                V + GL W    E ++ +       
Sbjct: 12  SGLVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIH 71

Query: 57  EILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRR 101
           +    V       GR  G  FV     +  + A       +  R 
Sbjct: 72  DGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRY 116

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 52.5 bits (126), Expect = 3e-09
 Identities = 19/101 (18%), Positives = 37/101 (36%), Gaps = 16/101 (15%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKV-FVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTG 70
           GSS SSG +   +P      ++V  +  L  E     +      FG++   +++      
Sbjct: 1   GSSGSSGDKMDGAP------SRVLHIRKLPGEVTETEVIALGLPFGKVTNILML------ 48

Query: 71  RSKGYGFVTFREPEAARRA---CADPTPFIDGRRANCNLAS 108
           + K   F+     EAA       +  TP +  +      ++
Sbjct: 49  KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSN 89

>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 = 52.5 bits (126), Expect = 3e-09
 Identities = 31/121 (25%), Positives = 42/121 (34%), Gaps = 16/121 (13%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG      P   +   +V V GL      + ++ +  + G++  A V  D     
Sbjct: 1   GSSGSSG----GPPSRRSEN-RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD----- 50

Query: 72  SKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPRP-QVLYGRLRPATLFS 128
             G G V F   E    A    D T F            +    P    YGR R +   S
Sbjct: 51  --GTGVVEFVRKEDMTYAVRKLDNTKF-RSHEGETAYIRVKVDGPRSPSYGRSRSSGPSS 107

Query: 129 G 129
           G
Sbjct: 108 G 108

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 54.3 bits (130), Expect = 4e-09
 Identities = 6/62 (9%), Positives = 11/62 (17%)

Query: 30  TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
               +       E   E      ++ G      V            G + +     A   
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALET 181

Query: 90  CA 91
             
Sbjct: 182 LG 183

>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 = 43.9 bits (103), Expect = 1e-05
 Identities = 11/57 (19%), Positives = 19/57 (33%), Gaps = 6/57 (10%)

Query: 34 VFVGGLAWETQSE-TMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          + V GL     +   +   F  +G + +   +  K      G   V   +  A  RA
Sbjct: 7  LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRA 58

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 50.6 bits (121), Expect = 1e-08
 Identities = 11/78 (14%), Positives = 26/78 (33%), Gaps = 9/78 (11%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA---C 90
           + +  L  +     +      FG++   +++      + K   F+     EAA       
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVNYY 72

Query: 91  ADPTPFIDGRRANCNLAS 108
              TP + G+      ++
Sbjct: 73  TSVTPVLRGQPIYIQFSN 90

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 51.0 bits (122), Expect = 1e-08
 Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 6/59 (10%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
          T +    L   T +  ++  F +FG +   ++              V F EP  AR+A 
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAF 63

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 50.2 bits (120), Expect = 1e-08
 Identities = 15/88 (17%), Positives = 30/88 (34%), Gaps = 6/88 (6%)

Query: 27  GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
           G      V+VG L  + +   ++R   + G      V         +   F+ + +  AA
Sbjct: 15  GAPLAADVYVGNLPRDARVSDLKRALRELG-----SVPLRLTWQGPRRRAFLHYPDSAAA 69

Query: 87  RRACADPTPF-IDGRRANCNLASLGRPR 113
           ++A +      +        LA   R +
Sbjct: 70  QQAVSCLQGLRLGTDTLRVALARQQRDK 97

>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 = 51.1 bits (122), Expect = 4e-08
 Identities = 18/121 (14%), Positives = 39/121 (32%), Gaps = 9/121 (7%)

Query: 34  VFVGGLA-WETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA--C 90
           + V  L       +++   F  +G++    ++ +K     K    V   +   A+ A   
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH 60

Query: 91  ADPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSGSTQATRGPYIGSFGYQQPLPY 150
            +      G+     L+     +        +  T   G++   R    GS  +Q   P 
Sbjct: 61  LNGHKL-HGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPP 119

Query: 151 N 151
           +
Sbjct: 120 S 120

>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 = 50.7 bits (121), Expect = 6e-08
 Identities = 13/89 (14%), Positives = 27/89 (30%), Gaps = 9/89 (10%)

Query: 1   MAYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE 60
             Y + P        S  FQ +  P        + +  +      E ++  F   G +++
Sbjct: 95  KDYGNSPLHRFKKPGSKNFQNIFPP-----SATLHLSNIPPSVSEEDLKVLFSSNGGVVK 149

Query: 61  AVVITDKNTGRSKGYGFVTFREPEAARRA 89
                 K+    +    +     E A +A
Sbjct: 150 GFKFFQKD----RKMALIQMGSVEEAVQA 174

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 47.9 bits (114), Expect = 1e-07
 Identities = 18/84 (21%), Positives = 27/84 (32%), Gaps = 10/84 (11%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA- 91
           +V V GL      + ++ +  + G++  A V  D       G G V F   E    A   
Sbjct: 18  RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRK 70

Query: 92  -DPTPFIDGRRANCNLASLGRPRP 114
            D T F            +    P
Sbjct: 71  LDNTKF-RSHEGETAYIRVKVDGP 93

>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 = 48.5 bits (115), Expect = 5e-07
 Identities = 13/90 (14%), Positives = 27/90 (30%), Gaps = 7/90 (7%)

Query: 2  AYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKV-FVGGLAWET-QSETMRRYFEQFGEIL 59
          ++             S    +  P        V  V  L  E    +++   F  +G++ 
Sbjct: 4  SHHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQ 63

Query: 60 EAVVITDKNTGRSKGYGFVTFREPEAARRA 89
             ++ +K     K    V   +   A+ A
Sbjct: 64 RVKILFNK-----KENALVQMADGNQAQLA 88

>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 = 47.7 bits (113), Expect = 8e-07
 Identities = 13/89 (14%), Positives = 27/89 (30%), Gaps = 9/89 (10%)

Query: 1   MAYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE 60
             Y + P        S  FQ +  P        + +  +      E ++  F   G +++
Sbjct: 126 KDYGNSPLHRFKKPGSKNFQNIFPP-----SATLHLSNIPPSVSEEDLKVLFSSNGGVVK 180

Query: 61  AVVITDKNTGRSKGYGFVTFREPEAARRA 89
                 K+    +    +     E A +A
Sbjct: 181 GFKFFQKD----RKMALIQMGSVEEAVQA 205

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 43.0 bits (101), Expect = 8e-06
 Identities = 22/106 (20%), Positives = 38/106 (35%), Gaps = 15/106 (14%)

Query: 12  GSSSSSGFQYLNSPF----GDTTYTKV-FVGGLAWETQSET-MRRYFEQFGEILEAVVIT 65
           GSS SSG +    P           +V  +  L     S++ + +  E +G+I   +++ 
Sbjct: 1   GSSGSSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM- 59

Query: 66  DKNTGRSKGYGFVTFREPEAARRA---CADPTPFIDGRRANCNLAS 108
                R K   F+     E A      C     +  GR    +L+ 
Sbjct: 60  -----RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSE 100

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 42.9 bits (100), Expect = 4e-05
 Identities = 15/67 (22%), Positives = 23/67 (34%), Gaps = 15/67 (22%)

Query: 32  TKVFVGGL---------AWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFRE 82
             ++VGG+                 +R  F + G+I     +       SK  GFV F+ 
Sbjct: 135 KTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKY 188

Query: 83  PEAARRA 89
              A  A
Sbjct: 189 QANAEFA 195

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	258
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.88
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.86
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.85
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.85
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.85
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.85
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.84
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.84
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.84
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.84
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.84
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.84
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.84
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.83
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.83
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.83
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.83
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.83
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.83
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.83
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.83
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.83
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.83
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.83
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.83
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.83
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.82
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.82
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.82
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.82
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.82
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.82
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.82
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.82
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.82
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.82
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.82
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.82
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.82
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.82
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.81
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.81
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.81
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.81
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.81
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.81
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.81
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.81
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.81
2div_A	99	TRNA selenocysteine associated protein; structural	99.81
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.81
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.81
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.81
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.81
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.81
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.8
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.8
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.8
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.8
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.8
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.8
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.8
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.8
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.8
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.8
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.8
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.8
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.8
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.8
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.8
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.8
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.79
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.79
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.79
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.79
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.79
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.79
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.79
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.79
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.79
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.79
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.78
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.78
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.78
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.78
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.78
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.78
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.77
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.77
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.77
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.77
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.77
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.77
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.77
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.77
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.77
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.77
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.77
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.77
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.76
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.76
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.76
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.76
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.76
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.76
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.76
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.76
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.76
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.76
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.75
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.75
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.75
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.75
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.75
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.74
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.74
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.74
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.74
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.74
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.74
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.59
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.74
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.74
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.73
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.73
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.73
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.73
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.72
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.72
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.72
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.72
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.72
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.71
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.71
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.71
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.71
1x5p_A	97	Negative elongation factor E; structure genomics,	99.71
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.71
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.7
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.7
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.7
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.7
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.7
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.7
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.7
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.7
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.69
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.69
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.68
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.68
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.68
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.68
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.68
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.68
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.68
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.68
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.68
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.68
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.67
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.67
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.66
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.66
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.66
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.66
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.66
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.64
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.64
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.63
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.63
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.63
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.62
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.62
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.61
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.61
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.61
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.61
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.6
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.59
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.58
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.57
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.56
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.55
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.55
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.55
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.55
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.55
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.54
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.53
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.52
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.51
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.49
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.49
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.49
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.47
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.47
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.47
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.46
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.46
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.44
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.43
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.42
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.35
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.22
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.19
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.07
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.85
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.8
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.32
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.31
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.64
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.45
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.39
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.1
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.8
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.2
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.1
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	95.17
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	94.56
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	93.96
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	87.52

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=1.6e-21  Score=149.96  Aligned_cols=88  Identities=60%  Similarity=1.043  Sum_probs=81.7

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEE
Q 025068           24 SPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRAN  103 (258)
Q Consensus        24 ~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~  103 (258)
                      .+..+...++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++.+|+|+.|+
T Consensus        10 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~   89 (116)
T 2cqd_A           10 GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKAN   89 (116)
T ss_dssp             CCCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECE
T ss_pred             CCcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCCcCCCEEEE
Confidence            44567778999999999999999999999999999999999999999999999999999999999999988799999999


Q ss_pred             EEeccCCC
Q 025068          104 CNLASLGR  111 (258)
Q Consensus       104 V~~a~~~~  111 (258)
                      |+++..+.
T Consensus        90 V~~a~~~~   97 (116)
T 2cqd_A           90 VNLAYLGA   97 (116)
T ss_dssp             EEESTTTC
T ss_pred             EEEcccCC
Confidence            99997543

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.86  E-value=1.2e-21  Score=150.41  Aligned_cols=91  Identities=25%  Similarity=0.333  Sum_probs=81.6

Q ss_pred             CCCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCce
Q 025068           23 NSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRR  101 (258)
Q Consensus        23 ~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~  101 (258)
                      ..+..+...++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.
T Consensus        17 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   96 (115)
T 2cpz_A           17 GSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKR   96 (115)
T ss_dssp             SCCCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             ccCcCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            344556677899999999999999999999999999999999999899999999999999999999998855 6799999


Q ss_pred             EEEEeccCCCCC
Q 025068          102 ANCNLASLGRPR  113 (258)
Q Consensus       102 i~V~~a~~~~~~  113 (258)
                      |+|+++..+..+
T Consensus        97 l~V~~a~~~~~~  108 (115)
T 2cpz_A           97 LKVQLKRSKNDS  108 (115)
T ss_dssp             CEEECCCCSCCC
T ss_pred             EEEEEcCCCCcC
Confidence            999999765443

>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=99.85  E-value=2.4e-21  Score=145.68  Aligned_cols=79  Identities=28%  Similarity=0.423  Sum_probs=74.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      ..++|||+|||.++||++|+++|++||.|++|+|++|+.++++||||||+|.+.++|++||+.++ ..|+|+.|+|++|+
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            35789999999999999999999999999999999999999999999999999999999999854 67999999999985

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.85  E-value=1.4e-21  Score=149.74  Aligned_cols=84  Identities=15%  Similarity=0.244  Sum_probs=77.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...++|||+||+++++|++|+++|++||.|++|+|++|+.|+++||||||+|++.++|++||+.++ ..|+|+.|+|+++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            456899999999999999999999999999999999999999999999999999999999999865 6799999999999


Q ss_pred             cCCCC
Q 025068          108 SLGRP  112 (258)
Q Consensus       108 ~~~~~  112 (258)
                      ..++.
T Consensus        84 ~~~~~   88 (110)
T 3s8s_A           84 IKGQQ   88 (110)
T ss_dssp             STTHH
T ss_pred             CCCcH
Confidence            65543

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.85  E-value=1.9e-20  Score=143.57  Aligned_cols=88  Identities=36%  Similarity=0.574  Sum_probs=80.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      +....++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            45668899999999999999999999999999999999999899999999999999999999999865 67999999999


Q ss_pred             eccCCCCCC
Q 025068          106 LASLGRPRP  114 (258)
Q Consensus       106 ~a~~~~~~~  114 (258)
                      ++..+..+.
T Consensus        91 ~a~~~~~~~   99 (115)
T 2dgo_A           91 WATRKPPAP   99 (115)
T ss_dssp             ESSCCCCCS
T ss_pred             EccCCCCCC
Confidence            998665543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.85  E-value=5e-21  Score=146.20  Aligned_cols=88  Identities=35%  Similarity=0.640  Sum_probs=77.8

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEE
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCN  105 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~  105 (258)
                      .++...++|||+||+.++++++|+++|++||.|++|+|++++.++++||||||+|.+.++|++||+.++..|+|+.|+|+
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~   99 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPK   99 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEE
Confidence            34566789999999999999999999999999999999999999999999999999999999999998878999999999


Q ss_pred             eccCCCCC
Q 025068          106 LASLGRPR  113 (258)
Q Consensus       106 ~a~~~~~~  113 (258)
                      ++..++.+
T Consensus       100 ~a~~~~~~  107 (109)
T 2rs2_A          100 VAFPRRAQ  107 (109)
T ss_dssp             ECCCCCCC
T ss_pred             EccCCCCC
Confidence            99766544

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=1.4e-20  Score=140.85  Aligned_cols=86  Identities=17%  Similarity=0.346  Sum_probs=78.0

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEE
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRAN  103 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~  103 (258)
                      ...+...++|||+||+.++++++|+++|++||.|++|+|+.++ +++++|||||+|.+.++|++||+.++ ..|+|+.|+
T Consensus        11 ~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   89 (100)
T 2do4_A           11 YSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIK   89 (100)
T ss_dssp             CSSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3445667899999999999999999999999999999999998 89999999999999999999998855 669999999


Q ss_pred             EEeccCCC
Q 025068          104 CNLASLGR  111 (258)
Q Consensus       104 V~~a~~~~  111 (258)
                      |+++..+.
T Consensus        90 v~~a~~~~   97 (100)
T 2do4_A           90 VAISNSGP   97 (100)
T ss_dssp             EEECCCCS
T ss_pred             EEECCCCC
Confidence            99996543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=1.8e-20  Score=139.97  Aligned_cols=87  Identities=28%  Similarity=0.551  Sum_probs=78.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEe
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNL  106 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~  106 (258)
                      ++...++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++..|+|+.|+|++
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~   85 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKR   85 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999444779999999999


Q ss_pred             ccCCCCC
Q 025068          107 ASLGRPR  113 (258)
Q Consensus       107 a~~~~~~  113 (258)
                      +..+..+
T Consensus        86 a~~~~~~   92 (99)
T 2dgs_A           86 AEPRDSK   92 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCCccc
Confidence            9765443

>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=99.84  E-value=4.7e-21  Score=150.87  Aligned_cols=92  Identities=25%  Similarity=0.425  Sum_probs=82.4

Q ss_pred             CCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCC
Q 025068           21 YLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDG   99 (258)
Q Consensus        21 ~~~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G   99 (258)
                      ......+....++|||+||+.++++++|+++|++||.|++|+|++|+.+++++|||||+|.+.++|++||+.++ ..|+|
T Consensus        36 ~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g  115 (129)
T 2kxn_B           36 HVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG  115 (129)
T ss_dssp             CCCCSSCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSS
T ss_pred             CCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            33444556678899999999999999999999999999999999999999999999999999999999999854 77999


Q ss_pred             ceEEEEeccCCCC
Q 025068          100 RRANCNLASLGRP  112 (258)
Q Consensus       100 ~~i~V~~a~~~~~  112 (258)
                      ++|+|+++..+++
T Consensus       116 ~~l~V~~a~~~~p  128 (129)
T 2kxn_B          116 RRIRVDFSITKRP  128 (129)
T ss_dssp             SCCEESCCSSSSC
T ss_pred             EEEEEEEecCCCC
Confidence            9999999976654

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.84  E-value=9.8e-21  Score=138.06  Aligned_cols=82  Identities=33%  Similarity=0.728  Sum_probs=76.9

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEE
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCN  105 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~  105 (258)
                      .++...++|||+|||.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++.+|+|+.|+|+
T Consensus         6 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            6 KNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPK   85 (87)
T ss_dssp             -CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEE
Confidence            45667889999999999999999999999999999999999999999999999999999999999888788999999999


Q ss_pred             ec
Q 025068          106 LA  107 (258)
Q Consensus       106 ~a  107 (258)
                      +|
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            76

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.84  E-value=1.5e-21  Score=144.40  Aligned_cols=81  Identities=20%  Similarity=0.322  Sum_probs=74.7

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCC-CEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-C-CccCCceEEEEec
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFG-EILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-T-PFIDGRRANCNLA  107 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG-~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~-~~i~G~~i~V~~a  107 (258)
                      +++|||+|||.++||++|+++|++|| .|++|+|++|+.|+++||||||+|.+.++|++||+.+ + ..|+|++|+|++|
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 8999999999999999999999999999999999885 4 3599999999999


Q ss_pred             cCCC
Q 025068          108 SLGR  111 (258)
Q Consensus       108 ~~~~  111 (258)
                      .++.
T Consensus        81 ~~~~   84 (91)
T 2lxi_A           81 DPKP   84 (91)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            6543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=1.2e-20  Score=141.89  Aligned_cols=89  Identities=25%  Similarity=0.432  Sum_probs=80.6

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCccCCceEE
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPFIDGRRAN  103 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~i~G~~i~  103 (258)
                      +.+....++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.+ +..|+|+.|+
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2dnm_A            7 GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELR   86 (103)
T ss_dssp             SSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCE
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            345566789999999999999999999999999999999999999999999999999999999999975 4779999999


Q ss_pred             EEeccCCCCC
Q 025068          104 CNLASLGRPR  113 (258)
Q Consensus       104 V~~a~~~~~~  113 (258)
                      |+++..++.+
T Consensus        87 V~~a~~~~~~   96 (103)
T 2dnm_A           87 VQVARYGRRD   96 (103)
T ss_dssp             EEECSSCCSC
T ss_pred             EEECCcCCCC
Confidence            9999765443

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=4.6e-20  Score=141.79  Aligned_cols=85  Identities=36%  Similarity=0.656  Sum_probs=78.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      +...++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++..|+|+.|+|+++
T Consensus        24 ~~~~~~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           24 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEEC
Confidence            34558999999999999999999999999999999999999999999999999999999999999557799999999999


Q ss_pred             cCCCC
Q 025068          108 SLGRP  112 (258)
Q Consensus       108 ~~~~~  112 (258)
                      ..+..
T Consensus       104 ~~~~~  108 (116)
T 1x4b_A          104 VAREE  108 (116)
T ss_dssp             SSCCC
T ss_pred             CCCcc
Confidence            76543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.83  E-value=2.4e-21  Score=144.83  Aligned_cols=84  Identities=17%  Similarity=0.280  Sum_probs=75.9

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCC--EEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCC-----ccC
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGE--ILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP-----FID   98 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~--I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~-----~i~   98 (258)
                      ..+...++|||+||++++|+++|+++|++||.  |.+|+|++|+.|+++||||||+|.+.++|++||+.++.     .|+
T Consensus         4 ~~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~   83 (95)
T 2lkz_A            4 HHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKID   83 (95)
T ss_dssp             CSSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEET
T ss_pred             ccCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceEC
Confidence            45667889999999999999999999999995  56999999999999999999999999999999998542     489


Q ss_pred             CceEEEEeccC
Q 025068           99 GRRANCNLASL  109 (258)
Q Consensus        99 G~~i~V~~a~~  109 (258)
                      ||+|.|++|+.
T Consensus        84 Gr~i~V~~Aks   94 (95)
T 2lkz_A           84 GKTIGVDFAKS   94 (95)
T ss_dssp             TEEEEEEECCC
T ss_pred             CEEEEEEEccC
Confidence            99999999953

>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=99.83  E-value=4.1e-20  Score=139.40  Aligned_cols=86  Identities=28%  Similarity=0.366  Sum_probs=79.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      +....++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            45567899999999999999999999999999999999999899999999999999999999999865 67999999999


Q ss_pred             eccCCCC
Q 025068          106 LASLGRP  112 (258)
Q Consensus       106 ~a~~~~~  112 (258)
                      ++..++.
T Consensus        91 ~a~~~~~   97 (105)
T 1x5u_A           91 KASAHNK   97 (105)
T ss_dssp             ETTTTSC
T ss_pred             ECCCCCc
Confidence            9975543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=1.4e-20  Score=142.11  Aligned_cols=87  Identities=37%  Similarity=0.728  Sum_probs=79.5

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEE
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCN  105 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~  105 (258)
                      .++...++|||+||++++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++..|+|+.|+|+
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~   90 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPK   90 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEE
Confidence            35667899999999999999999999999999999999999989999999999999999999999994467999999999


Q ss_pred             eccCCCC
Q 025068          106 LASLGRP  112 (258)
Q Consensus       106 ~a~~~~~  112 (258)
                      ++..+..
T Consensus        91 ~a~~~~~   97 (105)
T 2dh8_A           91 PCTPRGM   97 (105)
T ss_dssp             CSCCSSC
T ss_pred             EccCCCC
Confidence            9975543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=2.9e-20  Score=139.85  Aligned_cols=86  Identities=28%  Similarity=0.371  Sum_probs=79.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      +....++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45567899999999999999999999999999999999999899999999999999999999999765 67999999999


Q ss_pred             eccCCCC
Q 025068          106 LASLGRP  112 (258)
Q Consensus       106 ~a~~~~~  112 (258)
                      ++..+..
T Consensus        91 ~a~~~~~   97 (103)
T 2cq0_A           91 WAKPSTN   97 (103)
T ss_dssp             ESSCCCC
T ss_pred             ECCCCCC
Confidence            9976543

>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=99.83  E-value=6.1e-20  Score=138.07  Aligned_cols=87  Identities=34%  Similarity=0.642  Sum_probs=79.0

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEE
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANC  104 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V  104 (258)
                      +..+...++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+. .+.|+|+.|+|
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~g~~l~v   87 (103)
T 2cqg_A            9 KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ-RHMIDGRWCDC   87 (103)
T ss_dssp             SCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS-CEEETTEEEEE
T ss_pred             CCccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc-CCeeCCeEEEE
Confidence            34556678999999999999999999999999999999999998999999999999999999999995 46799999999


Q ss_pred             EeccCCCC
Q 025068          105 NLASLGRP  112 (258)
Q Consensus       105 ~~a~~~~~  112 (258)
                      +++..+..
T Consensus        88 ~~a~~~~~   95 (103)
T 2cqg_A           88 KLPNSKQS   95 (103)
T ss_dssp             ECCCTTCC
T ss_pred             EecCCCCc
Confidence            99976543

>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=99.83  E-value=4.5e-20  Score=140.31  Aligned_cols=85  Identities=20%  Similarity=0.348  Sum_probs=74.8

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceE
Q 025068           24 SPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRA  102 (258)
Q Consensus        24 ~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i  102 (258)
                      .+..+...++|||+||+.++++++|+++|++||.|++|+|+.+   ++++|||||+|.+.++|++||+.++ ..|+|+.|
T Consensus        15 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   91 (109)
T 1x4a_A           15 RGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRL   91 (109)
T ss_dssp             SCCCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            3345567889999999999999999999999999999999664   5689999999999999999998855 67999999


Q ss_pred             EEEeccCCC
Q 025068          103 NCNLASLGR  111 (258)
Q Consensus       103 ~V~~a~~~~  111 (258)
                      +|+++..++
T Consensus        92 ~V~~a~~~~  100 (109)
T 1x4a_A           92 RVEFPRSGR  100 (109)
T ss_dssp             EEECCCCCC
T ss_pred             EEEEcccCC
Confidence            999996554

>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=99.83  E-value=2.4e-20  Score=150.69  Aligned_cols=85  Identities=20%  Similarity=0.260  Sum_probs=78.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|++
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3467899999999999999999999999999999999999999999999999999999999999865 679999999999


Q ss_pred             ccCCCC
Q 025068          107 ASLGRP  112 (258)
Q Consensus       107 a~~~~~  112 (258)
                      +...+.
T Consensus       116 a~~~~~  121 (156)
T 1h2v_Z          116 DAGFKE  121 (156)
T ss_dssp             ESCCCT
T ss_pred             CCCCCC
Confidence            976544

>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=99.83  E-value=4.1e-20  Score=140.64  Aligned_cols=88  Identities=27%  Similarity=0.416  Sum_probs=79.8

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-------CCccC
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-------TPFID   98 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-------~~~i~   98 (258)
                      .+....++|||+||+.++++++|+++|++||.|++|+|++|+.+++++|||||+|.+.++|++||+.+       +..|+
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             CcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            34566789999999999999999999999999999999999999999999999999999999999985       45699


Q ss_pred             CceEEEEeccCCCCC
Q 025068           99 GRRANCNLASLGRPR  113 (258)
Q Consensus        99 G~~i~V~~a~~~~~~  113 (258)
                      |+.|+|+++..+..+
T Consensus        90 g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           90 GRQLKVDLAVTRDEA  104 (111)
T ss_dssp             SCEEEEECCCCCCCC
T ss_pred             CEEEEEEECCCCccC
Confidence            999999999765444

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.83  E-value=4.9e-20  Score=145.90  Aligned_cols=87  Identities=28%  Similarity=0.459  Sum_probs=79.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      ++...++|||+||+.++++++|+++|++||.|++|+|++++.++++||||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            45567899999999999999999999999999999999999999999999999999999999999865 56999999999


Q ss_pred             eccCCCCC
Q 025068          106 LASLGRPR  113 (258)
Q Consensus       106 ~a~~~~~~  113 (258)
                      ++..+..+
T Consensus       118 ~a~~~~~~  125 (139)
T 1u6f_A          118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             ECCCCCCC
Confidence            99765443

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.83  E-value=9.3e-20  Score=137.18  Aligned_cols=87  Identities=20%  Similarity=0.368  Sum_probs=77.5

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEE
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANC  104 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V  104 (258)
                      +..+...++|||+||+.++++++|+++|++|| |++|+|++++.+++++|||||+|.+.++|++||+.++..|+|+.|+|
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V   87 (103)
T 2dng_A            9 ELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRV   87 (103)
T ss_dssp             CCCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEE
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEE
Confidence            34456688999999999999999999999996 99999999999999999999999999999999943457799999999


Q ss_pred             EeccCCCC
Q 025068          105 NLASLGRP  112 (258)
Q Consensus       105 ~~a~~~~~  112 (258)
                      +++..+..
T Consensus        88 ~~a~~~~~   95 (103)
T 2dng_A           88 DIAEGRKQ   95 (103)
T ss_dssp             EECCCCCC
T ss_pred             EEecCCCC
Confidence            99975543

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.83  E-value=1.4e-20  Score=149.27  Aligned_cols=93  Identities=29%  Similarity=0.509  Sum_probs=83.4

Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCc
Q 025068           22 LNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGR  100 (258)
Q Consensus        22 ~~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~  100 (258)
                      ...+.+....++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+
T Consensus        38 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~  117 (135)
T 2lea_A           38 GRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGR  117 (135)
T ss_dssp             CCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSS
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            3445566778899999999999999999999999999999999999899999999999999999999999865 679999


Q ss_pred             eEEEEeccCCCCCC
Q 025068          101 RANCNLASLGRPRP  114 (258)
Q Consensus       101 ~i~V~~a~~~~~~~  114 (258)
                      .|+|++++.++++.
T Consensus       118 ~l~V~~a~~~~~~~  131 (135)
T 2lea_A          118 ELRVQMARYGRPPD  131 (135)
T ss_dssp             CCEEEECCCCCCCT
T ss_pred             EEEEEECCCCCCCc
Confidence            99999997665544

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.83  E-value=1e-20  Score=148.85  Aligned_cols=89  Identities=17%  Similarity=0.272  Sum_probs=79.5

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEE--EEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-C----c
Q 025068           24 SPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE--AVVITDKNTGRSKGYGFVTFREPEAARRACADPT-P----F   96 (258)
Q Consensus        24 ~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~--v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~----~   96 (258)
                      .+..+...++|||+||+++++|++|+++|++||.|+.  |+|++|+.|+++||||||+|.+. +|++||+.++ .    .
T Consensus        16 ~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~   94 (131)
T 2m2b_A           16 EPSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLT   94 (131)
T ss_dssp             CCCCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCcc
Confidence            3445667889999999999999999999999999976  99999999999999999999999 9999999855 6    8


Q ss_pred             cCCceEEEEeccCCCCC
Q 025068           97 IDGRRANCNLASLGRPR  113 (258)
Q Consensus        97 i~G~~i~V~~a~~~~~~  113 (258)
                      |+|+.|+|+++..++.+
T Consensus        95 ~~gr~l~V~~a~~~~~~  111 (131)
T 2m2b_A           95 IDGKTINVEFAKGSKRD  111 (131)
T ss_dssp             GGGCCCCCEECCCSCCC
T ss_pred             CCCEEEEEEECCCCCCC
Confidence            99999999999765433

>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=99.83  E-value=7.1e-20  Score=136.63  Aligned_cols=85  Identities=26%  Similarity=0.452  Sum_probs=78.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+|||.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            3457899999999999999999999999999999999999899999999999999999999998765 669999999999


Q ss_pred             ccCCCC
Q 025068          107 ASLGRP  112 (258)
Q Consensus       107 a~~~~~  112 (258)
                      +..++.
T Consensus        85 a~~~~~   90 (99)
T 1whw_A           85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             cCCCcc
Confidence            976544

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.82  E-value=6.2e-20  Score=138.73  Aligned_cols=88  Identities=24%  Similarity=0.413  Sum_probs=79.9

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeec-CCCCCcccEEEEEEcCHHHHHHHhcCC-C-CccCCceE
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITD-KNTGRSKGYGFVTFREPEAARRACADP-T-PFIDGRRA  102 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d-~~tg~skG~aFV~F~~~~~A~~Ai~~~-~-~~i~G~~i  102 (258)
                      ..+...++|||+||+.++++++|+++|++||.|++|+|+++ +.+++++|||||+|.+.++|++||+.+ + ..|+|+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l   89 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   89 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEE
Confidence            34567889999999999999999999999999999999999 788999999999999999999999986 4 67999999


Q ss_pred             EEEeccCCCCC
Q 025068          103 NCNLASLGRPR  113 (258)
Q Consensus       103 ~V~~a~~~~~~  113 (258)
                      +|+++..+...
T Consensus        90 ~v~~a~~~~~~  100 (107)
T 2cph_A           90 VLEWADSEVTV  100 (107)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEeCCCCCCC
Confidence            99999765443

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.82  E-value=3.8e-20  Score=142.53  Aligned_cols=84  Identities=26%  Similarity=0.392  Sum_probs=77.6

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceE
Q 025068           24 SPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRA  102 (258)
Q Consensus        24 ~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i  102 (258)
                      .+.++...++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|++|
T Consensus        33 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l  112 (118)
T 2khc_A           33 KQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRL  112 (118)
T ss_dssp             SSCCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEEC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34456677999999999999999999999999999999999999899999999999999999999999865 67999999


Q ss_pred             EEEec
Q 025068          103 NCNLA  107 (258)
Q Consensus       103 ~V~~a  107 (258)
                      +|+++
T Consensus       113 ~V~~a  117 (118)
T 2khc_A          113 KVQLK  117 (118)
T ss_dssp             CEEEC
T ss_pred             EEEec
Confidence            99987

>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=99.82  E-value=7e-20  Score=138.08  Aligned_cols=87  Identities=16%  Similarity=0.376  Sum_probs=77.5

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCC-CCcccEEEEEEcCHHHHHHHhcCCCCccCCceEE
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNT-GRSKGYGFVTFREPEAARRACADPTPFIDGRRAN  103 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~t-g~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~  103 (258)
                      +..+...++|||+||+.++++++|+++|++|| |++|+|++++.+ ++++|||||+|.+.++|++||..++..|+|+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~   87 (104)
T 1wi8_A            9 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIR   87 (104)
T ss_dssp             CCCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEE
Confidence            34556679999999999999999999999999 999999999987 9999999999999999999993345779999999


Q ss_pred             EEeccCCCC
Q 025068          104 CNLASLGRP  112 (258)
Q Consensus       104 V~~a~~~~~  112 (258)
                      |+++..++.
T Consensus        88 V~~a~~~~~   96 (104)
T 1wi8_A           88 VDVADQAQD   96 (104)
T ss_dssp             EEECCCCCC
T ss_pred             EEEccCCCC
Confidence            999976543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=1e-19  Score=134.65  Aligned_cols=83  Identities=35%  Similarity=0.593  Sum_probs=76.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~i~G~~i~V~~a  107 (258)
                      ...++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.+ +..|+|+.|+|+++
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            34689999999999999999999999999999999999999999999999999999999999975 47799999999999


Q ss_pred             cCCC
Q 025068          108 SLGR  111 (258)
Q Consensus       108 ~~~~  111 (258)
                      ..+.
T Consensus        83 ~~~~   86 (95)
T 2dnz_A           83 TERL   86 (95)
T ss_dssp             SCCC
T ss_pred             cccc
Confidence            6543

>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=99.82  E-value=7e-20  Score=141.37  Aligned_cols=85  Identities=29%  Similarity=0.529  Sum_probs=77.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      +....++|||+||+.++++++|+++|++||.|++|+|++++ +++++|||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus         3 e~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~   81 (116)
T 2fy1_A            3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVE   81 (116)
T ss_dssp             TTCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            45667899999999999999999999999999999999998 89999999999999999999999865 67999999999


Q ss_pred             eccCCCC
Q 025068          106 LASLGRP  112 (258)
Q Consensus       106 ~a~~~~~  112 (258)
                      ++..+..
T Consensus        82 ~a~~~~~   88 (116)
T 2fy1_A           82 QAKKPSF   88 (116)
T ss_dssp             ECCCSSC
T ss_pred             ECCCCCC
Confidence            9975543

>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=99.82  E-value=1.5e-20  Score=146.47  Aligned_cols=89  Identities=18%  Similarity=0.326  Sum_probs=77.6

Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCce
Q 025068           22 LNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRR  101 (258)
Q Consensus        22 ~~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~  101 (258)
                      ..........++|||+|||+++++++|+++|++||.|+++.++.+..+++++|||||+|.+.++|++||+.++..|+|+.
T Consensus        16 ~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~   95 (124)
T 1wel_A           16 SRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRF   95 (124)
T ss_dssp             CCCSSCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSC
T ss_pred             CCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcE
Confidence            33444556778999999999999999999999999999877777777899999999999999999999994446799999


Q ss_pred             EEEEeccCC
Q 025068          102 ANCNLASLG  110 (258)
Q Consensus       102 i~V~~a~~~  110 (258)
                      |+|.++..+
T Consensus        96 i~V~~a~~~  104 (124)
T 1wel_A           96 IQVHPITKK  104 (124)
T ss_dssp             BEEEEECHH
T ss_pred             EEEEECCHH
Confidence            999999654

>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=99.82  E-value=1.1e-19  Score=136.98  Aligned_cols=85  Identities=27%  Similarity=0.335  Sum_probs=76.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCC---ceEE
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDG---RRAN  103 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G---~~i~  103 (258)
                      +...++|||+||+.++++++|+++|++||.|++|+|++++ +++++|||||+|.+.++|++||+.++ ..|.+   +.|+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            3457899999999999999999999999999999999998 79999999999999999999999855 56787   9999


Q ss_pred             EEeccCCCCC
Q 025068          104 CNLASLGRPR  113 (258)
Q Consensus       104 V~~a~~~~~~  113 (258)
                      |+++..+..+
T Consensus        91 V~~a~~~~~~  100 (105)
T 2dnh_A           91 VKFADTDKES  100 (105)
T ss_dssp             EEESCSSCCC
T ss_pred             EEECccCccc
Confidence            9999765544

>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=99.82  E-value=2.9e-20  Score=143.20  Aligned_cols=82  Identities=29%  Similarity=0.479  Sum_probs=73.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccC
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASL  109 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~  109 (258)
                      .++|||+|||.+++|++|+++|++||.|++|+|++|+  +.+||||||+|.+.++|++||+.++ ..|+|+.|+|+++..
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            5689999999999999999999999999999999996  5589999999999999999999855 679999999999976


Q ss_pred             CCCCC
Q 025068          110 GRPRP  114 (258)
Q Consensus       110 ~~~~~  114 (258)
                      ++.+.
T Consensus        83 ~~~~~   87 (115)
T 4f25_A           83 RKERE   87 (115)
T ss_dssp             CCC--
T ss_pred             ccccc
Confidence            65443

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=5.2e-20  Score=136.50  Aligned_cols=84  Identities=26%  Similarity=0.454  Sum_probs=77.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEE-EEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEA-VVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v-~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ..++|||+|||.++++++|+++|++||.|++| +|++|+.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|+++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   83 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            46899999999999999999999999999999 999998899999999999999999999999866 6699999999999


Q ss_pred             cCCCCC
Q 025068          108 SLGRPR  113 (258)
Q Consensus       108 ~~~~~~  113 (258)
                      ..+..+
T Consensus        84 ~~~~~~   89 (96)
T 1x5t_A           84 FKKDSK   89 (96)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            765443

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=1.3e-19  Score=136.27  Aligned_cols=86  Identities=30%  Similarity=0.494  Sum_probs=78.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      ++...++|||+||+.++++++|+++|++||.|++|+|+++  +++++|||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVA   88 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            4557889999999999999999999999999999999998  79999999999999999999999854 67999999999


Q ss_pred             eccCCCCCC
Q 025068          106 LASLGRPRP  114 (258)
Q Consensus       106 ~a~~~~~~~  114 (258)
                      ++..++.+.
T Consensus        89 ~a~~~~~~~   97 (103)
T 2d9p_A           89 LAQRKEERQ   97 (103)
T ss_dssp             ECSSCCCCC
T ss_pred             EecccccCC
Confidence            997665443

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=8.4e-20  Score=134.97  Aligned_cols=83  Identities=27%  Similarity=0.414  Sum_probs=76.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      +....++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS   90 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999855 67999999999


Q ss_pred             eccC
Q 025068          106 LASL  109 (258)
Q Consensus       106 ~a~~  109 (258)
                      +++.
T Consensus        91 ~a~~   94 (95)
T 2cqc_A           91 GPSS   94 (95)
T ss_dssp             CCSC
T ss_pred             ecCC
Confidence            9853

>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=99.82  E-value=3.4e-20  Score=142.11  Aligned_cols=84  Identities=21%  Similarity=0.331  Sum_probs=76.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcC-CCCccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD-PTPFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~-~~~~i~G~~i~V~  105 (258)
                      ++...++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++|| . ++..|+|+.|+|+
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   99 (114)
T 2cq4_A           21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQ   99 (114)
T ss_dssp             THHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEE
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEE
Confidence            3456689999999999999999999999999999999999999999999999999999999999 6 4567999999999


Q ss_pred             eccCCC
Q 025068          106 LASLGR  111 (258)
Q Consensus       106 ~a~~~~  111 (258)
                      ++..++
T Consensus       100 ~a~~~~  105 (114)
T 2cq4_A          100 ASQAEK  105 (114)
T ss_dssp             EHHHHH
T ss_pred             ecCCCc
Confidence            996543

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=9.1e-20  Score=137.23  Aligned_cols=86  Identities=24%  Similarity=0.415  Sum_probs=78.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhc-CCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-Cc-cCCceEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQ-FGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PF-IDGRRAN  103 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~-fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~-i~G~~i~  103 (258)
                      +....++|||+||+.++++++|+++|++ ||.|++|+|++++ +++++|||||+|.+.++|++||+.++ .. |+|+.|+
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~   83 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVR   83 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEE
Confidence            3456789999999999999999999999 9999999999999 89999999999999999999999765 67 9999999


Q ss_pred             EEeccCCCCC
Q 025068          104 CNLASLGRPR  113 (258)
Q Consensus       104 V~~a~~~~~~  113 (258)
                      |+++..+..+
T Consensus        84 v~~a~~~~~~   93 (104)
T 2dhg_A           84 LSVAIPKASR   93 (104)
T ss_dssp             CCBCCCCCSC
T ss_pred             EEEccCCCcC
Confidence            9999765443

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=9.3e-20  Score=137.65  Aligned_cols=87  Identities=23%  Similarity=0.311  Sum_probs=79.2

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCccCCceEEE
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPFIDGRRANC  104 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~i~G~~i~V  104 (258)
                      ......++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.+ +..|+|+.|+|
T Consensus        18 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   97 (106)
T 1p27_B           18 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   97 (106)
T ss_dssp             CCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEE
Confidence            34456789999999999999999999999999999999999999999999999999999999999985 47799999999


Q ss_pred             EeccCCCC
Q 025068          105 NLASLGRP  112 (258)
Q Consensus       105 ~~a~~~~~  112 (258)
                      +++..+.+
T Consensus        98 ~~a~~~~~  105 (106)
T 1p27_B           98 DWCFVRGP  105 (106)
T ss_dssp             EESEESSC
T ss_pred             EeecCCCC
Confidence            99976543

>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=99.81  E-value=8.3e-20  Score=137.92  Aligned_cols=86  Identities=28%  Similarity=0.417  Sum_probs=78.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-Ccc---CCceE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFI---DGRRA  102 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i---~G~~i  102 (258)
                      .+...++|||+||+.++++++|+++|++||.|++|+|++|+.++++||||||+|.+.++|++||+.++ ..+   +++.|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            45668899999999999999999999999999999999999999999999999999999999999855 556   88999


Q ss_pred             EEEeccCCCC
Q 025068          103 NCNLASLGRP  112 (258)
Q Consensus       103 ~V~~a~~~~~  112 (258)
                      +|+++..++.
T Consensus        89 ~v~~a~~~~~   98 (106)
T 2dgp_A           89 QVKPADSESR   98 (106)
T ss_dssp             EEEECCCCSC
T ss_pred             EEEECCcccc
Confidence            9999976543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=9.5e-20  Score=134.55  Aligned_cols=81  Identities=22%  Similarity=0.479  Sum_probs=75.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+|||.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            4457899999999999999999999999999999999999999999999999999999999998765 669999999999


Q ss_pred             cc
Q 025068          107 AS  108 (258)
Q Consensus       107 a~  108 (258)
                      |+
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            83

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=9.6e-20  Score=136.64  Aligned_cols=85  Identities=34%  Similarity=0.647  Sum_probs=77.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+|||.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|++
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3457899999999999999999999999999999999999899999999999999999999998854 679999999999


Q ss_pred             ccCCCC
Q 025068          107 ASLGRP  112 (258)
Q Consensus       107 a~~~~~  112 (258)
                      +..+..
T Consensus        89 a~~~~~   94 (102)
T 1x5s_A           89 AGKSSD   94 (102)
T ss_dssp             EECCCC
T ss_pred             CCCCCC
Confidence            976543

>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=99.81  E-value=1.3e-20  Score=138.68  Aligned_cols=81  Identities=19%  Similarity=0.375  Sum_probs=70.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCC--CEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFG--EILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG--~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      .+|||+||++++++++|+++|++||  .|++|+|++|+.++++||||||+|.+.++|++||+.++ .+|+|+.|+|+++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999999999999999999999999999999998865 67999999999997


Q ss_pred             CCCC
Q 025068          109 LGRP  112 (258)
Q Consensus       109 ~~~~  112 (258)
                      ...+
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            5543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=3.3e-19  Score=136.32  Aligned_cols=86  Identities=23%  Similarity=0.385  Sum_probs=77.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      +....++|||+||+.++++++|+++|++||.|++|+|++++ +++++|||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            44557899999999999999999999999999999999998 59999999999999999999999854 67999999999


Q ss_pred             eccCCCCC
Q 025068          106 LASLGRPR  113 (258)
Q Consensus       106 ~a~~~~~~  113 (258)
                      ++....++
T Consensus        90 ~a~~~~~~   97 (114)
T 2do0_A           90 MDERALPK   97 (114)
T ss_dssp             ECSCCCCC
T ss_pred             EcccCCCC
Confidence            99755444

>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=99.81  E-value=1.3e-19  Score=130.73  Aligned_cols=79  Identities=34%  Similarity=0.524  Sum_probs=74.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccCC
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASLG  110 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~~  110 (258)
                      ++|||+|||.++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|+++.++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            689999999999999999999999999999999999899999999999999999999999854 7799999999999654

>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=99.81  E-value=8.1e-20  Score=132.89  Aligned_cols=82  Identities=35%  Similarity=0.528  Sum_probs=74.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|+++
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            356799999999999999999999999999999999998899999999999999999999999854 6799999999999


Q ss_pred             cCC
Q 025068          108 SLG  110 (258)
Q Consensus       108 ~~~  110 (258)
                      ..+
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            643

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=4.9e-20  Score=138.23  Aligned_cols=85  Identities=32%  Similarity=0.450  Sum_probs=77.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|+++
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            457899999999999999999999999999999999999899999999999999999999998855 6699999999999


Q ss_pred             cCCCCC
Q 025068          108 SLGRPR  113 (258)
Q Consensus       108 ~~~~~~  113 (258)
                      ..++.+
T Consensus        90 ~~~~~~   95 (102)
T 2cqb_A           90 KPMRIK   95 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            765443

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.81  E-value=9.1e-20  Score=135.78  Aligned_cols=84  Identities=25%  Similarity=0.482  Sum_probs=76.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCC---CCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEE
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKN---TGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANC  104 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~---tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V  104 (258)
                      ...++|||+||+.++++++|+++|++||.|++|+|++++.   |++++|||||+|.+.++|++||+.++ ..|+|+.|+|
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            3568999999999999999999999999999999999876   66999999999999999999999865 6799999999


Q ss_pred             EeccCCCC
Q 025068          105 NLASLGRP  112 (258)
Q Consensus       105 ~~a~~~~~  112 (258)
                      +++..+..
T Consensus        83 ~~a~~~~~   90 (98)
T 2cpf_A           83 RISERATK   90 (98)
T ss_dssp             ECSSCSSC
T ss_pred             EEccCCCC
Confidence            99975543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=1.5e-19  Score=134.90  Aligned_cols=82  Identities=22%  Similarity=0.350  Sum_probs=76.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEE-EEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCce----E
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEIL-EAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRR----A  102 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~-~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~----i  102 (258)
                      ...++|||+||+.++++++|+++|++||.|+ +|+|++|+.+++++|||||+|.+.++|++||+.++ ..|+|+.    |
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            3578999999999999999999999999999 99999999999999999999999999999999866 6699999    9


Q ss_pred             EEEeccCC
Q 025068          103 NCNLASLG  110 (258)
Q Consensus       103 ~V~~a~~~  110 (258)
                      +|++|...
T Consensus        87 ~v~~a~~~   94 (99)
T 2div_A           87 KLNYATYS   94 (99)
T ss_dssp             CEEETTCC
T ss_pred             EEeecCCC
Confidence            99999644

>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=99.81  E-value=2.1e-20  Score=143.65  Aligned_cols=83  Identities=16%  Similarity=0.279  Sum_probs=76.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCE-EEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEI-LEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I-~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~  106 (258)
                      +...++|||+|||+++++++|+++|++||.| .+|+|++|+ ++++||||||+|.+.++|++||+.++..|+|+.|+|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHV   90 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEEE
Confidence            4456899999999999999999999999999 899999999 89999999999999999999999955779999999999


Q ss_pred             ccCCC
Q 025068          107 ASLGR  111 (258)
Q Consensus       107 a~~~~  111 (258)
                      +..+.
T Consensus        91 a~~~~   95 (114)
T 2cpy_A           91 VTLED   95 (114)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            97554

>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=99.81  E-value=2.8e-19  Score=134.45  Aligned_cols=86  Identities=24%  Similarity=0.318  Sum_probs=76.3

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEE
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANC  104 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V  104 (258)
                      .++...++|||+||+.++++++|+++|++||.|++|+|++++.  .++|||||+|.+.++|++||+.++ ..|+|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   87 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEE
Confidence            3556789999999999999999999999999999999999964  478999999999999999999755 6699999999


Q ss_pred             EeccCCCCC
Q 025068          105 NLASLGRPR  113 (258)
Q Consensus       105 ~~a~~~~~~  113 (258)
                      +++..+..+
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cqi_A           88 NWATTPSSQ   96 (103)
T ss_dssp             EECCCTTCC
T ss_pred             EECCCCccc
Confidence            999765443

>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=99.81  E-value=1e-19  Score=138.41  Aligned_cols=89  Identities=25%  Similarity=0.338  Sum_probs=80.4

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEE
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRAN  103 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~  103 (258)
                      +......++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+
T Consensus        20 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   99 (110)
T 1oo0_B           20 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ   99 (110)
T ss_dssp             BCCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            3445667899999999999999999999999999999999999899999999999999999999999754 679999999


Q ss_pred             EEeccCCCCC
Q 025068          104 CNLASLGRPR  113 (258)
Q Consensus       104 V~~a~~~~~~  113 (258)
                      |+++..+.++
T Consensus       100 V~~a~~~~~~  109 (110)
T 1oo0_B          100 VDWCFVKGPK  109 (110)
T ss_dssp             EEESEESSCC
T ss_pred             EEEcccCCCC
Confidence            9999765443

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=8.1e-20  Score=139.65  Aligned_cols=88  Identities=25%  Similarity=0.399  Sum_probs=79.7

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEE--------EEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-C
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEIL--------EAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-P   95 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~--------~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~   95 (258)
                      +.++...++|||+||+.++++++|+++|++||.|+        +|+|++++.+++++|||||+|.+.++|++||+.++ .
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   88 (113)
T 2cpe_A            9 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   88 (113)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCC
Confidence            34566789999999999999999999999999999        69999998899999999999999999999999854 6


Q ss_pred             ccCCceEEEEeccCCCC
Q 025068           96 FIDGRRANCNLASLGRP  112 (258)
Q Consensus        96 ~i~G~~i~V~~a~~~~~  112 (258)
                      .|+|+.|+|+++..+..
T Consensus        89 ~~~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           89 DFQGSKLKVSLARKKPP  105 (113)
T ss_dssp             EETTEECEEECSSCCCC
T ss_pred             ccCCCEEEEEECCCCCC
Confidence            79999999999976543

>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=99.81  E-value=3.7e-19  Score=134.45  Aligned_cols=83  Identities=23%  Similarity=0.268  Sum_probs=75.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEE-EEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILE-AVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~-v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~  106 (258)
                      ....++|||+|||+++++++|+++|++||.|.+ |+|+++ .+++++|||||+|.+.++|++||+.++..|+|+.|+|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEE
Confidence            455789999999999999999999999999997 888888 689999999999999999999999966779999999999


Q ss_pred             ccCCC
Q 025068          107 ASLGR  111 (258)
Q Consensus       107 a~~~~  111 (258)
                      +..++
T Consensus        91 ~~~~~   95 (104)
T 1wg5_A           91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            86543

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.80  E-value=1.1e-19  Score=141.63  Aligned_cols=90  Identities=23%  Similarity=0.329  Sum_probs=81.0

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEE
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRAN  103 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~  103 (258)
                      +......++|||+||+.++++++|+++|++||.|++|+|+.++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+
T Consensus        16 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   95 (126)
T 3ex7_B           16 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPIS   95 (126)
T ss_dssp             BCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            3445567899999999999999999999999999999999999899999999999999999999998754 779999999


Q ss_pred             EEeccCCCCCC
Q 025068          104 CNLASLGRPRP  114 (258)
Q Consensus       104 V~~a~~~~~~~  114 (258)
                      |+++..+..+.
T Consensus        96 v~~a~~~~~~~  106 (126)
T 3ex7_B           96 VDWCFVRGPPK  106 (126)
T ss_dssp             EEESEESSSCC
T ss_pred             EEEecCCCCCC
Confidence            99997665443

>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=99.80  E-value=2.2e-19  Score=131.16  Aligned_cols=81  Identities=20%  Similarity=0.442  Sum_probs=74.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEeccC
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASL  109 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~~  109 (258)
                      +.++|||+|||.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||..++..|+|+.|+|++++.
T Consensus         5 ~~~~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            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEETTT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEccC
Confidence            46899999999999999999999999999999999999899999999999999999999993355779999999999965


Q ss_pred             C
Q 025068          110 G  110 (258)
Q Consensus       110 ~  110 (258)
                      +
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.80  E-value=7.3e-20  Score=136.31  Aligned_cols=83  Identities=20%  Similarity=0.279  Sum_probs=76.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      .+...++|||+|||.++++++|+++|++||.|++++++.++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   90 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   90 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            34557899999999999999999999999999999999998899999999999999999999998866 67999999999


Q ss_pred             eccC
Q 025068          106 LASL  109 (258)
Q Consensus       106 ~a~~  109 (258)
                      ++..
T Consensus        91 ~a~~   94 (98)
T 2cqp_A           91 LGSG   94 (98)
T ss_dssp             ESSC
T ss_pred             EcCC
Confidence            9853

>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=99.80  E-value=3.9e-19  Score=136.01  Aligned_cols=92  Identities=18%  Similarity=0.402  Sum_probs=79.0

Q ss_pred             CCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-C
Q 025068           17 SGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-P   95 (258)
Q Consensus        17 sg~~~~~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~   95 (258)
                      .+.........+...++|||+||+.++++++|+++|++||.|++|+|++++ +++++|||||+|.+.++|++||+.++ .
T Consensus        11 ~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~   89 (114)
T 1x5o_A           11 SGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGK   89 (114)
T ss_dssp             SCCCCCCCSCCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTC
T ss_pred             cccccchhcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCC
Confidence            333333444556678999999999999999999999999999999999998 89999999999999999999999855 5


Q ss_pred             cc--------CCceEEEEeccC
Q 025068           96 FI--------DGRRANCNLASL  109 (258)
Q Consensus        96 ~i--------~G~~i~V~~a~~  109 (258)
                      .|        .++.|.|+++.+
T Consensus        90 ~~~~~~~~~~~~~~l~v~~a~p  111 (114)
T 1x5o_A           90 FIKTPPGVSAPTEPLLCKFSGP  111 (114)
T ss_dssp             CCCCCTTSCCCSSCBEEEECCC
T ss_pred             EEcCCccccCCCCceeEEccCC
Confidence            57        578899999853

>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=99.80  E-value=6.2e-19  Score=132.53  Aligned_cols=86  Identities=29%  Similarity=0.504  Sum_probs=76.5

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEE
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANC  104 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V  104 (258)
                      ..+...++|||+||+.++++++|+++|++||.|++|+|++++.  .++|||||+|.+.++|++||+.++ ..|+|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   87 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            3456679999999999999999999999999999999999864  489999999999999999999854 6799999999


Q ss_pred             EeccCCCCC
Q 025068          105 NLASLGRPR  113 (258)
Q Consensus       105 ~~a~~~~~~  113 (258)
                      +++..+..+
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cq3_A           88 NNATARVMT   96 (103)
T ss_dssp             EECCSSCCC
T ss_pred             EEcccCCCC
Confidence            999765443

>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=99.80  E-value=4e-19  Score=134.78  Aligned_cols=84  Identities=18%  Similarity=0.300  Sum_probs=76.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCC-EEEEEEe-ecCCCCCcccEEEEEEcCHHHHHHHhcCCC---CccCCceEEE
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGE-ILEAVVI-TDKNTGRSKGYGFVTFREPEAARRACADPT---PFIDGRRANC  104 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~-I~~v~v~-~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~---~~i~G~~i~V  104 (258)
                      ..++|||+||+.++++++|+++|++||. |++|.|+ .++.++++||||||+|.+.++|++||+.++   ..|+|+.|+|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V   86 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAV   86 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEE
Confidence            4689999999999999999999999998 9999998 888889999999999999999999999864   5699999999


Q ss_pred             EeccCCCCC
Q 025068          105 NLASLGRPR  113 (258)
Q Consensus       105 ~~a~~~~~~  113 (258)
                      +++..+...
T Consensus        87 ~~a~~~~~~   95 (109)
T 2dis_A           87 DWAEPEIDV   95 (109)
T ss_dssp             EESCSSCST
T ss_pred             EEcCCCCCc
Confidence            999765443

>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=99.80  E-value=1.3e-19  Score=134.13  Aligned_cols=84  Identities=30%  Similarity=0.453  Sum_probs=75.8

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEE
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRAN  103 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~  103 (258)
                      +..+...++|||+||+.++++++|+++|++||.|++|+|++++. ++++|||||+|.+.++|++||+.++ ..|+|+.|+
T Consensus        10 ~~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (95)
T 2ywk_A           10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPIN   88 (95)
T ss_dssp             --CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEE
Confidence            34556789999999999999999999999999999999999985 9999999999999999999999754 679999999


Q ss_pred             EEeccC
Q 025068          104 CNLASL  109 (258)
Q Consensus       104 V~~a~~  109 (258)
                      |++++.
T Consensus        89 V~~a~~   94 (95)
T 2ywk_A           89 VSGPSS   94 (95)
T ss_dssp             EECCCC
T ss_pred             EEEcCC
Confidence            999853

>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=99.80  E-value=4.3e-20  Score=138.92  Aligned_cols=88  Identities=27%  Similarity=0.537  Sum_probs=80.1

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEE
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRAN  103 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~  103 (258)
                      |..+...++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+
T Consensus         2 p~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (104)
T 1p1t_A            2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALR   81 (104)
T ss_dssp             CCSHHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBE
T ss_pred             CCcCCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Confidence            4456677899999999999999999999999999999999999899999999999999999999998755 679999999


Q ss_pred             EEeccCCCC
Q 025068          104 CNLASLGRP  112 (258)
Q Consensus       104 V~~a~~~~~  112 (258)
                      |+++..++.
T Consensus        82 v~~a~~~~~   90 (104)
T 1p1t_A           82 VDNAASEKN   90 (104)
T ss_dssp             EEETTCTTH
T ss_pred             EEeCCCccc
Confidence            999976543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.9e-19  Score=136.32  Aligned_cols=82  Identities=17%  Similarity=0.260  Sum_probs=75.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEe
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNL  106 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~  106 (258)
                      .+...++|||+|||.++|+++|+++|++||.|++|.|++|+. +++||||||+|.+.++|++||+.++..|+|+.|.|.+
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~   85 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILF   85 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345678999999999999999999999999999999999987 9999999999999999999999555789999999998


Q ss_pred             ccC
Q 025068          107 ASL  109 (258)
Q Consensus       107 a~~  109 (258)
                      +..
T Consensus        86 ~~~   88 (103)
T 1s79_A           86 KDD   88 (103)
T ss_dssp             HHH
T ss_pred             chH
Confidence            753

>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=99.80  E-value=1.7e-19  Score=130.68  Aligned_cols=81  Identities=32%  Similarity=0.472  Sum_probs=75.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~i~G~~i~V~~  106 (258)
                      +...++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.+ +..|+|+.|+|++
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            345789999999999999999999999999999999999889999999999999999999999885 4679999999999


Q ss_pred             cc
Q 025068          107 AS  108 (258)
Q Consensus       107 a~  108 (258)
                      |+
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            83

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.80  E-value=1e-19  Score=147.78  Aligned_cols=82  Identities=18%  Similarity=0.394  Sum_probs=75.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCC--CEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFG--EILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG--~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      ...++|||+||+++++|++|+++|++||  .|++|+|++|+.++++||||||+|.+.++|++||+.++ ..|+|+.|+|+
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  99999999999999999999999999999999999965 67999999999


Q ss_pred             eccCC
Q 025068          106 LASLG  110 (258)
Q Consensus       106 ~a~~~  110 (258)
                      ++..+
T Consensus       133 ~a~~~  137 (156)
T 3n9u_C          133 PATRQ  137 (156)
T ss_dssp             ECCHH
T ss_pred             EcCCC
Confidence            99643

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=7.9e-20  Score=138.90  Aligned_cols=79  Identities=13%  Similarity=0.203  Sum_probs=70.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC--C-CccCCceEEE
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP--T-PFIDGRRANC  104 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~--~-~~i~G~~i~V  104 (258)
                      +...++|||+||+++++|++|+++|++||.|++|+|+++      ||||||+|++.++|++||+.+  + .+|+|+.|+|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            445789999999999999999999999999999999876      689999999999999999963  2 5699999999


Q ss_pred             EeccCCCC
Q 025068          105 NLASLGRP  112 (258)
Q Consensus       105 ~~a~~~~~  112 (258)
                      ++|..++.
T Consensus        87 ~~A~~~~~   94 (105)
T 1sjq_A           87 QFSNHKEL   94 (105)
T ss_dssp             CCCSSSSC
T ss_pred             EEcCCCCC
Confidence            99975543

>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=99.80  E-value=2.8e-19  Score=136.30  Aligned_cols=88  Identities=32%  Similarity=0.545  Sum_probs=80.4

Q ss_pred             CCCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCccCCce
Q 025068           23 NSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPFIDGRR  101 (258)
Q Consensus        23 ~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~i~G~~  101 (258)
                      +.+..+...++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.+ +..|+|+.
T Consensus        18 ~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~   97 (108)
T 2jrs_A           18 NLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRP   97 (108)
T ss_dssp             SSCCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSC
T ss_pred             ccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            44556677899999999999999999999999999999999999989999999999999999999999975 46799999


Q ss_pred             EEEEeccCC
Q 025068          102 ANCNLASLG  110 (258)
Q Consensus       102 i~V~~a~~~  110 (258)
                      |+|+++..+
T Consensus        98 l~V~~a~~k  106 (108)
T 2jrs_A           98 MKVGHVTER  106 (108)
T ss_dssp             CEEECSCSS
T ss_pred             EEEEEcccC
Confidence            999999654

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.80  E-value=5.7e-20  Score=130.67  Aligned_cols=76  Identities=39%  Similarity=0.759  Sum_probs=73.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      ++|||+|||.++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++||+.++..|+|+.|+|++|
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 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCCCccCCEEEEEEec
Confidence            5799999999999999999999999999999999998999999999999999999999999887799999999987

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.80  E-value=3.3e-19  Score=133.20  Aligned_cols=83  Identities=28%  Similarity=0.414  Sum_probs=76.4

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEE--------EEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCc
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE--------AVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPF   96 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~--------v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~   96 (258)
                      ......++|||+||+.++++++|+++|++||.|++        |+|++++.+++++|||||+|.+.++|++||+.+ +..
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            34456789999999999999999999999999999        999999999999999999999999999999975 477


Q ss_pred             cCCceEEEEecc
Q 025068           97 IDGRRANCNLAS  108 (258)
Q Consensus        97 i~G~~i~V~~a~  108 (258)
                      |+|+.|+|++|+
T Consensus        88 ~~g~~l~V~~A~   99 (99)
T 2la6_A           88 FSGNPIKVSFAT   99 (99)
T ss_dssp             SSSSBCEEEECC
T ss_pred             eCCcEEEEEecC
Confidence            999999999973

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.80  E-value=6.6e-20  Score=137.74  Aligned_cols=82  Identities=17%  Similarity=0.196  Sum_probs=76.1

Q ss_pred             CCCCcEEEEcCCCC------CCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCC-
Q 025068           28 DTTYTKVFVGGLAW------ETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDG-   99 (258)
Q Consensus        28 ~~~~~~lfVgnLp~------~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G-   99 (258)
                      +...++|||+|||.      ++++++|+++|++||.|++|+|++|+.|+++||||||+|.+.++|++||+.++ ..|+| 
T Consensus         3 ~~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~   82 (100)
T 3ns6_A            3 LGSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK   82 (100)
T ss_dssp             SCGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            34578999999999      99999999999999999999999999999999999999999999999999855 67999 


Q ss_pred             ceEEEEeccC
Q 025068          100 RRANCNLASL  109 (258)
Q Consensus       100 ~~i~V~~a~~  109 (258)
                      +.|+|+++..
T Consensus        83 r~l~V~~a~~   92 (100)
T 3ns6_A           83 HRLFLYTMKD   92 (100)
T ss_dssp             CBCEEEESHH
T ss_pred             eEEEEEECch
Confidence            9999999964

>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=99.79  E-value=2.7e-19  Score=132.90  Aligned_cols=81  Identities=25%  Similarity=0.489  Sum_probs=75.7

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccC
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASL  109 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~  109 (258)
                      .++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|+++..
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            5799999999999999999999999999999999999899999999999999999999998854 679999999999965


Q ss_pred             CC
Q 025068          110 GR  111 (258)
Q Consensus       110 ~~  111 (258)
                      ++
T Consensus        82 ~~   83 (96)
T 2x1f_A           82 SD   83 (96)
T ss_dssp             SS
T ss_pred             CC
Confidence            53

>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=99.79  E-value=4.6e-19  Score=133.85  Aligned_cols=81  Identities=22%  Similarity=0.266  Sum_probs=73.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      ....++|||+|||++++|++|+++|++||. ++|+|++|+ ++++||||||+|.+.++|++||+.++.+|++|.|+|.++
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEEC
Confidence            445689999999999999999999999995 599999998 899999999999999999999976557799999999998


Q ss_pred             cCC
Q 025068          108 SLG  110 (258)
Q Consensus       108 ~~~  110 (258)
                      ...
T Consensus        90 ~~~   92 (102)
T 1wez_A           90 STA   92 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.79  E-value=1.3e-19  Score=128.35  Aligned_cols=75  Identities=39%  Similarity=0.754  Sum_probs=71.0

Q ss_pred             EEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        33 ~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      +|||+|||.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++..|+|+.|+|++|
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 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            599999999999999999999999999999999998999999999999999999999996567899999999875

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.79  E-value=2.1e-19  Score=139.12  Aligned_cols=83  Identities=16%  Similarity=0.223  Sum_probs=75.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCC---EEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGE---ILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRAN  103 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~---I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~  103 (258)
                      +..+.++|||+||++++++++|+++|++||.   |++|+|++++. +++||||||+|.+.++|++||+.++.+|+|+.|+
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~   91 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHRYIE   91 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEE
Confidence            4556789999999999999999999999999   89999999986 9999999999999999999999544679999999


Q ss_pred             EEeccCC
Q 025068          104 CNLASLG  110 (258)
Q Consensus       104 V~~a~~~  110 (258)
                      |.++..+
T Consensus        92 V~~a~~~   98 (118)
T 2db1_A           92 VFKSHRT   98 (118)
T ss_dssp             EEEECHH
T ss_pred             EEECCHH
Confidence            9998644

>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=99.79  E-value=2.2e-19  Score=130.75  Aligned_cols=83  Identities=25%  Similarity=0.414  Sum_probs=75.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCC-cccEEEEEEcCHHHHHHHhcCC-CCccCCceEEEEec
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR-SKGYGFVTFREPEAARRACADP-TPFIDGRRANCNLA  107 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~-skG~aFV~F~~~~~A~~Ai~~~-~~~i~G~~i~V~~a  107 (258)
                      ..++|||+||+.++++++|+++|++||.|++|+|+.++.++. ++|||||+|.+.++|++||+.+ +..|+|+.|+|+++
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            468999999999999999999999999999999999987766 8999999999999999999984 47799999999999


Q ss_pred             cCCCC
Q 025068          108 SLGRP  112 (258)
Q Consensus       108 ~~~~~  112 (258)
                      ...++
T Consensus        83 ~~~~~   87 (88)
T 4a8x_A           83 LAPWP   87 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            65543

>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=99.79  E-value=5.3e-20  Score=136.19  Aligned_cols=81  Identities=19%  Similarity=0.245  Sum_probs=73.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...++|||+|||.++++++|+++|++||.|++++++.++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            346899999999999999999999999999999999998899999999999999999999999854 6799999999988


Q ss_pred             cC
Q 025068          108 SL  109 (258)
Q Consensus       108 ~~  109 (258)
                      ..
T Consensus        93 ~s   94 (95)
T 2ek1_A           93 SS   94 (95)
T ss_dssp             C-
T ss_pred             cC
Confidence            53

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=1e-18  Score=132.85  Aligned_cols=80  Identities=19%  Similarity=0.226  Sum_probs=71.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCC-----c
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDG-----R  100 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G-----~  100 (258)
                      .....++|||+||++++++++|+++|++||+|++|+|+++       |||||+|.+.++|++||+.++ .+|+|     +
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~   83 (108)
T 1x4c_A           11 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETA   83 (108)
T ss_dssp             CCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcce
Confidence            3456789999999999999999999999999999999886       799999999999999999866 56989     9


Q ss_pred             eEEEEeccCCCCC
Q 025068          101 RANCNLASLGRPR  113 (258)
Q Consensus       101 ~i~V~~a~~~~~~  113 (258)
                      .|+|+++..+...
T Consensus        84 ~i~V~~a~~~~~~   96 (108)
T 1x4c_A           84 YIRVKVDGPRSPS   96 (108)
T ss_dssp             EEEEEESSCCSCC
T ss_pred             EEEEEeCCCCCCC
Confidence            9999999765443

>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=99.79  E-value=3.5e-19  Score=134.67  Aligned_cols=83  Identities=29%  Similarity=0.395  Sum_probs=76.3

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCccCCceEE
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPFIDGRRAN  103 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~i~G~~i~  103 (258)
                      +......++|||+||+.++++++|+++|++||.|++|+|++++ +++++|||||+|.+.++|++||+.+ +..|+|+.|+
T Consensus        23 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  101 (107)
T 3ulh_A           23 GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMN  101 (107)
T ss_dssp             -CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            4455678899999999999999999999999999999999999 8999999999999999999999985 4779999999


Q ss_pred             EEecc
Q 025068          104 CNLAS  108 (258)
Q Consensus       104 V~~a~  108 (258)
                      |+++.
T Consensus       102 V~~a~  106 (107)
T 3ulh_A          102 IQLVT  106 (107)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99984

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.79  E-value=7e-19  Score=129.32  Aligned_cols=83  Identities=28%  Similarity=0.514  Sum_probs=75.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      .....++|||+|||.++++++|+++|++||.|++|+|+++  +++++|||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   81 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVR   81 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3445789999999999999999999999999999999985  79999999999999999999999854 67999999999


Q ss_pred             eccCCC
Q 025068          106 LASLGR  111 (258)
Q Consensus       106 ~a~~~~  111 (258)
                      ++....
T Consensus        82 ~a~~~~   87 (92)
T 2dgv_A           82 IDRNAS   87 (92)
T ss_dssp             ECSCCS
T ss_pred             EcCCCC
Confidence            996543

>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=99.79  E-value=7.6e-19  Score=141.84  Aligned_cols=88  Identities=30%  Similarity=0.538  Sum_probs=80.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      .....++|||+||+.++++++|+++|++||.|++|+|++|+.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus        66 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  145 (158)
T 2kn4_A           66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ  145 (158)
T ss_dssp             CCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            44567899999999999999999999999999999999999899999999999999999999999865 66999999999


Q ss_pred             eccCCCCCC
Q 025068          106 LASLGRPRP  114 (258)
Q Consensus       106 ~a~~~~~~~  114 (258)
                      ++..++++.
T Consensus       146 ~a~~~~~~~  154 (158)
T 2kn4_A          146 MARYGRPPD  154 (158)
T ss_dssp             EECCSSCCC
T ss_pred             ECCCCCCCC
Confidence            997665443

>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=99.78  E-value=1.1e-19  Score=128.65  Aligned_cols=75  Identities=31%  Similarity=0.581  Sum_probs=71.8

Q ss_pred             EEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        33 ~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      +|||+|||.++++++|+++|++||.|++|++++++.+++++|||||+|.+.++|++||+.++..|+|+.|+|++|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            599999999999999999999999999999999999999999999999999999999998778899999999875

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.78  E-value=7.6e-19  Score=136.36  Aligned_cols=82  Identities=22%  Similarity=0.414  Sum_probs=75.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEecc
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLAS  108 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~  108 (258)
                      ...++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++..|+|+.|+|+++.
T Consensus        34 ~~~~~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           34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECC
Confidence            35689999999999999999999999999999999999889999999999999999999999434477999999999996


Q ss_pred             CC
Q 025068          109 LG  110 (258)
Q Consensus       109 ~~  110 (258)
                      ..
T Consensus       114 ~~  115 (124)
T 2jwn_A          114 TN  115 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.78  E-value=5.8e-19  Score=151.91  Aligned_cols=81  Identities=19%  Similarity=0.381  Sum_probs=75.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCC--CEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFG--EILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG--~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ..++|||+||++++||++|+++|++||  .|++|+|++|+.|+++||||||+|.+.++|++||+.++ ++|+|+.|+|++
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            567899999999999999999999999  99999999999999999999999999999999999866 779999999999


Q ss_pred             ccCC
Q 025068          107 ASLG  110 (258)
Q Consensus       107 a~~~  110 (258)
                      |..+
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            9643

>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=99.78  E-value=2.5e-19  Score=134.39  Aligned_cols=84  Identities=19%  Similarity=0.408  Sum_probs=72.3

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecC-CCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEE
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDK-NTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANC  104 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~-~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V  104 (258)
                      ......++|||+||+.++++++|+++|++|| |++|+|++++ .+++++|||||+|.+.++|++||+.++..|+|+.|+|
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V   92 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRV   92 (100)
T ss_dssp             ------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEE
Confidence            3456789999999999999999999999999 9999999998 6899999999999999999999943557799999999


Q ss_pred             EeccCC
Q 025068          105 NLASLG  110 (258)
Q Consensus       105 ~~a~~~  110 (258)
                      +++..+
T Consensus        93 ~~a~~~   98 (100)
T 2j76_E           93 DVADQA   98 (100)
T ss_dssp             EECCCS
T ss_pred             EeccCC
Confidence            999643

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.78  E-value=1.1e-18  Score=137.65  Aligned_cols=81  Identities=32%  Similarity=0.476  Sum_probs=74.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      .+...++|||+|||.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999999999899999999999999999999998866 66999999998


Q ss_pred             ec
Q 025068          106 LA  107 (258)
Q Consensus       106 ~a  107 (258)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            75

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1.4e-18  Score=127.69  Aligned_cols=80  Identities=19%  Similarity=0.369  Sum_probs=73.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+|||.++++++|+++|++| .|++|+|+++ .+++++|||||+|.+.++|++||+ ++ ..|+|+.|+|.+
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            4567899999999999999999999999 9999999999 689999999999999999999999 66 569999999999


Q ss_pred             ccCC
Q 025068          107 ASLG  110 (258)
Q Consensus       107 a~~~  110 (258)
                      +..+
T Consensus        84 a~~~   87 (91)
T 2dgw_A           84 EKSG   87 (91)
T ss_dssp             ESSC
T ss_pred             CCcC
Confidence            9654

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.2e-19  Score=131.56  Aligned_cols=79  Identities=27%  Similarity=0.474  Sum_probs=72.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...++|||+|||.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|+++
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            457899999999999999999999999999999999999899999999999999999999999865 6689988877765

>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=99.77  E-value=9.8e-19  Score=130.15  Aligned_cols=78  Identities=13%  Similarity=0.143  Sum_probs=71.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHH----HHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEE
Q 025068           30 TYTKVFVGGLAWETQSETMR----RYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANC  104 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~----~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V  104 (258)
                      +.++|||+||++++++++|+    ++|++||.|++|+|++|+.+   ||||||+|.+.++|++||+.++ ..|+|+.|+|
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            46799999999999999999    99999999999999999865   8899999999999999999865 6699999999


Q ss_pred             EeccCC
Q 025068          105 NLASLG  110 (258)
Q Consensus       105 ~~a~~~  110 (258)
                      ++|..+
T Consensus        85 ~~a~~~   90 (96)
T 2dgx_A           85 SLATGA   90 (96)
T ss_dssp             EECCCS
T ss_pred             EEcCCC
Confidence            999544

>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=99.77  E-value=1.7e-18  Score=128.79  Aligned_cols=78  Identities=26%  Similarity=0.474  Sum_probs=69.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccC--CceEEE
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFID--GRRANC  104 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~--G~~i~V  104 (258)
                      ....++|||+||+.++++++|+++|++||.|++|+++++      ||||||+|.+.++|++||+.++ ..|+  |+.|+|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V   87 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEE
Confidence            345689999999999999999999999999999998764      6799999999999999999854 6788  999999


Q ss_pred             EeccCCC
Q 025068          105 NLASLGR  111 (258)
Q Consensus       105 ~~a~~~~  111 (258)
                      +++..+.
T Consensus        88 ~~a~~~~   94 (97)
T 1why_A           88 DFAKSGP   94 (97)
T ss_dssp             EECCCCC
T ss_pred             EECCCCC
Confidence            9996543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.77  E-value=3.7e-18  Score=132.69  Aligned_cols=85  Identities=27%  Similarity=0.373  Sum_probs=77.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      .....++|||+||+.++++++|+++|++||.|++|+|++++ +++++|||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999998 89999999999999999999999755 66999999999


Q ss_pred             eccCCCC
Q 025068          106 LASLGRP  112 (258)
Q Consensus       106 ~a~~~~~  112 (258)
                      +|.....
T Consensus       110 ~a~~~~~  116 (124)
T 2kt5_A          110 LVASQID  116 (124)
T ss_dssp             EECCTTC
T ss_pred             EeCCCCC
Confidence            9975543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.77  E-value=4.2e-19  Score=133.21  Aligned_cols=85  Identities=31%  Similarity=0.559  Sum_probs=77.8

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEE
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANC  104 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V  104 (258)
                      +..+...++|||+||+.++++++|+++|++||.|++|+|++++ +++++|||||+|.+.++|++||+ .+..|+|+.|.|
T Consensus         3 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~-~~~~~~g~~l~v   80 (102)
T 2xs2_A            3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKL   80 (102)
T ss_dssp             CCCEEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT-CCCEETTEECEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh-CCCeECCEEEEE
Confidence            3455667899999999999999999999999999999999998 89999999999999999999999 667799999999


Q ss_pred             EeccCCC
Q 025068          105 NLASLGR  111 (258)
Q Consensus       105 ~~a~~~~  111 (258)
                      .++..+.
T Consensus        81 ~~a~~~~   87 (102)
T 2xs2_A           81 GPAIRKQ   87 (102)
T ss_dssp             EEEEECC
T ss_pred             EECCcCc
Confidence            9997554

>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=99.77  E-value=3.7e-19  Score=139.65  Aligned_cols=81  Identities=23%  Similarity=0.313  Sum_probs=73.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEE--EEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEIL--EAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANC  104 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~--~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V  104 (258)
                      +....++|||+|||+++||++|+++|++| .|+  +|+|++|+. |++||||||+|.+.++|++||+.++.+|+||.|+|
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V  115 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGKHKERIGHRYIEV  115 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEE
Confidence            34457889999999999999999999999 677  899999987 99999999999999999999998778899999999


Q ss_pred             EeccC
Q 025068          105 NLASL  109 (258)
Q Consensus       105 ~~a~~  109 (258)
                      ..+..
T Consensus       116 ~~a~~  120 (126)
T 2hgm_A          116 FKSSQ  120 (126)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            98854

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=2e-18  Score=129.29  Aligned_cols=81  Identities=26%  Similarity=0.373  Sum_probs=71.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      .+...++|||+||+.++++++|+++|++||.|   +|+++ .+++++|||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            45568899999999999999999999999987   56666 579999999999999999999999765 66999999999


Q ss_pred             eccCCC
Q 025068          106 LASLGR  111 (258)
Q Consensus       106 ~a~~~~  111 (258)
                      ++..+.
T Consensus        87 ~a~~~~   92 (101)
T 2fc9_A           87 LQGPRG   92 (101)
T ss_dssp             ECSSCC
T ss_pred             EcCCCC
Confidence            996553

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=7.3e-19  Score=134.53  Aligned_cols=80  Identities=20%  Similarity=0.334  Sum_probs=72.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      ....++|||+|||+++++++|+++|+.| .|++|+|++|+. |++||||||+|.+.++|++||+.++++|+||.|+|..+
T Consensus        13 ~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a   90 (109)
T 2dnn_A           13 NPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPA   90 (109)
T ss_dssp             CHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEEC
Confidence            3456799999999999999999999999 899999999985 99999999999999999999965667799999999988


Q ss_pred             cC
Q 025068          108 SL  109 (258)
Q Consensus       108 ~~  109 (258)
                      ..
T Consensus        91 ~~   92 (109)
T 2dnn_A           91 TE   92 (109)
T ss_dssp             CH
T ss_pred             Cc
Confidence            53

>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=99.77  E-value=1e-18  Score=142.62  Aligned_cols=91  Identities=24%  Similarity=0.322  Sum_probs=79.2

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEE
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRAN  103 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~  103 (258)
                      +......++|||+||+.++++++|+++|++||.|++|.|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|.
T Consensus        66 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  145 (165)
T 1rk8_A           66 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ  145 (165)
T ss_dssp             CCCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            4445567899999999999999999999999999999999999999999999999999999999999855 669999999


Q ss_pred             EEeccCCCCCCC
Q 025068          104 CNLASLGRPRPQ  115 (258)
Q Consensus       104 V~~a~~~~~~~~  115 (258)
                      |.++..+..+..
T Consensus       146 V~~a~~~~~~~~  157 (165)
T 1rk8_A          146 VDWCFVKGPKRV  157 (165)
T ss_dssp             EEESEECC----
T ss_pred             EEEecCCCCCCC
Confidence            999987655443

>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=99.77  E-value=1.9e-19  Score=132.00  Aligned_cols=79  Identities=29%  Similarity=0.547  Sum_probs=72.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccCC
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASLG  110 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~~  110 (258)
                      ++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.+ |++||+.++ ..|+|+.|+|++|..+
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            68999999999999999999999999999999999999999999999999999 999999966 6699999999999754


Q ss_pred             C
Q 025068          111 R  111 (258)
Q Consensus       111 ~  111 (258)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            3

>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=99.77  E-value=2.4e-18  Score=129.85  Aligned_cols=80  Identities=14%  Similarity=0.152  Sum_probs=70.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC---CCccCCceEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP---TPFIDGRRAN  103 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~---~~~i~G~~i~  103 (258)
                      .....++|||+||+++++|++|+++|++||.|++|.|+++      ||||||+|++.++|++||+.+   ..+|+|+.|+
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   84 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   84 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEE
Confidence            3456789999999999999999999999999999998865      789999999999999999864   2569999999


Q ss_pred             EEeccCCCC
Q 025068          104 CNLASLGRP  112 (258)
Q Consensus       104 V~~a~~~~~  112 (258)
                      |+++..++.
T Consensus        85 V~~a~~~~~   93 (101)
T 2cq1_A           85 IQYSNHKEL   93 (101)
T ss_dssp             EEECSCSSC
T ss_pred             EEEcCcccC
Confidence            999975543

>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=99.77  E-value=6.2e-19  Score=134.76  Aligned_cols=84  Identities=25%  Similarity=0.348  Sum_probs=74.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHH---HHHhcCCCEEEEEEeecCCCC---CcccEEEEEEcCHHHHHHHhcCCC-CccCCc
Q 025068           28 DTTYTKVFVGGLAWETQSETMR---RYFEQFGEILEAVVITDKNTG---RSKGYGFVTFREPEAARRACADPT-PFIDGR  100 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~---~~F~~fG~I~~v~v~~d~~tg---~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~  100 (258)
                      ....++|||+|||+++++++|+   ++|++||.|++|+|++++.++   +++|||||+|.+.++|++||+.++ ..|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3457799999999999999999   999999999999999998754   456999999999999999999955 679999


Q ss_pred             eEEEEeccCCC
Q 025068          101 RANCNLASLGR  111 (258)
Q Consensus       101 ~i~V~~a~~~~  111 (258)
                      .|+|++|..+.
T Consensus        92 ~l~V~~a~~k~  102 (111)
T 2cpi_A           92 TLKASLGTTKY  102 (111)
T ss_dssp             EEEEESCCCCS
T ss_pred             EEEEEeccccc
Confidence            99999996553

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.76  E-value=1.8e-19  Score=134.99  Aligned_cols=83  Identities=18%  Similarity=0.251  Sum_probs=74.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+||+.++++++|+++|++||.|.+ .++.++.++++||||||+|.+.++|++||+ ++ ..|+|+.|+|++
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            445789999999999999999999999999988 777787789999999999999999999999 65 679999999999


Q ss_pred             ccCCCC
Q 025068          107 ASLGRP  112 (258)
Q Consensus       107 a~~~~~  112 (258)
                      +..++.
T Consensus        92 a~~~~~   97 (101)
T 1fj7_A           92 PKGRDG   97 (101)
T ss_dssp             CSCCCC
T ss_pred             cCCCCC
Confidence            965543

>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=99.76  E-value=4.5e-18  Score=129.01  Aligned_cols=79  Identities=22%  Similarity=0.282  Sum_probs=69.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC---CccCCceEEE
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT---PFIDGRRANC  104 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~---~~i~G~~i~V  104 (258)
                      ....++|||+||+++++|++|+++|++||.|++|.|+++      ||||||+|++.++|++||+.++   ..|+|++|+|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V   85 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            345789999999999999999999999999999998764      6899999999999999999743   3599999999


Q ss_pred             EeccCCCC
Q 025068          105 NLASLGRP  112 (258)
Q Consensus       105 ~~a~~~~~  112 (258)
                      +++..++.
T Consensus        86 ~~a~~~~~   93 (104)
T 1wex_A           86 NYSTSKRI   93 (104)
T ss_dssp             EECSSSSC
T ss_pred             EEccCccc
Confidence            99975543

>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=99.76  E-value=3.3e-18  Score=128.71  Aligned_cols=80  Identities=23%  Similarity=0.368  Sum_probs=70.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+||+.++++++|+++|++||.|++|+|+        ++||||+|.+.++|++||+.++ ..|+|+.|+|++
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   79 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF   79 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEE
Confidence            3457899999999999999999999999999999986        3499999999999999999855 679999999999


Q ss_pred             ccCCCCCCC
Q 025068          107 ASLGRPRPQ  115 (258)
Q Consensus       107 a~~~~~~~~  115 (258)
                      +..+..++.
T Consensus        80 a~~~~~~~~   88 (103)
T 2dgu_A           80 AKPPDQKRK   88 (103)
T ss_dssp             CCCCCCCCC
T ss_pred             cCCCcccch
Confidence            976655443

>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=99.76  E-value=1.9e-18  Score=134.22  Aligned_cols=81  Identities=14%  Similarity=0.221  Sum_probs=71.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC---CccCCceEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT---PFIDGRRAN  103 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~---~~i~G~~i~  103 (258)
                      .....++|||+||+++++|++|+++|++||.|++|+|+++      ||||||+|++.++|++||+.++   .+|+|+.|+
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY  100 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEE
Confidence            3455789999999999999999999999999999999876      6899999999999999999754   469999999


Q ss_pred             EEeccCCCCC
Q 025068          104 CNLASLGRPR  113 (258)
Q Consensus       104 V~~a~~~~~~  113 (258)
                      |++++.++.+
T Consensus       101 V~~a~~k~~~  110 (119)
T 2ad9_A          101 IQFSNHKELK  110 (119)
T ss_dssp             EEECSSSSCC
T ss_pred             EEEccCCCCC
Confidence            9999755443

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.2e-18  Score=132.87  Aligned_cols=85  Identities=28%  Similarity=0.517  Sum_probs=76.0

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceE
Q 025068           24 SPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRA  102 (258)
Q Consensus        24 ~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i  102 (258)
                      ....+...++|||+||+.++++++|+++|++||.|++|+|++++  +.+||||||+|.+.++|++||+.++ ..|+|+.|
T Consensus        22 ~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   99 (109)
T 2err_A           22 NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKI   99 (109)
T ss_dssp             CCSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEEC
T ss_pred             CccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34456678999999999999999999999999999999999985  4589999999999999999999854 67999999


Q ss_pred             EEEeccCC
Q 025068          103 NCNLASLG  110 (258)
Q Consensus       103 ~V~~a~~~  110 (258)
                      +|+++..+
T Consensus       100 ~V~~a~~~  107 (109)
T 2err_A          100 EVNNATAR  107 (109)
T ss_dssp             EEEECCCS
T ss_pred             EEEECCCC
Confidence            99999643

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.76  E-value=1.7e-18  Score=129.60  Aligned_cols=75  Identities=25%  Similarity=0.436  Sum_probs=69.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccCC
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASLG  110 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~~  110 (258)
                      ++|||+||+.++++++|+++|++||.|++|+|+++     ++|||||+|.+.++|++||+.++ ..|+|+.|+|+++..+
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            58999999999999999999999999999999887     68999999999999999999854 7799999999999765


Q ss_pred             C
Q 025068          111 R  111 (258)
Q Consensus       111 ~  111 (258)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.76  E-value=1.4e-18  Score=131.47  Aligned_cols=75  Identities=17%  Similarity=0.223  Sum_probs=68.0

Q ss_pred             CCcEEEEcCCCC-CCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC---CccCCceEEEE
Q 025068           30 TYTKVFVGGLAW-ETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT---PFIDGRRANCN  105 (258)
Q Consensus        30 ~~~~lfVgnLp~-~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~---~~i~G~~i~V~  105 (258)
                      ..++|||+||++ +++|++|+++|++||.|++|.|+++      ||||||+|++.++|++||+.++   .+|+|++|+|+
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   87 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVH   87 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEE
Confidence            578999999999 9999999999999999999999876      4799999999999999999754   35999999999


Q ss_pred             eccCC
Q 025068          106 LASLG  110 (258)
Q Consensus       106 ~a~~~  110 (258)
                      +|...
T Consensus        88 ~a~~~   92 (102)
T 1x4d_A           88 LSQKY   92 (102)
T ss_dssp             EECCC
T ss_pred             ECCCC
Confidence            99643

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=2.7e-18  Score=127.80  Aligned_cols=81  Identities=17%  Similarity=0.278  Sum_probs=70.8

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEE
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANC  104 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V  104 (258)
                      .+....++|||+||+.++++++|+++|++||.|. ++++.+    +++|||||+|.+.++|++||+.++ ..|+|+.|+|
T Consensus        14 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   88 (97)
T 2e5j_A           14 EGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRV   88 (97)
T ss_dssp             SSSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            3455678999999999999999999999999997 677654    678999999999999999998854 7799999999


Q ss_pred             EeccCCC
Q 025068          105 NLASLGR  111 (258)
Q Consensus       105 ~~a~~~~  111 (258)
                      +++..++
T Consensus        89 ~~a~~~~   95 (97)
T 2e5j_A           89 ALARQQR   95 (97)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9996553

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=2.5e-18  Score=128.82  Aligned_cols=82  Identities=33%  Similarity=0.503  Sum_probs=72.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      .....++|||+||+.++++++|+++|+.|   .+|++++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34567899999999999999999999987   368888998899999999999999999999999854 67999999999


Q ss_pred             eccCCC
Q 025068          106 LASLGR  111 (258)
Q Consensus       106 ~a~~~~  111 (258)
                      ++..+.
T Consensus        88 ~a~~~~   93 (102)
T 2fc8_A           88 WAKPKG   93 (102)
T ss_dssp             ECCCCC
T ss_pred             EecCCC
Confidence            996543

>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=99.76  E-value=9.8e-19  Score=138.97  Aligned_cols=83  Identities=16%  Similarity=0.206  Sum_probs=75.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCC---EEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGE---ILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRAN  103 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~---I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~  103 (258)
                      +..+.++|||+|||+++|+++|+++|++||.   |++|+|++|+. +++||||||+|.+.++|++||+.++.+|+||.|+
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~  118 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALKKDRESMGHRYIE  118 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEE
Confidence            4456789999999999999999999999999   89999999987 9999999999999999999999434679999999


Q ss_pred             EEeccCC
Q 025068          104 CNLASLG  110 (258)
Q Consensus       104 V~~a~~~  110 (258)
                      |.++..+
T Consensus       119 V~~a~~~  125 (136)
T 2hgl_A          119 VFKSHRT  125 (136)
T ss_dssp             EEECCHH
T ss_pred             EEECChH
Confidence            9998543

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.75  E-value=2.4e-18  Score=129.56  Aligned_cols=79  Identities=22%  Similarity=0.257  Sum_probs=69.6

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-C--ccCCceE
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-P--FIDGRRA  102 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~--~i~G~~i  102 (258)
                      ......++|||+|||.++++++|+++|++||.|++|+++++      ||||||+|++.++|++||+.++ .  .|.|++|
T Consensus        16 ~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i   89 (100)
T 3r27_A           16 HKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPA   89 (100)
T ss_dssp             -CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEE
T ss_pred             ccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEE
Confidence            34456789999999999999999999999999999999854      6899999999999999999865 3  3889999


Q ss_pred             EEEeccCC
Q 025068          103 NCNLASLG  110 (258)
Q Consensus       103 ~V~~a~~~  110 (258)
                      +|++++.+
T Consensus        90 ~V~~S~~k   97 (100)
T 3r27_A           90 FVNYSTSQ   97 (100)
T ss_dssp             EEEECSCS
T ss_pred             EEEecccc
Confidence            99999654

>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=99.75  E-value=1.7e-18  Score=132.57  Aligned_cols=88  Identities=18%  Similarity=0.208  Sum_probs=72.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      .....++|||+||+.++++++|+++|++||.|++|.+..+..+++++|||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~  100 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE  100 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34567899999999999999999999999998543322222278999999999999999999999855 67999999999


Q ss_pred             eccCCCCCC
Q 025068          106 LASLGRPRP  114 (258)
Q Consensus       106 ~a~~~~~~~  114 (258)
                      ++..++.+.
T Consensus       101 ~a~~~~~~~  109 (115)
T 2cpx_A          101 FGKNKKQRS  109 (115)
T ss_dssp             ECCCCSCCC
T ss_pred             EccCCCCCC
Confidence            997665443

>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=99.75  E-value=2.6e-18  Score=132.09  Aligned_cols=79  Identities=14%  Similarity=0.225  Sum_probs=69.7

Q ss_pred             CCCCCcEEEEcCCCCC-CcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC---CccCCceE
Q 025068           27 GDTTYTKVFVGGLAWE-TQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT---PFIDGRRA  102 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~-~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~---~~i~G~~i  102 (258)
                      .....++|||+||+++ ++|++|+++|++||.|++|.|++      +||||||+|.+.++|++||+.++   .+|+|++|
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l   94 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   94 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            3556789999999998 99999999999999999999975      37899999999999999999753   45999999


Q ss_pred             EEEeccCCC
Q 025068          103 NCNLASLGR  111 (258)
Q Consensus       103 ~V~~a~~~~  111 (258)
                      +|+++..++
T Consensus        95 ~V~~a~~~~  103 (112)
T 1x4f_A           95 KVDLSEKYK  103 (112)
T ss_dssp             EEEEECSCS
T ss_pred             EEEECcccc
Confidence            999996543

>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=99.75  E-value=6.3e-19  Score=140.58  Aligned_cols=84  Identities=20%  Similarity=0.234  Sum_probs=72.9

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEE
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCN  105 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~  105 (258)
                      ....+.++|||+|||+++||++|+++|++|| |++|+|++|+. +++||||||+|++.++|++||+.++.+|+++.|+|.
T Consensus        41 ~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~  118 (139)
T 2hgn_A           41 VQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELF  118 (139)
T ss_dssp             ----CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEE
Confidence            3455678999999999999999999999999 77999999986 999999999999999999999555578999999999


Q ss_pred             eccCCC
Q 025068          106 LASLGR  111 (258)
Q Consensus       106 ~a~~~~  111 (258)
                      .+..+.
T Consensus       119 ~a~~~~  124 (139)
T 2hgn_A          119 LNSTTG  124 (139)
T ss_dssp             ECCCSC
T ss_pred             ECCCCC
Confidence            986543

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.75  E-value=5.3e-18  Score=128.26  Aligned_cols=81  Identities=21%  Similarity=0.345  Sum_probs=72.7

Q ss_pred             CCCCCcEEEEcCCCCCC------cHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCC
Q 025068           27 GDTTYTKVFVGGLAWET------QSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDG   99 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~------te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G   99 (258)
                      .+...++|||+|||.++      ++++|+++|++||.|++|+|++  .+|++||||||+|.+.++|++||+.++ ..|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~--~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g   88 (105)
T 2nlw_A           11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK   88 (105)
T ss_dssp             CCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC--BTTBSCCEEEEEECSSSHHHHHHHHCSSEECST
T ss_pred             CCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC--CCCCeeeEEEEEECCHHHHHHHHHHhCCcccCC
Confidence            44457899999999999      7899999999999999999883  579999999999999999999999866 66999


Q ss_pred             c-eEEEEeccC
Q 025068          100 R-RANCNLASL  109 (258)
Q Consensus       100 ~-~i~V~~a~~  109 (258)
                      + .|+|+++..
T Consensus        89 ~~~l~V~~a~~   99 (105)
T 2nlw_A           89 QHTFRVNLFTD   99 (105)
T ss_dssp             TCEEEEECSCC
T ss_pred             CceEEEEEcch
Confidence            8 999999954

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=5.6e-19  Score=138.06  Aligned_cols=82  Identities=22%  Similarity=0.271  Sum_probs=74.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCE----EEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEE
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEI----LEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRAN  103 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I----~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~  103 (258)
                      ....++|||+|||+++|+++|+++|++||.|    ++|.|++|+ ++++||||||+|.+.++|++||+.+++.|++|.|+
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~   98 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIE   98 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEE
Confidence            3557899999999999999999999999976    689999995 79999999999999999999999866779999999


Q ss_pred             EEeccCC
Q 025068          104 CNLASLG  110 (258)
Q Consensus       104 V~~a~~~  110 (258)
                      |..+..+
T Consensus        99 V~~a~~~  105 (123)
T 2dha_A           99 LFRSTAA  105 (123)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9988543

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.5e-17  Score=121.93  Aligned_cols=77  Identities=30%  Similarity=0.509  Sum_probs=69.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+||+.++++++|+++|++||.|++|+|+        ||||||+|.+.++|++||+.++ ..|+|++|+|++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            3457899999999999999999999999999999987        5799999999999999998855 679999999999


Q ss_pred             ccCCCC
Q 025068          107 ASLGRP  112 (258)
Q Consensus       107 a~~~~~  112 (258)
                      +..+..
T Consensus        77 a~~~~~   82 (90)
T 2dnq_A           77 SKNKSK   82 (90)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            965543

>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=99.74  E-value=1.7e-18  Score=131.40  Aligned_cols=83  Identities=11%  Similarity=0.217  Sum_probs=75.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCC---EEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGE---ILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRAN  103 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~---I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~  103 (258)
                      +....++|||+||++++++++|+++|+.||.   |++|+|++|+. ++++|||||+|.+.++|++||+.++..|+|+.|+
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~   85 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMGQRYVE   85 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEE
Confidence            3456789999999999999999999999998   89999999987 9999999999999999999999544679999999


Q ss_pred             EEeccCC
Q 025068          104 CNLASLG  110 (258)
Q Consensus       104 V~~a~~~  110 (258)
                      |.++..+
T Consensus        86 V~~a~~~   92 (107)
T 2lmi_A           86 VYEINNE   92 (107)
T ss_dssp             CEECCHH
T ss_pred             EEECCHH
Confidence            9998643

>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=99.74  E-value=7.1e-18  Score=128.36  Aligned_cols=76  Identities=24%  Similarity=0.487  Sum_probs=68.0

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           28 DTTYTKVFVGGLAWE-TQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~-~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      ....++|||+||+++ +++++|+++|++||.|++|+|        ++|||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   95 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDIN   95 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            344589999999999 999999999999999999988        57899999999999999998855 67999999999


Q ss_pred             eccCCC
Q 025068          106 LASLGR  111 (258)
Q Consensus       106 ~a~~~~  111 (258)
                      ++...+
T Consensus        96 ~a~~~~  101 (110)
T 1wf1_A           96 MAGEPK  101 (110)
T ss_dssp             ESCCCC
T ss_pred             ECCCCC
Confidence            996443

>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=99.74  E-value=1.1e-17  Score=120.99  Aligned_cols=78  Identities=31%  Similarity=0.475  Sum_probs=70.2

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-C-CccCCceE
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-T-PFIDGRRA  102 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~-~~i~G~~i  102 (258)
                      +.++...++|||+||+.++++++|+++|++||.|++|+++++      ||||||+|.+.++|++||+.+ + ..|+|+.|
T Consensus         6 ~~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l   79 (85)
T 2ytc_A            6 SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRL   79 (85)
T ss_dssp             CCSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEEC
T ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEE
Confidence            345567889999999999999999999999999999999874      689999999999999999986 5 56999999


Q ss_pred             EEEecc
Q 025068          103 NCNLAS  108 (258)
Q Consensus       103 ~V~~a~  108 (258)
                      +|++|+
T Consensus        80 ~v~~ak   85 (85)
T 2ytc_A           80 NVKWGR   85 (85)
T ss_dssp             CEEECC
T ss_pred             EEEecC
Confidence            999973

>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=99.74  E-value=8.4e-18  Score=139.04  Aligned_cols=88  Identities=38%  Similarity=0.604  Sum_probs=79.1

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEE
Q 025068           24 SPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRAN  103 (258)
Q Consensus        24 ~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~  103 (258)
                      .+.+....++|||+|||.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++..|+|+.|.
T Consensus         6 ~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~   85 (196)
T 1l3k_A            6 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE   85 (196)
T ss_dssp             --CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECE
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEee
Confidence            34456678999999999999999999999999999999999999999999999999999999999999977889999999


Q ss_pred             EEeccCCC
Q 025068          104 CNLASLGR  111 (258)
Q Consensus       104 V~~a~~~~  111 (258)
                      |.++..+.
T Consensus        86 v~~~~~~~   93 (196)
T 1l3k_A           86 PKRAVSRE   93 (196)
T ss_dssp             EEECCC--
T ss_pred             eecccCcc
Confidence            99986543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.59  E-value=1.4e-19  Score=139.21  Aligned_cols=85  Identities=27%  Similarity=0.400  Sum_probs=77.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEE--------EEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-Ccc
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE--------AVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFI   97 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~--------v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i   97 (258)
                      ++...++|||+||+.++++++|+++|++||.|++        |+|++++.+++++|||||+|.+.++|++||+.++ ..|
T Consensus         3 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   82 (116)
T 2lcw_A            3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   82 (116)
Confidence            4556789999999999999999999999999999        9999998899999999999999999999999865 679


Q ss_pred             CCceEEEEeccCCC
Q 025068           98 DGRRANCNLASLGR  111 (258)
Q Consensus        98 ~G~~i~V~~a~~~~  111 (258)
                      +|+.|+|+++..+.
T Consensus        83 ~g~~l~V~~a~~~~   96 (116)
T 2lcw_A           83 SGNPIKVSFATRRA   96 (116)
Confidence            99999999996543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.74  E-value=4.2e-18  Score=122.61  Aligned_cols=73  Identities=21%  Similarity=0.370  Sum_probs=65.9

Q ss_pred             CcEEEEcCCCCCC------cHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCc-eE
Q 025068           31 YTKVFVGGLAWET------QSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGR-RA  102 (258)
Q Consensus        31 ~~~lfVgnLp~~~------te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~-~i  102 (258)
                      .++|||+|||.++      ++++|+++|++||.|++|+|++  .++++||||||+|.+.++|++||+.++ ..|+|+ .|
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 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC--BTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC--CCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            3689999999999      7899999999999999999873  479999999999999999999999866 669999 88


Q ss_pred             EEE
Q 025068          103 NCN  105 (258)
Q Consensus       103 ~V~  105 (258)
                      +|+
T Consensus        79 ~V~   81 (81)
T 2krb_A           79 RVN   81 (81)
T ss_dssp             CCC
T ss_pred             EeC
Confidence            763

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.74  E-value=5.1e-18  Score=129.29  Aligned_cols=83  Identities=22%  Similarity=0.400  Sum_probs=70.0

Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCc
Q 025068           22 LNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGR  100 (258)
Q Consensus        22 ~~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~  100 (258)
                      ...+..+...++|||+||+.++++++|+++|++||.|++|+|+        +|||||+|.+.++|++||+.++ ..|+|+
T Consensus        22 ~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~   93 (108)
T 2jvo_A           22 HHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQ   93 (108)
T ss_dssp             ------CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             ccccCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            3445567788999999999999999999999999999999987        6899999999999999999854 679999


Q ss_pred             eEEEEeccCCCC
Q 025068          101 RANCNLASLGRP  112 (258)
Q Consensus       101 ~i~V~~a~~~~~  112 (258)
                      .|+|+++..+..
T Consensus        94 ~l~V~~a~~~~~  105 (108)
T 2jvo_A           94 PLEVVYSKLPAK  105 (108)
T ss_dssp             ECEEESCSCCC-
T ss_pred             EEEEEEecCCCC
Confidence            999999965543

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.73  E-value=1.2e-17  Score=138.18  Aligned_cols=87  Identities=28%  Similarity=0.558  Sum_probs=76.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      ....++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|.+||+.++..|+|+.|.|+++
T Consensus       101 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~~~~~~~G~~i~v~~a  180 (196)
T 1l3k_A          101 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA  180 (196)
T ss_dssp             --CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHhCCcEECCEEEEEEec
Confidence            34568999999999999999999999999999999999998999999999999999999999998778899999999999


Q ss_pred             cCCCCCC
Q 025068          108 SLGRPRP  114 (258)
Q Consensus       108 ~~~~~~~  114 (258)
                      .++....
T Consensus       181 ~~k~~~~  187 (196)
T 1l3k_A          181 LSKQEMA  187 (196)
T ss_dssp             C------
T ss_pred             CChhHhc
Confidence            7665443

>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=99.73  E-value=9.9e-18  Score=127.34  Aligned_cols=79  Identities=30%  Similarity=0.534  Sum_probs=71.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      .+...++|||+||+.++++++|+++|++||.|++|+|+++      +|||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   94 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY   94 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            3456789999999999999999999999999999999876      6899999999999999998854 67999999999


Q ss_pred             eccCCC
Q 025068          106 LASLGR  111 (258)
Q Consensus       106 ~a~~~~  111 (258)
                      ++..+.
T Consensus        95 ~a~~~~  100 (109)
T 1x4g_A           95 WGKESP  100 (109)
T ss_dssp             CCCCCC
T ss_pred             ecCCCC
Confidence            996554

>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=99.73  E-value=1.4e-17  Score=124.30  Aligned_cols=77  Identities=27%  Similarity=0.465  Sum_probs=69.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+||+.++++++|+++|++||.|++|+|+++      ||||||+|.+.++|++||+.++ ..|+|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   85 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEE
Confidence            445789999999999999999999999999999999865      6899999999999999998854 679999999999


Q ss_pred             ccCC
Q 025068          107 ASLG  110 (258)
Q Consensus       107 a~~~  110 (258)
                      +..+
T Consensus        86 a~~~   89 (99)
T 2cpj_A           86 ACHS   89 (99)
T ss_dssp             SSCC
T ss_pred             cCCC
Confidence            9654

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.73  E-value=1.4e-17  Score=130.70  Aligned_cols=81  Identities=16%  Similarity=0.212  Sum_probs=71.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHH----HHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceE
Q 025068           28 DTTYTKVFVGGLAWETQSETMR----RYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRA  102 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~----~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i  102 (258)
                      ....++|||+||++++++++|+    ++|++||.|++|.+.+   ++++||||||+|.+.++|++||+.++ ..|.|+.|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l  102 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            4457899999999999999876    6999999999988754   58899999999999999999999865 67999999


Q ss_pred             EEEeccCCC
Q 025068          103 NCNLASLGR  111 (258)
Q Consensus       103 ~V~~a~~~~  111 (258)
                      +|++|..+.
T Consensus       103 ~V~~a~~~~  111 (127)
T 2a3j_A          103 VITFSETPQ  111 (127)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEccCcc
Confidence            999996543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1.8e-17  Score=122.01  Aligned_cols=77  Identities=25%  Similarity=0.445  Sum_probs=69.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      .....++|||+||+.++++++|+++|++||.|++|+|+++        ||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   77 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ   77 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS--------EEEEEESCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            4556789999999999999999999999999999999743        99999999999999999855 67999999999


Q ss_pred             eccCCC
Q 025068          106 LASLGR  111 (258)
Q Consensus       106 ~a~~~~  111 (258)
                      ++..+.
T Consensus        78 ~a~~~~   83 (92)
T 2dgt_A           78 LSTSRL   83 (92)
T ss_dssp             ESSCCC
T ss_pred             EccCCC
Confidence            996543

>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=99.72  E-value=1.2e-17  Score=122.97  Aligned_cols=79  Identities=24%  Similarity=0.471  Sum_probs=64.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEe
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNL  106 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~  106 (258)
                      .....++|||+||++++||++|+++|++||.|++|+|+++     +||||||+|++.++|+++... ...+.|+.|.|++
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~~~~~-~~~~~g~~v~v~~   80 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCGE-DLIIKGISVHISN   80 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHHHTTC-EEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHHHcCC-CcccCCEEEEEEE
Confidence            4566789999999999999999999999999999999875     789999999999999965433 3447899999999


Q ss_pred             ccCCC
Q 025068          107 ASLGR  111 (258)
Q Consensus       107 a~~~~  111 (258)
                      |.++.
T Consensus        81 a~~k~   85 (89)
T 3d2w_A           81 AEPKH   85 (89)
T ss_dssp             CC---
T ss_pred             cCCCC
Confidence            96543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.72  E-value=8.2e-18  Score=123.24  Aligned_cols=72  Identities=14%  Similarity=0.163  Sum_probs=66.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      ...|||+||++++||++|+++|.+||+|++++++.      +||||||+|.+.++|++||+.+| ..|+||.|+|++|+
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            56899999999999999999999999999999865      58999999999999999999966 66999999999984

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.72  E-value=1.7e-17  Score=140.41  Aligned_cols=81  Identities=27%  Similarity=0.404  Sum_probs=75.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      ..++|||+|||.++||++|+++|++||.|++|+|++|+.+++++|||||+|.+.++|++||+.++ ..+.|+.|+|.++.
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~   93 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   93 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccc
Confidence            45799999999999999999999999999999999999999999999999999999999999865 56999999999985


Q ss_pred             CC
Q 025068          109 LG  110 (258)
Q Consensus       109 ~~  110 (258)
                      ..
T Consensus        94 ~~   95 (213)
T 4f02_A           94 RD   95 (213)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=3.2e-17  Score=120.22  Aligned_cols=78  Identities=29%  Similarity=0.513  Sum_probs=69.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      .....++|||+||+.++++++|+++|++||.|++|+|+++        ||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   76 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNGKEVKGKRINVE   76 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS--------CEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3456789999999999999999999999999999999743        99999999999999999854 67999999999


Q ss_pred             eccCCCC
Q 025068          106 LASLGRP  112 (258)
Q Consensus       106 ~a~~~~~  112 (258)
                      ++..++.
T Consensus        77 ~a~~~~~   83 (90)
T 2dnp_A           77 LSTKGQK   83 (90)
T ss_dssp             ESCCCCC
T ss_pred             ECCCCCC
Confidence            9976543

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.71  E-value=8.9e-18  Score=128.89  Aligned_cols=78  Identities=13%  Similarity=0.030  Sum_probs=69.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCC-CEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFG-EILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG-~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ...++|||+|||+++++++|+++|++|| +|+.++|+.    .+++|||||+|.+.++|++||+.++ .+|+|+.|+|++
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~  101 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVER  101 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3567999999999999999999999999 999998854    3478999999999999999999866 669999999999


Q ss_pred             ccCC
Q 025068          107 ASLG  110 (258)
Q Consensus       107 a~~~  110 (258)
                      +...
T Consensus       102 a~~~  105 (111)
T 2jvr_A          102 DDNP  105 (111)
T ss_dssp             SCC-
T ss_pred             CCCC
Confidence            9643

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=1.3e-17  Score=127.91  Aligned_cols=79  Identities=24%  Similarity=0.373  Sum_probs=70.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCC---CCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEE
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNT---GRSKGYGFVTFREPEAARRACADPTPFIDGRRANCN  105 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~t---g~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~  105 (258)
                      ...++|||+||++++++++|+++|++||.|+ +.++.++.+   |++||||||+|.+.++|++||+.++ .++|+.|.|.
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~-~~~G~~~~~~   83 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL-EEDGKLYLCV   83 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE-EETTEEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh-hcCCcEEEec
Confidence            3468999999999999999999999999999 888888877   7999999999999999999999873 4899999888


Q ss_pred             eccC
Q 025068          106 LASL  109 (258)
Q Consensus       106 ~a~~  109 (258)
                      .+..
T Consensus        84 ~~~~   87 (114)
T 2dnl_A           84 SSPT   87 (114)
T ss_dssp             CCSS
T ss_pred             cCCC
Confidence            6643

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=6.4e-17  Score=119.60  Aligned_cols=77  Identities=21%  Similarity=0.391  Sum_probs=67.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...++|||+||++++++++|+++|++||.|++|  +.++.+++   ||||+|.+.++|++||+ ++ ..|+|+.|+|+++
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            346799999999999999999999999999987  66665666   99999999999999999 65 6799999999988


Q ss_pred             cCCC
Q 025068          108 SLGR  111 (258)
Q Consensus       108 ~~~~  111 (258)
                      ..++
T Consensus        80 ~~~~   83 (94)
T 2e5g_A           80 EQKE   83 (94)
T ss_dssp             CCSC
T ss_pred             CcCC
Confidence            6443

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.71  E-value=1.8e-17  Score=137.24  Aligned_cols=81  Identities=27%  Similarity=0.389  Sum_probs=75.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...++|||+||+.++++++|+++|++||.|++|+|+.++ +++++|||||+|.+.++|++||+.++ ..|+|+.|+|++|
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            456899999999999999999999999999999999998 89999999999999999999999765 6799999999999


Q ss_pred             cCC
Q 025068          108 SLG  110 (258)
Q Consensus       108 ~~~  110 (258)
                      ...
T Consensus       165 ~~~  167 (177)
T 2f3j_A          165 ASQ  167 (177)
T ss_dssp             SSG
T ss_pred             cCC
Confidence            643

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.4e-16  Score=118.48  Aligned_cols=77  Identities=21%  Similarity=0.334  Sum_probs=67.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+||  ++++++|+++|++||.|++|+|.      +++|||||+|.+.++|++||+.++ ..|+|+.|+|++
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            345689999996  89999999999999999999984      467899999999999999998866 569999999999


Q ss_pred             ccCCCC
Q 025068          107 ASLGRP  112 (258)
Q Consensus       107 a~~~~~  112 (258)
                      +..+..
T Consensus        84 a~~~~~   89 (97)
T 1x5p_A           84 ARKQPM   89 (97)
T ss_dssp             CSSCCC
T ss_pred             CCCCCC
Confidence            976543

>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=99.71  E-value=1.5e-17  Score=127.98  Aligned_cols=76  Identities=18%  Similarity=0.219  Sum_probs=64.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCce-----
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRR-----  101 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~-----  101 (258)
                      ....++|||+||+.++++++|+++|++||+|++|+|+++       |||||+|.+.++|++||+.++ .+|+|+.     
T Consensus        13 ~r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~   85 (115)
T 3beg_B           13 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   85 (115)
T ss_dssp             ----CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCB
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEE
Confidence            456789999999999999999999999999999999876       799999999999999999855 6799998     


Q ss_pred             EEEEeccCC
Q 025068          102 ANCNLASLG  110 (258)
Q Consensus       102 i~V~~a~~~  110 (258)
                      |+|+.+..+
T Consensus        86 i~v~~~~~~   94 (115)
T 3beg_B           86 IRVKVDGPR   94 (115)
T ss_dssp             CEEEECC--
T ss_pred             EEeccCCCC
Confidence            777776543

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.71  E-value=1.7e-17  Score=124.16  Aligned_cols=76  Identities=18%  Similarity=0.269  Sum_probs=68.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+||+.++++++|+++|++||.|++|+|+      ++||||||+|.+.++|++||+.++ ..|+|+.|+|++
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   97 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGW   97 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCB
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEe
Confidence            3456899999999999999999999999999999997      357899999999999999998854 679999999999


Q ss_pred             ccC
Q 025068          107 ASL  109 (258)
Q Consensus       107 a~~  109 (258)
                      ++.
T Consensus        98 a~~  100 (101)
T 2la4_A           98 GKE  100 (101)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            854

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1e-16  Score=119.58  Aligned_cols=77  Identities=23%  Similarity=0.346  Sum_probs=68.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcC--CCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQF--GEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRAN  103 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~f--G~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~  103 (258)
                      .....++|||+||+.++++++|+++|++|  |.|++|++.        +|||||+|.+.++|++||+.++ ..|+|+.|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIE   82 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEE
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEE
Confidence            34567899999999999999999999999  999999774        5699999999999999999755 669999999


Q ss_pred             EEeccCCC
Q 025068          104 CNLASLGR  111 (258)
Q Consensus       104 V~~a~~~~  111 (258)
                      |+++..+.
T Consensus        83 v~~a~~~~   90 (99)
T 2cpd_A           83 VTLAKPVD   90 (99)
T ss_dssp             EECCCCCC
T ss_pred             EEECCCCC
Confidence            99996543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.70  E-value=2e-17  Score=122.55  Aligned_cols=80  Identities=19%  Similarity=0.321  Sum_probs=70.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      .+...++|||+||+.++++++|+++|++||.|+.+     ..+++++|||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   86 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567899999999999999999999999988766     2368999999999999999999999866 66999999999


Q ss_pred             eccCCC
Q 025068          106 LASLGR  111 (258)
Q Consensus       106 ~a~~~~  111 (258)
                      ++..+.
T Consensus        87 ~a~~~~   92 (96)
T 1fjc_A           87 YTGEKG   92 (96)
T ss_dssp             ECSSSC
T ss_pred             EcCCCC
Confidence            996543

>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=99.70  E-value=2.1e-17  Score=120.65  Aligned_cols=78  Identities=22%  Similarity=0.488  Sum_probs=67.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEecc
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLAS  108 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~  108 (258)
                      ...++|||+|||.++++++|+++|++||.|++|+|+++     +||||||+|.+.++|++|+.. ...++++.|+|+++.
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE-DLIIKGISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC-EEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC-CceeCCEEEEEEecC
Confidence            34689999999999999999999999999999999765     689999999999999876554 345799999999996


Q ss_pred             CCCC
Q 025068          109 LGRP  112 (258)
Q Consensus       109 ~~~~  112 (258)
                      .++.
T Consensus        77 ~~~~   80 (88)
T 1wf0_A           77 PKHN   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            5543

>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=99.70  E-value=3.8e-17  Score=125.06  Aligned_cols=79  Identities=15%  Similarity=0.240  Sum_probs=71.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...++|||+|||.++++++|+++|++||.|++|.|+++   +.++|||||+|.+.++|++||+.++ ..|+|+.|+|.++
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            45679999999999999999999999999999999976   5569999999999999999999754 6799999999999


Q ss_pred             cCC
Q 025068          108 SLG  110 (258)
Q Consensus       108 ~~~  110 (258)
                      ..+
T Consensus        83 ~~~   85 (115)
T 3lqv_A           83 NAN   85 (115)
T ss_dssp             CHH
T ss_pred             cCC
Confidence            754

>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=99.70  E-value=1.1e-16  Score=149.86  Aligned_cols=83  Identities=24%  Similarity=0.512  Sum_probs=76.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...++|||+||+.+||+++|+++|++||.|+.|+|+.++.+++++|||||+|.+.++|++||+.++ .+|+|+.|.|+++
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            345799999999999999999999999999999999999899999999999999999999998866 6799999999999


Q ss_pred             cCCC
Q 025068          108 SLGR  111 (258)
Q Consensus       108 ~~~~  111 (258)
                      ..+.
T Consensus       180 ~~~~  183 (437)
T 3pgw_S          180 RGRT  183 (437)
T ss_pred             CCCC
Confidence            7543

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.70  E-value=2.1e-17  Score=122.49  Aligned_cols=82  Identities=18%  Similarity=0.318  Sum_probs=72.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHH----HHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCce
Q 025068           27 GDTTYTKVFVGGLAWETQSETMR----RYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRR  101 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~----~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~  101 (258)
                      +....++|||+||+.++++++|+    ++|++||.|++|+|++   +++++|||||+|.+.++|++||+.++ ..|+|+.
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   80 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcE
Confidence            34567899999999999999999    9999999999998874   57889999999999999999999854 6799999


Q ss_pred             EEEEeccCCC
Q 025068          102 ANCNLASLGR  111 (258)
Q Consensus       102 i~V~~a~~~~  111 (258)
                      |+|+++..+.
T Consensus        81 l~v~~a~~~~   90 (97)
T 1nu4_A           81 MRIQYAKTDS   90 (97)
T ss_dssp             CEEEECSSCC
T ss_pred             EEEEEccCCC
Confidence            9999997654

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=4.1e-17  Score=120.80  Aligned_cols=79  Identities=18%  Similarity=0.139  Sum_probs=69.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEE-EEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEA-VVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v-~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      ....++|||+||+.++++++|+++|++||.|++| .|++++.++.    |||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~----afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   87 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYSSKDQARQALDKLNGFQLENFTLKVA   87 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3456899999999999999999999999999999 5888875443    9999999999999999854 77999999999


Q ss_pred             eccCC
Q 025068          106 LASLG  110 (258)
Q Consensus       106 ~a~~~  110 (258)
                      ++..+
T Consensus        88 ~a~~~   92 (96)
T 2e44_A           88 YIPDE   92 (96)
T ss_dssp             ECCCC
T ss_pred             EcCcc
Confidence            99655

>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=99.70  E-value=2.8e-17  Score=121.16  Aligned_cols=77  Identities=18%  Similarity=0.353  Sum_probs=66.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCC-EEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC--CccCCceEEEE
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGE-ILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT--PFIDGRRANCN  105 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~-I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~--~~i~G~~i~V~  105 (258)
                      ...++|||+||+.++++++|+++|++||. |..+.+.       ++|||||+|.+.++|++||+.++  ..|+|+.|+|+
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            45689999999999999999999999999 5555552       47899999999999999999854  56999999999


Q ss_pred             eccCCCC
Q 025068          106 LASLGRP  112 (258)
Q Consensus       106 ~a~~~~~  112 (258)
                      ++..+..
T Consensus        79 ~a~~~~~   85 (93)
T 2cqh_A           79 YSVSKKL   85 (93)
T ss_dssp             ECCCCCC
T ss_pred             EccCccc
Confidence            9975543

>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=99.69  E-value=5.5e-17  Score=130.04  Aligned_cols=81  Identities=23%  Similarity=0.353  Sum_probs=72.6

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCccCCceEE
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPFIDGRRAN  103 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~i~G~~i~  103 (258)
                      .......++|||+||++++++++|+++|++||.|++|+|+++     ++|||||+|.+.++|++||+.+ +..|+|+.|+
T Consensus        67 ~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  141 (150)
T 2i2y_A           67 RDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVR  141 (150)
T ss_dssp             SSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            334566789999999999999999999999999999999876     5899999999999999999975 4679999999


Q ss_pred             EEeccCC
Q 025068          104 CNLASLG  110 (258)
Q Consensus       104 V~~a~~~  110 (258)
                      |+++..+
T Consensus       142 v~~a~~~  148 (150)
T 2i2y_A          142 VELSNGE  148 (150)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCC
Confidence            9999654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.69  E-value=4.1e-17  Score=127.45  Aligned_cols=79  Identities=19%  Similarity=0.254  Sum_probs=70.0

Q ss_pred             cEEEEcCC----CCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcC----HHH----HHHHhc--CCC-Cc
Q 025068           32 TKVFVGGL----AWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFRE----PEA----ARRACA--DPT-PF   96 (258)
Q Consensus        32 ~~lfVgnL----p~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~----~~~----A~~Ai~--~~~-~~   96 (258)
                      ++|||+||    +++++|++|+++|+.||+|.+|+++.|+.||+++|||||+|.|    .++    |.+||.  .++ ..
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    433    889988  545 56


Q ss_pred             cCCceEEEEeccCC
Q 025068           97 IDGRRANCNLASLG  110 (258)
Q Consensus        97 i~G~~i~V~~a~~~  110 (258)
                      |+|+.|+|++....
T Consensus        83 I~Gr~irV~ln~~g   96 (136)
T 2j8a_A           83 IMGFKFEVILNKHS   96 (136)
T ss_dssp             ETTEEEEEEECCTT
T ss_pred             ecCcEEEEEECccc
Confidence            99999999987543

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.68  E-value=1.8e-16  Score=132.98  Aligned_cols=83  Identities=22%  Similarity=0.480  Sum_probs=76.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|.+||+.++ ..|+|+.|+|+++
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            345799999999999999999999999999999999999899999999999999999999999854 7799999999999


Q ss_pred             cCCC
Q 025068          108 SLGR  111 (258)
Q Consensus       108 ~~~~  111 (258)
                      ..+.
T Consensus       203 ~~~~  206 (216)
T 2qfj_A          203 VTPP  206 (216)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            7553

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.68  E-value=6.1e-17  Score=120.28  Aligned_cols=76  Identities=21%  Similarity=0.456  Sum_probs=67.5

Q ss_pred             CCCCcEEEEcCCCC-CCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           28 DTTYTKVFVGGLAW-ETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        28 ~~~~~~lfVgnLp~-~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      ....++|||+||+. ++++++|+++|++||.|++|+|.        ||||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            44578999999998 99999999999999999999883        6899999999999999999854 67999999999


Q ss_pred             eccCCC
Q 025068          106 LASLGR  111 (258)
Q Consensus       106 ~a~~~~  111 (258)
                      ++..+.
T Consensus        79 ~a~~~~   84 (96)
T 2kvi_A           79 VSSSNA   84 (96)
T ss_dssp             EEECCC
T ss_pred             EcCcCC
Confidence            997554

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.68  E-value=1.9e-16  Score=127.01  Aligned_cols=82  Identities=33%  Similarity=0.527  Sum_probs=76.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      .....++|||+||+.++++++|+++|++||.|+++++++++.+++++|+|||+|.+.++|.+||+.++ ..|+|+.|+|+
T Consensus        83 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  162 (166)
T 3md3_A           83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN  162 (166)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999855 67999999999


Q ss_pred             ecc
Q 025068          106 LAS  108 (258)
Q Consensus       106 ~a~  108 (258)
                      +|+
T Consensus       163 ~a~  165 (166)
T 3md3_A          163 WAA  165 (166)
T ss_dssp             ESC
T ss_pred             ecC
Confidence            985

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.68  E-value=1.4e-16  Score=130.05  Aligned_cols=82  Identities=16%  Similarity=0.322  Sum_probs=70.8

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCC--ceE
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDG--RRA  102 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G--~~i  102 (258)
                      ....+..+|||+||++++++++|+++|++||+|++|+|..++    ++|||||+|++.++|++||+.++ ..|.+  +.|
T Consensus        41 ~~ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L  116 (164)
T 1sjr_A           41 AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTL  116 (164)
T ss_dssp             CCCCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCE
T ss_pred             CCCCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEE
Confidence            344567789999999999999999999999999999987542    57899999999999999999876 56855  999


Q ss_pred             EEEeccCCC
Q 025068          103 NCNLASLGR  111 (258)
Q Consensus       103 ~V~~a~~~~  111 (258)
                      +|++++.++
T Consensus       117 ~V~~Ak~~~  125 (164)
T 1sjr_A          117 RIDFSKLTS  125 (164)
T ss_dssp             EEEECSSSS
T ss_pred             EEEEecCCc
Confidence            999997553

>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=99.68  E-value=4.6e-17  Score=131.22  Aligned_cols=81  Identities=31%  Similarity=0.631  Sum_probs=75.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEeccC
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASL  109 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~~  109 (258)
                      ..++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+..+..|+|+.|+|++|.+
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~V~~a~p  165 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEP  165 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHHCSEECSSSSCEEEEECCC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHhCCCEEeCCeEEEEeecCC
Confidence            45699999999999999999999999999999999998899999999999999999999999544679999999999965


Q ss_pred             C
Q 025068          110 G  110 (258)
Q Consensus       110 ~  110 (258)
                      +
T Consensus       166 k  166 (167)
T 2cjk_A          166 R  166 (167)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.68  E-value=1.6e-16  Score=118.56  Aligned_cols=76  Identities=22%  Similarity=0.517  Sum_probs=67.6

Q ss_pred             CCCCCcEEEEcCCCC-CCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEE
Q 025068           27 GDTTYTKVFVGGLAW-ETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANC  104 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~-~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V  104 (258)
                      .....++|||+||+. ++++++|+++|++||.|++|+|.        +|||||+|.+.++|++||+.++ ..|+|+.|+|
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL   89 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345678999999998 99999999999999999999882        7899999999999999999855 6699999999


Q ss_pred             EeccCC
Q 025068          105 NLASLG  110 (258)
Q Consensus       105 ~~a~~~  110 (258)
                      ++++.+
T Consensus        90 ~~a~~~   95 (97)
T 2xnq_A           90 EVSSSN   95 (97)
T ss_dssp             EECCCC
T ss_pred             EecCCC
Confidence            998543

>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=99.68  E-value=6.1e-17  Score=123.83  Aligned_cols=77  Identities=19%  Similarity=0.236  Sum_probs=69.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      +...++|||+||+.++++++|+++|++||.|++|.|++      ++|||||+|.+.++|++||+.++ ..|+|+.|+|++
T Consensus         7 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   80 (111)
T 1whx_A            7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEW   80 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            33568999999999999999999999999999998864      46799999999999999999865 679999999999


Q ss_pred             ccCC
Q 025068          107 ASLG  110 (258)
Q Consensus       107 a~~~  110 (258)
                      +...
T Consensus        81 a~~~   84 (111)
T 1whx_A           81 APIG   84 (111)
T ss_dssp             EETT
T ss_pred             CCCC
Confidence            9654

>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=99.68  E-value=1.9e-16  Score=127.13  Aligned_cols=80  Identities=29%  Similarity=0.432  Sum_probs=74.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCccCCceEEEEeccC
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPFIDGRRANCNLASL  109 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~i~G~~i~V~~a~~  109 (258)
                      .++|||+|||.++++++|+++|++||.|.+|++++++.+++++|||||+|.+.++|++||+.+ +..+.|+.|+|.++..
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            579999999999999999999999999999999999989999999999999999999999975 4679999999999864


Q ss_pred             C
Q 025068          110 G  110 (258)
Q Consensus       110 ~  110 (258)
                      .
T Consensus        82 ~   82 (167)
T 1fxl_A           82 S   82 (167)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.68  E-value=9e-18  Score=133.61  Aligned_cols=87  Identities=21%  Similarity=0.368  Sum_probs=71.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEE--E---eecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCce
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAV--V---ITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRR  101 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~--v---~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~  101 (258)
                      ....++|||+||+.++++++|+++|++||.|.+|.  +   ++...+++++|||||+|.+.++|++||+.++ ..|+|+.
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            44568999999999999999999999999987641  1   1112368999999999999999999999855 6699999


Q ss_pred             EEEEeccCCCCCC
Q 025068          102 ANCNLASLGRPRP  114 (258)
Q Consensus       102 i~V~~a~~~~~~~  114 (258)
                      |+|++|...+++.
T Consensus       122 l~V~~a~~~~~~~  134 (143)
T 3egn_A          122 MVVQFARSARPKQ  134 (143)
T ss_dssp             CEEEECCCSCC--
T ss_pred             EEEEECCCCCCcc
Confidence            9999997665544

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.68  E-value=5.6e-16  Score=128.18  Aligned_cols=84  Identities=24%  Similarity=0.418  Sum_probs=77.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+||+.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|++
T Consensus       111 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  190 (198)
T 2yh0_A          111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  190 (198)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4567899999999999999999999999999999999998899999999999999999999999854 679999999999


Q ss_pred             ccCCC
Q 025068          107 ASLGR  111 (258)
Q Consensus       107 a~~~~  111 (258)
                      +..+.
T Consensus       191 a~~~~  195 (198)
T 2yh0_A          191 ASVGA  195 (198)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            96543

>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=99.67  E-value=1.5e-16  Score=128.08  Aligned_cols=82  Identities=24%  Similarity=0.343  Sum_probs=75.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~i~G~~i~V~~a~  108 (258)
                      ..++|||+|||.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.+ +..|+|+.|+|.++.
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            3579999999999999999999999999999999999989999999999999999999999875 467999999999996


Q ss_pred             CCC
Q 025068          109 LGR  111 (258)
Q Consensus       109 ~~~  111 (258)
                      .+.
T Consensus        82 ~~~   84 (168)
T 1b7f_A           82 PGG   84 (168)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            543

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.67  E-value=3e-17  Score=138.91  Aligned_cols=80  Identities=29%  Similarity=0.475  Sum_probs=73.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      ..++|||+||+.++++++|+++|++||.|++|+|++|+  +.+||||||+|.+.++|++||+.++ .+|+|++|+|++|.
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            45789999999999999999999999999999999985  5689999999999999999999855 77999999999996


Q ss_pred             CCC
Q 025068          109 LGR  111 (258)
Q Consensus       109 ~~~  111 (258)
                      +++
T Consensus       180 ~~~  182 (213)
T 4f02_A          180 SRK  182 (213)
T ss_dssp             CHH
T ss_pred             CCc
Confidence            543

>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=99.66  E-value=1.1e-16  Score=128.97  Aligned_cols=79  Identities=30%  Similarity=0.729  Sum_probs=73.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEeccC
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASL  109 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~~  109 (258)
                      ..++|||+|||.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+. .+.++|+.|.|.++..
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~g~~i~v~~~~~   80 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT-QHILDGKVIDPKRAIP   80 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS-CCEETTEECCCEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc-ccccCCeEcccccccc
Confidence            468999999999999999999999999999999999998999999999999999999999996 4679999999998854

>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=99.66  E-value=3.1e-16  Score=126.89  Aligned_cols=80  Identities=24%  Similarity=0.399  Sum_probs=74.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...++|||+|||.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.++ ..|+|+.|+|++|
T Consensus        92 ~~~~~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           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            346899999999999999999999999999999999998899999999999999999999999854 6799999999997


Q ss_pred             c
Q 025068          108 S  108 (258)
Q Consensus       108 ~  108 (258)
                      .
T Consensus       172 s  172 (172)
T 2g4b_A          172 S  172 (172)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.66  E-value=4e-16  Score=130.73  Aligned_cols=79  Identities=16%  Similarity=0.242  Sum_probs=74.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEeccC
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASL  109 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~~  109 (258)
                      ..++|||+|||.++++++|+++|++||.|.+|+|++++ ++++||||||+|++.++|++||+.++..|+|+.|.|.++..
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD  186 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHH
Confidence            35899999999999999999999999999999999987 49999999999999999999999988899999999998854

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.66  E-value=1.4e-15  Score=118.88  Aligned_cols=77  Identities=14%  Similarity=0.153  Sum_probs=66.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccE-EEEEEcCHHHHHHHhcCCC-CccCC--ceEEE
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGY-GFVTFREPEAARRACADPT-PFIDG--RRANC  104 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~-aFV~F~~~~~A~~Ai~~~~-~~i~G--~~i~V  104 (258)
                      .....|||+||++.+++++|+++|++||.|++|+|+..      .|| |||+|.+.++|++||+.++ ..|.|  +.|+|
T Consensus        23 s~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V   96 (124)
T 2e5i_A           23 NKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKI   96 (124)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEE
T ss_pred             CcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEE
Confidence            34456789999999999999999999999999998652      276 9999999999999999965 66877  68999


Q ss_pred             EeccCCC
Q 025068          105 NLASLGR  111 (258)
Q Consensus       105 ~~a~~~~  111 (258)
                      ++|+.+.
T Consensus        97 ~~Ak~~~  103 (124)
T 2e5i_A           97 EYARPTR  103 (124)
T ss_dssp             ECCSCSC
T ss_pred             EEecCCc
Confidence            9996553

>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=99.66  E-value=1.2e-16  Score=116.80  Aligned_cols=73  Identities=18%  Similarity=0.219  Sum_probs=66.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      ..++|||+|||+++++++|+++|++| .|++|+|.      ++||||||+|.+.++|++||+.++ ..++|++|+|+++.
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            46789999999999999999999999 99999884      578999999999999999999865 66999999999985


Q ss_pred             C
Q 025068          109 L  109 (258)
Q Consensus       109 ~  109 (258)
                      .
T Consensus        77 ~   77 (88)
T 1wg1_A           77 T   77 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.64  E-value=4.5e-16  Score=130.49  Aligned_cols=83  Identities=29%  Similarity=0.437  Sum_probs=73.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~i~G~~i~V~~  106 (258)
                      ....++|||+|||.++++++|+++|++||.|++|+|++++.+++++|||||+|.+.++|++||+.+ +..|+|+.|+|.+
T Consensus        25 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~  104 (216)
T 2qfj_A           25 LAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGR  104 (216)
T ss_dssp             HHHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEEC
T ss_pred             cCcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEec
Confidence            345689999999999999999999999999999999999989999999999999999999999975 4679999999998


Q ss_pred             ccCC
Q 025068          107 ASLG  110 (258)
Q Consensus       107 a~~~  110 (258)
                      +...
T Consensus       105 ~~~~  108 (216)
T 2qfj_A          105 PSNI  108 (216)
T ss_dssp             CSCC
T ss_pred             CCCc
Confidence            7644

>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=99.64  E-value=3.1e-16  Score=120.69  Aligned_cols=75  Identities=19%  Similarity=0.282  Sum_probs=65.8

Q ss_pred             CCCCcEEEE--cCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-Ccc-----CC
Q 025068           28 DTTYTKVFV--GGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFI-----DG   99 (258)
Q Consensus        28 ~~~~~~lfV--gnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i-----~G   99 (258)
                      +...++|||  +||+++++|++|+++|++||+|++|.|+.+      ||||||+|.+.++|++||+.++ .+|     .+
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            345678999  779999999999999999999999987643      6899999999999999999866 556     68


Q ss_pred             ceEEEEecc
Q 025068          100 RRANCNLAS  108 (258)
Q Consensus       100 ~~i~V~~a~  108 (258)
                      +.|+|.++.
T Consensus        96 ~~l~v~~a~  104 (114)
T 2cq2_A           96 ITLYLNFVE  104 (114)
T ss_dssp             EECEEEEES
T ss_pred             cEEEEEecc
Confidence            899999985

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.63  E-value=1.4e-15  Score=122.45  Aligned_cols=80  Identities=25%  Similarity=0.467  Sum_probs=73.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCC--ceEEE
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDG--RRANC  104 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G--~~i~V  104 (258)
                      ....++|||+||+.++++++|+++|++||.|++++|++++.+++++|+|||+|.+.++|.+|++.++ ..|+|  ++|+|
T Consensus        86 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V  165 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV  165 (168)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEE
Confidence            3457899999999999999999999999999999999999889999999999999999999999855 66877  99999


Q ss_pred             Eec
Q 025068          105 NLA  107 (258)
Q Consensus       105 ~~a  107 (258)
                      ++|
T Consensus       166 ~~A  168 (168)
T 1b7f_A          166 RLA  168 (168)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.63  E-value=7.2e-16  Score=111.79  Aligned_cols=71  Identities=20%  Similarity=0.427  Sum_probs=64.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcC----C-------CEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCc
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQF----G-------EILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPF   96 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~f----G-------~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~   96 (258)
                      ...++|||+||+.++++++|+++|++|    |       .|.++++.++      ||||||+|.+.++|++|| .+ +..
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       9999998755      789999999999999999 64 467


Q ss_pred             cCCceEEEEe
Q 025068           97 IDGRRANCNL  106 (258)
Q Consensus        97 i~G~~i~V~~  106 (258)
                      |+|+.|+|+.
T Consensus        77 ~~g~~l~V~r   86 (87)
T 2hzc_A           77 FQGQSLKIRR   86 (87)
T ss_dssp             ETTEECEEEC
T ss_pred             ECCeEEEEeC
Confidence            9999999974

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.63  E-value=8.5e-16  Score=123.15  Aligned_cols=79  Identities=23%  Similarity=0.386  Sum_probs=71.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccCC
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASLG  110 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~~  110 (258)
                      ++|||+|||.++++++|+++|++||.|++|+|++++. ++++|||||+|.+.++|++||+.++ ..+.|+.|+|.++...
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC--CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC-CCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            5899999999999999999999999999999999984 8899999999999999999997754 6799999999999654


Q ss_pred             C
Q 025068          111 R  111 (258)
Q Consensus       111 ~  111 (258)
                      .
T Consensus        80 ~   80 (166)
T 3md3_A           80 Q   80 (166)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.62  E-value=1.7e-15  Score=132.70  Aligned_cols=83  Identities=19%  Similarity=0.304  Sum_probs=74.0

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHH----HHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCc
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMR----RYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGR  100 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~----~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~  100 (258)
                      .+....++|||+||+.++++++|+    ++|++||.|++|+|++   ++++||||||+|.+.++|++||+.++ ..|.|+
T Consensus         4 ~~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   80 (282)
T 3pgw_A            4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK   80 (282)
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCc
Confidence            345668899999999999999977    8999999999999886   58899999999999999999998865 669999


Q ss_pred             eEEEEeccCCC
Q 025068          101 RANCNLASLGR  111 (258)
Q Consensus       101 ~i~V~~a~~~~  111 (258)
                      .|+|+++..+.
T Consensus        81 ~l~v~~a~~~~   91 (282)
T 3pgw_A           81 PMRIQYAKTDS   91 (282)
T ss_pred             EEEEEEeccCc
Confidence            99999996544

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.62  E-value=1.5e-15  Score=119.51  Aligned_cols=79  Identities=15%  Similarity=0.356  Sum_probs=69.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccE-EEEEEcCHHHHHHHhcCCC-CccCC--ceEE
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGY-GFVTFREPEAARRACADPT-PFIDG--RRAN  103 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~-aFV~F~~~~~A~~Ai~~~~-~~i~G--~~i~  103 (258)
                      ..+.-+|||+||+..+|+++|+++|++||.|++|+|+++     .+|| |||+|.+.++|++||+.++ ..|.+  +.|+
T Consensus        25 ps~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~Lr   99 (130)
T 3zzy_A           25 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR   99 (130)
T ss_dssp             CCSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEE
T ss_pred             CCceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEE
Confidence            345678899999999999999999999999999988764     2677 9999999999999999966 56877  8999


Q ss_pred             EEeccCCC
Q 025068          104 CNLASLGR  111 (258)
Q Consensus       104 V~~a~~~~  111 (258)
                      |++++.++
T Consensus       100 I~~ak~~~  107 (130)
T 3zzy_A          100 IDFSKLTS  107 (130)
T ss_dssp             EEECSCSS
T ss_pred             EEecCCCc
Confidence            99997553

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.61  E-value=1.9e-15  Score=122.28  Aligned_cols=82  Identities=28%  Similarity=0.362  Sum_probs=72.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCC--CcccEEEEEEcCHHHHHHHhcCCC-CccC---CceEE
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTG--RSKGYGFVTFREPEAARRACADPT-PFID---GRRAN  103 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg--~skG~aFV~F~~~~~A~~Ai~~~~-~~i~---G~~i~  103 (258)
                      +.++|||+|||.++++++|+++|++||.|++|+|++++.++  +++|||||+|.+.++|++||+.++ ..+.   ++.|.
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            46899999999999999999999999999999999999876  899999999999999999999855 3443   67788


Q ss_pred             EEeccCCC
Q 025068          104 CNLASLGR  111 (258)
Q Consensus       104 V~~a~~~~  111 (258)
                      +..+....
T Consensus        82 ~~~~~~~~   89 (175)
T 3nmr_A           82 MKPADSEK   89 (175)
T ss_dssp             EEECGGGC
T ss_pred             Eccccccc
Confidence            88876443

>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=99.61  E-value=1.2e-15  Score=129.01  Aligned_cols=76  Identities=18%  Similarity=0.270  Sum_probs=69.3

Q ss_pred             CCcEEEEcCCC-CCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           30 TYTKVFVGGLA-WETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        30 ~~~~lfVgnLp-~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ..++|||+||+ +++++++|+++|++||.|++|+|++++     ||||||+|.+.++|++||+.++ ..|.|+.|+|.++
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 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            46799999999 899999999999999999999998763     7999999999999999999865 6799999999999


Q ss_pred             cCC
Q 025068          108 SLG  110 (258)
Q Consensus       108 ~~~  110 (258)
                      +.+
T Consensus        78 ~~~   80 (205)
T 3tyt_A           78 KQP   80 (205)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            644

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.61  E-value=2.4e-15  Score=120.60  Aligned_cols=80  Identities=24%  Similarity=0.439  Sum_probs=72.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCce--EEE
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRR--ANC  104 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~--i~V  104 (258)
                      ....++|||+||+.++++++|+++|++||.|++++++.++.+++++|+|||+|.+.++|++|++.++ ..|+|+.  |+|
T Consensus        85 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v  164 (167)
T 1fxl_A           85 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV  164 (167)
T ss_dssp             GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEE
Confidence            3456799999999999999999999999999999999999889999999999999999999999855 6799865  788


Q ss_pred             Eec
Q 025068          105 NLA  107 (258)
Q Consensus       105 ~~a  107 (258)
                      ++|
T Consensus       165 ~~A  167 (167)
T 1fxl_A          165 KFA  167 (167)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            775

>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=99.60  E-value=3.3e-15  Score=120.88  Aligned_cols=79  Identities=24%  Similarity=0.361  Sum_probs=71.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccC---CceEEE
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFID---GRRANC  104 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~---G~~i~V  104 (258)
                      ...++|||+||+.++++++|+++|++||.|++|+|++++ +++++|||||+|.+.++|++||+.++ ..+.   +++|+|
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V  171 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV  171 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEE
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEE
Confidence            367899999999999999999999999999999999997 59999999999999999999999865 4444   499999


Q ss_pred             Eecc
Q 025068          105 NLAS  108 (258)
Q Consensus       105 ~~a~  108 (258)
                      ++|.
T Consensus       172 ~~ad  175 (175)
T 3nmr_A          172 KFAD  175 (175)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9983

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.59  E-value=4e-15  Score=112.87  Aligned_cols=80  Identities=16%  Similarity=0.233  Sum_probs=69.7

Q ss_pred             CCCcEEEEcCCCC-----CCcHHHHHHHHhcCCCEEEEEEeecCCC-CCcccEEEEEEcCHHHHHHHhcCCC-CccCCce
Q 025068           29 TTYTKVFVGGLAW-----ETQSETMRRYFEQFGEILEAVVITDKNT-GRSKGYGFVTFREPEAARRACADPT-PFIDGRR  101 (258)
Q Consensus        29 ~~~~~lfVgnLp~-----~~te~~L~~~F~~fG~I~~v~v~~d~~t-g~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~  101 (258)
                      ...++|+|.||-.     +-++++|+++|++||.|++|+|++++.+ ++++||+||+|.+.++|.+||+.++ ..++||.
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            3467899999953     2378999999999999999999998754 6899999999999999999999965 6799999


Q ss_pred             EEEEecc
Q 025068          102 ANCNLAS  108 (258)
Q Consensus       102 i~V~~a~  108 (258)
                      |+|+++.
T Consensus        86 i~v~~a~   92 (105)
T 2pe8_A           86 VKACFYN   92 (105)
T ss_dssp             CEEEECC
T ss_pred             EEEEEcC
Confidence            9999985

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=4.6e-15  Score=109.77  Aligned_cols=71  Identities=23%  Similarity=0.316  Sum_probs=61.9

Q ss_pred             CcEEEEcCCCCCCcHHH----HHHHHhcC-CCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEE
Q 025068           31 YTKVFVGGLAWETQSET----MRRYFEQF-GEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANC  104 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~----L~~~F~~f-G~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V  104 (258)
                      .+.|||+||++++++++    |+++|++| |+|.+|       |+   |+|||+|.+.++|++|++.++ ..|.||.|+|
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            33499999999999998    55899999 599998       34   999999999999999999965 6799999999


Q ss_pred             EeccCCC
Q 025068          105 NLASLGR  111 (258)
Q Consensus       105 ~~a~~~~  111 (258)
                      ++|+.++
T Consensus        79 ~~A~~~s   85 (96)
T 2diu_A           79 SFTPKNR   85 (96)
T ss_dssp             ESSCCSC
T ss_pred             EecCCCc
Confidence            9996554

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.57  E-value=2.9e-15  Score=129.46  Aligned_cols=78  Identities=21%  Similarity=0.298  Sum_probs=68.5

Q ss_pred             CCCCcEEEEcCCCCCC---------cHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-Ccc
Q 025068           28 DTTYTKVFVGGLAWET---------QSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFI   97 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~---------te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i   97 (258)
                      +...++|||+||+.++         +|++|+++|++||+|++|+|+.+      ||||||+|.+.++|++||+.++ ..|
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            5578899999999998         79999999999999999999864      7899999999999999999865 557


Q ss_pred             ------------CCceEEEEeccCCC
Q 025068           98 ------------DGRRANCNLASLGR  111 (258)
Q Consensus        98 ------------~G~~i~V~~a~~~~  111 (258)
                                  .|+.|.|++|....
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             eccccccccccCCCCEEEEEEccCCC
Confidence                        89999999997543

>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=99.56  E-value=8e-16  Score=125.12  Aligned_cols=85  Identities=16%  Similarity=0.217  Sum_probs=72.4

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEE
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCN  105 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~  105 (258)
                      .+....++|||+|||.++++++|+++|++||.|.. .++++..+++++|||||+|.+.++|++||+.++..|.|+.|+|.
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~   86 (175)
T 1fje_B            8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLE   86 (175)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEe
Confidence            34567889999999999999999999999998776 34555557899999999999999999999644467999999999


Q ss_pred             eccCCC
Q 025068          106 LASLGR  111 (258)
Q Consensus       106 ~a~~~~  111 (258)
                      ++..+.
T Consensus        87 ~~~~~~   92 (175)
T 1fje_B           87 KPKGRD   92 (175)
T ss_dssp             CCCCSS
T ss_pred             cCCCcc
Confidence            997544

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.55  E-value=3.1e-14  Score=124.63  Aligned_cols=77  Identities=19%  Similarity=0.223  Sum_probs=69.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccC-CceEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFID-GRRANC  104 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~-G~~i~V  104 (258)
                      .....++|||+||+.++++++|+++|++||.|++|+|+.++     +|||||+|.+.++|++||+.++ ..|+ |+.|+|
T Consensus       203 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v  277 (282)
T 3pgw_A          203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKI  277 (282)
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEE
Confidence            34467899999999999999999999999999999998764     5899999999999999999866 5688 999999


Q ss_pred             Eecc
Q 025068          105 NLAS  108 (258)
Q Consensus       105 ~~a~  108 (258)
                      ++++
T Consensus       278 ~~ak  281 (282)
T 3pgw_A          278 SFAK  281 (282)
T ss_pred             EEec
Confidence            9984

>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=99.55  E-value=9.4e-15  Score=128.54  Aligned_cols=82  Identities=20%  Similarity=0.324  Sum_probs=73.5

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHHHhcCCCEEEEEEeecCC-CCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEE
Q 025068           28 DTTYTKVFVGGLAWE-TQSETMRRYFEQFGEILEAVVITDKN-TGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANC  104 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~-~te~~L~~~F~~fG~I~~v~v~~d~~-tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V  104 (258)
                      ....++|||+||+.+ +++++|+++|++||.|++|+|+++.. |++++|||||+|.+.++|.+|| .++ ..|+|+.|.|
T Consensus       207 ~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V  285 (292)
T 2ghp_A          207 TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISV  285 (292)
T ss_dssp             CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEE
T ss_pred             CCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEE
Confidence            445689999999999 99999999999999999999999886 6999999999999999999999 755 6699999999


Q ss_pred             EeccCC
Q 025068          105 NLASLG  110 (258)
Q Consensus       105 ~~a~~~  110 (258)
                      .++.++
T Consensus       286 ~~a~~k  291 (292)
T 2ghp_A          286 SLADKK  291 (292)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            999654

>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=99.55  E-value=3.2e-14  Score=108.62  Aligned_cols=78  Identities=21%  Similarity=0.319  Sum_probs=66.0

Q ss_pred             CCCcEEEEcCCCCCCc-----------HHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-Cc
Q 025068           29 TTYTKVFVGGLAWETQ-----------SETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PF   96 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~t-----------e~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~   96 (258)
                      ...++|+|.||-...+           +++|+++|++||.|++|.| .++   .++|||||+|.+.++|++||+.++ ..
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            4578999999944432           6899999999999999955 554   379999999999999999998866 66


Q ss_pred             cCCceEEEEeccCC
Q 025068           97 IDGRRANCNLASLG  110 (258)
Q Consensus        97 i~G~~i~V~~a~~~  110 (258)
                      |+|+.|+|+++..+
T Consensus        89 ~~gr~l~v~~a~~~  102 (112)
T 2dit_A           89 FGGRQITAQAWDGT  102 (112)
T ss_dssp             ETTEECEEEECCSC
T ss_pred             ECCcEEEEEEeCCC
Confidence            99999999999654

>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=99.55  E-value=8.9e-15  Score=118.89  Aligned_cols=78  Identities=19%  Similarity=0.338  Sum_probs=69.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+||+.++++++|+++|++||.|..+     ..+++++|||||+|.+.++|.+||+.++ ..|+|+.|+|++
T Consensus        96 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  170 (175)
T 1fje_B           96 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY  170 (175)
T ss_dssp             TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEE
T ss_pred             cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEe
Confidence            4467899999999999999999999999988766     3478999999999999999999999855 679999999999


Q ss_pred             ccCC
Q 025068          107 ASLG  110 (258)
Q Consensus       107 a~~~  110 (258)
                      |..+
T Consensus       171 a~~k  174 (175)
T 1fje_B          171 TGEK  174 (175)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            9643

>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=99.55  E-value=1.8e-14  Score=123.00  Aligned_cols=78  Identities=14%  Similarity=0.232  Sum_probs=70.9

Q ss_pred             CCCCcEEEEcCCCC-CCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCccCCceEEEE
Q 025068           28 DTTYTKVFVGGLAW-ETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPFIDGRRANCN  105 (258)
Q Consensus        28 ~~~~~~lfVgnLp~-~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~i~G~~i~V~  105 (258)
                      ....++|||+|||. ++++++|+++|++||.|++|+|++++     +|||||+|.+.++|++||+.+ +..|.|+.|+|.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~  105 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRIT  105 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34678999999999 99999999999999999999999875     789999999999999999874 467999999999


Q ss_pred             eccCC
Q 025068          106 LASLG  110 (258)
Q Consensus       106 ~a~~~  110 (258)
                      ++..+
T Consensus       106 ~a~~~  110 (229)
T 2adc_A          106 LSKHQ  110 (229)
T ss_dssp             CCSCC
T ss_pred             EecCc
Confidence            99754

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.54  E-value=2.7e-14  Score=125.10  Aligned_cols=82  Identities=23%  Similarity=0.381  Sum_probs=76.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      ..++|||+|||.++++++|+++|++||.|.+++|++++.+++++|||||+|.+.++|.+||+.++ ..|+|+.|.|.++.
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            45799999999999999999999999999999999999899999999999999999999998754 67999999999997


Q ss_pred             CCC
Q 025068          109 LGR  111 (258)
Q Consensus       109 ~~~  111 (258)
                      .+.
T Consensus       174 ~~~  176 (284)
T 3smz_A          174 AGQ  176 (284)
T ss_dssp             GGG
T ss_pred             CCC
Confidence            554

>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=99.53  E-value=1.6e-14  Score=126.58  Aligned_cols=86  Identities=14%  Similarity=0.170  Sum_probs=77.7

Q ss_pred             CCCCcEEEEcCCCCCC-cHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           28 DTTYTKVFVGGLAWET-QSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~-te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      ....++|||+|||.++ ++++|+++|++||.|++|+|+++. +++++|+|||+|.+.++|.+||+.++ ..|+|+.|+|+
T Consensus       181 ~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  259 (284)
T 3smz_A          181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVS  259 (284)
T ss_dssp             TTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEE
Confidence            4567899999999995 999999999999999999999997 69999999999999999999999855 67999999999


Q ss_pred             eccCCCCCC
Q 025068          106 LASLGRPRP  114 (258)
Q Consensus       106 ~a~~~~~~~  114 (258)
                      ++.++..++
T Consensus       260 ~a~~~~~~~  268 (284)
T 3smz_A          260 FCAPGPPGR  268 (284)
T ss_dssp             ECCSSSCHH
T ss_pred             EecCCCccc
Confidence            997766543

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=2.1e-13  Score=102.45  Aligned_cols=76  Identities=16%  Similarity=0.154  Sum_probs=62.9

Q ss_pred             CcEEEEcCCC-------CCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEE
Q 025068           31 YTKVFVGGLA-------WETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRAN  103 (258)
Q Consensus        31 ~~~lfVgnLp-------~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~  103 (258)
                      .++|-|.-..       .++++++|+++|++||.|++|.|+     +++||||||+|.+.++|++||+.+ ..+.++.|+
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~-~~~~g~~l~   83 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNE-VGLVDNPLK   83 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTC-CBCSSSBCE
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhc-CCCCCCeEE
Confidence            4466665433       468999999999999999999987     467999999999999999999984 347899999


Q ss_pred             EEeccCCCC
Q 025068          104 CNLASLGRP  112 (258)
Q Consensus       104 V~~a~~~~~  112 (258)
                      |+++..+..
T Consensus        84 V~~a~~~~~   92 (100)
T 2d9o_A           84 ISWLEGQPQ   92 (100)
T ss_dssp             EECSSCCCC
T ss_pred             EEEccCCCC
Confidence            999965543

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.51  E-value=2.4e-14  Score=118.84  Aligned_cols=77  Identities=14%  Similarity=0.233  Sum_probs=69.7

Q ss_pred             CCcEEEEcCCCC-CCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCccCCceEEEEec
Q 025068           30 TYTKVFVGGLAW-ETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPFIDGRRANCNLA  107 (258)
Q Consensus        30 ~~~~lfVgnLp~-~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~i~G~~i~V~~a  107 (258)
                      ..++|||+|||. ++++++|+++|++||.|++|+|++++     +|||||+|.+.++|++||+.+ +..|+|+.|+|.++
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            357999999999 99999999999999999999998875     789999999999999999974 46799999999999


Q ss_pred             cCCC
Q 025068          108 SLGR  111 (258)
Q Consensus       108 ~~~~  111 (258)
                      ..+.
T Consensus        77 ~~~~   80 (198)
T 1qm9_A           77 KHQN   80 (198)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            7543

>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=99.49  E-value=6.2e-14  Score=123.26  Aligned_cols=83  Identities=14%  Similarity=0.197  Sum_probs=68.4

Q ss_pred             CCCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceE
Q 025068           23 NSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRA  102 (258)
Q Consensus        23 ~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i  102 (258)
                      ..+..+...++|||+|||.++++++|+++|++||.|.+|+|++++.+  ++|||||+|.+.++|++||+.++..|+|+.|
T Consensus        33 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i  110 (292)
T 2ghp_A           33 EALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAITKTHKVVGQNEI  110 (292)
T ss_dssp             ---------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEEC
T ss_pred             cccccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHHhCCcEeCCcEE
Confidence            34455677899999999999999999999999999999999998743  5899999999999999999755577999999


Q ss_pred             EEEec
Q 025068          103 NCNLA  107 (258)
Q Consensus       103 ~V~~a  107 (258)
                      .|.++
T Consensus       111 ~v~~~  115 (292)
T 2ghp_A          111 IVSHL  115 (292)
T ss_dssp             EEEEC
T ss_pred             EEEEC
Confidence            99987

>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=99.49  E-value=8.2e-14  Score=112.53  Aligned_cols=75  Identities=19%  Similarity=0.368  Sum_probs=65.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcC----C-------CEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccC
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQF----G-------EILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFID   98 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~f----G-------~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~   98 (258)
                      +.++|||+|||.++++++|+++|++|    |       .|.++++.      +++|||||+|.+.++|++||+.++..|+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~~~~~~~~~   76 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAMAFDGIIFQ   76 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHGGGTTCEET
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHHHhCCcEec
Confidence            46899999999999999999999999    6       77777764      3478999999999999999944557799


Q ss_pred             CceEEEEeccCC
Q 025068           99 GRRANCNLASLG  110 (258)
Q Consensus        99 G~~i~V~~a~~~  110 (258)
                      |+.|+|.++...
T Consensus        77 g~~i~v~~~~~~   88 (172)
T 2g4b_A           77 GQSLKIRRPHDY   88 (172)
T ss_dssp             TEECEEECCSSC
T ss_pred             CceeeecCCccc
Confidence            999999987644

>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=99.49  E-value=4.5e-14  Score=122.91  Aligned_cols=80  Identities=28%  Similarity=0.321  Sum_probs=72.3

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCc-cC---CceEEEE
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPF-ID---GRRANCN  105 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~-i~---G~~i~V~  105 (258)
                      .++|||+||+.++|+++|+++|++||.|++|+|+.|. +++++|||||+|.+.++|.+||+.+ +.. +.   ++.|.|+
T Consensus        96 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~  174 (261)
T 3sde_A           96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVE  174 (261)
T ss_dssp             SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEE
T ss_pred             CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCC-CCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEe
Confidence            5789999999999999999999999999999999995 7999999999999999999999996 433 33   9999999


Q ss_pred             eccCCC
Q 025068          106 LASLGR  111 (258)
Q Consensus       106 ~a~~~~  111 (258)
                      ++....
T Consensus       175 ~~~~~~  180 (261)
T 3sde_A          175 PMEQFD  180 (261)
T ss_dssp             ECCCEE
T ss_pred             eccccC
Confidence            997543

>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=1e-13  Score=114.41  Aligned_cols=77  Identities=19%  Similarity=0.402  Sum_probs=64.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcC----C-------CEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccC
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQF----G-------EILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFID   98 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~f----G-------~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~   98 (258)
                      ..++|||+|||.++++++|+++|++|    |       .|.++++      ++++|||||+|.+.++|++||+.++..|+
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al~l~g~~~~   76 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAMAFDGIIFQ   76 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHGGGTTEEET
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHHHhcCCEEc
Confidence            46899999999999999999999999    5       5666655      45689999999999999999943456799


Q ss_pred             CceEEEEeccCCCC
Q 025068           99 GRRANCNLASLGRP  112 (258)
Q Consensus        99 G~~i~V~~a~~~~~  112 (258)
                      |+.|+|.++.....
T Consensus        77 g~~i~v~~~~~~~~   90 (198)
T 2yh0_A           77 GQSLKIRRPHDYQP   90 (198)
T ss_dssp             TEEEEEECCCCCCC
T ss_pred             CceEEEeCCCCCCC
Confidence            99999999865543

>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=99.47  E-value=6.6e-14  Score=106.07  Aligned_cols=80  Identities=14%  Similarity=0.079  Sum_probs=68.2

Q ss_pred             CCCcEEEEcCC--CCCCc--------HHHHHHHHhcCCCEEEEEEeecCCC--CCcccEEEEEEcCHHHHHHHhcCCC-C
Q 025068           29 TTYTKVFVGGL--AWETQ--------SETMRRYFEQFGEILEAVVITDKNT--GRSKGYGFVTFREPEAARRACADPT-P   95 (258)
Q Consensus        29 ~~~~~lfVgnL--p~~~t--------e~~L~~~F~~fG~I~~v~v~~d~~t--g~skG~aFV~F~~~~~A~~Ai~~~~-~   95 (258)
                      ..++.|.|.|+  +.++.        +++|++.|++||.|++|+|++++.+  ++++|++||+|.+.++|++||+.++ .
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            35678999998  33443        3689999999999999999998764  4689999999999999999999966 6


Q ss_pred             ccCCceEEEEecc
Q 025068           96 FIDGRRANCNLAS  108 (258)
Q Consensus        96 ~i~G~~i~V~~a~  108 (258)
                      .++||.|+|+++.
T Consensus        83 ~f~GR~i~v~~~~   95 (105)
T 3v4m_A           83 KFANRVVVTKYCD   95 (105)
T ss_dssp             EETTEECEEEEEC
T ss_pred             EeCCCEEEEEEeC
Confidence            6999999999874

>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=99.47  E-value=3.3e-14  Score=120.05  Aligned_cols=76  Identities=11%  Similarity=0.078  Sum_probs=66.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCE--EEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCc----eE
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEI--LEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGR----RA  102 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I--~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~----~i  102 (258)
                      ..++|||+|||+++|+++|+++|++||.|  ++++|+.++  ++++|+|||+|.+.++|.+||..++ .+|+|+    ++
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~  199 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY  199 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCE
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcce
Confidence            45789999999999999999999999999  899998885  5667999999999999999999966 557776    56


Q ss_pred             EEEec
Q 025068          103 NCNLA  107 (258)
Q Consensus       103 ~V~~a  107 (258)
                      .|++|
T Consensus       200 ~vk~~  204 (205)
T 3tyt_A          200 TLKLC  204 (205)
T ss_dssp             ECEEE
T ss_pred             EEEec
Confidence            66665

>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=99.46  E-value=1.6e-14  Score=109.21  Aligned_cols=71  Identities=25%  Similarity=0.429  Sum_probs=62.3

Q ss_pred             EcCCCCCCcHHHHHHHH------------hcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceE
Q 025068           36 VGGLAWETQSETMRRYF------------EQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRA  102 (258)
Q Consensus        36 VgnLp~~~te~~L~~~F------------~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i  102 (258)
                      +.+|++++++++|++.|            ++||.|++|+|++++. +++||||||+|.+.++|++|++.++ ..++||.|
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 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56777788888777766            9999999999999874 8999999999999999999999865 67999999


Q ss_pred             EEEec
Q 025068          103 NCNLA  107 (258)
Q Consensus       103 ~V~~a  107 (258)
                      +|+++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.46  E-value=1.7e-13  Score=119.23  Aligned_cols=76  Identities=28%  Similarity=0.489  Sum_probs=68.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+|||.++|+++|+++|++||.|.+|+|.++      +|||||+|.+.++|++||+.++ ..|.|+.|+|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            345679999999999999999999999999999999654      6899999999999999999754 679999999999


Q ss_pred             ccC
Q 025068          107 ASL  109 (258)
Q Consensus       107 a~~  109 (258)
                      +..
T Consensus        93 a~~   95 (261)
T 3sde_A           93 ATH   95 (261)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            853

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.44  E-value=3.6e-13  Score=114.87  Aligned_cols=75  Identities=9%  Similarity=0.135  Sum_probs=67.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCC-CEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccC-CceEEEEe
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFG-EILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFID-GRRANCNL  106 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG-~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~-G~~i~V~~  106 (258)
                      ..++|||+||+.++++++|+++|++|| .|++|+|+.+     .+|+|||+|.+.++|++||+.++ ..|+ |+.|+|++
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~  224 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  224 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEE
Confidence            468999999999999999999999999 9999999653     36899999999999999999855 6788 99999999


Q ss_pred             ccC
Q 025068          107 ASL  109 (258)
Q Consensus       107 a~~  109 (258)
                      +++
T Consensus       225 a~~  227 (229)
T 2adc_A          225 SKS  227 (229)
T ss_dssp             CSS
T ss_pred             ecC
Confidence            964

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.43  E-value=1.8e-13  Score=113.52  Aligned_cols=75  Identities=9%  Similarity=0.135  Sum_probs=67.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCC-CEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccC-CceEEEEe
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFG-EILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFID-GRRANCNL  106 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG-~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~-G~~i~V~~  106 (258)
                      ..++|||+||+.++++++|+++|++|| .|++|+|+.+.     +|+|||+|.+.++|.+||+.++ ..|+ |+.|+|++
T Consensus       119 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  193 (198)
T 1qm9_A          119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  193 (198)
T ss_dssp             CCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEe
Confidence            478999999999999999999999999 99999997642     7899999999999999999855 6688 99999999


Q ss_pred             ccC
Q 025068          107 ASL  109 (258)
Q Consensus       107 a~~  109 (258)
                      +++
T Consensus       194 a~~  196 (198)
T 1qm9_A          194 SKS  196 (198)
T ss_dssp             ECC
T ss_pred             ecc
Confidence            854

>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=99.42  E-value=2.6e-13  Score=105.04  Aligned_cols=79  Identities=13%  Similarity=0.199  Sum_probs=68.1

Q ss_pred             CCcEEEEcCCCC--C---CcHHHHHHHHhcCCCEEEEEEeecCC----CCCcccEEEEEEcCHHHHHHHhcCCC-CccCC
Q 025068           30 TYTKVFVGGLAW--E---TQSETMRRYFEQFGEILEAVVITDKN----TGRSKGYGFVTFREPEAARRACADPT-PFIDG   99 (258)
Q Consensus        30 ~~~~lfVgnLp~--~---~te~~L~~~F~~fG~I~~v~v~~d~~----tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G   99 (258)
                      .++.|+|.|+-.  +   -.+++|++.|++||.|++|+|++++.    +++++|++||+|.+.++|.+||+.++ ..++|
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            467899999832  2   24689999999999999999999864    46788999999999999999999966 66999


Q ss_pred             ceEEEEecc
Q 025068          100 RRANCNLAS  108 (258)
Q Consensus       100 ~~i~V~~a~  108 (258)
                      |.|+|+++.
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999999874

>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=99.35  E-value=1.5e-12  Score=118.00  Aligned_cols=75  Identities=17%  Similarity=0.252  Sum_probs=62.7

Q ss_pred             CCCCcEEEEcC--CCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-Ccc---CCc-
Q 025068           28 DTTYTKVFVGG--LAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFI---DGR-  100 (258)
Q Consensus        28 ~~~~~~lfVgn--Lp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i---~G~-  100 (258)
                      +...++|||+|  |+.++||++|+++|++||+|++|.+..      +||||||+|++.++|++||+.+| .++   .|+ 
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            45678999999  588999999999999999999987643      47899999999999999999976 444   345 


Q ss_pred             -eEEEEecc
Q 025068          101 -RANCNLAS  108 (258)
Q Consensus       101 -~i~V~~a~  108 (258)
                       .|+|+++.
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             57888773

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.22  E-value=4.7e-11  Score=92.47  Aligned_cols=84  Identities=14%  Similarity=0.168  Sum_probs=71.1

Q ss_pred             CCCCCCCCCCCCCcEEEEcCCCCC-CcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcC-HHHHHHHhcCCC--
Q 025068           19 FQYLNSPFGDTTYTKVFVGGLAWE-TQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFRE-PEAARRACADPT--   94 (258)
Q Consensus        19 ~~~~~~p~~~~~~~~lfVgnLp~~-~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~-~~~A~~Ai~~~~--   94 (258)
                      +++......-...+.|+|+||+.+ +++++|+++|++||+|..|+++++..      .|||+|.+ .++|.+||+.++  
T Consensus         6 ~~~~~~~~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~   79 (121)
T 1owx_A            6 HHHHHGSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNG   79 (121)
T ss_dssp             ---CCCCCSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTS
T ss_pred             cccccCcccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcC
Confidence            345566677788999999999999 99999999999999999999998865      59999999 889999998853  


Q ss_pred             -CccCCceEEEEecc
Q 025068           95 -PFIDGRRANCNLAS  108 (258)
Q Consensus        95 -~~i~G~~i~V~~a~  108 (258)
                       .+|++..+.+++..
T Consensus        80 ~~~i~g~~~~~evL~   94 (121)
T 1owx_A           80 NLQLRNKEVTWEVLE   94 (121)
T ss_dssp             CBCTTSSSEEEEECC
T ss_pred             CcEEeCcEEEEEECC
Confidence             45999999887663

>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=99.19  E-value=2.5e-11  Score=93.23  Aligned_cols=75  Identities=11%  Similarity=0.115  Sum_probs=61.4

Q ss_pred             CCcEEEEcCCCCCC----------cHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccC
Q 025068           30 TYTKVFVGGLAWET----------QSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFID   98 (258)
Q Consensus        30 ~~~~lfVgnLp~~~----------te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~   98 (258)
                      .++.|.|.|+=..-          .+++|++.|++||.|++|.|.++.    .+|++||+|.+.++|++||+.++ ..++
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            35677888772211          235789999999999999987653    58999999999999999999966 6699


Q ss_pred             CceEEEEecc
Q 025068           99 GRRANCNLAS  108 (258)
Q Consensus        99 G~~i~V~~a~  108 (258)
                      ||.|+|+++.
T Consensus        82 GR~i~v~~~~   91 (114)
T 3s6e_A           82 GKMITAAYVP   91 (114)
T ss_dssp             TEECEEEEEC
T ss_pred             CEEEEEEEEc
Confidence            9999999985

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.07  E-value=5.5e-10  Score=81.75  Aligned_cols=71  Identities=23%  Similarity=0.188  Sum_probs=58.2

Q ss_pred             CcEEEEcCCC----CCCcH----HHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceE
Q 025068           31 YTKVFVGGLA----WETQS----ETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRA  102 (258)
Q Consensus        31 ~~~lfVgnLp----~~~te----~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i  102 (258)
                      .-+|+|.-++    .++-+    .+|.+.|++||+|..++|+.|+        +||+|.+.++|.+||+.++..|+||.|
T Consensus         7 d~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~mnG~~v~Gr~L   78 (91)
T 2dnr_A            7 GGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLSLNGKELLNRTI   78 (91)
T ss_dssp             SCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGGGTTCEETTEEE
T ss_pred             CCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHhcCCeEeCCeEE
Confidence            4467777665    23333    5799999999999999999884        899999999999999944467999999


Q ss_pred             EEEeccC
Q 025068          103 NCNLASL  109 (258)
Q Consensus       103 ~V~~a~~  109 (258)
                      +|+++++
T Consensus        79 kV~lkt~   85 (91)
T 2dnr_A           79 TIALKSP   85 (91)
T ss_dssp             EEEECCC
T ss_pred             EEEeCCC
Confidence            9999864

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.85  E-value=3.8e-09  Score=89.36  Aligned_cols=67  Identities=13%  Similarity=0.238  Sum_probs=58.8

Q ss_pred             CCcHHHHHHHHhcCCCEEEEEEeecCC----CCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           42 ETQSETMRRYFEQFGEILEAVVITDKN----TGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        42 ~~te~~L~~~F~~fG~I~~v~v~~d~~----tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      +-.+++|++.|++||.|++++|+++..    +++++|++||+|.+.++|++||+.++ ..++||.|.|.+..
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            346788999999999999999986643    45899999999999999999999966 66999999999974

>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=98.80  E-value=5.1e-09  Score=77.02  Aligned_cols=70  Identities=16%  Similarity=0.135  Sum_probs=58.1

Q ss_pred             CcEEEEcCCCCC-----C-cH---HHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCce
Q 025068           31 YTKVFVGGLAWE-----T-QS---ETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRR  101 (258)
Q Consensus        31 ~~~lfVgnLp~~-----~-te---~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~  101 (258)
                      .-+|+|.-++.+     + ++   .+|.+.|+.||+|..++++.|+        +||+|.+.++|.+||+.++..|+||.
T Consensus        15 D~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~ldG~~v~Gr~   86 (95)
T 1ufw_A           15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLDVDGMKVKGRA   86 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHHGGGSEETTEE
T ss_pred             CCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHhcCCeeeCCeE
Confidence            558889877642     2 22   4689999999999999999984        89999999999999994447799999


Q ss_pred             EEEEecc
Q 025068          102 ANCNLAS  108 (258)
Q Consensus       102 i~V~~a~  108 (258)
                      |+|++..
T Consensus        87 L~V~~k~   93 (95)
T 1ufw_A           87 VKISGPS   93 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEeccC
Confidence            9999864

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.32  E-value=1.5e-06  Score=65.42  Aligned_cols=74  Identities=12%  Similarity=0.158  Sum_probs=64.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcC-----CCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcC-CCCccCCce
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQF-----GEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD-PTPFIDGRR  101 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~f-----G~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~-~~~~i~G~~  101 (258)
                      ++..++|-|-|||+.++++.|+.+++++     |.|+.+.++.|..      -|+|+|.|...|-||.-. ++.+|+||+
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~------GAivef~d~~~AgKasLaL~G~ef~gr~   91 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN------GAIIIFRDSKFAAKMLMILNGSQFQGKV   91 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT------EEEEECSCHHHHHHHHHHHSSEEETTEE
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC------ceEEEEccchhhHHHHhhcCCeeecCeE
Confidence            4457788889999999999999999999     9999999988864      799999999999888866 557799999


Q ss_pred             EEEEec
Q 025068          102 ANCNLA  107 (258)
Q Consensus       102 i~V~~a  107 (258)
                      |+|.-.
T Consensus        92 Lr~gTv   97 (117)
T 2l9w_A           92 IRSGTI   97 (117)
T ss_dssp             EEEECH
T ss_pred             EEecCH
Confidence            999754

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.31  E-value=1.1e-05  Score=60.03  Aligned_cols=76  Identities=29%  Similarity=0.319  Sum_probs=64.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhc-----CCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEE
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQ-----FGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCN  105 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~-----fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~  105 (258)
                      -++|.|.|||.+++++.|+-+|++     -|+|++++...        +-|+|+|.+.+.|++.|+...+.|.+..|.|.
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~H~L~~~~LsV~   79 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQADHELHGAQLSLR   79 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSCCBSSSSBCEEE
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCcceecCeEEEEE
Confidence            468999999999999999999987     26888887643        37899999999999999998899999999998


Q ss_pred             eccCCCCCC
Q 025068          106 LASLGRPRP  114 (258)
Q Consensus       106 ~a~~~~~~~  114 (258)
                      ....+.+++
T Consensus        80 P~~~~~~~r   88 (104)
T 2dhx_A           80 PAPPRAPAR   88 (104)
T ss_dssp             ECCCCCCCC
T ss_pred             cCCCCCcce
Confidence            776555443

>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=97.64  E-value=0.00023  Score=53.01  Aligned_cols=74  Identities=9%  Similarity=0.032  Sum_probs=61.4

Q ss_pred             CCcEEEEcCCCCCC-c----HHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCc-cCCceEE
Q 025068           30 TYTKVFVGGLAWET-Q----SETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRRAN  103 (258)
Q Consensus        30 ~~~~lfVgnLp~~~-t----e~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~-i~G~~i~  103 (258)
                      -.++|+|.||+.++ +    .+.++++|..|+++......+.-.      -..|.|.+.++|.+|-.+++.+ ++|++|+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR------Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK------RVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT------EEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce------EEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            35789999998865 2    256799999999999888877642      5689999999999999998755 9999999


Q ss_pred             EEeccC
Q 025068          104 CNLASL  109 (258)
Q Consensus       104 V~~a~~  109 (258)
                      |-++..
T Consensus        78 ~YFgq~   83 (104)
T 1wey_A           78 LYFAQT   83 (104)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            999963

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.45  E-value=0.00047  Score=50.68  Aligned_cols=54  Identities=22%  Similarity=0.374  Sum_probs=45.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcC
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD   92 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~   92 (258)
                      ..+.++| ++|.++...||.++|+.||. ..|+++.|-       .|||.|.+++.|..|+..
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~   68 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNT   68 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEETT-------EEEEECSCHHHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHh
Confidence            3455666 99999999999999999994 457788774       799999999999998875

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.39  E-value=0.00074  Score=51.55  Aligned_cols=74  Identities=18%  Similarity=0.200  Sum_probs=58.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCC-ceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDG-RRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G-~~i~V~  105 (258)
                      +....+-|.|-+.+.+. .+.|.+.|++||+|.+......      ..+-.|.|+++.+|++||.+++..|++ -.|-|.
T Consensus        20 ~~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~~------~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~   92 (119)
T 1wwh_A           20 DHLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALSKDGRIFGESIMIGVK   92 (119)
T ss_dssp             -CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHTTTTCEETTTEECEEE
T ss_pred             CCCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCCC------CCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEE
Confidence            34457789999999985 5667788999999998876211      248899999999999999998888875 556666


Q ss_pred             ec
Q 025068          106 LA  107 (258)
Q Consensus       106 ~a  107 (258)
                      ..
T Consensus        93 p~   94 (119)
T 1wwh_A           93 PC   94 (119)
T ss_dssp             EC
T ss_pred             EC
Confidence            64

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.10  E-value=0.00063  Score=50.14  Aligned_cols=53  Identities=23%  Similarity=0.366  Sum_probs=45.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcC
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD   92 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~   92 (258)
                      .+.++| ++|.++...||.++|+.|| -..|+++.|-       .|||.|.+++.|..|+..
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~   58 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNT   58 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHh
Confidence            345566 9999999999999999999 5568888874       799999999999998884

>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=96.80  E-value=0.0046  Score=44.94  Aligned_cols=65  Identities=11%  Similarity=0.060  Sum_probs=51.4

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCC--cccEEEEEEcCHHHHHHHhcC-CCCc
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR--SKGYGFVTFREPEAARRACAD-PTPF   96 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~--skG~aFV~F~~~~~A~~Ai~~-~~~~   96 (258)
                      ++|-|++||..+||+++.+.++...++.-...+..+.+.+  .-.-|+|.|.+.|++....+. .++.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~   69 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYV   69 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcE
Confidence            6899999999999999999999988877666666553332  225789999999999888877 4444

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.20  E-value=0.0022  Score=59.94  Aligned_cols=58  Identities=19%  Similarity=0.271  Sum_probs=44.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP   93 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~   93 (258)
                      ..++|||. ++.++++++|.++|++||.|.++..-+++  |   -|+.|+|.+.+++.+++...
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~--g---~~~~vef~~~~~~~~~~~~~  109 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF--G---LYAVVEFCQKESIGSLQNGT  109 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS--S---EEEEEECC---CCHHHHSSC
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC--C---eEEEEEeCCHHHHHHHHhcc
Confidence            45789997 79999999999999999999998776543  2   59999999999999888764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.10  E-value=0.0067  Score=46.93  Aligned_cols=77  Identities=19%  Similarity=0.292  Sum_probs=55.2

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEE-EEEeecC--------CCC-----CcccEEEEEEcCHHHHHHHhcCCCCc
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILE-AVVITDK--------NTG-----RSKGYGFVTFREPEAARRACADPTPF   96 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~-v~v~~d~--------~tg-----~skG~aFV~F~~~~~A~~Ai~~~~~~   96 (258)
                      ..-|.|=+.|.+.+ ..+.+.|++||.|.+ ..+.++.        .+.     ....+-.|+|++..+|.+||.+++..
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~i   85 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGAV   85 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTCE
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCeE
Confidence            34577778877754 567778999999976 2221100        000     12457899999999999999999999


Q ss_pred             cCCceEEEEecc
Q 025068           97 IDGRRANCNLAS  108 (258)
Q Consensus        97 i~G~~i~V~~a~  108 (258)
                      |+|..|-|...+
T Consensus        86 i~G~mIGV~Py~   97 (132)
T 3p3d_A           86 FNGVLLGVIPYT   97 (132)
T ss_dssp             ETTEECEEEECC
T ss_pred             eCcEEEEEEECC
Confidence            999988888774

>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=95.17  E-value=0.017  Score=45.21  Aligned_cols=33  Identities=12%  Similarity=0.061  Sum_probs=28.1

Q ss_pred             EEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC
Q 025068           60 EAVVITDKNTGRSKGYGFVTFREPEAARRACADPT   94 (258)
Q Consensus        60 ~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~   94 (258)
                      .++|+++.  .+++||+||+|.+.++|++||+.++
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~   34 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYA   34 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhc
Confidence            46788885  4799999999999999999997743

>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=94.56  E-value=0.0087  Score=46.67  Aligned_cols=40  Identities=15%  Similarity=0.055  Sum_probs=34.7

Q ss_pred             CCCcccEEEEEEcCHHHHHHHhcCC-C-CccCCceEEEEeccC
Q 025068           69 TGRSKGYGFVTFREPEAARRACADP-T-PFIDGRRANCNLASL  109 (258)
Q Consensus        69 tg~skG~aFV~F~~~~~A~~Ai~~~-~-~~i~G~~i~V~~a~~  109 (258)
                      ..+.+|+++|+|.+.++|++||+.+ + ..|+| .|.+..+..
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            3577899999999999999999887 6 66999 999998754

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=93.96  E-value=0.034  Score=40.71  Aligned_cols=64  Identities=9%  Similarity=0.005  Sum_probs=44.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCC-C-cccEEEEEEcCHHHHHHHhcCCC
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTG-R-SKGYGFVTFREPEAARRACADPT   94 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg-~-skG~aFV~F~~~~~A~~Ai~~~~   94 (258)
                      .-+|.|+.||+.+||+++.+.++..-++.-...+..+.+- . .-.-|+|.|++.|+...-.+..+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~   74 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFD   74 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHST
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcC
Confidence            4589999999999999999888776554332222222221 1 12568999999999988887743

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=87.52  E-value=0.94  Score=42.61  Aligned_cols=55  Identities=22%  Similarity=0.369  Sum_probs=44.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP   93 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~   93 (258)
                      ....++|+ ++..+...+|.++|+.||. .+|+++.|.       .+||.|.+.+.|..++...
T Consensus       439 R~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widdt-------~a~V~~~~~~~a~~~l~~~  493 (507)
T 3d45_A          439 RDHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNTS  493 (507)
T ss_dssp             GGGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSSS-------EEEEECSCHHHHHHHHHHH
T ss_pred             cCcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcCC-------eEEEEECCHHHHHHHHHHH
Confidence            34566665 8899999999999999995 456666653       6999999999999888763

---

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	258
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-20
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-20
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	7e-20
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-19
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	9e-19
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	7e-18
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	7e-18
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-17
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-16
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	6e-16
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-15
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	4e-15
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-14
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-14
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-12
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-14
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	5e-14
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-14
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	9e-14
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-13
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-12
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-12
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	3e-12
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-12
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-12
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-12
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	5e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	5e-12
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	6e-12
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	1e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-11
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-11
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-11
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	5e-11
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	9e-11
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-10
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-10
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-10
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-10
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-10
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	4e-10
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	4e-10
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	5e-10
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	9e-10
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-09
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-09
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-09
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-09
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-09
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	5e-09
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-09
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-08
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-08
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-08
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	4e-08
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-08
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	8e-08
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-07
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	2e-07
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	5e-07
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	9e-07
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 9e-07
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-06
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-05
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-04
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	1e-04
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	2e-04
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-04
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	4e-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-04
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	0.001
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	0.003

>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 = 80.8 bits (199), Expect = 2e-20
 Identities = 30/75 (40%), Positives = 46/75 (61%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+F+GGL+W+T  E +R YF QFGE+ E +V+ D  T RS+G+GFVTF +     +  A 
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 93  PTPFIDGRRANCNLA 107
               +D +  +  +A
Sbjct: 62  SRHELDSKTIDPKVA 76

>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 = 79.2 bits (195), Expect = 5e-20
 Identities = 23/75 (30%), Positives = 39/75 (52%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVGGL+ +T  E +R YF  FGE+    +  D  T + +G+ F+TF+E E  ++    
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 93  PTPFIDGRRANCNLA 107
               +   +    +A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>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 = 79.2 bits (195), Expect = 7e-20
 Identities = 30/76 (39%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           + + V GL W+T  + ++ YF  FGE+L   V  D  TG SKG+GFV F E E   +  +
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 92  DPTPFIDGRRANCNLA 107
                IDGR  +C L 
Sbjct: 69  QRH-MIDGRWCDCKLP 83

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 76.6 bits (188), Expect = 7e-19
 Identities = 26/75 (34%), Positives = 47/75 (62%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+F+GGL+W+T  + ++ YF +FGE+++  +  D  TGRS+G+GFV F+E E+  +    
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 93  PTPFIDGRRANCNLA 107
               ++G+  +   A
Sbjct: 61  KEHKLNGKVIDPKRA 75

>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 = 77.1 bits (189), Expect = 9e-19
 Identities = 55/95 (57%), Positives = 70/95 (73%), Gaps = 1/95 (1%)

Query: 22  LNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFR 81
           ++    DTT+TK+FVGGL + T   ++R+YFE FG+I EAVVITD+ TG+S+GYGFVT  
Sbjct: 1   MHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMA 60

Query: 82  EPEAARRACADPTPFIDGRRANCNLASLG-RPRPQ 115
           +  AA RAC DP P IDGR+AN NLA LG +PR  
Sbjct: 61  DRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSL 95

>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 = 74.7 bits (183), Expect = 7e-18
 Identities = 32/85 (37%), Positives = 49/85 (57%), Gaps = 3/85 (3%)

Query: 31  YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
           + K+F+GGL++ET  E++R Y+EQ+G++ + VV+ D  + RS+G+GFVTF        A 
Sbjct: 20  FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 79

Query: 91  ADPTPFIDGRRANCNLASLGRPRPQ 115
           A     IDGR      A     R +
Sbjct: 80  AARPHSIDGRVVEPKRA---VAREE 101

>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 = 74.2 bits (182), Expect = 7e-18
 Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 3/80 (3%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKN-TGRSKGYGFVTFREPEAARRAC 90
           +K+ V  + ++     +R  F  FGE+    +      TG  +G+GFV F   + A++A 
Sbjct: 9   SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 68

Query: 91  ADPT--PFIDGRRANCNLAS 108
                   + GRR     A 
Sbjct: 69  NALCHSTHLYGRRLVLEWAD 88

>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 = 72.8 bits (178), Expect = 2e-17
 Identities = 31/75 (41%), Positives = 46/75 (61%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+F+GGL++ET  E++R +FEQ+G + + VV+ D NT RS+G+GFVT+   E    A   
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 93  PTPFIDGRRANCNLA 107
               +DGR      A
Sbjct: 68  RPHKVDGRVVEPKRA 82

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.4 bits (169), Expect = 3e-16
 Identities = 24/78 (30%), Positives = 44/78 (56%)

Query: 30  TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
           T  K+FVGG+  +T+   +R YFEQ+G+I    ++TD+ +G+ +G+ FVTF + ++  + 
Sbjct: 1   TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 60

Query: 90  CADPTPFIDGRRANCNLA 107
                  ++G       A
Sbjct: 61  VIQKYHTVNGHNCEVRKA 78

>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 = 68.6 bits (167), Expect = 6e-16
 Identities = 29/75 (38%), Positives = 45/75 (60%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVGGL+  T  E ++ YFEQFG++ +A+++ DK T R +G+GFVTF   +   + C  
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 93  PTPFIDGRRANCNLA 107
               I+ +   C  A
Sbjct: 61  HFHEINNKMVECKKA 75

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.7 bits (165), Expect = 2e-15
 Identities = 19/82 (23%), Positives = 35/82 (42%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             VF   LA   +   +  +F   G++ +  +I+D+N+ RSKG  +V F E ++   A  
Sbjct: 19  RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG 78

Query: 92  DPTPFIDGRRANCNLASLGRPR 113
                + G       +   + R
Sbjct: 79  LTGQRLLGVPIIVQASQAEKNR 100

>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 = 66.5 bits (162), Expect = 4e-15
 Identities = 22/76 (28%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
            ++VG L  +     +   F   G IL   V  D  T RS GY +V F++P  A RA   
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 93  PTPF-IDGRRANCNLA 107
                I G+      +
Sbjct: 62  MNFDVIKGKPVRIMWS 77

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.4 bits (159), Expect = 1e-14
 Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 1/79 (1%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+F+GGL      + ++     FG +    ++ D  TG SKGY F  + +     +A A 
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 93  PTPF-IDGRRANCNLASLG 110
                +  ++     AS+G
Sbjct: 63  LNGMQLGDKKLLVQRASVG 81

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.9 bits (162), Expect = 3e-14
 Identities = 25/91 (27%), Positives = 47/91 (51%), Gaps = 3/91 (3%)

Query: 25  PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPE 84
           P    T  K+FVGG+  +T+   +R YFEQ+G+I    ++TD+ +G+ +G+ FVTF + +
Sbjct: 91  PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 150

Query: 85  AARRACADPTPFIDGRRANCNLASLGRPRPQ 115
           +  +        ++G       A     + +
Sbjct: 151 SVDKIVIQKYHTVNGHNCEVRKA---LSKQE 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 = 62.3 bits (150), Expect = 1e-12
 Identities = 31/76 (40%), Positives = 46/76 (60%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+F+GGL++ET  E++R +FEQ+G + + VV+ D NT RS+G+GFVT+   E    A   
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 93  PTPFIDGRRANCNLAS 108
               +DGR      A 
Sbjct: 68  RPHKVDGRVVEPKRAV 83

>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 = 64.6 bits (157), Expect = 3e-14
 Identities = 18/85 (21%), Positives = 35/85 (41%), Gaps = 1/85 (1%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             ++VG L++ T  E +   F + G+I + ++  DK    + G+ FV +     A  A  
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 92  DPTPF-IDGRRANCNLASLGRPRPQ 115
                 +D R    +  +  +   Q
Sbjct: 68  YINGTRLDDRIIRTDWDAGFKEGRQ 92

>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 = 63.5 bits (154), Expect = 5e-14
 Identities = 27/86 (31%), Positives = 40/86 (46%), Gaps = 1/86 (1%)

Query: 29  TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
           TT   ++VGGLA E   + +   F  FG+I +  +  D  T + +G+ FV F   E A  
Sbjct: 3   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62

Query: 89  ACADPTPF-IDGRRANCNLASLGRPR 113
           A  +     + GR    NLA   R +
Sbjct: 63  AIDNMNESELFGRTIRVNLAKPMRIK 88

>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 = 63.6 bits (154), Expect = 7e-14
 Identities = 14/87 (16%), Positives = 29/87 (33%), Gaps = 5/87 (5%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVV-----ITDKNTGRSKGYGFVTFREPEAAR 87
           +++VG + +    E M  +F     +          +      + K + F+ FR  +   
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 88  RACADPTPFIDGRRANCNLASLGRPRP 114
           +A A       G+          +P P
Sbjct: 63  QAMAFDGIIFQGQSLKIRRPHDYQPLP 89

>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 = 63.2 bits (153), Expect = 9e-14
 Identities = 16/90 (17%), Positives = 34/90 (37%), Gaps = 8/90 (8%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAV--VITDKNTGRSKGYGFVTFREPEAARRA 89
            ++F+GG+    + E +     +  E +  V    +  +  +++G+ FV +    AA  A
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 90  CA---DPTPFIDGRRANCNLASLGRPRPQV 116
                     + G +   + A    P   V
Sbjct: 62  RRKLMPGRIQLWGHQIAVDWA---EPEIDV 88

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 63.0 bits (153), Expect = 1e-13
 Identities = 17/58 (29%), Positives = 31/58 (53%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
          T ++V  L      + +   F ++G I++  ++ DK TGR +G  FV + + E A+ A
Sbjct: 7  TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 64

>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 = 60.3 bits (146), Expect = 1e-12
 Identities = 27/104 (25%), Positives = 43/104 (41%), Gaps = 15/104 (14%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWE-TQSETMRRYFEQFGEILEAVVITDKNTG 70
           GSS SSG          +  ++VF+G L     +   +   F ++G+I+   V       
Sbjct: 1   GSSGSSG-----KTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH------ 49

Query: 71  RSKGYGFVTFREPEAARRACADPTPF-IDGRRANCNLASLGRPR 113
             KG+ FV +     AR A A      I G+  + NLA+  +  
Sbjct: 50  --KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVN 91

>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 = 59.3 bits (143), Expect = 2e-12
 Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 5/84 (5%)

Query: 35  FVGGLAWETQSETMRRYFEQFGEILEAVVITDKN---TGRSKGYGFVTFREPEAARRACA 91
           F+  L + T  ET++  F + G I    +   KN      S G+GFV +++PE A++A  
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 92  DPTPF-IDGRRANCNLASLGRPRP 114
                 +DG +    ++     +P
Sbjct: 62  QLQGHTVDGHKLEVRISE-RATKP 84

>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 = 58.9 bits (142), Expect = 3e-12
 Identities = 19/89 (21%), Positives = 39/89 (43%), Gaps = 9/89 (10%)

Query: 27  GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
           G +  + VFVG    +   + +R +F Q+G++++            + + FVTF + + A
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDV-----FIPKPFRAFAFVTFADDQIA 55

Query: 87  RRACADPTPFIDGRRANCNLASLGRPRPQ 115
           +  C +    I G   + + A    P+  
Sbjct: 56  QSLCGEDL-IIKGISVHISNA---EPKHN 80

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.4 bits (143), Expect = 3e-12
 Identities = 23/100 (23%), Positives = 40/100 (40%), Gaps = 12/100 (12%)

Query: 25  PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVI--------TDKNTGRSKGYG 76
           P  D+  + ++V GL      + +  +F+Q G +               DK TG+ KG  
Sbjct: 2   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 61

Query: 77  FVTFREPEAARRACADPTPF-IDGRRANCNLASLGRPRPQ 115
            V++ +P  A+ A          G +   +LA   R +P 
Sbjct: 62  TVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA---RKKPP 98

>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 = 58.9 bits (142), Expect = 3e-12
 Identities = 20/80 (25%), Positives = 30/80 (37%), Gaps = 1/80 (1%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           T + V  L  +     +   F   G I    ++ D  TG S GY FV F     ++RA  
Sbjct: 3   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

Query: 92  DPTPF-IDGRRANCNLASLG 110
                 +  +R   + A  G
Sbjct: 63  VLNGITVRNKRLKVSYARPG 82

>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 = 58.4 bits (141), Expect = 3e-12
 Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 2/77 (2%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+ V  L +      ++  F +FG + +A V  D  +GRS G   V F     A +A   
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 60

Query: 93  PTPF-IDGRRANCNLAS 108
                +DGR  N  L +
Sbjct: 61  YNGVPLDGRPMNIQLVT 77

>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 = 58.5 bits (141), Expect = 4e-12
 Identities = 16/85 (18%), Positives = 28/85 (32%), Gaps = 1/85 (1%)

Query: 24  SPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREP 83
           +  G    T + V  + +    + +  +F  +  I  +V +     G   G   V F   
Sbjct: 2   ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 61

Query: 84  EAARRACAD-PTPFIDGRRANCNLA 107
           + A  A  D     I  R+    L 
Sbjct: 62  DEATAAVIDLNDRPIGSRKVKLVLG 86

>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 = 58.2 bits (140), Expect = 5e-12
 Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 5/84 (5%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVI-TDKNTGRSKGYGFVTFREPEAARRACAD 92
           +F+G L  E   + +   F  FG IL+   I  D +TG SKGY F+ F   +A+  A   
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 93  PTP-FIDGRRANCNLASLGRPRPQ 115
               ++  R    + A     +  
Sbjct: 61  MNGQYLCNRPITVSYA---FKKDS 81

>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 = 58.5 bits (141), Expect = 5e-12
 Identities = 29/101 (28%), Positives = 47/101 (46%), Gaps = 11/101 (10%)

Query: 16  SSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGY 75
           SSG     +    +T  ++ V  + +  +   +R+ F QFG+IL+  +I ++    SKG+
Sbjct: 1   SSG-----NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGF 53

Query: 76  GFVTFREPEAARRACADPTPF-IDGRRANCNLASLGRPRPQ 115
           GFVTF     A RA        ++GR+   N A     R  
Sbjct: 54  GFVTFENSADADRAREKLHGTVVEGRKIEVNNA---TARVM 91

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.1 bits (140), Expect = 6e-12
 Identities = 24/78 (30%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             V+VGGL  +     +   F Q G ++   +  D+ TG+ +GYGFV F   E A  A  
Sbjct: 10  ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 69

Query: 92  DPTPF-IDGRRANCNLAS 108
                 + G+    N AS
Sbjct: 70  IMDMIKLYGKPIRVNKAS 87

>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 = 57.9 bits (139), Expect = 1e-11
 Identities = 13/81 (16%), Positives = 32/81 (39%)

Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
           ++      +  + +      + ++ E       AV +   N G+  G   V F+  + AR
Sbjct: 5   NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDAR 64

Query: 88  RACADPTPFIDGRRANCNLAS 108
           ++       ++GR A  ++ +
Sbjct: 65  KSERLHRKKLNGREAFVHVVT 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 = 57.4 bits (138), Expect = 1e-11
 Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 1/70 (1%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             ++V GL      + + + F Q+G I+ + ++ D+ TG S+G GF+ F +   A  A  
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 92  DPTPF-IDGR 100
                   G 
Sbjct: 67  GLNGQKPSGA 76

>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 = 57.3 bits (138), Expect = 2e-11
 Identities = 17/85 (20%), Positives = 36/85 (42%), Gaps = 4/85 (4%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             +++  L ++  +E M   F ++G I +   I   NT  ++G  +V + +   A+ AC 
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNACD 64

Query: 92  DPTPF-IDGRRANCNLASLGRPRPQ 115
             + F +  R       +  R   +
Sbjct: 65  HLSGFNVCNRYLVVLYYNANRAFQK 89

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.7 bits (136), Expect = 3e-11
 Identities = 22/103 (21%), Positives = 43/103 (41%), Gaps = 5/103 (4%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG +   SP         F+G L ++   E+++ +F         +     N  R
Sbjct: 1   GSSGSSGSRLPKSP-----PYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPER 55

Query: 72  SKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPRP 114
            KG+G+  F + ++   A +     +  +R   ++A   + + 
Sbjct: 56  LKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKD 98

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.4 bits (135), Expect = 4e-11
 Identities = 27/97 (27%), Positives = 37/97 (38%), Gaps = 5/97 (5%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG    NSP        V + GL +    E + ++F     +   + +     GR
Sbjct: 1   GSSGSSG----NSP-DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGR 55

Query: 72  SKGYGFVTFREPEAARRACADPTPFIDGRRANCNLAS 108
           S G  FV F   E A +A       I  R      +S
Sbjct: 56  STGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS 92

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 5e-11
 Identities = 24/98 (24%), Positives = 39/98 (39%), Gaps = 5/98 (5%)

Query: 17  SGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYG 76
           SG   +  P G+    +++VG L  + +++ +   F ++G I     I  KN      + 
Sbjct: 1   SGGGVIRGPAGNND-CRIYVGNLPPDIRTKDIEDVFYKYGAI---RDIDLKNRRGGPPFA 56

Query: 77  FVTFREPEAARRACADPTPF-IDGRRANCNLASLGRPR 113
           FV F +P  A  A      +  DG R        GR  
Sbjct: 57  FVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGT 94

>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 = 54.7 bits (131), Expect = 9e-11
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             + V GL+  T    +R  F ++G I +  ++ D+ + RS+G+ FV F   + A+ A  
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 92  DPTPF-IDGRR 101
                 +DGRR
Sbjct: 70  RANGMELDGRR 80

>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 = 55.0 bits (132), Expect = 1e-10
 Identities = 25/84 (29%), Positives = 34/84 (40%), Gaps = 10/84 (11%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             V+ GG+A     + MR+ F  FG+I+E  V         KGY FV F   E+A  A  
Sbjct: 19  CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVRFSTHESAAHAIV 72

Query: 92  DPTPF-IDGRRANCNLASLGRPRP 114
                 I+G    C      +  P
Sbjct: 73  SVNGTTIEGHVVKCYWG---KESP 93

>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 = 54.4 bits (130), Expect = 1e-10
 Identities = 29/77 (37%), Positives = 49/77 (63%), Gaps = 1/77 (1%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
           K+FVGGL+++T  +++ + F ++G+I E VV+ D+ T RS+G+GFVTF   + A+ A   
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 93  PTPF-IDGRRANCNLAS 108
                +DGR+   + A 
Sbjct: 67  MNGKSVDGRQIRVDQAG 83

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.0 bits (129), Expect = 2e-10
 Identities = 23/77 (29%), Positives = 34/77 (44%), Gaps = 1/77 (1%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           T + V  L      E  R  F   GEI    ++ DK TG+S GYGFV + +P+ A +A  
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 92  DPTPF-IDGRRANCNLA 107
                 +  +    + A
Sbjct: 63  TLNGLRLQTKTIKVSYA 79

>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 = 53.5 bits (128), Expect = 3e-10
 Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 4/83 (4%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             + V  L+ +T+   ++  F  FG I    +  DK TG+SKG+ F++F   E A RA A
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 92  DPTPF-IDGRRANCNLASLGRPR 113
             + F  D    N   A   +P 
Sbjct: 69  GVSGFGYDHLILNVEWA---KPS 88

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (128), Expect = 3e-10
 Identities = 17/84 (20%), Positives = 27/84 (32%), Gaps = 10/84 (11%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
            ++V  L   T  E + + F              +   + + Y FV F   E A  A   
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNI------KPGAVERVKKIRDYAFVHFSNREDAVEAMKA 63

Query: 93  PTPF-IDGRRANCNLASLGRPRPQ 115
                +DG      LA   +P  +
Sbjct: 64  LNGKVLDGSPIEVTLA---KPVDK 84

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 53.4 bits (127), Expect = 4e-10
 Identities = 14/79 (17%), Positives = 27/79 (34%), Gaps = 1/79 (1%)

Query: 29  TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
           TT   +F+G L        ++    +       + + D  TG ++ +G+V F   E   +
Sbjct: 11  TTPFNLFIGNLNPNKSVAELKVAISELFAK-NDLAVVDVRTGTNRKFGYVDFESAEDLEK 69

Query: 89  ACADPTPFIDGRRANCNLA 107
           A       + G        
Sbjct: 70  ALELTGLKVFGNEIKLEKP 88

>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 = 53.6 bits (128), Expect = 4e-10
 Identities = 29/105 (27%), Positives = 47/105 (44%), Gaps = 13/105 (12%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG              ++FV  L++ +  E + + F  +G + E     D  T +
Sbjct: 1   GSSGSSGS------------GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKK 48

Query: 72  SKGYGFVTFREPEAARRACADPTPF-IDGRRANCNLASLGRPRPQ 115
            KG+ FVTF  PE A +A A+       GR  +   +++ +   Q
Sbjct: 49  PKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQ 93

>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 = 52.8 bits (126), Expect = 4e-10
 Identities = 13/85 (15%), Positives = 28/85 (32%), Gaps = 11/85 (12%)

Query: 33  KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA- 91
           K+++G L+    ++ +R+ F                     GY FV + +   A RA   
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKL------PLAGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 92  -DPTPFIDGRRANCNLASLGRPRPQ 115
                 + G+    + +     +  
Sbjct: 57  LSGKVELHGKIMEVDYS---VSKKL 78

>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 = 52.9 bits (126), Expect = 5e-10
 Identities = 24/91 (26%), Positives = 43/91 (47%), Gaps = 10/91 (10%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             VF+  L+++++ E +    +QFG++    V+   +T  SKG  F  F   EAA++  A
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 92  DPTPF-------IDGRRANCNLASLGRPRPQ 115
             +         +DGR+   +LA     R +
Sbjct: 69  AASLEAEGGGLKLDGRQLKVDLA---VTRDE 96

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 52.1 bits (124), Expect = 9e-10
 Identities = 18/85 (21%), Positives = 33/85 (38%), Gaps = 5/85 (5%)

Query: 32  TKVFVGGLAWE-TQSETMRRYFEQFGEILEAVVITD-KNTGRSKGYGFVTFREPEAARRA 89
            ++ +  L+ E      +R  FE FG I +  +    K    +    F+ F   ++A RA
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 90  CADPTPFIDGRRANCNLASLGRPRP 114
                  +  R  + +LA     +P
Sbjct: 65  LQMNRSLLGNREISVSLA---DKKP 86

>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 = 52.0 bits (124), Expect = 1e-09
 Identities = 22/85 (25%), Positives = 33/85 (38%), Gaps = 5/85 (5%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             ++VG L+ +     + + F Q G      +IT+     +  Y FV F E   A  A A
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALA 66

Query: 92  DPTPF-IDGRRANCNLASLGRPRPQ 115
                 I G+    N A+   P  Q
Sbjct: 67  AMNGRKILGKEVKVNWAT--TPSSQ 89

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 2e-09
 Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 1/80 (1%)

Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
           D     V++ G   +   + ++ + E  G++L  + +        KG  FV F   E+A+
Sbjct: 3   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIESAK 61

Query: 88  RACADPTPFIDGRRANCNLA 107
           +    P              
Sbjct: 62  KFVETPGQKYKETDLLILFK 81

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.1 bits (122), Expect = 2e-09
 Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 7/81 (8%)

Query: 29  TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
           T  +++FVG L  +   E MR+ FE++G+  E  +  DK       +GF+       A  
Sbjct: 6   TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEI 59

Query: 89  ACAD-PTPFIDGRRANCNLAS 108
           A  +     + G++     A 
Sbjct: 60  AKVELDNMPLRGKQLRVRFAC 80

>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 = 51.6 bits (123), Expect = 2e-09
 Identities = 30/114 (26%), Positives = 45/114 (39%), Gaps = 17/114 (14%)

Query: 1   MAYQSIPGPGSGSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILE 60
           +  QSI   GS      G               +F+  L  E   + + + F  FG ++ 
Sbjct: 1   LTQQSIGAAGSQKEGPEG-------------ANLFIYHLPQEFGDQDLLQMFMPFGNVVS 47

Query: 61  AVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRRANCNLASLGRPR 113
           A V  DK T  SK +GFV++  P +A+ A      F I  +R    L    R +
Sbjct: 48  AKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK---RSK 98

>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 = 50.4 bits (120), Expect = 4e-09
 Identities = 25/85 (29%), Positives = 37/85 (43%), Gaps = 6/85 (7%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             +F+  L     ++ +   F  FG IL   V+ D+N   SKGYGFV F   EAA RA  
Sbjct: 9   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIE 66

Query: 92  DPTPF-IDGRRANCNLASLGRPRPQ 115
                 ++ R+         + R +
Sbjct: 67  KMNGMLLNDRKVFVGRF---KSRKE 88

>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 = 49.9 bits (119), Expect = 5e-09
 Identities = 14/70 (20%), Positives = 26/70 (37%), Gaps = 7/70 (10%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           T V V G    + S  +   F Q+G IL+ V+        +  +  + ++    AR+A +
Sbjct: 5   TWVTVFGFPQASASYILL-QFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS 57

Query: 92  DPTPFIDGRR 101
                     
Sbjct: 58  KDGRIFGESI 67

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 50.4 bits (120), Expect = 5e-09
 Identities = 15/84 (17%), Positives = 28/84 (33%), Gaps = 6/84 (7%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             +    L++    + ++  FE   EI           G+SKG  ++ F+    A +   
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEKNLE 71

Query: 92  DPTPF-IDGRRANCNLASLGRPRP 114
           +     IDGR  +           
Sbjct: 72  EKQGAEIDGRSVSLYYTGEKGGTR 95

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 48.6 bits (115), Expect = 1e-08
 Identities = 7/77 (9%), Positives = 23/77 (29%), Gaps = 1/77 (1%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             +++           +R   +    +  ++ +       S+ + ++     E AR    
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 92  DPTPF-IDGRRANCNLA 107
                 I+G      ++
Sbjct: 62  KLNGLKIEGYTLVTKVS 78

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 1e-08
 Identities = 26/97 (26%), Positives = 33/97 (34%), Gaps = 7/97 (7%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG     S F  TT   V + GL +      +  +F     +   +       GR
Sbjct: 1   GSSGSSG-----SSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIE--IGPDGR 53

Query: 72  SKGYGFVTFREPEAARRACADPTPFIDGRRANCNLAS 108
             G   V F   E A  A A     +  R     L S
Sbjct: 54  VTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNS 90

>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 = 47.9 bits (113), Expect = 2e-08
 Identities = 12/77 (15%), Positives = 25/77 (32%), Gaps = 2/77 (2%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
           T V V  L        + +YF+  G I+   V    +  ++  +  + F   + A  A  
Sbjct: 1   TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALAAIT 58

Query: 92  DPTPFIDGRRANCNLAS 108
                +       +  +
Sbjct: 59  KTHKVVGQNEIIVSHLT 75

>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 = 47.7 bits (113), Expect = 4e-08
 Identities = 12/78 (15%), Positives = 29/78 (37%), Gaps = 2/78 (2%)

Query: 32  TKVFVGGLAWETQSETMRR-YFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
             +++  L  + + + +++     F    + + I    + + +G  FV F+E  +A  A 
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 91  ADPTPF-IDGRRANCNLA 107
                F    +      A
Sbjct: 64  RSMQGFPFYDKPMRIQYA 81

>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 = 48.1 bits (114), Expect = 5e-08
 Identities = 11/63 (17%), Positives = 29/63 (46%), Gaps = 4/63 (6%)

Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
          G +   ++ V  L +    + + + F +FG +L+ +  T      ++    + + +P +A
Sbjct: 3  GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSA 58

Query: 87 RRA 89
          + A
Sbjct: 59 QHA 61

>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 = 47.1 bits (111), Expect = 8e-08
 Identities = 24/92 (26%), Positives = 45/92 (48%), Gaps = 1/92 (1%)

Query: 25  PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPE 84
           P  D +   VFVG + +E   E ++  F + G ++   ++ D+ TG+ KGYGF  +++ E
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 85  AARRACADPTPF-IDGRRANCNLASLGRPRPQ 115
            A  A  +       GR    + A+  + + +
Sbjct: 62  TALSAMRNLNGREFSGRALRVDNAASEKNKEE 93

>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 = 46.6 bits (110), Expect = 1e-07
 Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 1/77 (1%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             +FV  +  E Q + ++  F  +GEI    +  D+ TG SKGY  V +   + A  A  
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 92  DPTPF-IDGRRANCNLA 107
                 I G+    +  
Sbjct: 68  ALNGAEIMGQTIQVDWC 84

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.4 bits (109), Expect = 2e-07
 Identities = 19/94 (20%), Positives = 41/94 (43%)

Query: 15  SSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKG 74
           S SG +   S         V++ GL +E +++ +  +F++   + +++ I     G++ G
Sbjct: 2   SPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATG 61

Query: 75  YGFVTFREPEAARRACADPTPFIDGRRANCNLAS 108
            GFV FR     + A      ++  R    +  +
Sbjct: 62  EGFVEFRNEADYKAALCRHKQYMGNRFIQVHPIT 95

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.4 bits (104), Expect = 5e-07
 Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 7/79 (8%)

Query: 33  KVFVGGLAWETQSETMRRYFE---QFGEILEAVVITDKNTGRS---KGYGFVTFREPEAA 86
            VFV GL+       + +  E   +FG+I + V+    +   S       +VT+   E A
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 87  RRACADPTPF-IDGRRANC 104
            RA        +DGR    
Sbjct: 70  LRAIQCVNNVVVDGRTLKA 88

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (103), Expect = 9e-07
 Identities = 16/85 (18%), Positives = 31/85 (36%), Gaps = 4/85 (4%)

Query: 32  TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
             +++  L+       +   F +F E     +     TGR +G  F+TF   E A +A  
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 92  DPTPF-IDGRRANCNLASLGRPRPQ 115
               + + G+          + + Q
Sbjct: 79  LVNGYKLYGKILVIEFG---KNKKQ 100

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 9e-07
 Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 2/80 (2%)

Query: 28  DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
            +  + V +     E   E      E++GE+ E + + D       G  +V FR  E A 
Sbjct: 24  RSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEE-MNVCDNLGDHLVGNVYVKFRREEDAE 82

Query: 88  RACADPT-PFIDGRRANCNL 106
           +A  D    + +G+  +  L
Sbjct: 83  KAVIDLNNRWFNGQPIHAEL 102

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.8 bits (103), Expect = 1e-06
 Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 5/68 (7%)

Query: 41  WETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP-FIDG 99
                E +R    +FG+I + ++          G   V+FR+PE A          +  G
Sbjct: 29  LNEIREDLRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYCIQTLDGRWFGG 84

Query: 100 RRANCNLA 107
           R+      
Sbjct: 85  RQITAQAW 92

>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 = 42.1 bits (98), Expect = 3e-06
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 34  VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA-- 91
           +++ GL   T  + + +  + +G+I+    I DK T + KGYGFV F  P AA++A    
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 92  DPTPFIDGRRA 102
             +     + A
Sbjct: 61  KASGV-QAQMA 70

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (95), Expect = 1e-05
 Identities = 16/80 (20%), Positives = 27/80 (33%), Gaps = 8/80 (10%)

Query: 29  TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
           T    V  GGL        +    E+ G +   ++  +K       Y F  +R  E ++R
Sbjct: 18  TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKR 71

Query: 89  ACA--DPTPFIDGRRANCNL 106
           A    +    +D       L
Sbjct: 72  AYVTLNGKEVVDDLGQKITL 91

>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 = 41.0 bits (95), Expect = 2e-05
 Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 1/86 (1%)

Query: 30  TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
               + V  +        +R+ FE++G I    ++ D+ T +S+GYGFV F+   +A++A
Sbjct: 41  VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA 100

Query: 90  CADPTPF-IDGRRANCNLASLGRPRP 114
            A    F I  +R    LA+ G  RP
Sbjct: 101 IAGLNGFNILNKRLKVALAASGHQRP 126

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.4 bits (91), Expect = 5e-05
 Identities = 25/100 (25%), Positives = 39/100 (39%), Gaps = 14/100 (14%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG  +  S         V V GL        +    E+FG I   +++  K    
Sbjct: 1   GSSGSSGSHHKVSV-----SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR--- 52

Query: 72  SKGYGFVTFREPEAARRA---CADPTPFIDGRRANCNLAS 108
                 V F   ++A+      AD   +I G++A  N ++
Sbjct: 53  ---QALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYST 89

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 1e-04
 Identities = 13/82 (15%), Positives = 27/82 (32%), Gaps = 8/82 (9%)

Query: 27  GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
           G +  + + V  L  ++  + +    + +        +      R+K   FVT    E A
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQA 53

Query: 87  RRACADPTPF-IDGRRANCNLA 107
           + A      +   G+     L 
Sbjct: 54  QNAIQMFHQYSFRGKDLIVQLQ 75

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (87), Expect = 1e-04
 Identities = 12/91 (13%), Positives = 25/91 (27%), Gaps = 11/91 (12%)

Query: 19  FQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFV 78
           FQ +  P        + +  +      E ++  F   G     VV   K   + +    +
Sbjct: 3   FQNIFPP-----SATLHLSNIPPSVSEEDLKVLFSSNGG----VVKGFKFFQKDRKMALI 53

Query: 79  TFREPEAARRA--CADPTPFIDGRRANCNLA 107
                E A +A          +      + +
Sbjct: 54  QMGSVEEAVQALIDLHNHDLGENHHLRVSFS 84

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.9 bits (87), Expect = 2e-04
 Identities = 14/62 (22%), Positives = 20/62 (32%), Gaps = 7/62 (11%)

Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREP-EAARRAC 90
             F G L  +T  E +   F   GEI     +           G + F+E  + A    
Sbjct: 12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKA 65

Query: 91 AD 92
           D
Sbjct: 66 KD 67

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.1 bits (85), Expect = 3e-04
 Identities = 20/105 (19%), Positives = 31/105 (29%), Gaps = 15/105 (14%)

Query: 12  GSSSSSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGR 71
           GSS SSG      P    +  +V V GL      + ++ +  +                +
Sbjct: 1   GSSGSSG-----GPPTRRSDFRVLVSGLPPSGSWQDLKDHMREA-------GDVCYADVQ 48

Query: 72  SKGYGFVTFREPEAARRACA--DPTPFIDGRRANCNLASLGRPRP 114
             G G V +   E    A    D T F        +   +   R 
Sbjct: 49  KDGMGMVEYLRKEDMEYALRKLDDTKF-RSHEGETSYIRVYPERS 92

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.7 bits (84), Expect = 4e-04
 Identities = 16/93 (17%), Positives = 31/93 (33%), Gaps = 2/93 (2%)

Query: 16  SSGFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGY 75
           +SG Q   +   +   T +++  L      + +    + FG++  +  I   ++G S+G 
Sbjct: 3   ASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQV-ISTRILRDSSGTSRGV 61

Query: 76  GFVTFREPEAARRACADPT-PFIDGRRANCNLA 107
           GF      E            FI          
Sbjct: 62  GFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT 94

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.1 bits (83), Expect = 7e-04
 Identities = 10/73 (13%), Positives = 19/73 (26%), Gaps = 3/73 (4%)

Query: 39  LAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGF--VTFREPEAARRACAD-PTP 95
             +E   E +R    ++G +    +    +     G G   V F      ++A       
Sbjct: 22  EEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR 81

Query: 96  FIDGRRANCNLAS 108
               R        
Sbjct: 82  KFANRVVVTKYCD 94

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.2 bits (80), Expect = 0.001
 Identities = 11/97 (11%), Positives = 21/97 (21%), Gaps = 12/97 (12%)

Query: 27  GDTTYTKVFVGGLAWETQSET-----MRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFR 81
           G +  + +       +  SE+         F  + +                    + F 
Sbjct: 1   GSSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFS 54

Query: 82  EPEAARRACADPTPF-IDGRRANCNLASLGRPRPQVL 117
            P +A  A          G+      A         L
Sbjct: 55  NPLSAADARLRLHKTEFLGKEMKLYFAQTLHIGSSHL 91

>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 = 34.3 bits (78), Expect = 0.003
 Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 11/80 (13%)

Query: 12 GSSSSSGFQYLNSPFGDTT-YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTG 70
          GSS SSG       +G     T+++VGGL   T    + R F++FG I     +   +  
Sbjct: 1  GSSGSSG----KIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS-- 54

Query: 71 RSKGYGFVTFREPEAARRAC 90
              + ++ +   +AA+ AC
Sbjct: 55 ----FAYIQYESLDAAQAAC 70

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	258
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.89
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.87
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.87
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.87
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.86
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.86
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.86
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.86
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.86
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.85
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.85
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.85
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.85
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.85
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.85
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.85
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.85
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.85
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.84
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.84
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.84
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.84
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.83
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.83
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.83
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.83
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.83
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.82
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.82
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.82
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.82
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.82
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.82
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.81
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.81
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.81
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.8
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.8
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.79
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.79
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.78
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.78
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.78
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.78
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.77
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.77
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.77
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.77
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.76
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.75
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.75
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.74
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.74
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.74
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.73
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.73
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.73
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.73
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.72
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.72
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.72
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.71
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.71
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.71
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.71
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.71
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.7
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.7
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.69
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.69
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.69
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.68
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.67
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.67
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.66
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.64
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.61
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.6
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.59
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.55
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.48
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.45
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.41
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.37
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.23
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.23
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.95
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.79
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.5

>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=99.89  E-value=3.4e-23  Score=155.26  Aligned_cols=87  Identities=61%  Similarity=1.057  Sum_probs=81.0

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEE
Q 025068           24 SPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRAN  103 (258)
Q Consensus        24 ~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~  103 (258)
                      .+..|.+.++|||+|||++++|++|+++|++||.|++|+|++|+.|+++||||||+|.+.++|++||+.++++|+|+.|+
T Consensus         3 ~~~~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~   82 (103)
T d2cqda1           3 GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKAN   82 (103)
T ss_dssp             CCCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECE
T ss_pred             CCCCCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEE
Confidence            34556677899999999999999999999999999999999999999999999999999999999999988889999999


Q ss_pred             EEeccCC
Q 025068          104 CNLASLG  110 (258)
Q Consensus       104 V~~a~~~  110 (258)
                      |++|..+
T Consensus        83 V~~a~~~   89 (103)
T d2cqda1          83 VNLAYLG   89 (103)
T ss_dssp             EEESTTT
T ss_pred             EEEcCCC
Confidence            9999754

>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=99.87  E-value=2e-22  Score=145.58  Aligned_cols=81  Identities=38%  Similarity=0.643  Sum_probs=76.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      .+..++|||+|||.++++++|+++|++||.|.+++|++|+.++++||||||+|.+.++|++||+.+++.|+|+.|+|+.|
T Consensus         3 pe~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           3 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEEC
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEee
Confidence            34568999999999999999999999999999999999999999999999999999999999998888899999999988


Q ss_pred             c
Q 025068          108 S  108 (258)
Q Consensus       108 ~  108 (258)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            4

>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=99.87  E-value=2.7e-22  Score=146.80  Aligned_cols=84  Identities=36%  Similarity=0.675  Sum_probs=76.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      ....++|||+|||+++||++|+++|++||.|++|+|++|+.|+++||||||+|.+.++|++||+.+ +.|+|+.|.|++|
T Consensus         5 ~~~~~~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           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR-HMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC-EEETTEEEEEECC
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC-CccCCEEeEEEeC
Confidence            345678999999999999999999999999999999999999999999999999999999999865 4799999999999


Q ss_pred             cCCCC
Q 025068          108 SLGRP  112 (258)
Q Consensus       108 ~~~~~  112 (258)
                      ..++.
T Consensus        84 ~~k~~   88 (90)
T d2cqga1          84 NSKQS   88 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            76543

>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=99.87  E-value=1.4e-22  Score=143.48  Aligned_cols=75  Identities=31%  Similarity=0.581  Sum_probs=72.5

Q ss_pred             EEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        33 ~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      +|||+|||+++||++|+++|++||.|++|+|++|+.|+++||||||+|.+.++|++||+.++++|+|+.|.|+.|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEEC
Confidence            699999999999999999999999999999999999999999999999999999999998888999999999876

>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=99.86  E-value=9.4e-23  Score=145.00  Aligned_cols=76  Identities=39%  Similarity=0.759  Sum_probs=73.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      |+|||+|||+++||++|+++|++||.|++++|++|+.|+++||||||+|.+.++|++||+.+++.|+||.|+|+.|
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 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            6899999999999999999999999999999999999999999999999999999999997668899999999987

>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=99.86  E-value=1.2e-21  Score=145.61  Aligned_cols=83  Identities=27%  Similarity=0.463  Sum_probs=77.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...++|||+||++++++++|+++|++||.|++|+|++|+.++++||||||+|.+.++|++||+.++ ..|+|+.|+|+++
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            346789999999999999999999999999999999999999999999999999999999999866 6699999999999


Q ss_pred             cCCC
Q 025068          108 SLGR  111 (258)
Q Consensus       108 ~~~~  111 (258)
                      ..++
T Consensus        86 ~~~~   89 (99)
T d1whwa_          86 TIKK   89 (99)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            7553

>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=99.86  E-value=1e-21  Score=144.43  Aligned_cols=84  Identities=29%  Similarity=0.380  Sum_probs=77.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+|||.++++++|+++|++||.|++|+|++|+.|+++||||||+|.+.++|++||+.++ ..|+|+.|+|++
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3446799999999999999999999999999999999999999999999999999999999998865 669999999999


Q ss_pred             ccCCC
Q 025068          107 ASLGR  111 (258)
Q Consensus       107 a~~~~  111 (258)
                      |..++
T Consensus        86 A~~~~   90 (93)
T d1x5ua1          86 ASAHN   90 (93)
T ss_dssp             TTTTS
T ss_pred             cCCCC
Confidence            96543

>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=99.86  E-value=6.7e-22  Score=141.75  Aligned_cols=79  Identities=24%  Similarity=0.333  Sum_probs=74.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccC
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASL  109 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~  109 (258)
                      +++|||+|||.++++++|+++|++||.|++|+|++|+.++++||||||+|.+.++|++||+.++ ..|+|+.|+|++|++
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            5789999999999999999999999999999999999999999999999999999999999855 679999999999954

>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=99.86  E-value=6.4e-22  Score=139.82  Aligned_cols=75  Identities=35%  Similarity=0.773  Sum_probs=71.6

Q ss_pred             EEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        33 ~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      +|||+|||++++|++|+++|++||.|++|+|++|+.|+++||||||+|.+.++|++||+.+++.|+|+.|+|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            599999999999999999999999999999999999999999999999999999999998778899999999764

>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=99.85  E-value=1e-21  Score=142.91  Aligned_cols=84  Identities=24%  Similarity=0.302  Sum_probs=76.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      .....++|||+||+.++++++|+++|++||.|++|+|++|+.++++||||||+|.+.++|++||+.++ ..|+|+.|+|+
T Consensus         3 ~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~   82 (88)
T d1rk8a_           3 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD   82 (88)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34456799999999999999999999999999999999999999999999999999999999999854 67999999999


Q ss_pred             eccCC
Q 025068          106 LASLG  110 (258)
Q Consensus       106 ~a~~~  110 (258)
                      +|..+
T Consensus        83 ~a~~k   87 (88)
T d1rk8a_          83 WCFVK   87 (88)
T ss_dssp             ESEEC
T ss_pred             EecCC
Confidence            99654

>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=99.85  E-value=2e-21  Score=142.86  Aligned_cols=82  Identities=21%  Similarity=0.277  Sum_probs=76.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ..+++|||+|||.++|+++|+++|++||.|++|+|++++.++++||||||+|.+.++|++||+.++ ..|+|+.|+|+++
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            357899999999999999999999999999999999999999999999999999999999999865 6699999999998


Q ss_pred             cCC
Q 025068          108 SLG  110 (258)
Q Consensus       108 ~~~  110 (258)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            543

>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=99.85  E-value=1.5e-21  Score=145.88  Aligned_cols=83  Identities=27%  Similarity=0.372  Sum_probs=76.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccC
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASL  109 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~  109 (258)
                      .++|||+|||+++++++|+++|++||.|.+++++.++.++++||||||+|.+.++|++||+.++ ..|+|+.|+|++|.+
T Consensus        18 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~   97 (102)
T d2cpza1          18 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRS   97 (102)
T ss_dssp             TCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCC
Confidence            4689999999999999999999999999999999999999999999999999999999998855 679999999999976


Q ss_pred             CCCC
Q 025068          110 GRPR  113 (258)
Q Consensus       110 ~~~~  113 (258)
                      +..+
T Consensus        98 k~~~  101 (102)
T d2cpza1          98 KNDS  101 (102)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            6543

>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=99.85  E-value=3.8e-22  Score=145.51  Aligned_cols=83  Identities=31%  Similarity=0.440  Sum_probs=76.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      +.++|||+|||+++++++|+++|++||.|++|+|++|+.++++||||||+|.+.++|++||+.++ ..|+|+.|+|++|.
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            46799999999999999999999999999999999999999999999999999999999999854 66999999999997


Q ss_pred             CCCC
Q 025068          109 LGRP  112 (258)
Q Consensus       109 ~~~~  112 (258)
                      +++.
T Consensus        84 p~~~   87 (89)
T d2cqba1          84 PMRI   87 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            5543

>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=99.85  E-value=2.1e-21  Score=138.66  Aligned_cols=76  Identities=29%  Similarity=0.438  Sum_probs=72.7

Q ss_pred             EEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        33 ~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      +|||+|||.++||++|+++|++||.|.+|+|++|+.|++++|||||+|.+.++|++||+.++ ..|+|++|+|++|+
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            69999999999999999999999999999999999999999999999999999999999866 66999999999984

>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=99.85  E-value=7.1e-21  Score=149.62  Aligned_cols=85  Identities=28%  Similarity=0.476  Sum_probs=77.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...++|||+|||++++|++|+++|++||.|++|+|++|+.|+++||||||+|.+.++|++||+.++ .+|+|++|+|++|
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            345789999999999999999999999999999999999999999999999999999999999865 6799999999999


Q ss_pred             cCCCCC
Q 025068          108 SLGRPR  113 (258)
Q Consensus       108 ~~~~~~  113 (258)
                      ..+..+
T Consensus       120 ~~~~~~  125 (139)
T d1u6fa1         120 ASGHQR  125 (139)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            765443

>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=99.85  E-value=2.8e-21  Score=137.49  Aligned_cols=78  Identities=31%  Similarity=0.650  Sum_probs=74.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      +.++|||+|||+++|+++|+++|++||.|.+++++.++.+++++|||||+|.+.+++++|++.++++|+|+.|+|+.|
T Consensus         1 t~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           1 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             CCCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            468999999999999999999999999999999999999999999999999999999999987778899999999987

>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=99.85  E-value=1.8e-21  Score=140.71  Aligned_cols=79  Identities=25%  Similarity=0.452  Sum_probs=74.6

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccCC
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASLG  110 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~~  110 (258)
                      .+|||+|||+++||++|+++|++||+|++|+|++|+.||++||||||+|.+.++|++||+.++ ..|+|+.|+|++|...
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            479999999999999999999999999999999999999999999999999999999999865 6799999999999643

>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=99.85  E-value=1.6e-21  Score=146.09  Aligned_cols=83  Identities=37%  Similarity=0.672  Sum_probs=77.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEecc
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLAS  108 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~  108 (258)
                      +..++|||+|||+++++++|+++|++||.|+++.|++|+.++++||||||+|.+.++|++||+.+++.|+|+.|.|++|.
T Consensus        18 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          18 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCS
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECc
Confidence            34579999999999999999999999999999999999999999999999999999999999887788999999999997


Q ss_pred             CCC
Q 025068          109 LGR  111 (258)
Q Consensus       109 ~~~  111 (258)
                      +++
T Consensus        98 ~ke  100 (103)
T d1x4ba1          98 ARE  100 (103)
T ss_dssp             SCC
T ss_pred             ccC
Confidence            654

>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=99.84  E-value=4.7e-21  Score=138.36  Aligned_cols=81  Identities=25%  Similarity=0.458  Sum_probs=74.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCC--ceEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDG--RRAN  103 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G--~~i~  103 (258)
                      ++.+.++|||+|||.+++|++|+++|++||.|++|+|++|+.++++||||||+|.+.++|++||+.++ ..+.|  ++|+
T Consensus         2 ~~~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~   81 (85)
T d1b7fa2           2 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLS   81 (85)
T ss_dssp             STTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEE
Confidence            34567789999999999999999999999999999999999999999999999999999999999855 55665  8899


Q ss_pred             EEec
Q 025068          104 CNLA  107 (258)
Q Consensus       104 V~~a  107 (258)
                      |++|
T Consensus        82 V~~A   85 (85)
T d1b7fa2          82 VRLA   85 (85)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            9986

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=3.5e-21  Score=140.56  Aligned_cols=82  Identities=29%  Similarity=0.398  Sum_probs=76.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...++|||+|||.++++++|+++|++||.|++|+|++|+.++++||||||+|.+.++|++||+.++ ..|+|+.|+|++|
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            356789999999999999999999999999999999999999999999999999999999999866 5699999999999


Q ss_pred             cCC
Q 025068          108 SLG  110 (258)
Q Consensus       108 ~~~  110 (258)
                      +++
T Consensus        86 kp~   88 (90)
T d2cq0a1          86 KPS   88 (90)
T ss_dssp             SCC
T ss_pred             eCC
Confidence            543

>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=99.84  E-value=8.7e-22  Score=147.50  Aligned_cols=87  Identities=28%  Similarity=0.547  Sum_probs=79.3

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEE
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRAN  103 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~  103 (258)
                      |..+...++|||+||+.++++++|+++|++||+|++|+|++++.|+++||||||+|.+.++|++||+.++ ..|+|+.|+
T Consensus         2 P~~~~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~   81 (104)
T d1p1ta_           2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALR   81 (104)
T ss_dssp             CCSHHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBE
T ss_pred             CCCCCCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            4455567899999999999999999999999999999999999999999999999999999999999865 679999999


Q ss_pred             EEeccCCC
Q 025068          104 CNLASLGR  111 (258)
Q Consensus       104 V~~a~~~~  111 (258)
                      |++|..++
T Consensus        82 V~~a~~~~   89 (104)
T d1p1ta_          82 VDNAASEK   89 (104)
T ss_dssp             EEETTCTT
T ss_pred             EEECCCCC
Confidence            99996543

>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=99.84  E-value=6.3e-21  Score=136.48  Aligned_cols=78  Identities=29%  Similarity=0.451  Sum_probs=73.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCccCCceEEEEecc
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPFIDGRRANCNLAS  108 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~i~G~~i~V~~a~  108 (258)
                      .++|||+|||.+++|++|+++|++||.|++|+|++|+.+++++|||||+|.+.++|++||+.+ +..|+|+.|+|++|+
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~Ak   80 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            357999999999999999999999999999999999989999999999999999999999985 467999999999985

>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=99.83  E-value=5.1e-21  Score=139.51  Aligned_cols=84  Identities=35%  Similarity=0.650  Sum_probs=77.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~i~G~~i~V~~a  107 (258)
                      .+.++|||+|||+++++++|+++|++||.|+++.+++++.+++++|||||+|.+.++|++||+.+ +..|+|++|+|++|
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            34678999999999999999999999999999999999999999999999999999999999884 57799999999999


Q ss_pred             cCCCC
Q 025068          108 SLGRP  112 (258)
Q Consensus       108 ~~~~~  112 (258)
                      .++..
T Consensus        83 ~~~~~   87 (90)
T d1x5sa1          83 GKSSD   87 (90)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            76543

>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=99.83  E-value=9.5e-21  Score=136.84  Aligned_cols=78  Identities=24%  Similarity=0.452  Sum_probs=71.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCC--ceEEEEe
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDG--RRANCNL  106 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G--~~i~V~~  106 (258)
                      +.++|||+|||.++|+++|+++|++||+|++|+|++|+.++++||||||+|.+.++|++||+.++ ..++|  ++|+|++
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            46789999999999999999999999999999999999999999999999999999999999855 66887  5689988


Q ss_pred             c
Q 025068          107 A  107 (258)
Q Consensus       107 a  107 (258)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          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=99.83  E-value=8.1e-21  Score=139.80  Aligned_cols=83  Identities=25%  Similarity=0.457  Sum_probs=75.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCC-CCCcccEEEEEEcCHHHHHHHhcCC-C-CccCCceEEEE
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKN-TGRSKGYGFVTFREPEAARRACADP-T-PFIDGRRANCN  105 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~-tg~skG~aFV~F~~~~~A~~Ai~~~-~-~~i~G~~i~V~  105 (258)
                      ...++|||+|||.+++|++|+++|++||.|++|+|++++. +|++||||||+|.+.++|++||+.+ + ..|+|++|+|+
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            4567899999999999999999999999999999998854 7999999999999999999999985 5 56999999999


Q ss_pred             eccCCC
Q 025068          106 LASLGR  111 (258)
Q Consensus       106 ~a~~~~  111 (258)
                      +|..+.
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            996543

>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=99.83  E-value=9.7e-22  Score=146.80  Aligned_cols=82  Identities=22%  Similarity=0.320  Sum_probs=75.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      +.+.++|||+||+.+++|++|+++|+.||.|++|+|++|+.++++||||||+|.+.++|++||+.++..|+|+.|+|+++
T Consensus        15 ~~~~~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          15 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQAS   94 (101)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEH
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEEC
Confidence            33457999999999999999999999999999999999999999999999999999999999975557799999999998


Q ss_pred             cC
Q 025068          108 SL  109 (258)
Q Consensus       108 ~~  109 (258)
                      ..
T Consensus        95 ~~   96 (101)
T d2cq4a1          95 QA   96 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>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=99.83  E-value=6.1e-21  Score=137.04  Aligned_cols=79  Identities=28%  Similarity=0.482  Sum_probs=72.5

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCEEEE-EEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccCCC
Q 025068           34 VFVGGLAWETQSETMRRYFEQFGEILEA-VVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASLGR  111 (258)
Q Consensus        34 lfVgnLp~~~te~~L~~~F~~fG~I~~v-~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~~~  111 (258)
                      |||+|||.+++|++|+++|++||.|.++ +|++|+.+++++|||||+|.+.++|++||+.++ ..|+|++|+|++|.+++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            8999999999999999999999999765 789999999999999999999999999999866 66999999999997654


Q ss_pred             C
Q 025068          112 P  112 (258)
Q Consensus       112 ~  112 (258)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.83  E-value=1.7e-20  Score=136.63  Aligned_cols=80  Identities=29%  Similarity=0.477  Sum_probs=72.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccC
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASL  109 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~  109 (258)
                      ..+|||+|||.++++++|+++|++||.|++|+|+.++  +.++|||||+|.+.++|++||+.++ ..|+|+.|+|++|.+
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            4589999999999999999999999999999999986  4578999999999999999999876 669999999999976


Q ss_pred             CCC
Q 025068          110 GRP  112 (258)
Q Consensus       110 ~~~  112 (258)
                      ++.
T Consensus        86 ~~~   88 (89)
T d1cvja2          86 RKE   88 (89)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            543

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1.1e-20  Score=135.71  Aligned_cols=75  Identities=28%  Similarity=0.472  Sum_probs=70.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEE
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANC  104 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V  104 (258)
                      ..++|||+||+.++||++|+++|++||.|++|+|++|+.+++++|||||+|.+.++|++||+.++ ..|+|++|+|
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            45789999999999999999999999999999999999999999999999999999999998855 6699999987

>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=99.82  E-value=2.1e-20  Score=136.38  Aligned_cols=83  Identities=25%  Similarity=0.344  Sum_probs=74.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      ++...++|||+|||.+++|++|+++|++||.|++|+|++|+.+  .+|||||+|.+.++|++||+.++ ..|.|+.|+|.
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~   81 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   81 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            4556789999999999999999999999999999999999754  37899999999999999999855 56999999999


Q ss_pred             eccCCC
Q 025068          106 LASLGR  111 (258)
Q Consensus       106 ~a~~~~  111 (258)
                      +|.++.
T Consensus        82 ~a~~~~   87 (90)
T d2cqia1          82 WATTPS   87 (90)
T ss_dssp             ECCCTT
T ss_pred             EcCCCC
Confidence            996543

>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=99.82  E-value=4.8e-20  Score=137.78  Aligned_cols=84  Identities=18%  Similarity=0.402  Sum_probs=72.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecC-CCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDK-NTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~-~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~  106 (258)
                      +...++|||+|||+++||++|+++|++|| |++++++.++ .++++||||||+|.+.++|++|++.++.+|+|+.|+|++
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34468999999999999999999999999 7788777765 468899999999999999998887666789999999999


Q ss_pred             ccCCCC
Q 025068          107 ASLGRP  112 (258)
Q Consensus       107 a~~~~~  112 (258)
                      |..++.
T Consensus        91 a~~~~~   96 (104)
T d1wi8a_          91 ADQAQD   96 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            965543

>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=99.82  E-value=2.2e-20  Score=137.87  Aligned_cols=86  Identities=29%  Similarity=0.470  Sum_probs=76.9

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-------Ccc
Q 025068           25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-------PFI   97 (258)
Q Consensus        25 p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-------~~i   97 (258)
                      |.+..+.++|||+|||+++||++|+++|++||.|.++.++.++.+++++|||||+|.+.++|++||+.++       ..|
T Consensus         2 P~~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~   81 (98)
T d1x4ha1           2 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL   81 (98)
T ss_dssp             CCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEES
T ss_pred             ccCCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEE
Confidence            3445567899999999999999999999999999999999999999999999999999999999998643       348


Q ss_pred             CCceEEEEeccCC
Q 025068           98 DGRRANCNLASLG  110 (258)
Q Consensus        98 ~G~~i~V~~a~~~  110 (258)
                      +|+.|+|++|.++
T Consensus        82 ~gr~l~v~~a~~k   94 (98)
T d1x4ha1          82 DGRQLKVDLAVTR   94 (98)
T ss_dssp             SSCEEEEECCCCC
T ss_pred             CCEEEEEEECCCC
Confidence            8999999999654

>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=99.82  E-value=1.2e-20  Score=132.64  Aligned_cols=75  Identities=39%  Similarity=0.754  Sum_probs=71.5

Q ss_pred             EEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        33 ~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      +|||+|||.++||++|+++|++||.|+.+.+++++.+++++|||||+|.+.++|++||+.+++.|+|+.|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEEC
Confidence            599999999999999999999999999999999999999999999999999999999986668899999999976

>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=99.82  E-value=2e-20  Score=134.89  Aligned_cols=76  Identities=28%  Similarity=0.560  Sum_probs=70.0

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCC---CcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccC
Q 025068           34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTG---RSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASL  109 (258)
Q Consensus        34 lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg---~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~  109 (258)
                      |||+|||+++|+++|+++|++||.|++|+|++++.++   ++||||||+|.+.++|++||+.++ ..|+|+.|+|++|.+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            8999999999999999999999999999999987665   478999999999999999998865 679999999999853

>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=99.82  E-value=1.9e-20  Score=133.07  Aligned_cols=75  Identities=29%  Similarity=0.457  Sum_probs=71.0

Q ss_pred             EEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        33 ~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      +|||+|||.++++++|+++|++||.|++|+|++++ +++++|||||+|.+.++|++||+.++ ..++|+.|+|++|.
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            69999999999999999999999999999999997 79999999999999999999999854 77999999999985

>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=99.81  E-value=2.9e-20  Score=138.08  Aligned_cols=89  Identities=25%  Similarity=0.396  Sum_probs=79.2

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEE--------EEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-
Q 025068           24 SPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEIL--------EAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-   94 (258)
Q Consensus        24 ~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~--------~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-   94 (258)
                      +|.++...++|||+|||.++||++|+++|++||.|.        .+.+.+++.+++++|||||+|.+.++|++||+.++ 
T Consensus         1 dp~~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g   80 (101)
T d2cpea1           1 DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDG   80 (101)
T ss_dssp             CCCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCC
Confidence            366778889999999999999999999999999874        56778888899999999999999999999999854 


Q ss_pred             CccCCceEEEEeccCCCC
Q 025068           95 PFIDGRRANCNLASLGRP  112 (258)
Q Consensus        95 ~~i~G~~i~V~~a~~~~~  112 (258)
                      ..|+|+.|+|++|..+.+
T Consensus        81 ~~~~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          81 KDFQGSKLKVSLARKKPP   98 (101)
T ss_dssp             CEETTEECEEECSSCCCC
T ss_pred             CEECCEEEEEEEcCCCCC
Confidence            679999999999976543

>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=99.81  E-value=1.9e-20  Score=133.84  Aligned_cols=79  Identities=9%  Similarity=0.174  Sum_probs=67.2

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccC
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASL  109 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~  109 (258)
                      +++|||+|||+++|+++|+++|++||.|..++++.++.+++++|||||+|.+.++|++||+.++ ..|+|++|+|+++++
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            4799999999999999999999999999999998888889999999999999999999999854 679999999999853

>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=99.81  E-value=1.2e-19  Score=133.12  Aligned_cols=82  Identities=30%  Similarity=0.558  Sum_probs=73.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      .+...++|||+|||.++++++|+++|++||.|++|+|++++  +.+||||||+|.+.++|++||+.++ .+|+|+.|+|+
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~   84 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   84 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45567789999999999999999999999999999999986  4479999999999999999999854 67999999999


Q ss_pred             eccCC
Q 025068          106 LASLG  110 (258)
Q Consensus       106 ~a~~~  110 (258)
                      +|.++
T Consensus        85 ~A~~r   89 (93)
T d2cq3a1          85 NATAR   89 (93)
T ss_dssp             ECCSS
T ss_pred             ecCcC
Confidence            99654

>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=99.80  E-value=2.7e-19  Score=133.83  Aligned_cols=85  Identities=21%  Similarity=0.252  Sum_probs=75.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      ..+...|||+|||+++||++|+++|+.+|.|..+.++.+..+++++|+|||+|.++++|++||+.+++.|+||.|+|..+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEEC
Confidence            44566899999999999999999999999999877777777899999999999999999999986667899999999999


Q ss_pred             cCCCC
Q 025068          108 SLGRP  112 (258)
Q Consensus       108 ~~~~~  112 (258)
                      ..++.
T Consensus        92 ~~~~~   96 (104)
T d1wg5a_          92 SRAEV   96 (104)
T ss_dssp             CTTTS
T ss_pred             CHHHh
Confidence            65543

>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=99.80  E-value=5.5e-20  Score=133.03  Aligned_cols=81  Identities=21%  Similarity=0.317  Sum_probs=69.0

Q ss_pred             CCcEEEEcCCCCCCc-HHHHHHHHhcCCCEEEEEEeec-CCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           30 TYTKVFVGGLAWETQ-SETMRRYFEQFGEILEAVVITD-KNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        30 ~~~~lfVgnLp~~~t-e~~L~~~F~~fG~I~~v~v~~d-~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      ..++|||+|||.+++ |++|+++|++||.|++|+|+.+ +.++++||||||+|.+.++|++||+.++..|+|+.|+|++|
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEEc
Confidence            468999999999975 6679999999999999998764 56799999999999999999999975557799999999999


Q ss_pred             cCC
Q 025068          108 SLG  110 (258)
Q Consensus       108 ~~~  110 (258)
                      .++
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.5e-19  Score=129.32  Aligned_cols=78  Identities=17%  Similarity=0.262  Sum_probs=72.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~  108 (258)
                      ..++|||+|||.++|+++|+++|++||.|++|+|.+++ ++++||||||+|.+.++|++||+.++..+.|+.|.|.++.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            46799999999999999999999999999999998886 7999999999999999999999877788999999999863

>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=99.79  E-value=2.8e-19  Score=131.77  Aligned_cols=83  Identities=18%  Similarity=0.307  Sum_probs=73.2

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCC-EEEEEEeecC-CCCCcccEEEEEEcCHHHHHHHhcCCC---CccCCceEEEE
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGE-ILEAVVITDK-NTGRSKGYGFVTFREPEAARRACADPT---PFIDGRRANCN  105 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~-I~~v~v~~d~-~tg~skG~aFV~F~~~~~A~~Ai~~~~---~~i~G~~i~V~  105 (258)
                      +|+|||+|||.++++++|+++|++||. |+++.|++|. .++++||||||+|.+.++|.+||+.++   ..+.|+.|+|+
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            479999999999999999999999995 9999999885 468999999999999999999999864   23689999999


Q ss_pred             eccCCCCC
Q 025068          106 LASLGRPR  113 (258)
Q Consensus       106 ~a~~~~~~  113 (258)
                      +|.+++..
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99765433

>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=99.78  E-value=1.5e-19  Score=134.51  Aligned_cols=90  Identities=17%  Similarity=0.349  Sum_probs=77.6

Q ss_pred             CCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCc
Q 025068           18 GFQYLNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPF   96 (258)
Q Consensus        18 g~~~~~~p~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~   96 (258)
                      +.+...+...+.+.++|||+|||.++++++|+++|++||.|+++.++.+. +++++|||||+|.+.++|++||+.+ +.+
T Consensus         5 g~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~   83 (101)
T d1x5oa1           5 GVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKF   83 (101)
T ss_dssp             CCCCCCCSCCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCC
T ss_pred             ccccchhccccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCE
Confidence            33444444556677899999999999999999999999999999999886 7899999999999999999999985 477


Q ss_pred             cCCceEEEEecc
Q 025068           97 IDGRRANCNLAS  108 (258)
Q Consensus        97 i~G~~i~V~~a~  108 (258)
                      |.||++.|..+.
T Consensus        84 i~gr~~~v~~~~   95 (101)
T d1x5oa1          84 IKTPPGVSAPTE   95 (101)
T ss_dssp             CCCCTTSCCCSS
T ss_pred             ECCcCCccCCCC
Confidence            999998887663

>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=99.78  E-value=1.3e-20  Score=137.99  Aligned_cols=82  Identities=17%  Similarity=0.229  Sum_probs=73.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEe
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNL  106 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~  106 (258)
                      +....++|||+|||.++++++|+++|++||.|++++|+.++ ++++||||||+|.+.++|++||+.++.+|+|+.|+|++
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~-~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEK   87 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEE-EETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecC-CCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEe
Confidence            34456799999999999999999999999999999887654 79999999999999999999997555779999999999


Q ss_pred             ccC
Q 025068          107 ASL  109 (258)
Q Consensus       107 a~~  109 (258)
                      |+.
T Consensus        88 ak~   90 (91)
T d1fjeb1          88 PKG   90 (91)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            854

>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=99.78  E-value=3.7e-19  Score=132.65  Aligned_cols=83  Identities=22%  Similarity=0.243  Sum_probs=72.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEe
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNL  106 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~  106 (258)
                      ...+.++|||+|||+++||++|+++|+.++ |.+|.++++. +++++|||||+|.+.++|++||+.+++.|+||.|+|.+
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~   88 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFL   88 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345567899999999999999999999997 5578888886 58999999999999999999998666889999999999


Q ss_pred             ccCCC
Q 025068          107 ASLGR  111 (258)
Q Consensus       107 a~~~~  111 (258)
                      +..+.
T Consensus        89 s~~~~   93 (102)
T d1weza_          89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             cCCCC
Confidence            86543

>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=99.78  E-value=5.4e-19  Score=130.03  Aligned_cols=80  Identities=20%  Similarity=0.371  Sum_probs=70.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+|||.++++++|+++|++||.|+.+++..+   ..+|+||||+|++.++|++||+.++ .+|+|++|+|++
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            345678999999999999999999999999999987654   5678999999999999999999855 779999999999


Q ss_pred             ccCC
Q 025068          107 ASLG  110 (258)
Q Consensus       107 a~~~  110 (258)
                      |+..
T Consensus        88 a~~~   91 (95)
T d1x4aa1          88 PRSG   91 (95)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8543

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.9e-19  Score=130.67  Aligned_cols=77  Identities=22%  Similarity=0.478  Sum_probs=67.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEecc
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLAS  108 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~  108 (258)
                      ...++|||+|||+++||++|+++|++||.|.+|++.     .++++||||+|++.++|++||. .+++|+|+.|+|++|.
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG-EDLIIKGISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEECCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh-CCCEECCEEeEEEeCC
Confidence            346799999999999999999999999999999764     4468999999999999999997 4467999999999996


Q ss_pred             CCC
Q 025068          109 LGR  111 (258)
Q Consensus       109 ~~~  111 (258)
                      ++.
T Consensus        77 ~k~   79 (88)
T d1wf0a_          77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.77  E-value=8.3e-20  Score=135.85  Aligned_cols=83  Identities=18%  Similarity=0.206  Sum_probs=76.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      .+++|||+|||.++++++|+++|++||.|..+.++.+..+++++|||||+|.+.++|++||+.++ ..|.|+.|+|++|+
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            46799999999999999999999999999999999888889999999999999999999999865 67999999999997


Q ss_pred             CCCC
Q 025068          109 LGRP  112 (258)
Q Consensus       109 ~~~~  112 (258)
                      .++.
T Consensus        97 ~k~~  100 (102)
T d2cpxa1          97 NKKQ  100 (102)
T ss_dssp             CCSC
T ss_pred             Cccc
Confidence            6543

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=8.7e-19  Score=129.79  Aligned_cols=76  Identities=28%  Similarity=0.496  Sum_probs=66.8

Q ss_pred             CCCCCcEEEEcCCC-CCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEE
Q 025068           27 GDTTYTKVFVGGLA-WETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANC  104 (258)
Q Consensus        27 ~~~~~~~lfVgnLp-~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V  104 (258)
                      .+...++|||+||+ ..+++++|+++|++||.|++|+|        +||||||+|++.++|++||+.++ .+|+|++|+|
T Consensus        11 ~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V   82 (98)
T d1wf2a_          11 PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDI   82 (98)
T ss_dssp             CSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEE
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34456789999996 57889999999999999999988        36899999999999999999976 6799999999


Q ss_pred             EeccCC
Q 025068          105 NLASLG  110 (258)
Q Consensus       105 ~~a~~~  110 (258)
                      +++..+
T Consensus        83 ~~a~~~   88 (98)
T d1wf2a_          83 NLAAEP   88 (98)
T ss_dssp             EETTSC
T ss_pred             EECCCC
Confidence            999644

>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=99.77  E-value=9e-19  Score=123.42  Aligned_cols=74  Identities=16%  Similarity=0.240  Sum_probs=67.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      ++|||+|||.++++++|+++|+.||.|++|+++.++.  ..++||||+|++.++|++||+.+++.|+|++|.|+.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            5899999999999999999999999999999999874  3457999999999999999987778899999999876

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.4e-18  Score=131.64  Aligned_cols=78  Identities=17%  Similarity=0.274  Sum_probs=70.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      +.+++|||+|||.++++++|+++|++||.|++|++..+   +++||||||+|.+.++|.+||+.++ ..|+|+.|.|.++
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34679999999999999999999999999999998765   6679999999999999999999855 6799999999998


Q ss_pred             cC
Q 025068          108 SL  109 (258)
Q Consensus       108 ~~  109 (258)
                      ..
T Consensus        82 ~~   83 (114)
T d2f9da1          82 NA   83 (114)
T ss_dssp             CH
T ss_pred             CC
Confidence            64

>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=99.75  E-value=1.1e-18  Score=128.60  Aligned_cols=80  Identities=19%  Similarity=0.305  Sum_probs=70.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEe
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNL  106 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~  106 (258)
                      ....++|||+||+.++++++|+++|++||.|..++.     +++++|||||+|.+.++|++||+.++ ..|+|+.|+|.+
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            445789999999999999999999999998876542     68899999999999999999999866 679999999999


Q ss_pred             ccCCCC
Q 025068          107 ASLGRP  112 (258)
Q Consensus       107 a~~~~~  112 (258)
                      +.++..
T Consensus        88 a~~k~~   93 (96)
T d1fjca_          88 TGEKGG   93 (96)
T ss_dssp             CSSSCC
T ss_pred             eCCCCC
Confidence            976543

>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=99.75  E-value=1.9e-18  Score=127.46  Aligned_cols=74  Identities=32%  Similarity=0.560  Sum_probs=68.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC-CCccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP-TPFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~-~~~i~G~~i~V~~a~  108 (258)
                      ..++|||+||+.++++++|+++|++||.|++|+|++|      ||||||+|.+.++|++||..+ +..|+|+.|+|++++
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      679999999999999999985 467999999999985


Q ss_pred             C
Q 025068          109 L  109 (258)
Q Consensus       109 ~  109 (258)
                      .
T Consensus        91 ~   91 (96)
T d1x4ga1          91 E   91 (96)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.74  E-value=1.2e-18  Score=125.62  Aligned_cols=78  Identities=19%  Similarity=0.276  Sum_probs=68.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ..++|||+|||.++++++|+++|+.||.|.++.++.+..+++++|+|||+|.+.++|++||++++ ..|+||+|+|+++
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            45689999999999999999999999999875444444579999999999999999999999855 7799999999985

>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=99.74  E-value=5e-18  Score=127.44  Aligned_cols=75  Identities=15%  Similarity=0.250  Sum_probs=67.7

Q ss_pred             CcEEEEcCCCC-CCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           31 YTKVFVGGLAW-ETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        31 ~~~lfVgnLp~-~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      +++|||+||++ .+++++|+++|++||.|++|+|++++     ||||||+|++.++|++||+.++ ..|+|+.|+|+++.
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 59999999999999999999998874     7899999999999999999865 67999999999986


Q ss_pred             CC
Q 025068          109 LG  110 (258)
Q Consensus       109 ~~  110 (258)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.74  E-value=4.8e-19  Score=123.57  Aligned_cols=70  Identities=30%  Similarity=0.566  Sum_probs=65.7

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEE
Q 025068           34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRAN  103 (258)
Q Consensus        34 lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~  103 (258)
                      |||+|||.++|+++|+++|++||.|.++++++++.+++++|+|||+|.+.++|++||+.++ ..|+|+.|+
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            7999999999999999999999999999999999999999999999999999999999865 668888763

>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=99.73  E-value=7.2e-19  Score=125.36  Aligned_cols=75  Identities=20%  Similarity=0.354  Sum_probs=66.4

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-C-ccCCceEEEEeccC
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-P-FIDGRRANCNLASL  109 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~-~i~G~~i~V~~a~~  109 (258)
                      ++|||+|||.++||++|+++|++||.|.+++++++      ||||||+|.+.++|++||+.++ . .|+|+.|+|++|.+
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            47999999999999999999999999987777654      6899999999999999999865 4 49999999999976


Q ss_pred             CCC
Q 025068          110 GRP  112 (258)
Q Consensus       110 ~~~  112 (258)
                      ++.
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            544

>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=99.73  E-value=7.5e-18  Score=120.75  Aligned_cols=77  Identities=18%  Similarity=0.212  Sum_probs=68.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-Ccc-CCceEEE
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFI-DGRRANC  104 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i-~G~~i~V  104 (258)
                      ++..+++|||+|||.++++++|+++|++||.|++|++++++     +|||||+|.+.++|++|++.++ ..| +|+.|+|
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v   78 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKI   78 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEE
Confidence            34457899999999999999999999999999999997653     6899999999999999999865 556 5789999


Q ss_pred             Eecc
Q 025068          105 NLAS  108 (258)
Q Consensus       105 ~~a~  108 (258)
                      ++|+
T Consensus        79 ~~ak   82 (83)
T d2b0ga1          79 TFAK   82 (83)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9984

>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=99.73  E-value=1.6e-18  Score=126.01  Aligned_cols=76  Identities=28%  Similarity=0.409  Sum_probs=68.0

Q ss_pred             CCcEEEEcCCCCCCcHHHH---HHHHhcCCCEEEEEEeecCCCCCcc---cEEEEEEcCHHHHHHHhcCCC-CccCCceE
Q 025068           30 TYTKVFVGGLAWETQSETM---RRYFEQFGEILEAVVITDKNTGRSK---GYGFVTFREPEAARRACADPT-PFIDGRRA  102 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L---~~~F~~fG~I~~v~v~~d~~tg~sk---G~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i  102 (258)
                      ..++|||+|||.++++++|   +++|++||.|++|+|++|+.++.++   |||||+|++.++|++||+.++ ..|+|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            3567999999999999999   6789999999999999998776554   899999999999999999865 66999999


Q ss_pred             EEE
Q 025068          103 NCN  105 (258)
Q Consensus       103 ~V~  105 (258)
                      +|+
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            985

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=4.4e-18  Score=128.07  Aligned_cols=76  Identities=20%  Similarity=0.233  Sum_probs=67.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      ..++|||+|||.++++++|+++|++||+|++|.|.      ++||||||+|.+.++|++||+.++ ..|.|++|+|+++.
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            35799999999999999999999999999999873      357899999999999999999855 67999999999986


Q ss_pred             CCC
Q 025068          109 LGR  111 (258)
Q Consensus       109 ~~~  111 (258)
                      ...
T Consensus        83 ~~~   85 (111)
T d1whxa_          83 IGV   85 (111)
T ss_dssp             TTT
T ss_pred             CCc
Confidence            543

>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=99.72  E-value=7.1e-19  Score=131.13  Aligned_cols=81  Identities=17%  Similarity=0.265  Sum_probs=70.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEeccC
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASL  109 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~~  109 (258)
                      ...+|||+|||+++|+++|+++|+.||.|..+.++.+..+|+++|+|||+|.+.++|++||+.++..|+|+.|.|..+..
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~~~   86 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVTL   86 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEECH
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEECCH
Confidence            34579999999999999999999999999876555565689999999999999999999998655779999999998854


Q ss_pred             C
Q 025068          110 G  110 (258)
Q Consensus       110 ~  110 (258)
                      +
T Consensus        87 ~   87 (103)
T d2cpya1          87 E   87 (103)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.72  E-value=6.1e-18  Score=125.14  Aligned_cols=79  Identities=15%  Similarity=0.161  Sum_probs=69.5

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEE
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANC  104 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V  104 (258)
                      ....+.++|||+|||+++++++|+++|++||+|++|+|.+       +|||||+|.+.++|++||+.++ .+|+|+.|+|
T Consensus        10 ~~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v   82 (98)
T d1wg4a_          10 PTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGET   82 (98)
T ss_dssp             CCCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEE
Confidence            3455677899999999999999999999999999999864       4799999999999999999865 6699999999


Q ss_pred             EeccCCC
Q 025068          105 NLASLGR  111 (258)
Q Consensus       105 ~~a~~~~  111 (258)
                      .++..+.
T Consensus        83 ~~~~~~~   89 (98)
T d1wg4a_          83 SYIRVYP   89 (98)
T ss_dssp             EEEEEEC
T ss_pred             EEEecCC
Confidence            9986443

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=7.1e-18  Score=121.55  Aligned_cols=76  Identities=22%  Similarity=0.295  Sum_probs=67.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ...++|||+|||.++++++|+++|++||.|..+++.      ++||||||+|.+.++|.+||..++ ..|+|+.|+|++|
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~a   79 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   79 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            345799999999999999999999999998887764      357899999999999999999865 6699999999999


Q ss_pred             cCC
Q 025068          108 SLG  110 (258)
Q Consensus       108 ~~~  110 (258)
                      +++
T Consensus        80 kP~   82 (86)
T d2cpda1          80 KPV   82 (86)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            644

>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=99.71  E-value=3.4e-17  Score=120.67  Aligned_cols=75  Identities=27%  Similarity=0.497  Sum_probs=66.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCC--ceEEEE
Q 025068           29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDG--RRANCN  105 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G--~~i~V~  105 (258)
                      ...++|||+||+.++++++|+++|++||.|++|+++++      |+||||+|.+.++|++|++.++ ..|+|  ++|+|+
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            34679999999999999999999999999999999765      5699999999999999999955 56765  589999


Q ss_pred             eccC
Q 025068          106 LASL  109 (258)
Q Consensus       106 ~a~~  109 (258)
                      +|+.
T Consensus        89 ~ak~   92 (97)
T d1whya_          89 FAKS   92 (97)
T ss_dssp             ECCC
T ss_pred             eCCC
Confidence            9954

>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=99.71  E-value=1.3e-17  Score=120.40  Aligned_cols=75  Identities=27%  Similarity=0.486  Sum_probs=68.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      ..++|||+|||.++++++|+++|++||.|.+|+++++      |+||||+|++.++|++||+.++ ..|+|+.|+|++|.
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            3568999999999999999999999999999999866      5799999999999999999955 77999999999996


Q ss_pred             CC
Q 025068          109 LG  110 (258)
Q Consensus       109 ~~  110 (258)
                      .+
T Consensus        81 ~~   82 (86)
T d2cpja1          81 HS   82 (86)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>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=99.71  E-value=4.8e-17  Score=121.36  Aligned_cols=79  Identities=22%  Similarity=0.280  Sum_probs=69.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC--C-CccCCceEEE
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP--T-PFIDGRRANC  104 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~--~-~~i~G~~i~V  104 (258)
                      ....++|||+|||.+++|++|+++|++||.|++|++.++      |++|||+|++.++|++||+.+  + ..+.|++|+|
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v   85 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEE
Confidence            345789999999999999999999999999999998754      579999999999999999874  2 4589999999


Q ss_pred             EeccCCCC
Q 025068          105 NLASLGRP  112 (258)
Q Consensus       105 ~~a~~~~~  112 (258)
                      .+++.++.
T Consensus        86 ~~s~~~~~   93 (104)
T d1wexa_          86 NYSTSKRI   93 (104)
T ss_dssp             EECSSSSC
T ss_pred             EEcCCCcc
Confidence            99965543

>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=99.71  E-value=2.3e-17  Score=133.98  Aligned_cols=84  Identities=29%  Similarity=0.581  Sum_probs=77.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEe
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNL  106 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~  106 (258)
                      .....++|||+|||.++|+++|+++|+.||.|+.+.|++|+.+++++|||||+|.+.++|.+||+.+++.|+|+.|+|++
T Consensus        93 ~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~~~~~~G~~i~V~~  172 (183)
T d1u1qa_          93 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK  172 (183)
T ss_dssp             TTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSSCEEETTEEEEEEE
T ss_pred             cccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHHhCCCeECCEEEEEEe
Confidence            45567899999999999999999999999999999999999999999999999999999999998767779999999999


Q ss_pred             ccCC
Q 025068          107 ASLG  110 (258)
Q Consensus       107 a~~~  110 (258)
                      |.++
T Consensus       173 A~~k  176 (183)
T d1u1qa_         173 ALSK  176 (183)
T ss_dssp             CCCH
T ss_pred             cCCc
Confidence            8654

>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=99.71  E-value=8e-18  Score=127.37  Aligned_cols=83  Identities=18%  Similarity=0.369  Sum_probs=72.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      ....++|||+|||+++|+++|+++|+.+|.|..+.++.+..+|+++|+|||+|.+.++|++||+.++..|+|+.|.|..+
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEc
Confidence            34566899999999999999999999999998766666666899999999999999999999986667799999999988


Q ss_pred             cCC
Q 025068          108 SLG  110 (258)
Q Consensus       108 ~~~  110 (258)
                      ..+
T Consensus        95 ~~~   97 (112)
T d1wela1          95 TKK   97 (112)
T ss_dssp             CHH
T ss_pred             ChH
Confidence            543

>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=99.70  E-value=2.8e-18  Score=124.15  Aligned_cols=72  Identities=19%  Similarity=0.246  Sum_probs=64.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccCC
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASLG  110 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~~  110 (258)
                      ++|||+|||.++++++|+++|++||.|++|+|++|       |||||+|.+.++|++||+.++ .+|+|+.|+|.++..+
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            47999999999999999999999999999998654       799999999999999998854 7799999999887544

>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=99.70  E-value=1.1e-17  Score=121.27  Aligned_cols=73  Identities=18%  Similarity=0.231  Sum_probs=62.7

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccC
Q 025068           31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASL  109 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~  109 (258)
                      .++|||+|||.++++++|+++|++|| ++.+.+      +++||||||+|.+.++|++||+.++ .+|+|++|+|+++..
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999 333333      4568999999999999999999865 669999999999954


Q ss_pred             C
Q 025068          110 G  110 (258)
Q Consensus       110 ~  110 (258)
                      +
T Consensus        78 ~   78 (88)
T d1wg1a_          78 D   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.69  E-value=3.2e-17  Score=123.15  Aligned_cols=80  Identities=15%  Similarity=0.312  Sum_probs=69.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-Ccc--CCceEEE
Q 025068           28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFI--DGRRANC  104 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i--~G~~i~V  104 (258)
                      .....+|||+||+.++||++|+++|++||.|++|+|++++    ++|+|||+|.+.++|++||+.++ ..|  .++.|+|
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v   79 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI   79 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEE
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEE
Confidence            3456789999999999999999999999999999998874    48999999999999999999865 555  5788999


Q ss_pred             EeccCCC
Q 025068          105 NLASLGR  111 (258)
Q Consensus       105 ~~a~~~~  111 (258)
                      .+++.+.
T Consensus        80 ~~s~~~~   86 (108)
T d2adba1          80 DFSKLTS   86 (108)
T ss_dssp             EECSSCS
T ss_pred             EecCCcc
Confidence            9886543

>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=99.69  E-value=5.3e-17  Score=117.37  Aligned_cols=76  Identities=9%  Similarity=0.192  Sum_probs=66.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-Ccc-CCceEEEEec
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFI-DGRRANCNLA  107 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i-~G~~i~V~~a  107 (258)
                      .+++|||+|||.++++++|+++|++||.|.++.++.+    +.+++|||+|++.++|.+|+..++ ..| +|+.|+|+++
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 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            3678999999999999999999999999998877654    457899999999999999999865 556 6899999998


Q ss_pred             cC
Q 025068          108 SL  109 (258)
Q Consensus       108 ~~  109 (258)
                      +.
T Consensus        85 k~   86 (88)
T d2adca2          85 KS   86 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>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=99.69  E-value=1.7e-17  Score=120.95  Aligned_cols=77  Identities=19%  Similarity=0.358  Sum_probs=68.2

Q ss_pred             CcEEEEcCCCCCCcHHHHHH----HHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEE
Q 025068           31 YTKVFVGGLAWETQSETMRR----YFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCN  105 (258)
Q Consensus        31 ~~~lfVgnLp~~~te~~L~~----~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~  105 (258)
                      +++|||+|||.++++++|++    +|++||+|++|++.+   +++++|||||+|.+.++|.+||+.++ ..|+|+.|+|.
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~   79 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   79 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            57999999999999999865    579999999998754   47789999999999999999999855 67999999999


Q ss_pred             eccCC
Q 025068          106 LASLG  110 (258)
Q Consensus       106 ~a~~~  110 (258)
                      +|+.+
T Consensus        80 ~ak~~   84 (91)
T d1nu4a_          80 YAKTD   84 (91)
T ss_dssp             ECSSC
T ss_pred             EeCCC
Confidence            99654

>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=99.68  E-value=4.1e-17  Score=115.77  Aligned_cols=72  Identities=22%  Similarity=0.367  Sum_probs=64.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      ..++|||+||+  +||++|+++|++||.|++|++.++      ++||||+|.+.++|++||+.++ ..|+|+.|+|++|+
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            45789999995  899999999999999999998754      5699999999999999999855 77999999999995


Q ss_pred             C
Q 025068          109 L  109 (258)
Q Consensus       109 ~  109 (258)
                      +
T Consensus        76 ~   76 (79)
T d2bz2a1          76 K   76 (79)
T ss_dssp             S
T ss_pred             C
Confidence            3

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.5e-16  Score=114.97  Aligned_cols=79  Identities=14%  Similarity=0.169  Sum_probs=69.7

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC---CCccCCceE
Q 025068           26 FGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP---TPFIDGRRA  102 (258)
Q Consensus        26 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~---~~~i~G~~i  102 (258)
                      .+....++|||+|||.++++++|+++|++||.|.+++++++      +++|||+|.+.++|++|++.+   +..+.|++|
T Consensus         3 ~~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l   76 (88)
T d2cq1a1           3 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPI   76 (88)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEE
Confidence            35567889999999999999999999999999999998765      469999999999999999863   356999999


Q ss_pred             EEEeccCC
Q 025068          103 NCNLASLG  110 (258)
Q Consensus       103 ~V~~a~~~  110 (258)
                      +|++++.+
T Consensus        77 ~v~~sk~~   84 (88)
T d2cq1a1          77 YIQYSNHK   84 (88)
T ss_dssp             EEEECSCS
T ss_pred             EEEECCCC
Confidence            99999644

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=8.1e-17  Score=113.18  Aligned_cols=69  Identities=19%  Similarity=0.300  Sum_probs=61.1

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEeccC
Q 025068           34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLASL  109 (258)
Q Consensus        34 lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~~  109 (258)
                      |||+|||.++++++|+++|++|| +..+++      +++||||||+|.+.++|++||+.++ ..++|++|+|+++..
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 555554      4568899999999999999999865 569999999999954

>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=99.66  E-value=2.2e-18  Score=125.29  Aligned_cols=76  Identities=16%  Similarity=0.298  Sum_probs=65.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEe-----ecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEe
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVI-----TDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNL  106 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~-----~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~  106 (258)
                      ++|||+|||.++||++|+++|++||.|.++.+.     .+..++++||||||+|.+.++|++|++.++..|+|+.|+|+.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V~r   81 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR   81 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCCBC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEECC
Confidence            689999999999999999999999987766543     345678899999999999999999997555789999999975


Q ss_pred             c
Q 025068          107 A  107 (258)
Q Consensus       107 a  107 (258)
                      +
T Consensus        82 ~   82 (90)
T d1u2fa_          82 P   82 (90)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=2.7e-16  Score=116.29  Aligned_cols=77  Identities=14%  Similarity=0.236  Sum_probs=67.1

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcC---CCCccCCceEE
Q 025068           28 DTTYTKVFVGGLAWE-TQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD---PTPFIDGRRAN  103 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~-~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~---~~~~i~G~~i~  103 (258)
                      ....++|||+|||.+ +|+++|+++|++||.|+++.++++      ||+|||+|.+.++|.+||+.   .+..|+|+.|+
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            345679999999985 899999999999999999999865      57999999999999999973   33569999999


Q ss_pred             EEeccCC
Q 025068          104 CNLASLG  110 (258)
Q Consensus       104 V~~a~~~  110 (258)
                      |++|+.+
T Consensus        89 V~~s~~~   95 (99)
T d1x4fa1          89 VDLSEKY   95 (99)
T ss_dssp             EEEECSC
T ss_pred             EEEcCCc
Confidence            9999644

>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=99.61  E-value=8.6e-16  Score=114.62  Aligned_cols=77  Identities=9%  Similarity=0.009  Sum_probs=66.1

Q ss_pred             CCCcEEEEcCCCCCC-c----HHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceE
Q 025068           29 TTYTKVFVGGLAWET-Q----SETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRA  102 (258)
Q Consensus        29 ~~~~~lfVgnLp~~~-t----e~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i  102 (258)
                      ...++|||+||+.++ +    +++|+++|+.||.|++++++++      +++|||+|.+.++|++||+.++ ..|+|+.|
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 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            346789999999876 3    3569999999999999999754      6699999999999999999977 56999999


Q ss_pred             EEEeccCCC
Q 025068          103 NCNLASLGR  111 (258)
Q Consensus       103 ~V~~a~~~~  111 (258)
                      +|.+|+...
T Consensus        77 ~v~~a~~~~   85 (104)
T d1weya_          77 KLYFAQTLH   85 (104)
T ss_dssp             EEECCCCSS
T ss_pred             EEeecccCC
Confidence            999996443

>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=99.60  E-value=6e-16  Score=112.23  Aligned_cols=76  Identities=17%  Similarity=0.215  Sum_probs=67.0

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCC--C-CccCCceEE
Q 025068           28 DTTYTKVFVGGLAWE-TQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP--T-PFIDGRRAN  103 (258)
Q Consensus        28 ~~~~~~lfVgnLp~~-~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~--~-~~i~G~~i~  103 (258)
                      .+..++|||+||+.. +|++||+++|++||.|++|+++.++      ++|||+|++.++|++|++.+  + ..++|++|+
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            456789999999986 8999999999999999999998764      59999999999999999863  3 469999999


Q ss_pred             EEeccC
Q 025068          104 CNLASL  109 (258)
Q Consensus       104 V~~a~~  109 (258)
                      |++|++
T Consensus        79 V~~s~~   84 (89)
T d1x4da1          79 VHLSQK   84 (89)
T ss_dssp             EEEECC
T ss_pred             EEECCC
Confidence            999964

>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=99.59  E-value=1.4e-15  Score=123.22  Aligned_cols=81  Identities=38%  Similarity=0.634  Sum_probs=75.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEeccC
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASL  109 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a~~  109 (258)
                      ..++|||+|||.++|+++|+++|++||.|++++|+++..++.++|+|||+|.+.++|++|+..++..++.+.+.+.....
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhh
Confidence            45899999999999999999999999999999999999999999999999999999999999988889999988887654


Q ss_pred             C
Q 025068          110 G  110 (258)
Q Consensus       110 ~  110 (258)
                      .
T Consensus        85 ~   85 (183)
T d1u1qa_          85 R   85 (183)
T ss_dssp             T
T ss_pred             c
Confidence            4

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=1.6e-16  Score=118.67  Aligned_cols=75  Identities=24%  Similarity=0.301  Sum_probs=69.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEec
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      +.++|.++..+++|++|+++|++||.|++|+|+++. ++++||+|||+|.+.++|.+||+.++ ..++||+|+|++.
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 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            468888999999999999999999999999998875 79999999999999999999999955 7799999999875

>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=99.48  E-value=2.7e-14  Score=107.81  Aligned_cols=73  Identities=21%  Similarity=0.222  Sum_probs=60.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCH-HHHHHHhcCCC-CccCCceEEEEec
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREP-EAARRACADPT-PFIDGRRANCNLA  107 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~-~~A~~Ai~~~~-~~i~G~~i~V~~a  107 (258)
                      ....+||+||++++|+++|+++|++||+|.+|+|+++      +|||||+|.+. ++|.+|+..++ ..|.++.+.|.++
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            3456799999999999999999999999999999865      67999999985 77888888865 4566666666665


Q ss_pred             c
Q 025068          108 S  108 (258)
Q Consensus       108 ~  108 (258)
                      .
T Consensus        84 ~   84 (113)
T d1owxa_          84 V   84 (113)
T ss_dssp             E
T ss_pred             e
Confidence            4

>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=99.45  E-value=1.1e-13  Score=98.29  Aligned_cols=73  Identities=19%  Similarity=0.201  Sum_probs=60.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCce-EEEEecc
Q 025068           30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRR-ANCNLAS  108 (258)
Q Consensus        30 ~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~-i~V~~a~  108 (258)
                      +.+.|+|++||.+++++.| ++|++||+|.++++.      +.|+|+||+|.++++|++||+.++..|+|+. |.|+.+.
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCC
Confidence            4678999999999987656 579999999999874      4468999999999999999976667799985 5688764


Q ss_pred             C
Q 025068          109 L  109 (258)
Q Consensus       109 ~  109 (258)
                      .
T Consensus        76 ~   76 (81)
T d1wwha1          76 D   76 (81)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.41  E-value=1.5e-13  Score=101.62  Aligned_cols=67  Identities=18%  Similarity=0.264  Sum_probs=56.5

Q ss_pred             CCCcEEEEcC--CCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-Cc-cCCce
Q 025068           29 TTYTKVFVGG--LAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PF-IDGRR  101 (258)
Q Consensus        29 ~~~~~lfVgn--Lp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~-i~G~~  101 (258)
                      ...++|||.|  |+.++||++|+++|++||.|++|+++.+      |+||||+|.+.++|++|++.++ .. +++..
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~~~~~   86 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLG   86 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTS
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCCCCCCC
Confidence            3457888855  9999999999999999999999988765      5699999999999999999976 44 34433

>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=99.37  E-value=7.1e-13  Score=97.52  Aligned_cols=80  Identities=19%  Similarity=0.296  Sum_probs=66.5

Q ss_pred             CCCCCcEEEEcCC--CCCCc---------HHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-
Q 025068           27 GDTTYTKVFVGGL--AWETQ---------SETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-   94 (258)
Q Consensus        27 ~~~~~~~lfVgnL--p~~~t---------e~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-   94 (258)
                      ....+++|+|.||  +.++.         +++|++.|++||.|++|++..+    ..+|++||+|++.++|.+|+..++ 
T Consensus         4 ~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng   79 (99)
T d2dita1           4 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDG   79 (99)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCC
Confidence            4456889999999  54432         3679999999999999988765    357999999999999999999976 


Q ss_pred             CccCCceEEEEeccCC
Q 025068           95 PFIDGRRANCNLASLG  110 (258)
Q Consensus        95 ~~i~G~~i~V~~a~~~  110 (258)
                      ..++||.|+|+++..+
T Consensus        80 ~~~~gr~i~v~~~~g~   95 (99)
T d2dita1          80 RWFGGRQITAQAWDGT   95 (99)
T ss_dssp             CEETTEECEEEECCSC
T ss_pred             cEECCEEEEEEEeCCc
Confidence            6699999999998543

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.23  E-value=3.9e-12  Score=94.25  Aligned_cols=79  Identities=14%  Similarity=0.081  Sum_probs=65.7

Q ss_pred             CCcEEEEcCC--CCCCc--------HHHHHHHHhcCCCEEEEEEeecCCCC--CcccEEEEEEcCHHHHHHHhcCCC-Cc
Q 025068           30 TYTKVFVGGL--AWETQ--------SETMRRYFEQFGEILEAVVITDKNTG--RSKGYGFVTFREPEAARRACADPT-PF   96 (258)
Q Consensus        30 ~~~~lfVgnL--p~~~t--------e~~L~~~F~~fG~I~~v~v~~d~~tg--~skG~aFV~F~~~~~A~~Ai~~~~-~~   96 (258)
                      .++.|.|.||  +.++.        .++|++.|++||.|++|+|.++..+.  ..+|++||+|.+.++|.+|+..++ ..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            3678999999  44432        35689999999999999998876543  356899999999999999999965 67


Q ss_pred             cCCceEEEEecc
Q 025068           97 IDGRRANCNLAS  108 (258)
Q Consensus        97 i~G~~i~V~~a~  108 (258)
                      ++||.|.|.+..
T Consensus        83 f~gR~v~v~f~~   94 (104)
T d1o0pa_          83 FANRVVVTKYCD   94 (104)
T ss_dssp             SSSSCCEEEEEC
T ss_pred             ECCeEEEEEEcC
Confidence            999999999974

>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=97.23  E-value=0.00034  Score=48.86  Aligned_cols=53  Identities=15%  Similarity=0.175  Sum_probs=47.8

Q ss_pred             HHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCCCccCCceEEEEec
Q 025068           47 TMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLA  107 (258)
Q Consensus        47 ~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~~~i~G~~i~V~~a  107 (258)
                      +|.+.|+.||+|.-++++.|        --.|+|.+-+.|.+|+.....+|.|+.|+|...
T Consensus        40 ~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          40 ELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDVDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHGGGSEETTEEEEEECC
T ss_pred             HHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhccCCeEEcceEEEEecC
Confidence            57788899999999999888        469999999999999999989999999999865

>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=96.95  E-value=0.00082  Score=44.61  Aligned_cols=60  Identities=13%  Similarity=0.158  Sum_probs=49.0

Q ss_pred             HHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcCCC-CccCCceEEEEecc
Q 025068           46 ETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT-PFIDGRRANCNLAS  108 (258)
Q Consensus        46 ~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~~~-~~i~G~~i~V~~a~  108 (258)
                      +.|.+.|.+++.|.++.|....+ +..  .|-|...+.++|.-||..++ ..|++|+|.|++++
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~d-g~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTD-YQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCS-TTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccC-CcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            34667788999999998865532 333  68999999999999999977 66999999999984

>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=96.79  E-value=0.0023  Score=44.82  Aligned_cols=65  Identities=11%  Similarity=0.069  Sum_probs=52.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCc--ccEEEEEEcCHHHHHHHhcC-CCCc
Q 025068           32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRS--KGYGFVTFREPEAARRACAD-PTPF   96 (258)
Q Consensus        32 ~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~s--kG~aFV~F~~~~~A~~Ai~~-~~~~   96 (258)
                      ++|.|++||+..||+++.+.+...+++.-......+.+-+.  -.-|+|.|.+.+++....+. .++.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~   69 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYV   69 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcE
Confidence            68999999999999999999999999887776666544332  25789999999999888877 4444

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.50  E-value=0.0052  Score=43.27  Aligned_cols=58  Identities=22%  Similarity=0.310  Sum_probs=47.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHHhcCCCEEEEEEeecCCCCCcccEEEEEEcCHHHHHHHhcC
Q 025068           27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD   92 (258)
Q Consensus        27 ~~~~~~~lfVgnLp~~~te~~L~~~F~~fG~I~~v~v~~d~~tg~skG~aFV~F~~~~~A~~Ai~~   92 (258)
                      +......||.-..|.++...||.++|+.||.|. |.++.|.       -|||...+.|+|+.++..
T Consensus        11 ~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~~~~v~~~   68 (100)
T d1whva_          11 LQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNT   68 (100)
T ss_dssp             CCCCCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHH
T ss_pred             CCCCcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHHHHHHHHH
Confidence            444556788888999999999999999999876 4455553       799999999998888764