Citrus Sinensis ID: 030012

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180----
Protein Sequence
MRPGALGLVDTAGVGVHPEPGMVGITAVASVKGYSSPLPDPNLIGQRRDIAPGINPTIPDVINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHFPFHLPSDGDEKCTPR
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHccccccEEEEEEEEccccccccccccEEEEEEccHHHHHHHHHHHccccccccccccccEEEEEcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHccccccEEEEEEEccccccccccEEEEEEEcccHHHHHHHHHHHcccEcccccccccEEEEEEEccccccccccccccccc
Coil and Loop (DISEMBL)
mrpgalglvdtagvgvhpepgmVGITAVASvkgyssplpdpnligqrrdiapginptipdvingvpsslrnnagsplkkgesnllfvdglptdctrrevshlfrpfvgyreirvihkeprrtgdrAMVLCfvefddpkcaRTAMDalhgykfddkkpdsptlkiqfahfpfhlpsdgdekctpr
Flexible Loop (DISEMBL)
MRPGALGLVDTAGVGVHPEPGMVGITAVASVKGYSSPLPDPNLIGQRRDIAPGINPTIPDVINGVPSSLRNNAGSPLKKGESNLLFVDGLPTdctrrevshlfrpfvgyreirvihkeprrtgdraMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAhfpfhlpsdgdekctpr
Low Complexity Region (SEG)
MRPGALGLVDTAGVGVHPEPGMVGITAVASVKGYSSPLPDPNLIGQRRDIAPGINPTIPDVINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHFPFHLPSDGDEKCTPR
Disordered region (IsUnstruct)
*******LVDTAGVGVHPEPGMVGITAVASVKGY***************IAPGINPTIPDVI********************NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFD********LKIQFAHFPFH************
Disordered Region (DISOPRED)
***********************************************************************************LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHK******DRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLK*********************
Disordered Region (DISEMBL)
MRPGALGLVDTAGVGVHPEPGMVGITAVASVKGYSSPLPDPNLIGQRRDIAPGINPTIPDVINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHFPFHLPS*********
Disordered Region (DISPRO)
**PGALGLVDTAGVGVHPEPGMVGITAVASVKGYSSPLPDPNLIGQRRDIAPGINPTIPD**************SPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHF***************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRPGALGLVDTAGVGVHPEPGMVGITAVASVKGYSSPLPDPNLIGQRRDIAPGINPTIPDVINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHFPFHLPSDGDEKCTPR
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	184	2.2.26 [Sep-21-2011]
Q93062	196	RNA-binding protein with	no	no	0.434	0.408	0.397	1e-08
Q8VC52	206	RNA-binding protein with	yes	no	0.445	0.398	0.406	1e-08
Q9WVB0	197	RNA-binding protein with	no	no	0.434	0.406	0.397	1e-08
Q9W6I1	200	RNA-binding protein with	yes	no	0.413	0.38	0.404	3e-08
Q9YGP5	196	RNA-binding protein with	N/A	no	0.391	0.367	0.411	5e-08
Q6ZRY4	209	RNA-binding protein with	no	no	0.413	0.363	0.393	2e-07
B8AM21	232	U2 small nuclear ribonucl	N/A	no	0.369	0.293	0.328	8e-07
Q10MR0	232	U2 small nuclear ribonucl	no	no	0.369	0.293	0.328	8e-07
O22922	232	U2 small nuclear ribonucl	no	no	0.565	0.448	0.309	1e-06
Q8H1S6	229	U2 small nuclear ribonucl	no	no	0.369	0.296	0.315	8e-06

>sp|Q93062|RBPMS_HUMAN RNA-binding protein with multiple splicing OS=Homo sapiens GN=RBPMS PE=1 SV=1

 Score = 59.7 bits (143), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 37/93 (39%), Positives = 51/93 (54%), Gaps = 13/93 (13%)

Query: 77  LKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYR--EIRVIHKEPRRTGDRAMVLCFVEF 134
           L++ E   LFV GLP D   RE+  LFRPF GY    I++  K+P         + FV F
Sbjct: 18  LQEEEVRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQP---------VGFVSF 68

Query: 135 DDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           D    A  A +AL+G +FD + P   TL+++FA
Sbjct: 69  DSRSEAEAAKNALNGIRFDPEIPQ--TLRLEFA 99

Acts as a coactivator of transcriptional activity. Required to increase TGFB1/Smad-mediated transactivation. Acts through SMAD2, SMAD3 and SMAD4 to increase transcriptional activity. Increases phosphorylation of SMAD2 and SMAD3 on their C-terminal SSXS motif, possibly through recruitment of TGFBR1. Promotes the nuclear accumulation of SMAD2, SMAD3 and SMAD4 proteins. Binds to poly(A) RNA.
Homo sapiens (taxid: 9606)

>sp|Q8VC52|RBPS2_MOUSE RNA-binding protein with multiple splicing 2 OS=Mus musculus GN=Rbpms2 PE=1 SV=1

 Score = 59.3 bits (142), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 39/96 (40%), Positives = 54/96 (56%), Gaps = 14/96 (14%)

Query: 74  GSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYR--EIRVIHKEPRRTGDRAMVLCF 131
           GSPL++ E   LFV GLP D   RE+  LFRPF GY    I++  ++P         + F
Sbjct: 17  GSPLEE-EVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSRQP---------VGF 66

Query: 132 VEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           V FD    A  A +AL+G +FD + P   TL+++FA
Sbjct: 67  VIFDSRAGAEAAKNALNGIRFDPENPQ--TLRLEFA 100

Mus musculus (taxid: 10090)

>sp|Q9WVB0|RBPMS_MOUSE RNA-binding protein with multiple splicing OS=Mus musculus GN=Rbpms PE=2 SV=2

 Score = 59.3 bits (142), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 37/93 (39%), Positives = 51/93 (54%), Gaps = 13/93 (13%)

Query: 77  LKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYR--EIRVIHKEPRRTGDRAMVLCFVEF 134
           L++ E   LFV GLP D   RE+  LFRPF GY    I++  K+P         + FV F
Sbjct: 18  LQEEEVRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQP---------VGFVSF 68

Query: 135 DDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           D    A  A +AL+G +FD + P   TL+++FA
Sbjct: 69  DSRSEAEAAKNALNGIRFDPEIPQ--TLRLEFA 99

Acts as a coactivator of transcriptional activity. Required to increase TGFB1/Smad-mediated transactivation. Acts through SMAD2, SMAD3 and SMAD4 to increase transcriptional activity. Increases phosphorylation of SMAD2 and SMAD3 on their C-terminal SSXS motif, possibly through recruitment of TGFBR1. Promotes the nuclear accumulation of SMAD2, SMAD3 and SMAD4 proteins. Binds to poly(A) RNA.

Mus musculus (taxid: 10090)

>sp|Q9W6I1|RBPMS_CHICK RNA-binding protein with multiple splicing OS=Gallus gallus GN=RBPMS PE=2 SV=1

 Score = 58.2 bits (139), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 36/89 (40%), Positives = 48/89 (53%), Gaps = 13/89 (14%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYRE--IRVIHKEPRRTGDRAMVLCFVEFDDPK 138
           E   LFV GLP D   RE+  LFRPF GY    I++  K+P         + FV FD   
Sbjct: 20  EVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSKQP---------VGFVTFDSRA 70

Query: 139 CARTAMDALHGYKFDDKKPDSPTLKIQFA 167
            A  A +AL+G +FD + P   TL+++FA
Sbjct: 71  GAEAAKNALNGIRFDPENPQ--TLRLEFA 97

Acts as a coactivator of transcriptional activity. Binds RNA.

Gallus gallus (taxid: 9031)

>sp|Q9YGP5|RBPMS_XENLA RNA-binding protein with multiple splicing OS=Xenopus laevis GN=rbpms PE=2 SV=1

 Score = 57.4 bits (137), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 35/85 (41%), Positives = 48/85 (56%), Gaps = 13/85 (15%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYRE--IRVIHKEPRRTGDRAMVLCFVEFDDPKCART 142
           LFV GLP D   RE+  LFRPF GY    I++  K+P         + FV FD+   A  
Sbjct: 22  LFVSGLPIDIKPRELYLLFRPFKGYEGSLIKLTSKQP---------VGFVTFDNRAGAEA 72

Query: 143 AMDALHGYKFDDKKPDSPTLKIQFA 167
           A +AL+G +FD + P   TL+++FA
Sbjct: 73  AKNALNGIRFDPENPQ--TLRLEFA 95

Acts as a coactivator of transcriptional activity. Binds RNA.

Xenopus laevis (taxid: 8355)

>sp|Q6ZRY4|RBPS2_HUMAN RNA-binding protein with multiple splicing 2 OS=Homo sapiens GN=RBPMS2 PE=2 SV=1

 Score = 55.1 bits (131), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/89 (39%), Positives = 48/89 (53%), Gaps = 13/89 (14%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYR--EIRVIHKEPRRTGDRAMVLCFVEFDDPK 138
           E   LFV GLP D   RE+  LFRPF GY    I++  ++P         + FV FD   
Sbjct: 29  EVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTARQP---------VGFVIFDSRA 79

Query: 139 CARTAMDALHGYKFDDKKPDSPTLKIQFA 167
            A  A +AL+G +FD + P   TL+++FA
Sbjct: 80  GAEAAKNALNGIRFDPENPQ--TLRLEFA 106

Homo sapiens (taxid: 9606)

>sp|B8AM21|RU2B_ORYSI U2 small nuclear ribonucleoprotein B'' OS=Oryza sativa subsp. indica GN=OsI_11177 PE=3 SV=1

 Score = 53.5 bits (127), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 8/76 (10%)

Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           +N+LF+  LP + T   +  LF+ + G+RE+R+I  +P         + FVE++D   + 
Sbjct: 157 NNILFIQNLPAETTSMMLQILFQQYPGFREVRMIEAKPG--------IAFVEYEDDSQSM 208

Query: 142 TAMDALHGYKFDDKKP 157
            AM AL G+K     P
Sbjct: 209 VAMQALQGFKITPYNP 224

Involved in nuclear pre-mRNA splicing.

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q10MR0|RU2B_ORYSJ U2 small nuclear ribonucleoprotein B'' OS=Oryza sativa subsp. japonica GN=Os03g0298800 PE=2 SV=1

 Score = 53.5 bits (127), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 8/76 (10%)

Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           +N+LF+  LP + T   +  LF+ + G+RE+R+I  +P         + FVE++D   + 
Sbjct: 157 NNILFIQNLPAETTSMMLQILFQQYPGFREVRMIEAKPG--------IAFVEYEDDSQSM 208

Query: 142 TAMDALHGYKFDDKKP 157
            AM AL G+K     P
Sbjct: 209 VAMQALQGFKITPYNP 224

Involved in nuclear pre-mRNA splicing.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|O22922|RU2B1_ARATH U2 small nuclear ribonucleoprotein B'' OS=Arabidopsis thaliana GN=U2B'' PE=1 SV=1

 Score = 52.8 bits (125), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 35/113 (30%), Positives = 54/113 (47%), Gaps = 9/113 (7%)

Query: 45  GQRRDIAPGINPTIPDVINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFR 104
            QR + A G +   P   NGVP+     +G       +N+LF+  LP + T   +  LF 
Sbjct: 121 SQRPNTANGPSANGPSANNGVPAPSFQPSGQETMPP-NNILFIQNLPHETTSMMLQLLFE 179

Query: 105 PFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP 157
            + G++EIR+I  +P         + FVE++D   A  AM  L G+K   + P
Sbjct: 180 QYPGFKEIRMIDAKPG--------IAFVEYEDDVQASIAMQPLQGFKITPQNP 224

Involved in nuclear pre-mRNA splicing.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8H1S6|RU2B2_ARATH U2 small nuclear ribonucleoprotein B'' 2 OS=Arabidopsis thaliana GN=At1g06960 PE=1 SV=1

 Score = 50.1 bits (118), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 8/76 (10%)

Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           +N+LF+  LP +     +  LF  + G++EIR+I  +P         + FVE++D   + 
Sbjct: 154 NNILFIHNLPIETNSMMLQLLFEQYPGFKEIRMIEAKPG--------IAFVEYEDDVQSS 205

Query: 142 TAMDALHGYKFDDKKP 157
            AM AL G+K   + P
Sbjct: 206 MAMQALQGFKITPQNP 221

Involved in nuclear pre-mRNA splicing.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	184
343887275	231	RRM-containing protein [Citrus unshiu]	0.940	0.748	0.864	9e-84
225429574	239	PREDICTED: uncharacterized protein LOC10	0.945	0.728	0.653	8e-60
224088786	476	predicted protein [Populus trichocarpa]	0.978	0.378	0.563	1e-56
449447147	246	PREDICTED: uncharacterized protein LOC10	0.961	0.719	0.592	6e-53
225429572	229	PREDICTED: uncharacterized protein LOC10	0.891	0.716	0.607	2e-51
356514689	228	PREDICTED: uncharacterized protein LOC10	0.885	0.714	0.596	3e-49
363807398	220	uncharacterized protein LOC100816255 [Gl	0.836	0.7	0.616	6e-48
255550095	243	conserved hypothetical protein [Ricinus	0.956	0.724	0.551	2e-45
388521817	229	unknown [Lotus japonicus]	0.782	0.628	0.627	1e-44
357465775	229	RNA-binding protein with multiple splici	0.864	0.694	0.552	2e-44

>gi|343887275|dbj|BAK61821.1| RRM-containing protein [Citrus unshiu]

 Score =  314 bits (805), Expect = 9e-84,   Method: Compositional matrix adjust.
 Identities = 159/184 (86%), Positives = 164/184 (89%), Gaps = 11/184 (5%)

Query: 1   MRPGALGLVDTAGVGVHPEPGMVGITAVASVKGYSSPLPDPNLIGQRRDIAPGINPTIPD 60
           MRPGALGLVDTAGVGVHPEPGMVGITAVASVKGYSSPLPDPNLIGQRRDIAPGINPTIPD
Sbjct: 59  MRPGALGLVDTAGVGVHPEPGMVGITAVASVKGYSSPLPDPNLIGQRRDIAPGINPTIPD 118

Query: 61  VINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPR 120
           VINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVS +           +++    
Sbjct: 119 VINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSRI-----------LLNVSST 167

Query: 121 RTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHFPFHLPSDGDEK 180
            +GDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP LKIQFAHFPF LPSDGDEK
Sbjct: 168 CSGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPALKIQFAHFPFRLPSDGDEK 227

Query: 181 CTPR 184
            TPR
Sbjct: 228 RTPR 231

Source: Citrus unshiu

Species: Citrus unshiu

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225429574|ref|XP_002280068.1| PREDICTED: uncharacterized protein LOC100257637 isoform 1 [Vitis vinifera] gi|296081671|emb|CBI20676.3| unnamed protein product [Vitis vinifera]

 Score =  234 bits (598), Expect = 8e-60,   Method: Compositional matrix adjust.
 Identities = 115/176 (65%), Positives = 138/176 (78%), Gaps = 2/176 (1%)

Query: 1   MRPGALGLVDTAGVGVHPEPGMVGITAVASVKGYSSPLPDPNLIGQRRDIAPGINPTIPD 60
           +RPGA    D  G+ V P+P + G TA  ++KGY +P+ DPNLIGQRRD+A GI+P IPD
Sbjct: 59  VRPGAHDFDDIMGIRVPPKPVIGGFTATTNIKGYPNPVEDPNLIGQRRDVAHGISPGIPD 118

Query: 61  VINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPR 120
           +    PSS  N    P    ESN+LFVDGLP DCTRREV HLFRPF+G++EIRV+HKEPR
Sbjct: 119 IER--PSSFGNVESLPPPVQESNILFVDGLPKDCTRREVGHLFRPFIGFKEIRVVHKEPR 176

Query: 121 RTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHFPFHLPSD 176
            +GD+AMVLCFVEF+D  C+RTA++AL GYKFDDKKPDSPTL+IQFAHFPF LPSD
Sbjct: 177 HSGDKAMVLCFVEFNDASCSRTALEALQGYKFDDKKPDSPTLRIQFAHFPFRLPSD 232

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224088786|ref|XP_002308540.1| predicted protein [Populus trichocarpa] gi|222854516|gb|EEE92063.1| predicted protein [Populus trichocarpa]

 Score =  224 bits (571), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 120/213 (56%), Positives = 140/213 (65%), Gaps = 33/213 (15%)

Query: 1   MRPGALGLVDTAGVGVHPEPGMVGITAVASVKGYSSPLPDPNLIGQRRDIA--------P 52
           ++ G+ GL   +GVG  PEP + G+   AS KGYSSPL DP+L+ QR D +        P
Sbjct: 59  LQLGSYGLNGYSGVGFRPEPVIGGVMPGASGKGYSSPLEDPSLLAQRGDASMHAIGGAIP 118

Query: 53  G-------------------------INPTIPDVINGVPSSLRNNAGSPLKKGESNLLFV 87
           G                         +   IPD+IN  P SLR+  G P+ KGESN+LFV
Sbjct: 119 GSTGKGYPSPLEDPSLLSQRGDASVRVTAAIPDMINDRPGSLRSADGPPVPKGESNILFV 178

Query: 88  DGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDAL 147
           DGLPTDCTRREV HLFRPF+GY+EIRV+HKE R++GDRA VLCFVEF D  CA TAM+AL
Sbjct: 179 DGLPTDCTRREVGHLFRPFIGYKEIRVVHKEARKSGDRATVLCFVEFTDANCAATAMEAL 238

Query: 148 HGYKFDDKKPDSPTLKIQFAHFPFHLPSDGDEK 180
            GYKFDDKKPDSPTLKIQFA FPF  PSD D K
Sbjct: 239 QGYKFDDKKPDSPTLKIQFARFPFRPPSDRDGK 271

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447147|ref|XP_004141330.1| PREDICTED: uncharacterized protein LOC101211987 [Cucumis sativus] gi|449486681|ref|XP_004157367.1| PREDICTED: uncharacterized protein LOC101228687 [Cucumis sativus]

 Score =  212 bits (539), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 109/184 (59%), Positives = 134/184 (72%), Gaps = 7/184 (3%)

Query: 3   PGALGLVDTAGVGVHPEPGMVGITAVASVKGYSSPLPDPNLIGQRRDIAPGINPTI---P 59
           PGA G  D  G   +PEP + G+T+  S  GY+SP  D +L  QR+DIA G +P +    
Sbjct: 63  PGAYGYTDLGGNSKYPEPVIGGVTSGGSATGYASPFAD-SLASQRQDIAVGSSPGVMGRA 121

Query: 60  DVINGVPSSL---RNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIH 116
           D+ +   +SL   R     P    ESN+LFVDGLPTDCTRREV HLFRPF+GY++IRV+H
Sbjct: 122 DIGHERANSLNLIRTAECDPSPLRESNVLFVDGLPTDCTRREVGHLFRPFMGYKDIRVVH 181

Query: 117 KEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHFPFHLPSD 176
           KEPRRTGD+AMVLCFVEF + K ++ AM+AL GYKFDDKKPDSP LKIQFAHFPFHLPS+
Sbjct: 182 KEPRRTGDKAMVLCFVEFVEAKFSQAAMEALQGYKFDDKKPDSPVLKIQFAHFPFHLPSN 241

Query: 177 GDEK 180
            D++
Sbjct: 242 HDDR 245

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225429572|ref|XP_002280083.1| PREDICTED: uncharacterized protein LOC100257637 isoform 2 [Vitis vinifera]

 Score =  207 bits (527), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 107/176 (60%), Positives = 128/176 (72%), Gaps = 12/176 (6%)

Query: 1   MRPGALGLVDTAGVGVHPEPGMVGITAVASVKGYSSPLPDPNLIGQRRDIAPGINPTIPD 60
           +RPGA    D  G+ V P+P + G TA  ++KGY +P+ DPNLIGQRRD+A GI+P IPD
Sbjct: 59  VRPGAHDFDDIMGIRVPPKPVIGGFTATTNIKGYPNPVEDPNLIGQRRDVAHGISPGIPD 118

Query: 61  VINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPR 120
           +    PSS  N    P    ESN+LFVDGLP DCTRREV           +IRV+HKEPR
Sbjct: 119 IER--PSSFGNVESLPPPVQESNILFVDGLPKDCTRREVG----------QIRVVHKEPR 166

Query: 121 RTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHFPFHLPSD 176
            +GD+AMVLCFVEF+D  C+RTA++AL GYKFDDKKPDSPTL+IQFAHFPF LPSD
Sbjct: 167 HSGDKAMVLCFVEFNDASCSRTALEALQGYKFDDKKPDSPTLRIQFAHFPFRLPSD 222

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356514689|ref|XP_003526036.1| PREDICTED: uncharacterized protein LOC100809186 [Glycine max]

 Score =  200 bits (508), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 105/176 (59%), Positives = 124/176 (70%), Gaps = 13/176 (7%)

Query: 10  DTAGVGVHPEPGMVGITAVASVKGYSSPLPDPNLIGQRRDIAP-GINPTIPDVINGVPSS 68
           DT G  VH EP          VKGYS PL DP+   ++RD  P  I   +PDV +  P+S
Sbjct: 59  DTFGSRVHSEP----------VKGYS-PLADPD-PSKKRDTTPLSITHGVPDVNSERPAS 106

Query: 69  LRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMV 128
             +  G P+   +SN+LFV GLP DCTRREV HLFRPF+GY++IRV+HKEPRR+GD+AM 
Sbjct: 107 KSSYDGLPISAADSNILFVGGLPNDCTRREVGHLFRPFIGYKDIRVVHKEPRRSGDKAMT 166

Query: 129 LCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHFPFHLPSDGDEKCTPR 184
           LCFVEF D KCA TAM+AL GYKFDDKKPDSPTLKI+FAHFPF LPSD     + R
Sbjct: 167 LCFVEFVDSKCALTAMEALQGYKFDDKKPDSPTLKIEFAHFPFRLPSDHGSSLSTR 222

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363807398|ref|NP_001242381.1| uncharacterized protein LOC100816255 [Glycine max] gi|255647054|gb|ACU23995.1| unknown [Glycine max]

 Score =  195 bits (496), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 103/167 (61%), Positives = 120/167 (71%), Gaps = 13/167 (7%)

Query: 11  TAGVGVHPEPGMVGITAVASVKGYSSPLPDPNLIGQRRDIAP-GINPTIPDVINGVPSSL 69
           T G  VH EP          VKGYS PL DP L  ++RD  P GIN  +PDV +  P+S 
Sbjct: 59  TLGSRVHSEP----------VKGYS-PLADPCL-SKKRDTTPLGINNGVPDVSSERPASK 106

Query: 70  RNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL 129
            +  G P+   +SN+LFV GLP DCTRREV HLFRPF+GY++IRV+HKEPRR+GD+AM L
Sbjct: 107 SSYDGLPISAADSNILFVGGLPKDCTRREVGHLFRPFIGYKDIRVVHKEPRRSGDKAMTL 166

Query: 130 CFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHFPFHLPSD 176
           CFVEF D  CA TA++ L GYKFDDKKPDSPTLKIQ AHFPF LPSD
Sbjct: 167 CFVEFVDSNCALTALETLQGYKFDDKKPDSPTLKIQPAHFPFRLPSD 213

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255550095|ref|XP_002516098.1| conserved hypothetical protein [Ricinus communis] gi|223544584|gb|EEF46100.1| conserved hypothetical protein [Ricinus communis]

 Score =  187 bits (474), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 101/183 (55%), Positives = 128/183 (69%), Gaps = 7/183 (3%)

Query: 2   RPGALGLVDTAGVGVHPEPGMVGITAVASVKGYSSPLPDPNLIGQR-RDIAPGINP-TIP 59
           +P + GL ++    +   P   G+   AS +GY SPL DP+L   R RD +  +    IP
Sbjct: 58  QPVSYGLNNSNNDDI---PVRSGVIPGASSRGYLSPLNDPSLPSHRLRDTSVNVTTLAIP 114

Query: 60  DVINGVP-SSLRNNAGSP-LKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHK 117
           DVIN  P + LR NA SP + + ESN+LFVDGLPTDCTRREV HLFRPF+GY++I+VIH+
Sbjct: 115 DVINDQPPNYLRINADSPSVSRTESNILFVDGLPTDCTRREVGHLFRPFIGYKDIKVIHR 174

Query: 118 EPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHFPFHLPSDG 177
           EPRR GD+AMV CFVEF D KCA TAM+AL GYKFDD++ +SP L+I  A FPF  P D 
Sbjct: 175 EPRRDGDKAMVYCFVEFADAKCAITAMEALQGYKFDDRRSNSPVLRIHLARFPFRPPHDR 234

Query: 178 DEK 180
           +E+
Sbjct: 235 NEQ 237

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388521817|gb|AFK48970.1| unknown [Lotus japonicus]

 Score =  184 bits (467), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 96/153 (62%), Positives = 114/153 (74%), Gaps = 9/153 (5%)

Query: 30  SVKGYSSPLPDPNLIGQRRDIAPGINPTIPDVINGVPSSLRNNAGSPLKKGESNLLFVDG 89
           ++KGYS PL DP ++  +RD + G+NP   DV +  P    N  G      +SN+LFVD 
Sbjct: 86  NIKGYS-PLDDP-VLRTKRDTSLGVNP---DVSSERPIPKANREG----LADSNVLFVDV 136

Query: 90  LPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHG 149
           LP DCTRREV HLFRPF+GY++IRV+HKEPRR+GD+AMVLCFVEFDD KCA TAM+AL G
Sbjct: 137 LPRDCTRREVGHLFRPFIGYKDIRVVHKEPRRSGDKAMVLCFVEFDDSKCALTAMEALQG 196

Query: 150 YKFDDKKPDSPTLKIQFAHFPFHLPSDGDEKCT 182
           YKFDDKKPDS TLKIQFAHFPF  P+D     T
Sbjct: 197 YKFDDKKPDSRTLKIQFAHFPFRPPADNGTTTT 229

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357465775|ref|XP_003603172.1| RNA-binding protein with multiple splicing [Medicago truncatula] gi|355492220|gb|AES73423.1| RNA-binding protein with multiple splicing [Medicago truncatula]

 Score =  183 bits (465), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 95/172 (55%), Positives = 116/172 (67%), Gaps = 13/172 (7%)

Query: 7   GLVDTAGVGVHPEPGMVGITAVASVKGYSSPLPDPNLIGQRRDIAPGINPTIPDVI--NG 64
           G+ DT G  VH E                +PL D +L   +RD   G++  +PD I  N 
Sbjct: 66  GVDDTRGSRVHSEHNATSY----------NPLEDVDL-STKRDALLGVSTGVPDPIANNE 114

Query: 65  VPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGD 124
              S  N    P+   ESN+LFV GLP DCTRREV HLFRPF+GY++I+V+HKEPRR+GD
Sbjct: 115 RSISKSNYDALPVSAAESNILFVGGLPKDCTRREVGHLFRPFIGYKDIKVVHKEPRRSGD 174

Query: 125 RAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHFPFHLPSD 176
           +AM+ CFVEF +PKCA TAM+AL GYKFDDKKPDSPTLKI+FAHFPF  P+D
Sbjct: 175 KAMIFCFVEFTEPKCALTAMEALQGYKFDDKKPDSPTLKIKFAHFPFRPPTD 226

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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	184
TAIR|locus:2025232	233	AT1G76940 [Arabidopsis thalian	0.527	0.416	0.515	3.3e-24
TAIR|locus:2014937	421	AT1G21320 [Arabidopsis thalian	0.510	0.223	0.520	1.7e-23
UNIPROTKB|F1P2M9	198	RBPMS2 "Uncharacterized protei	0.5	0.464	0.405	3.2e-10
MGI|MGI:1919223	206	Rbpms2 "RNA binding protein wi	0.445	0.398	0.416	8.4e-10
ZFIN|ZDB-GENE-040426-741	200	rbpms2b "RNA binding protein w	0.494	0.455	0.4	1.4e-09
UNIPROTKB|Q9YGP5	196	rbpms "RNA-binding protein wit	0.505	0.474	0.370	2.2e-09
MGI|MGI:1334446	197	Rbpms "RNA binding protein gen	0.516	0.482	0.381	2.2e-09
ZFIN|ZDB-GENE-040718-106	199	rbpms2a "RNA binding protein w	0.478	0.442	0.403	2.2e-09
UNIPROTKB|Q9W6I1	200	RBPMS "RNA-binding protein wit	0.456	0.42	0.397	2.9e-09
UNIPROTKB|F1MAV3	219	RBPMS "Uncharacterized protein	0.510	0.429	0.379	2.9e-09

TAIR|locus:2025232 AT1G76940 [Arabidopsis thaliana (taxid:3702)]

 Score = 277 (102.6 bits), Expect = 3.3e-24, P = 3.3e-24
 Identities = 51/99 (51%), Positives = 73/99 (73%)

Query:    77 LKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPR-RTGDRAMVLCFVEFD 135
             L    SN L+V+GLP++C+RREV+H+FRPFVGYRE+R++ K+ + R GD  +VLCFV+F 
Sbjct:   130 LPSDASNTLYVEGLPSNCSRREVAHIFRPFVGYREVRLVTKDSKHRNGD-PIVLCFVDFT 188

Query:   136 DPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHFPFHLP 174
             +P CA TA+ AL GY+ D+ + DS  L++QF+  P   P
Sbjct:   189 NPACAATALSALQGYRMDENESDSKFLRLQFSRKPGSRP 227

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2014937 AT1G21320 [Arabidopsis thaliana (taxid:3702)]

 Score = 272 (100.8 bits), Expect = 1.7e-23, P = 1.7e-23
 Identities = 50/96 (52%), Positives = 72/96 (75%)

Query:    76 PLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPR-RTGDRAMVLCFVEF 134
             PL    SN L+V+GLP++C+RREVSH+FRPFVGYRE+R++ ++ + R+GD   VLCFV+F
Sbjct:   316 PLPPDVSNTLYVEGLPSNCSRREVSHIFRPFVGYREVRLVTQDSKHRSGDPT-VLCFVDF 374

Query:   135 DDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHFP 170
             ++  CA TA+ AL  Y+ D+ +PDS  L++QF   P
Sbjct:   375 ENSACAATALSALQDYRMDEDEPDSKILRLQFFRNP 410

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|F1P2M9 RBPMS2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 145 (56.1 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 43/106 (40%), Positives = 55/106 (51%)

Query:    65 VPSSLRNNAGSPLKKG-ESNLLFVDGLPTDCTRREVSHLFRPFVGYRE--IRVIHKEPRR 121
             VP     N  S L+ G E   LFV GLP D   RE+  LFRPF GY    I++  K+P  
Sbjct:     1 VPWKCDRNVNSRLELGQEVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSKQP-- 58

Query:   122 TGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
              G       FV FD    A  A +AL+G +FD + P   TL+++FA
Sbjct:    59 VG-------FVTFDSRAGAEAAKNALNGIRFDPENPQ--TLRLEFA 95

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

MGI|MGI:1919223 Rbpms2 "RNA binding protein with multiple splicing 2" [Mus musculus (taxid:10090)]

 Score = 141 (54.7 bits), Expect = 8.4e-10, P = 8.4e-10
 Identities = 40/96 (41%), Positives = 54/96 (56%)

Query:    74 GSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYRE--IRVIHKEPRRTGDRAMVLCF 131
             GSPL++ E   LFV GLP D   RE+  LFRPF GY    I++  ++P   G       F
Sbjct:    17 GSPLEE-EVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSRQP--VG-------F 66

Query:   132 VEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
             V FD    A  A +AL+G +FD + P   TL+++FA
Sbjct:    67 VIFDSRAGAEAAKNALNGIRFDPENPQ--TLRLEFA 100

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

ZFIN|ZDB-GENE-040426-741 rbpms2b "RNA binding protein with multiple splicing 2b" [Danio rerio (taxid:7955)]

 Score = 139 (54.0 bits), Expect = 1.4e-09, P = 1.4e-09
 Identities = 42/105 (40%), Positives = 55/105 (52%)

Query:    65 VPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYRE--IRVIHKEPRRT 122
             V S    N    L++ E   LFV GLPTD   RE+  LFRPF GY    I++  K+P   
Sbjct:     3 VKSDSEPNNNVSLEE-EVRTLFVSGLPTDIKPRELYLLFRPFKGYEGSLIKLTSKQP--V 59

Query:   123 GDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
             G       FV FD    A  A +AL+G +FD + P   TL+++FA
Sbjct:    60 G-------FVTFDSRSGAEAAKNALNGVRFDPENPQ--TLRLEFA 95

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|Q9YGP5 rbpms "RNA-binding protein with multiple splicing" [Xenopus laevis (taxid:8355)]

 Score = 137 (53.3 bits), Expect = 2.2e-09, P = 2.2e-09
 Identities = 40/108 (37%), Positives = 60/108 (55%)

Query:    62 INGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYRE--IRVIHKEP 119
             ++G+ S   +N  + +++ E   LFV GLP D   RE+  LFRPF GY    I++  K+P
Sbjct:     1 MSGIKSDTEHNNNN-IEE-EVRTLFVSGLPIDIKPRELYLLFRPFKGYEGSLIKLTSKQP 58

Query:   120 RRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
                G       FV FD+   A  A +AL+G +FD + P   TL+++FA
Sbjct:    59 --VG-------FVTFDNRAGAEAAKNALNGIRFDPENPQ--TLRLEFA 95

GO:0003713 "transcription coactivator activity" evidence=ISS

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

GO:0010862 "positive regulation of pathway-restricted SMAD protein phosphorylation" evidence=ISS

GO:0060391 "positive regulation of SMAD protein import into nucleus" evidence=ISS

MGI|MGI:1334446 Rbpms "RNA binding protein gene with multiple splicing" [Mus musculus (taxid:10090)]

 Score = 137 (53.3 bits), Expect = 2.2e-09, P = 2.2e-09
 Identities = 42/110 (38%), Positives = 58/110 (52%)

Query:    62 INGVPSSLRNNAGSP--LKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYRE--IRVIHK 117
             +NG   + + N  S   L++ E   LFV GLP D   RE+  LFRPF GY    I++  K
Sbjct:     1 MNGGGKAEKENTPSEANLQEEEVRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSK 60

Query:   118 EPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
             +P   G       FV FD    A  A +AL+G +FD + P   TL+++FA
Sbjct:    61 QP--VG-------FVSFDSRSEAEAAKNALNGIRFDPEIPQ--TLRLEFA 99

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=ISO

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

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

GO:0010862 "positive regulation of pathway-restricted SMAD protein phosphorylation" evidence=ISO

GO:0060391 "positive regulation of SMAD protein import into nucleus" evidence=ISO

ZFIN|ZDB-GENE-040718-106 rbpms2a "RNA binding protein with multiple splicing 2a" [Danio rerio (taxid:7955)]

 Score = 137 (53.3 bits), Expect = 2.2e-09, P = 2.2e-09
 Identities = 42/104 (40%), Positives = 55/104 (52%)

Query:    67 SSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYRE--IRVIHKEPRRTGD 124
             S    N    L++ E   LFV GLP D   RE+  LFRPF GY    I++  K+P   G 
Sbjct:     5 SDSETNTSVSLEE-EVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSKQP--VG- 60

Query:   125 RAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP-TLKIQFA 167
                   FV FD    A  A +AL+G +FD   P+SP TL+++FA
Sbjct:    61 ------FVTFDSRSGAEAAKNALNGIRFD---PESPQTLRLEFA 95

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|Q9W6I1 RBPMS "RNA-binding protein with multiple splicing" [Gallus gallus (taxid:9031)]

 Score = 136 (52.9 bits), Expect = 2.9e-09, P = 2.9e-09
 Identities = 39/98 (39%), Positives = 53/98 (54%)

Query:    72 NAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYRE--IRVIHKEPRRTGDRAMVL 129
             N G  +++ E   LFV GLP D   RE+  LFRPF GY    I++  K+P   G      
Sbjct:    12 NGGGNVEE-EVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSKQP--VG------ 62

Query:   130 CFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
              FV FD    A  A +AL+G +FD + P   TL+++FA
Sbjct:    63 -FVTFDSRAGAEAAKNALNGIRFDPENPQ--TLRLEFA 97

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=ISS

GO:0010862 "positive regulation of pathway-restricted SMAD protein phosphorylation" evidence=ISS

GO:0060391 "positive regulation of SMAD protein import into nucleus" evidence=ISS

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

UNIPROTKB|F1MAV3 RBPMS "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 136 (52.9 bits), Expect = 2.9e-09, P = 2.9e-09
 Identities = 41/108 (37%), Positives = 55/108 (50%)

Query:    63 NGVPSSLRNNAGSP-LKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYRE--IRVIHKEP 119
             NG  +   N      L++ E   LFV GLP D   RE+  LFRPF GY    I++  K+P
Sbjct:     3 NGSKAEKENTPNEANLQEEEVRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQP 62

Query:   120 RRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
                G       FV FD    A  A +AL+G +FD + P   TL+++FA
Sbjct:    63 --VG-------FVSFDSRSEAEAAKNALNGIRFDPEIPQ--TLRLEFA 99

GO:0060391 "positive regulation of SMAD protein import into nucleus" evidence=IEA

GO:0010862 "positive regulation of pathway-restricted SMAD protein phosphorylation" evidence=IEA

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

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00032221001 SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (332 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	184
cd12420	79	cd12420, RRM_RBPMS_like, RNA recognition motif in	1e-31
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-13
smart00360	73	smart00360, RRM, RNA recognition motif	4e-13
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-13
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	6e-12
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	2e-10
cd12683	76	cd12683, RRM_RBPMS2, RNA recognition motif in vert	9e-10
cd12682	76	cd12682, RRM_RBPMS, RNA recognition motif in verte	5e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-08
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	6e-08
cd12684	83	cd12684, RRM_cpo, RNA recognition motif in Drosoph	8e-08
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	8e-08
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-07
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	1e-06
cd12480	80	cd12480, RRM2_U1A, RNA recognition motif 2 found i	2e-06
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-06
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	3e-06
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	4e-06
cd12481	80	cd12481, RRM2_U2B, RNA recognition motif 2 found i	5e-06
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	1e-05
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	1e-05
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-05
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	2e-05
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	2e-05
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	3e-05
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	8e-05
cd12479	80	cd12479, RRM2_SNF, RNA recognition motif 2 found i	8e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	8e-05
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	9e-05
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	1e-04
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	1e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	2e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	2e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	3e-04
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	3e-04
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-04
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	5e-04
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	5e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-04
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	7e-04
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	0.001
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	0.002
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	0.002
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	0.002
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	0.002
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	0.003
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	0.004

>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding protein with multiple splicing (RBP-MS)-like proteins

 Score =  108 bits (273), Expect = 1e-31
 Identities = 37/83 (44%), Positives = 50/83 (60%), Gaps = 4/83 (4%)

Query: 83  NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCART 142
             LFV GLP+D   RE++HLFRPF GY   R++ KE  + G     + FV+F   +CA  
Sbjct: 1   RTLFVSGLPSDVKERELAHLFRPFPGYEASRLVFKE--KKGGEKQPVGFVDFSSAQCAAA 58

Query: 143 AMDALHGYKFDDKKPDSPTLKIQ 165
           AMDAL GY+FD     S  L+++
Sbjct: 59  AMDALQGYRFDP--DTSSVLRLE 79

This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4. Length = 79

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

 Score = 61.1 bits (149), Expect = 3e-13
 Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           LFV  LP D T  ++  LF  F     IR++  E  R+        FVEF+D + A  A+
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRS----KGFAFVEFEDEEDAEKAL 56

Query: 145 DALHGYKFDDKK 156
           +AL+G +   ++
Sbjct: 57  EALNGKELGGRE 68

(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|214636 smart00360, RRM, RNA recognition motif

 Score = 61.1 bits (149), Expect = 4e-13
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           LFV  LP D T  E+  LF  F     +R++     +   ++    FVEF+  + A  A+
Sbjct: 2   LFVGNLPPDTTEEELRELFSKFGKVESVRLVRD---KETGKSKGFAFVEFESEEDAEKAL 58

Query: 145 DALHGYKFDDKK 156
           +AL+G + D + 
Sbjct: 59  EALNGKELDGRP 70

Length = 73

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

 Score = 61.2 bits (149), Expect = 4e-13
 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 4/72 (5%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           LFV  LP D T  ++  LF  F     +R++  +  ++   A    FVEF+ P+ A  A+
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFA----FVEFESPEDAEKAL 56

Query: 145 DALHGYKFDDKK 156
           +AL+G + D +K
Sbjct: 57  EALNGKELDGRK 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|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 58.0 bits (141), Expect = 6e-12
 Identities = 24/70 (34%), Positives = 40/70 (57%), Gaps = 9/70 (12%)

Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           + +LF+  LP + T+  +  LF  F G++E+R++   PRR       + FVEF+  + A 
Sbjct: 2   NKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLV---PRRG------IAFVEFETEEQAT 52

Query: 142 TAMDALHGYK 151
            A+ AL G+K
Sbjct: 53  VALQALQGFK 62

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

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

 Score = 54.1 bits (131), Expect = 2e-10
 Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 9/86 (10%)

Query: 83  NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCART 142
           N LFV  L  + T  E+  LF    G+R +++ +K           +CFVEF+D   A  
Sbjct: 3   NTLFVANLGPNTTEEELRQLFSRQPGFRRLKMHNKG-------GGPVCFVEFEDVSFATQ 55

Query: 143 AMDALHGYKFDDKKPDSPTLKIQFAH 168
           A+++L G        D   ++I++A 
Sbjct: 56  ALNSLQGAVLSSS--DRGGIRIEYAK 79

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

>gnl|CDD|241127 cd12683, RRM_RBPMS2, RNA recognition motif in vertebrate RNA-binding protein with multiple splicing 2 (RBP-MS2)

 Score = 52.7 bits (126), Expect = 9e-10
 Identities = 34/84 (40%), Positives = 46/84 (54%), Gaps = 13/84 (15%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYRE--IRVIHKEPRRTGDRAMVLCFVEFDDPKCART 142
           LFV GLP D   RE+  LFRPF GY    I++  K+P         + FV FD    A  
Sbjct: 4   LFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSKQP---------VGFVTFDSRAGAEA 54

Query: 143 AMDALHGYKFDDKKPDSPTLKIQF 166
           A +AL+G +FD + P   TL+++F
Sbjct: 55  AKNALNGIRFDPENPQ--TLRLEF 76

This subfamily corresponds to the RRM of RBP-MS2, encoded by RBPMS2 gene, a paralog of RNA-binding protein with multiple splicing (RBP-MS). The biological function of RBP-MS2 remains unclear. Like RBP-MS, RBP-MS2 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>gnl|CDD|241126 cd12682, RRM_RBPMS, RNA recognition motif in vertebrate RNA-binding protein with multiple splicing (RBP-MS)

 Score = 50.4 bits (120), Expect = 5e-09
 Identities = 34/84 (40%), Positives = 46/84 (54%), Gaps = 13/84 (15%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYRE--IRVIHKEPRRTGDRAMVLCFVEFDDPKCART 142
           LFV GLP D   RE+  LFRPF GY    I++  K+P         + FV FD    A  
Sbjct: 4   LFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQP---------VGFVSFDSRSEAEA 54

Query: 143 AMDALHGYKFDDKKPDSPTLKIQF 166
           A +AL+G +FD + P   TL+++F
Sbjct: 55  AKNALNGIRFDPEIPQ--TLRLEF 76

This subfamily corresponds to the RRM of RBP-MS, also termed heart and RRM expressed sequence (hermes), an RNA-binding proteins found in various vertebrate species. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RBP-MS physically interacts with Smad2, Smad3 and Smad4 and plays a role in regulation of Smad-mediated transcriptional activity. In addition, RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. . Length = 76

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

 Score = 51.5 bits (122), Expect = 4e-08
 Identities = 25/79 (31%), Positives = 43/79 (54%), Gaps = 3/79 (3%)

Query: 78  KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDP 137
            K E+N LFV  LP D T  ++  LF+ F   + +R++    R TG ++    FVEF+  
Sbjct: 111 SKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRD--RETG-KSRGFAFVEFESE 167

Query: 138 KCARTAMDALHGYKFDDKK 156
           + A  A++ L+G + + + 
Sbjct: 168 ESAEKAIEELNGKELEGRP 186

Length = 306

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

 Score = 47.1 bits (113), Expect = 6e-08
 Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 13/69 (18%)

Query: 99  VSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD 158
           +  LF PF    +I+++ K+P           FVEF   + A  A+  L+G  F  +   
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPGF--------AFVEFSTEEAAEKAVQYLNGVLFGGR--- 49

Query: 159 SPTLKIQFA 167
              L++ ++
Sbjct: 50  --PLRVDYS 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|241128 cd12684, RRM_cpo, RNA recognition motif in Drosophila couch potato (cpo) coding RNA-binding protein and similar proteins

 Score = 47.4 bits (112), Expect = 8e-08
 Identities = 31/84 (36%), Positives = 42/84 (50%), Gaps = 6/84 (7%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           LFV GLP D   RE+  LFR + GY    +  K   + G     + FV F+    A  A 
Sbjct: 4   LFVSGLPMDAKPRELYLLFRAYKGYEGSLL--KVTSKNGKTTSPVGFVTFETRAGAEAAK 61

Query: 145 DALHGYKFDDKKPDSP-TLKIQFA 167
             L G +FD   PD P T++++FA
Sbjct: 62  QDLQGVRFD---PDIPQTIRLEFA 82

This subfamily corresponds to the RRM of Cpo, an RNA-binding protein encoded by Drosophila couch potato (cpo) gene. Cpo contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It may control the processing of RNA molecules required for the proper functioning of the peripheral nervous system (PNS). . Length = 83

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

 Score = 47.3 bits (113), Expect = 8e-08
 Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 8/83 (9%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L V+ LP D T+ E+  LF         +++    R TG +++   FV++ D   A+ A+
Sbjct: 3   LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRD--RITG-QSLGYGFVDYVDENDAQKAI 59

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
           + L+G++  +K      LK+ +A
Sbjct: 60  NTLNGFEIRNK-----RLKVSYA 77

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

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

 Score = 46.0 bits (110), Expect = 2e-07
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 5/72 (6%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L+V  LP   T  ++   F P+     +R++  + R  G       FVEF  P+ A  A+
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGF-----AFVEFASPEDAEAAL 55

Query: 145 DALHGYKFDDKK 156
             L+G   D + 
Sbjct: 56  KKLNGLVLDGRT 67

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

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

 Score = 44.1 bits (105), Expect = 1e-06
 Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 8/76 (10%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRV-IHKEPRRTGDRAMVLCFVEFDDPKC 139
            + +L+V  LP   +  E+  LF  +   R+IR+   KE R T        FV ++D   
Sbjct: 1   VNRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGT-------AFVVYEDIYD 53

Query: 140 ARTAMDALHGYKFDDK 155
           A+ A D L G+   ++
Sbjct: 54  AKNACDHLSGFNVANR 69

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|240924 cd12480, RRM2_U1A, RNA recognition motif 2 found in vertebrate U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A)

 Score = 43.5 bits (102), Expect = 2e-06
 Identities = 28/86 (32%), Positives = 44/86 (51%), Gaps = 12/86 (13%)

Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           +++LF+  LP +     +S LF  F G++E+R++   P R       + FVEFD+   A 
Sbjct: 5   NHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV---PGRHD-----IAFVEFDNEVQAG 56

Query: 142 TAMDALHGYKFDDKKPDSPTLKIQFA 167
            A +AL G+K          +KI FA
Sbjct: 57  AAREALQGFKITQSN----AMKISFA 78

This subgroup corresponds to the RRM2 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). U1A also binds to a flavivirus NS5 protein and plays an important role in virus replication. It contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and it may be free for binding other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 80

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

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 3/69 (4%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L+V  LP + T  ++  LF  F      RVI    R TG R+    FVE +  + A  A+
Sbjct: 2   LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITD--RETG-RSRGFGFVEMETAEEANAAI 58

Query: 145 DALHGYKFD 153
           + L+G  F 
Sbjct: 59  EKLNGTDFG 67

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

 Score = 42.9 bits (101), Expect = 3e-06
 Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 4/65 (6%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           + V  LP + T+++V  LF  +   + +RV    P++    A    FVEF   K A  AM
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRV----PKKFDQSARGFAFVEFSTAKEALNAM 58

Query: 145 DALHG 149
           +AL  
Sbjct: 59  NALKD 63

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

>gnl|CDD|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 = 42.6 bits (101), Expect = 4e-06
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 4/65 (6%)

Query: 83  NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCART 142
             L V  +P + T++E+  LF PF   + +R+    P++         FVEF   + A+ 
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRL----PKKFDGSHRGFAFVEFVTKQEAQN 56

Query: 143 AMDAL 147
           AM+AL
Sbjct: 57  AMEAL 61

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|240925 cd12481, RRM2_U2B, RNA recognition motif 2 found in vertebrate U2 small nuclear ribonucleoprotein B" (U2B")

 Score = 42.7 bits (100), Expect = 5e-06
 Identities = 28/84 (33%), Positives = 44/84 (52%), Gaps = 12/84 (14%)

Query: 84  LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTA 143
           +LF++ LP +     +S LF  F G++E+R++   P R       + FVEF++   A  A
Sbjct: 7   ILFLNNLPEETNEMMLSMLFNQFPGFKEVRLV---PGRHD-----IAFVEFENEAQAGAA 58

Query: 144 MDALHGYKFDDKKPDSPTLKIQFA 167
            DAL G+K       S  +KI +A
Sbjct: 59  RDALQGFKIT----PSHAMKITYA 78

This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B"), a unique protein that comprises the U2 snRNP. It was initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus. . Length = 80

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 41.8 bits (98), Expect = 1e-05
 Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 7/86 (8%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHK-EPRRTGDR-AMVLCFVEFDDPKCART 142
           LFV  L    T + ++  F+   G+   RV  K +P+R G   +M   FV F   + A+ 
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 143 AMDALHGYKFDDKKPDSPTLKIQFAH 168
           A+ A+ G+  D       TL ++F+H
Sbjct: 63  ALKAMDGFVLDGH-----TLVVKFSH 83

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

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

 Score = 41.3 bits (97), Expect = 1e-05
 Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 12/73 (16%)

Query: 85  LFVDGLPTDCTR-REVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTA 143
           LFV G     TR  ++  LF PF       ++  + R+T        FVEF+D + A  A
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFG-----PLVRCDIRKT------FAFVEFEDSEDATKA 50

Query: 144 MDALHGYKFDDKK 156
           ++ALHG + D   
Sbjct: 51  LEALHGSRIDGSV 63

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

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

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 2/72 (2%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVI-HKEPRRTGDR-AMVLCFVEFDDPKCART 142
           LFV  L    T   +   F    G R + +   K+P+  G   +M   FVEF   + A+ 
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 143 AMDALHGYKFDD 154
           A+  L G   D 
Sbjct: 63  ALKRLQGTVLDG 74

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

 Score = 40.3 bits (95), Expect = 2e-05
 Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 12/66 (18%)

Query: 85  LFVDGLPTD-CTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTA 143
           +FV  L TD  ++ ++  +F  +     I + HK             FV+FD+ + AR A
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGISL-HKG----------YGFVQFDNEEDARAA 51

Query: 144 MDALHG 149
           +   +G
Sbjct: 52  VAGENG 57

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|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 41.0 bits (97), Expect = 2e-05
 Identities = 21/73 (28%), Positives = 27/73 (36%), Gaps = 13/73 (17%)

Query: 99  VSHLFRPFVGYREIRVI---HKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDK 155
           V  L + F  Y  +  I    K          V   V+FD  + A  A  AL+G    D 
Sbjct: 15  VDVLHQVFSPYGAVEKILIFEKNTG-------VQALVQFDSVESAENAKKALNGRNIYD- 66

Query: 156 KPDSPTLKIQFAH 168
                TL IQF+ 
Sbjct: 67  --GCCTLDIQFSR 77

This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. . Length = 85

>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 = 40.2 bits (95), Expect = 3e-05
 Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 7/68 (10%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYRE--IRVIHKEPRRTGDRAMVLCFVEFDDPKCART 142
           + + GLP   T  ++   F       +    V   + R TG+      +VEF  P+ AR 
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGE-----AYVEFASPEDARR 56

Query: 143 AMDALHGY 150
           A+   +  
Sbjct: 57  ALRKHNNK 64

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

 Score = 39.5 bits (93), Expect = 8e-05
 Identities = 14/27 (51%), Positives = 18/27 (66%)

Query: 129 LCFVEFDDPKCARTAMDALHGYKFDDK 155
             FVEF  P+ A+ A+ AL+GYK D K
Sbjct: 52  YAFVEFATPEEAKEAVKALNGYKLDKK 78

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|240923 cd12479, RRM2_SNF, RNA recognition motif 2 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 39.3 bits (91), Expect = 8e-05
 Identities = 28/88 (31%), Positives = 46/88 (52%), Gaps = 16/88 (18%)

Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           + +LF+  LP +     +S LF  F G++E+R++   P R       + FVEF++   + 
Sbjct: 5   NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLV---PGRHD-----IAFVEFENEVQSA 56

Query: 142 TAMDALHGYKFDDKKPDSPT--LKIQFA 167
            A +AL G+K       +PT  +KI FA
Sbjct: 57  AAKEALQGFKI------TPTHAMKITFA 78

This subgroup corresponds to the RRM2 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 80

>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 = 39.2 bits (92), Expect = 8e-05
 Identities = 22/81 (27%), Positives = 42/81 (51%), Gaps = 8/81 (9%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           LF+  LP + T +++  LF PF      +V      +   ++    FV +D+P+ A+ A+
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVD---KNTGQSKCFGFVSYDNPESAQAAI 57

Query: 145 DALHGYKFDDKKPDSPTLKIQ 165
            A++G++   K+     LK+Q
Sbjct: 58  KAMNGFQVGGKR-----LKVQ 73

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

 Score = 38.9 bits (91), Expect = 9e-05
 Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 6/77 (7%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIR-VIHKEPRRTGDRAMVLCFVEFDDPKC 139
           E + LFV GLP   T+ E+  LF+     + +R V ++  +  G     L +VE+++   
Sbjct: 1   EKHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKG-----LAYVEYENESS 55

Query: 140 ARTAMDALHGYKFDDKK 156
           A  A+  + G +  +K 
Sbjct: 56  ASQAVLKMDGTEIKEKT 72

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

 Score = 38.2 bits (89), Expect = 1e-04
 Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 11/72 (15%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L+V   P D +   +  +F P+   +E+++I               FVEF+  + A  A 
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMISN-----------FAFVEFESLESAIRAK 50

Query: 145 DALHGYKFDDKK 156
           D++HG   ++  
Sbjct: 51  DSVHGKVLNNNP 62

This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 67

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 38.2 bits (89), Expect = 1e-04
 Identities = 21/70 (30%), Positives = 31/70 (44%), Gaps = 6/70 (8%)

Query: 84  LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTA 143
            ++V  LP D   REV  LF  +    +I +      +   R     F+EF+D + A  A
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDL------KLPPRPPGYAFIEFEDARDAEDA 54

Query: 144 MDALHGYKFD 153
           +    GY FD
Sbjct: 55  IRGRDGYDFD 64

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 24/69 (34%), Positives = 34/69 (49%), Gaps = 6/69 (8%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           ++V  LP D   R++  LF  +   + I +  K  RR    A    FVEF+DP+ A  A+
Sbjct: 2   IYVGNLPGDIRERDIEDLFYKYGPIKAIDL--KNRRRGPPFA----FVEFEDPRDAEDAV 55

Query: 145 DALHGYKFD 153
               GY FD
Sbjct: 56  RGRDGYDFD 64

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 2/63 (3%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           + V  +P + T +E+  LF  F   + +R+  K       R     FV+F   + A+ A 
Sbjct: 3   ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRG--FGFVDFITKQDAKRAF 60

Query: 145 DAL 147
            AL
Sbjct: 61  KAL 63

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 40.3 bits (94), Expect = 3e-04
 Identities = 26/120 (21%), Positives = 43/120 (35%), Gaps = 11/120 (9%)

Query: 50  IAPGINPTIPDVINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGY 109
           I P ++   PD        L N+          + +++  LP      ++  L   F   
Sbjct: 266 ITPEVSQKNPDDNAKNVEKLVNSTTVL---DSKDRIYIGNLPLYLGEDQIKELLESFGDL 322

Query: 110 REIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHF 169
           +   +I  +   TG  +    F E+ DP     A+ AL+G    D K     L +Q A  
Sbjct: 323 KAFNLI--KDIATGL-SKGYAFCEYKDPSVTDVAIAALNGKDTGDNK-----LHVQRACV 374

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|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 = 37.5 bits (88), Expect = 3e-04
 Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 3/65 (4%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           LFV  LP   T  +V  LF  +    E+ +I ++      +     FV+F   + A+ A+
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTII-RDKDTGQSKGC--AFVKFSSREEAQKAI 58

Query: 145 DALHG 149
           +ALHG
Sbjct: 59  EALHG 63

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|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 = 37.3 bits (87), Expect = 4e-04
 Identities = 21/73 (28%), Positives = 26/73 (35%), Gaps = 11/73 (15%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRV----IHKEPRRTGDRAMVLCFVEFDDPKCA 140
           LFV  LP   T  E+  LF  F    E+ +      K  +          FV F  P+ A
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFA-------FVSFMFPEHA 54

Query: 141 RTAMDALHGYKFD 153
             A   L G  F 
Sbjct: 55  VKAYSELDGSIFQ 67

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

 Score = 36.9 bits (86), Expect = 5e-04
 Identities = 20/66 (30%), Positives = 37/66 (56%), Gaps = 3/66 (4%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L+V  L  + T  ++  +F PF G  E   + ++P  TG R+    F++F D + A+ A+
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPF-GEIEFVQLQRDPE-TG-RSKGYGFIQFADAEDAKKAL 57

Query: 145 DALHGY 150
           + L+G+
Sbjct: 58  EQLNGF 63

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|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 = 36.8 bits (86), Expect = 5e-04
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 5/74 (6%)

Query: 83  NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGD-RAMVLCFVEFDDPKCAR 141
           N LFV GL T  T +E+  LF  F    E+ ++ K+P  TG+ R     FV F+  + A 
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLM-KDP-ETGESRG--FGFVTFESVEDAD 57

Query: 142 TAMDALHGYKFDDK 155
            A+  L+G + + +
Sbjct: 58  AAIRDLNGKELEGR 71

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

 Score = 39.0 bits (91), Expect = 6e-04
 Identities = 16/74 (21%), Positives = 27/74 (36%), Gaps = 4/74 (5%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L+V  L       ++  LF  F       V+     R+        FV F+  + A  A+
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRS----RGFAFVNFEKHEDAAKAV 236

Query: 145 DALHGYKFDDKKPD 158
           + ++G K    K  
Sbjct: 237 EEMNGKKIGLAKEG 250

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|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 36.4 bits (85), Expect = 7e-04
 Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 5/38 (13%)

Query: 131 FVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAH 168
           FV F D + A  A+ AL G+ F DK      ++IQ+A 
Sbjct: 46  FVVFKDVESATNALRALQGFPFYDKP-----MRIQYAK 78

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|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 = 35.7 bits (83), Expect = 0.001
 Identities = 9/29 (31%), Positives = 13/29 (44%)

Query: 130 CFVEFDDPKCARTAMDALHGYKFDDKKPD 158
            +VEF     A    + L G +F+ KK  
Sbjct: 45  AYVEFASEAAAAAVKEKLEGREFNGKKCV 73

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

 Score = 35.6 bits (83), Expect = 0.002
 Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 3/67 (4%)

Query: 87  VDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDA 146
           V  L  D    ++  LFRPF      RV   + + TG ++    FV F   + A  A++ 
Sbjct: 4   VTNLSEDADEDDLRELFRPF--GPISRVYLAKDKETG-QSRGFAFVTFHTREDAERAIEK 60

Query: 147 LHGYKFD 153
           L+G+ +D
Sbjct: 61  LNGFGYD 67

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

>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 20/84 (23%), Positives = 34/84 (40%), Gaps = 13/84 (15%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVI-HKEPRRTGDRAMVLCFVEFDDPKCARTA 143
           L V  LP + +  +   L + F G   +RV+  +   +         F  FD+ + A  A
Sbjct: 2   LLVRHLPPELSEDDKEDLLKHF-GASSVRVMSRRGKLKNT------AFATFDNEQAASQA 54

Query: 144 MDALHGYKFDDKKPDSPTLKIQFA 167
           +  LH  K   K      L +++A
Sbjct: 55  LSRLHQLKILGK-----RLVVEYA 73

This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. . Length = 73

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

 Score = 35.4 bits (82), Expect = 0.002
 Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 3/72 (4%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCA 140
           E+  LFV  LP  C   ++  LF  F    E+ V   + +    +     +V F DP+ A
Sbjct: 1   ETGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAI-DKKSGKSKG--FAYVLFLDPEDA 57

Query: 141 RTAMDALHGYKF 152
             A   L G  F
Sbjct: 58  VKAYKELDGKVF 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|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 35.0 bits (81), Expect = 0.002
 Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 11/65 (16%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           +++  LP     R+V   F+   GY  IR I+    + G       FVEF+DP+ A  A+
Sbjct: 2   VYIGRLPYRARERDVERFFK---GYGRIREIN---LKNG-----FGFVEFEDPRDADDAV 50

Query: 145 DALHG 149
             L+G
Sbjct: 51  YELNG 55

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

 Score = 35.0 bits (81), Expect = 0.003
 Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 5/71 (7%)

Query: 86  FVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMD 145
           FV  LP +  + ++  +F+     + +R++     +  D+    C+VEF+D +  + A++
Sbjct: 5   FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRD---KETDKFKGFCYVEFEDVESLKEALE 60

Query: 146 ALHGYKFDDKK 156
              G  FDD+ 
Sbjct: 61  -YDGALFDDRS 70

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

>gnl|CDD|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 = 34.4 bits (79), Expect = 0.004
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 8/81 (9%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           LF+  LP +    E+  +F PF      +V      R  +++    FV FD+P  A+ A+
Sbjct: 7   LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVD---RATNQSKCFGFVSFDNPASAQAAI 63

Query: 145 DALHGYKFDDKKPDSPTLKIQ 165
            A++G++   K+     LK+Q
Sbjct: 64  QAMNGFQIGMKR-----LKVQ 79

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	184
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.82
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.74
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.72
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.72
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.71
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.67
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.67
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.66
KOG0122	270	consensus Translation initiation factor 3, subunit	99.65
PLN03120	260	nucleic acid binding protein; Provisional	99.65
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.63
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.63
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.62
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.62
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.61
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.6
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.6
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.59
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.58
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.58
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.57
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.57
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.57
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.56
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.56
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.56
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.56
PLN03121	243	nucleic acid binding protein; Provisional	99.55
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.55
PLN03213	759	repressor of silencing 3; Provisional	99.54
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.54
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.53
smart00362	72	RRM_2 RNA recognition motif.	99.53
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.52
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.52
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.5
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.49
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.48
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.48
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.48
smart00360	71	RRM RNA recognition motif.	99.48
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.46
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.46
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.45
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.44
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.42
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.42
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.41
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.37
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.37
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.35
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.35
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.34
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.33
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.31
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.31
smart00361	70	RRM_1 RNA recognition motif.	99.27
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.27
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.25
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.24
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.23
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.22
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.2
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.17
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.16
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.16
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.16
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.12
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.11
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.07
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.05
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.93
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.88
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.88
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.84
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.83
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.79
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.75
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.75
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.71
KOG0151	877	consensus Predicted splicing regulator, contains R	98.7
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.68
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.65
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.52
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.49
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.48
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.47
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.45
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.43
KOG0226	290	consensus RNA-binding proteins [General function p	98.42
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.32
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.19
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.04
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.98
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.95
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.91
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	97.84
KOG4210	285	consensus Nuclear localization sequence binding pr	97.81
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.71
KOG2314	698	consensus Translation initiation factor 3, subunit	97.68
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.66
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.64
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.61
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.54
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.43
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.42
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.41
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.4
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.4
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.28
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.24
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.16
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.14
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.13
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	97.03
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	96.99
KOG3152	278	consensus TBP-binding protein, activator of basal	96.94
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.9
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	96.87
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.71
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.68
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.64
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.45
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.4
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.39
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.37
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.1
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.86
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	95.72
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	95.68
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	95.6
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	95.37
KOG2068	327	consensus MOT2 transcription factor [Transcription	95.09
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.81
KOG2591	684	consensus c-Mpl binding protein, contains La domai	94.38
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.35
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	93.87
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	92.2
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	91.61
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	91.41
KOG4660	549	consensus Protein Mei2, essential for commitment t	90.72
KOG4210	285	consensus Nuclear localization sequence binding pr	90.43
KOG2135	526	consensus Proteins containing the RNA recognition	89.39
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	89.03
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	86.8
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	85.48

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.82  E-value=1.5e-19  Score=134.74  Aligned_cols=83  Identities=22%  Similarity=0.356  Sum_probs=76.2

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ...+++|||+|||++++|++|+++|++||.|.+|+++.+.   .+++++|||||+|.+.++|++|++.||+.+|.++.  
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~---~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~--  105 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDR---ETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRH--  105 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecC---CCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEE--
Confidence            4567899999999999999999999999999999998853   34789999999999999999999999999999997  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |+|+|++.
T Consensus       106 ---l~V~~a~~  113 (144)
T PLN03134        106 ---IRVNPAND  113 (144)
T ss_pred             ---EEEEeCCc
Confidence               99999965

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.74  E-value=2.8e-17  Score=138.08  Aligned_cols=83  Identities=24%  Similarity=0.416  Sum_probs=75.6

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ..+.+|||+|||+++++++|+++|++||.|.+++++.+.   .++.++|||||+|.+.++|.+||+.|||+.+.|+.   
T Consensus       267 ~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~---~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~---  340 (352)
T TIGR01661       267 GAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDL---TTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRV---  340 (352)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcC---CCCCccceEEEEECCHHHHHHHHHHhCCCEECCeE---
Confidence            445689999999999999999999999999999999853   23789999999999999999999999999999998   


Q ss_pred             CceEEEeecCC
Q 030012          160 PTLKIQFAHFP  170 (184)
Q Consensus       160 ~~l~V~~a~~~  170 (184)
                        |+|+|..+.
T Consensus       341 --i~V~~~~~~  349 (352)
T TIGR01661       341 --LQVSFKTNK  349 (352)
T ss_pred             --EEEEEccCC
Confidence              999998653

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.72  E-value=2.9e-17  Score=138.05  Aligned_cols=83  Identities=22%  Similarity=0.422  Sum_probs=75.9

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ...+|||+|||.+++|++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.|||..+.|+.    
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~~----   74 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDK---VTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKT----   74 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcC---CCCccceEEEEEECcHHHHHHHHhhcccEEECCee----
Confidence            46799999999999999999999999999999999853   33789999999999999999999999999999998    


Q ss_pred             ceEEEeecCCC
Q 030012          161 TLKIQFAHFPF  171 (184)
Q Consensus       161 ~l~V~~a~~~~  171 (184)
                       |+|.|++...
T Consensus        75 -i~v~~a~~~~   84 (352)
T TIGR01661        75 -IKVSYARPSS   84 (352)
T ss_pred             -EEEEeecccc
Confidence             9999997543

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.72  E-value=3e-17  Score=138.16  Aligned_cols=85  Identities=26%  Similarity=0.407  Sum_probs=77.1

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++||++|+++|+.||.|++|+|+.+.   .+++++|||||+|.++++|++|++.|||.++.++. 
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~---~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~-  178 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDY---KTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKR-  178 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC---CCCccCcEEEEEEccHHHHHHHHHHcCCCccCCce-
Confidence            44567899999999999999999999999999999998853   34789999999999999999999999999999997 


Q ss_pred             CCCceEEEeecCC
Q 030012          158 DSPTLKIQFAHFP  170 (184)
Q Consensus       158 ~~~~l~V~~a~~~  170 (184)
                          |+|.|++..
T Consensus       179 ----i~V~~a~p~  187 (346)
T TIGR01659       179 ----LKVSYARPG  187 (346)
T ss_pred             ----eeeeccccc
Confidence                999999754

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).

>PF00076 RRM_1: RNA recognition motif

Probab=99.71  E-value=6.9e-17  Score=104.69  Aligned_cols=68  Identities=31%  Similarity=0.580  Sum_probs=63.5

Q ss_pred             EEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           85 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        85 lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      |||+|||.++|+++|+++|++||.|..+.+..+.    .++.++||||+|.+.++|++|++.|||..+.++.
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~----~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~   68 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNS----SGKSKGYAFVEFESEEDAEKALEELNGKKINGRK   68 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEET----TSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccc----cccccceEEEEEcCHHHHHHHHHHcCCCEECccC
Confidence            7999999999999999999999999999998752    2688999999999999999999999999999975

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.67  E-value=5.3e-16  Score=130.67  Aligned_cols=84  Identities=18%  Similarity=0.302  Sum_probs=74.3

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ..++|||+|||+++||++|+++|++||.|++|+|+.++   .+++++|||||+|.+.++|++||+.||+..+.+..   .
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~---~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~---~  265 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDK---LTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGS---Q  265 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecC---CCCccceEEEEEECCHHHHHHHHHHhCCCccCCCc---e
Confidence            45789999999999999999999999999999998743   34789999999999999999999999999998752   3


Q ss_pred             ceEEEeecCC
Q 030012          161 TLKIQFAHFP  170 (184)
Q Consensus       161 ~l~V~~a~~~  170 (184)
                      +|+|.|++..
T Consensus       266 ~l~V~~a~~~  275 (346)
T TIGR01659       266 PLTVRLAEEH  275 (346)
T ss_pred             eEEEEECCcc
Confidence            5999999753

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).

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.67  E-value=1.5e-16  Score=113.83  Aligned_cols=83  Identities=22%  Similarity=0.316  Sum_probs=74.1

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ...+++||||||++.++||+|.++|+++|+|+.|.+-.+.   ....+.|||||+|.+.++|+.|++-++|..++.+.  
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr---~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~--  107 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDR---FKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRP--  107 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEecccc---CCcCccceEEEEEecchhHHHHHHHhccCcccccc--
Confidence            4568999999999999999999999999999998776643   33568899999999999999999999999999996  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |+++|...
T Consensus       108 ---ir~D~D~G  115 (153)
T KOG0121|consen  108 ---IRIDWDAG  115 (153)
T ss_pred             ---eeeecccc
Confidence               99999753

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.66  E-value=3.9e-16  Score=117.16  Aligned_cols=79  Identities=23%  Similarity=0.406  Sum_probs=71.5

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      -.++||||||+..+++.||+.+|..||.+.+|.|...        +.|||||||++..+|+.|+..|+|..|.|.+    
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn--------PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r----   76 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN--------PPGFAFVEFEDPRDAEDAVRYLDGKDICGSR----   76 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec--------CCCceEEeccCcccHHHHHhhcCCccccCce----
Confidence            4689999999999999999999999999999988652        3469999999999999999999999999998    


Q ss_pred             ceEEEeecCCCC
Q 030012          161 TLKIQFAHFPFH  172 (184)
Q Consensus       161 ~l~V~~a~~~~~  172 (184)
                       |+|++.+....
T Consensus        77 -~rVE~S~G~~r   87 (195)
T KOG0107|consen   77 -IRVELSTGRPR   87 (195)
T ss_pred             -EEEEeecCCcc
Confidence             99999986544

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.65  E-value=6.2e-16  Score=121.45  Aligned_cols=83  Identities=22%  Similarity=0.436  Sum_probs=76.3

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      -+..++|-|.||+.+++|++|+++|.+||.|..+.|.++   +.+|.+||||||.|+++++|.+||+.|||+-++.-.  
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylard---K~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LI--  260 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARD---KETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLI--  260 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEc---cccCcccceEEEEEecHHHHHHHHHHccCcccceEE--
Confidence            346789999999999999999999999999999999985   445899999999999999999999999999998876  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |+|+|+++
T Consensus       261 ---LrvEwskP  268 (270)
T KOG0122|consen  261 ---LRVEWSKP  268 (270)
T ss_pred             ---EEEEecCC
Confidence               99999975

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.65  E-value=1.3e-15  Score=122.09  Aligned_cols=77  Identities=21%  Similarity=0.270  Sum_probs=70.1

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCc
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPT  161 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~  161 (184)
                      .++|||+||++.++|++|+++|+.||.|.+|+|+.+.      .++|||||+|.+.++|+.|+. |+|..|.|+.     
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~------~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~-----   71 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN------ERSQIAYVTFKDPQGAETALL-LSGATIVDQS-----   71 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC------CCCCEEEEEeCcHHHHHHHHH-hcCCeeCCce-----
Confidence            5799999999999999999999999999999998752      246799999999999999995 9999999998     


Q ss_pred             eEEEeecCC
Q 030012          162 LKIQFAHFP  170 (184)
Q Consensus       162 l~V~~a~~~  170 (184)
                      |+|+++...
T Consensus        72 V~Vt~a~~~   80 (260)
T PLN03120         72 VTITPAEDY   80 (260)
T ss_pred             EEEEeccCC
Confidence            999999753

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.63  E-value=7.9e-16  Score=120.30  Aligned_cols=79  Identities=24%  Similarity=0.335  Sum_probs=68.9

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCc
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPT  161 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~  161 (184)
                      -.+||||+|+|+++.|+|+++|++||+|++..++.+   +.+|++|||+||+|.|.++|++|++- -.-.|+||+     
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd---~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~-----   82 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITD---KNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRK-----   82 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEec---cCCccccceeeEEeecHHHHHHHhcC-CCCcccccc-----
Confidence            468999999999999999999999999999999985   44589999999999999999999963 347889987     


Q ss_pred             eEEEeecC
Q 030012          162 LKIQFAHF  169 (184)
Q Consensus       162 l~V~~a~~  169 (184)
                      -.++.|.-
T Consensus        83 aNcnlA~l   90 (247)
T KOG0149|consen   83 ANCNLASL   90 (247)
T ss_pred             cccchhhh
Confidence            66666654

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.63  E-value=1.8e-15  Score=134.58  Aligned_cols=83  Identities=14%  Similarity=0.303  Sum_probs=76.1

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ..++|||+||++++++++|+++|+.||.|++|++.++.   .+++++|||||+|++.++|.+|++.||++++.|+.    
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~---~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~----  275 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAP---TGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQY----  275 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecC---CCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeE----
Confidence            45799999999999999999999999999999999853   34789999999999999999999999999999998    


Q ss_pred             ceEEEeecCCC
Q 030012          161 TLKIQFAHFPF  171 (184)
Q Consensus       161 ~l~V~~a~~~~  171 (184)
                       |+|.++..+.
T Consensus       276 -LrV~kAi~pP  285 (612)
T TIGR01645       276 -LRVGKCVTPP  285 (612)
T ss_pred             -EEEEecCCCc
Confidence             9999998643

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.

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.62  E-value=3.7e-16  Score=131.03  Aligned_cols=89  Identities=26%  Similarity=0.364  Sum_probs=79.8

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcC-CeeCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHG-YKFDDKKPD  158 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g-~~~~g~~~~  158 (184)
                      ...++||||.|+..+||.|++++|++||.|++|.|++++.    +.+||||||+|.+.+.|..||+.||| +++.|.   
T Consensus       122 ~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~----~~sRGcaFV~fstke~A~~Aika~ng~~tmeGc---  194 (510)
T KOG0144|consen  122 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD----GLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGC---  194 (510)
T ss_pred             ccchhhhhhhccccccHHHHHHHHHhhCccchhhheeccc----ccccceeEEEEehHHHHHHHHHhhccceeeccC---
Confidence            3478999999999999999999999999999999998754    78999999999999999999999999 778887   


Q ss_pred             CCceEEEeecCCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~~  175 (184)
                      +.||.|.||...+.+..
T Consensus       195 s~PLVVkFADtqkdk~~  211 (510)
T KOG0144|consen  195 SQPLVVKFADTQKDKDG  211 (510)
T ss_pred             CCceEEEecccCCCchH
Confidence            58999999987665543

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.62  E-value=4.4e-15  Score=119.56  Aligned_cols=94  Identities=17%  Similarity=0.316  Sum_probs=82.5

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ..++-+||||+-|+.+++|++|+..|+.||.|+.|+|+.+   +.+|+++|||||+|+++.+...|.+..+|.+|+|++ 
T Consensus        97 ~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d---~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrr-  172 (335)
T KOG0113|consen   97 IGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRD---KVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRR-  172 (335)
T ss_pred             cCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeee---cccCCccceEEEEeccHHHHHHHHHhccCceecCcE-
Confidence            4567789999999999999999999999999999999995   445899999999999999999999999999999998 


Q ss_pred             CCCceEEEeecC-------CCCCCCCCCC
Q 030012          158 DSPTLKIQFAHF-------PFHLPSDGDE  179 (184)
Q Consensus       158 ~~~~l~V~~a~~-------~~~~~~~~~~  179 (184)
                          |.|++-+.       |++..+..++
T Consensus       173 ----i~VDvERgRTvkgW~PRRLGGGLGg  197 (335)
T KOG0113|consen  173 ----ILVDVERGRTVKGWLPRRLGGGLGG  197 (335)
T ss_pred             ----EEEEecccccccccccccccCCcCC
Confidence                99998764       5555544444

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.61  E-value=2.9e-15  Score=121.96  Aligned_cols=81  Identities=22%  Similarity=0.381  Sum_probs=74.9

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ..+..++|+|+|||+...|-||+.+|++||.|.+|+|+..|.     -+|||+||+|++.++|++|-++|||..+.||+ 
T Consensus        92 s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNER-----GSKGFGFVTmen~~dadRARa~LHgt~VEGRk-  165 (376)
T KOG0125|consen   92 SKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNER-----GSKGFGFVTMENPADADRARAELHGTVVEGRK-  165 (376)
T ss_pred             CCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccC-----CCCccceEEecChhhHHHHHHHhhcceeeceE-
Confidence            456678999999999999999999999999999999998764     26899999999999999999999999999999 


Q ss_pred             CCCceEEEeec
Q 030012          158 DSPTLKIQFAH  168 (184)
Q Consensus       158 ~~~~l~V~~a~  168 (184)
                          |.|+.|.
T Consensus       166 ----IEVn~AT  172 (376)
T KOG0125|consen  166 ----IEVNNAT  172 (376)
T ss_pred             ----EEEeccc
Confidence                9999874

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.60  E-value=4e-15  Score=132.34  Aligned_cols=82  Identities=16%  Similarity=0.334  Sum_probs=74.5

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ...++|||+||++++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+.   
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D---~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~---  178 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWD---PATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRN---  178 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeec---CCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecce---
Confidence            34579999999999999999999999999999999884   334789999999999999999999999999999998   


Q ss_pred             CceEEEeecC
Q 030012          160 PTLKIQFAHF  169 (184)
Q Consensus       160 ~~l~V~~a~~  169 (184)
                        |+|.+..+
T Consensus       179 --IkV~rp~~  186 (612)
T TIGR01645       179 --IKVGRPSN  186 (612)
T ss_pred             --eeeccccc
Confidence              99987654

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=99.60  E-value=7.6e-15  Score=95.66  Aligned_cols=68  Identities=25%  Similarity=0.557  Sum_probs=61.0

Q ss_pred             EEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           85 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        85 lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      |||+|||+++++++|+++|+.||.|..+++...   +. +..+++|||+|.+.++|++|++.+++..+.|+.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~---~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~   68 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKN---KD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRK   68 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEES---TT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEee---ec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEE
Confidence            799999999999999999999999999999874   33 578999999999999999999999999999975

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 ....

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.59  E-value=7.1e-15  Score=123.40  Aligned_cols=89  Identities=22%  Similarity=0.415  Sum_probs=77.5

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcC-CeeCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHG-YKFDDKKP  157 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g-~~~~g~~~  157 (184)
                      +...-+||||-+|..++|+||+++|++||.|.+|.|++|   +.++.++|||||+|.+.++|.+|+.+||. +.+.|-  
T Consensus        31 d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kD---k~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~--  105 (510)
T KOG0144|consen   31 DGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKD---KSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGM--  105 (510)
T ss_pred             CchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecc---cccCcccceEEEEeccHHHHHHHHHHhhcccccCCC--
Confidence            344569999999999999999999999999999999995   44479999999999999999999999987 555554  


Q ss_pred             CCCceEEEeecCCCCC
Q 030012          158 DSPTLKIQFAHFPFHL  173 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~  173 (184)
                       .++|+|.||..++.+
T Consensus       106 -~~pvqvk~Ad~E~er  120 (510)
T KOG0144|consen  106 -HHPVQVKYADGERER  120 (510)
T ss_pred             -Ccceeecccchhhhc
Confidence             589999999877655

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.58  E-value=5.5e-15  Score=106.78  Aligned_cols=83  Identities=20%  Similarity=0.384  Sum_probs=76.1

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ..-.++.|||.++..++||++|.+.|..||+|+++.|-.+   +.+|-.+|||+|+|++.+.|++|++.+||..+.+++ 
T Consensus        68 rSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLD---RRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~-  143 (170)
T KOG0130|consen   68 RSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLD---RRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQN-  143 (170)
T ss_pred             cceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccc---cccccccceeeeehHhHHHHHHHHHhccchhhhCCc-
Confidence            3456789999999999999999999999999999998774   445899999999999999999999999999999998 


Q ss_pred             CCCceEEEeec
Q 030012          158 DSPTLKIQFAH  168 (184)
Q Consensus       158 ~~~~l~V~~a~  168 (184)
                          |.|+|+-
T Consensus       144 ----v~VDw~F  150 (170)
T KOG0130|consen  144 ----VSVDWCF  150 (170)
T ss_pred             ----eeEEEEE
Confidence                9999984

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.58  E-value=4.8e-15  Score=112.37  Aligned_cols=81  Identities=30%  Similarity=0.545  Sum_probs=72.2

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ...++|||+|||.++.|.||+++|.+||.|.+|.|...    .  ..-.||||+|++..+|+.||..-+|+.++|.+   
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r----~--g~ppfafVeFEd~RDAeDAiygRdGYdydg~r---   74 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR----P--GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCR---   74 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC----C--CCCCeeEEEecCccchhhhhhcccccccCcce---
Confidence            45689999999999999999999999999999998542    1  23459999999999999999999999999998   


Q ss_pred             CceEEEeecCCC
Q 030012          160 PTLKIQFAHFPF  171 (184)
Q Consensus       160 ~~l~V~~a~~~~  171 (184)
                        |+|+|++..+
T Consensus        75 --LRVEfprggr   84 (241)
T KOG0105|consen   75 --LRVEFPRGGR   84 (241)
T ss_pred             --EEEEeccCCC
Confidence              9999998764

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.57  E-value=2.1e-14  Score=126.34  Aligned_cols=83  Identities=22%  Similarity=0.382  Sum_probs=75.3

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.+.   .+|.++|||||+|.+.++|+.|++.|||..+.|+.   
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~---~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~---  366 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDI---ATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNK---  366 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC---CCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeE---
Confidence            345799999999999999999999999999999998743   34789999999999999999999999999999998   


Q ss_pred             CceEEEeecCC
Q 030012          160 PTLKIQFAHFP  170 (184)
Q Consensus       160 ~~l~V~~a~~~  170 (184)
                        |.|.++...
T Consensus       367 --l~v~~a~~~  375 (509)
T TIGR01642       367 --LHVQRACVG  375 (509)
T ss_pred             --EEEEECccC
Confidence              999998643

Members of this subfamily are found in plants, metazoa and fungi.

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.57  E-value=7.5e-15  Score=112.99  Aligned_cols=82  Identities=22%  Similarity=0.395  Sum_probs=75.0

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      +.-..|-|-||.+.++.++|+.+|++||.|-+|.|.++.   .+..++|||||.|.+..+|+.|+++|+|.+++|+.   
T Consensus        11 ~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr---~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRe---   84 (256)
T KOG4207|consen   11 EGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDR---YTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRE---   84 (256)
T ss_pred             ccceeEEecceeccCCHHHHHHHHHHhCcccceeccccc---ccccccceeEEEeeecchHHHHHHhhcceeeccce---
Confidence            444688999999999999999999999999999998853   34689999999999999999999999999999998   


Q ss_pred             CceEEEeecC
Q 030012          160 PTLKIQFAHF  169 (184)
Q Consensus       160 ~~l~V~~a~~  169 (184)
                        |+|++|+.
T Consensus        85 --lrVq~ary   92 (256)
T KOG4207|consen   85 --LRVQMARY   92 (256)
T ss_pred             --eeehhhhc
Confidence              99999975

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.57  E-value=2.9e-14  Score=98.62  Aligned_cols=80  Identities=26%  Similarity=0.437  Sum_probs=72.3

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      +...++.|||.|||+.+|.|+..++|.+||.|+.|++-..      ...+|.|||.|++..+|.+|++.|+|+.+.++- 
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~------k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ry-   86 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNT------KETRGTAFVVYEDIFDAKKACDHLSGYNVDNRY-   86 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCc------cCcCceEEEEehHhhhHHHHHHHhcccccCCce-
Confidence            4567899999999999999999999999999999999653      235789999999999999999999999999997 


Q ss_pred             CCCceEEEeec
Q 030012          158 DSPTLKIQFAH  168 (184)
Q Consensus       158 ~~~~l~V~~a~  168 (184)
                          |.|-|..
T Consensus        87 ----l~vlyyq   93 (124)
T KOG0114|consen   87 ----LVVLYYQ   93 (124)
T ss_pred             ----EEEEecC
Confidence                9888864

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.56  E-value=1.7e-14  Score=125.32  Aligned_cols=79  Identities=22%  Similarity=0.505  Sum_probs=73.4

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCc
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPT  161 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~  161 (184)
                      .++|||+|||..+++++|+++|++||.|..|+++.+.   .+|+++|||||+|.+.++|.+|++.|||+.+.|+.     
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~---~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~-----  257 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDP---ETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRP-----  257 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcC---CCCccceEEEEEECCHHHHHHHHHhcCCcEECCEE-----
Confidence            6899999999999999999999999999999998753   33688999999999999999999999999999997     


Q ss_pred             eEEEeec
Q 030012          162 LKIQFAH  168 (184)
Q Consensus       162 l~V~~a~  168 (184)
                      |+|.|+.
T Consensus       258 i~v~~a~  264 (457)
T TIGR01622       258 IKVGYAQ  264 (457)
T ss_pred             EEEEEcc
Confidence            9999975

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=99.56  E-value=1.4e-14  Score=128.58  Aligned_cols=80  Identities=23%  Similarity=0.331  Sum_probs=70.7

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeC-CCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFD-DKKP  157 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~-g~~~  157 (184)
                      ....++|||+|||++++|++|+++|++||.|.+|+|+.+.+    ++++|||||+|.+.++|++||+.||+.++. ++. 
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~s----G~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~-  129 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFS----GQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRL-  129 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCC----CCccceEEEEeCCHHHHHHHHHHcCCCeecCCcc-
Confidence            34568999999999999999999999999999999998633    789999999999999999999999999996 444 


Q ss_pred             CCCceEEEee
Q 030012          158 DSPTLKIQFA  167 (184)
Q Consensus       158 ~~~~l~V~~a  167 (184)
                          |.|.++
T Consensus       130 ----l~V~~S  135 (578)
T TIGR01648       130 ----LGVCIS  135 (578)
T ss_pred             ----cccccc
Confidence                666654

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

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

Probab=99.56  E-value=2.3e-14  Score=127.71  Aligned_cols=81  Identities=23%  Similarity=0.338  Sum_probs=74.9

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ....+|||+||++++++++|+++|++||.|.+|+++.+.+    ++++|||||+|.+.++|++|++.|||..+.|+.   
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~----g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~---  355 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEK----GVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKP---  355 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCC----CCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCce---
Confidence            4567899999999999999999999999999999998633    788999999999999999999999999999997   


Q ss_pred             CceEEEeecC
Q 030012          160 PTLKIQFAHF  169 (184)
Q Consensus       160 ~~l~V~~a~~  169 (184)
                        |.|.||..
T Consensus       356 --l~V~~a~~  363 (562)
T TIGR01628       356 --LYVALAQR  363 (562)
T ss_pred             --eEEEeccC
Confidence              99999875

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.56  E-value=2e-14  Score=114.53  Aligned_cols=81  Identities=16%  Similarity=0.313  Sum_probs=74.0

Q ss_pred             CCCCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCC
Q 030012           76 PLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDK  155 (184)
Q Consensus        76 ~~~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~  155 (184)
                      +.....+++|||||++..+||++|++.|+.||.|.+||+.++         +||+||.|++.|+|..||..+|+.+|.|.
T Consensus       158 NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~---------qGYaFVrF~tkEaAahAIv~mNntei~G~  228 (321)
T KOG0148|consen  158 NQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD---------QGYAFVRFETKEAAAHAIVQMNNTEIGGQ  228 (321)
T ss_pred             ccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc---------cceEEEEecchhhHHHHHHHhcCceeCce
Confidence            335677899999999999999999999999999999999753         56999999999999999999999999999


Q ss_pred             CCCCCceEEEeecCC
Q 030012          156 KPDSPTLKIQFAHFP  170 (184)
Q Consensus       156 ~~~~~~l~V~~a~~~  170 (184)
                      -     +++.|.|..
T Consensus       229 ~-----VkCsWGKe~  238 (321)
T KOG0148|consen  229 L-----VRCSWGKEG  238 (321)
T ss_pred             E-----EEEeccccC
Confidence            7     999999863

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.55  E-value=4.2e-14  Score=111.98  Aligned_cols=78  Identities=19%  Similarity=0.230  Sum_probs=69.6

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ..+.+|||+||++.+||++|+++|+.||.|.+|+|+++      ++.++||||+|.+.++++.|+ .|+|..|.++.   
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D------~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~---   72 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS------GEYACTAYVTFKDAYALETAV-LLSGATIVDQR---   72 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC------CCcceEEEEEECCHHHHHHHH-hcCCCeeCCce---
Confidence            34689999999999999999999999999999999875      344579999999999999999 69999999997   


Q ss_pred             CceEEEeecC
Q 030012          160 PTLKIQFAHF  169 (184)
Q Consensus       160 ~~l~V~~a~~  169 (184)
                        |.|.-+..
T Consensus        73 --I~It~~~~   80 (243)
T PLN03121         73 --VCITRWGQ   80 (243)
T ss_pred             --EEEEeCcc
Confidence              88887654

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

Probab=99.55  E-value=2.4e-14  Score=127.68  Aligned_cols=77  Identities=25%  Similarity=0.466  Sum_probs=71.7

Q ss_pred             EEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceE
Q 030012           84 LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLK  163 (184)
Q Consensus        84 ~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~  163 (184)
                      +|||+|||.++||++|+++|++||.|.+|++.++..   +++++|||||+|.+.++|++|++.|++..+.|+.     |+
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~---t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~-----i~   73 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSV---TRRSLGYGYVNFQNPADAERALETMNFKRLGGKP-----IR   73 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC---CCCcceEEEEEECCHHHHHHHHHHhCCCEECCee-----EE
Confidence            799999999999999999999999999999988533   3688999999999999999999999999999987     99


Q ss_pred             EEeec
Q 030012          164 IQFAH  168 (184)
Q Consensus       164 V~~a~  168 (184)
                      |.|+.
T Consensus        74 i~~s~   78 (562)
T TIGR01628        74 IMWSQ   78 (562)
T ss_pred             eeccc
Confidence            99985

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>PLN03213 repressor of silencing 3; Provisional

Probab=99.54  E-value=2.4e-14  Score=122.19  Aligned_cols=78  Identities=15%  Similarity=0.353  Sum_probs=70.8

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCH--HHHHHHHHHhcCCeeCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDP--KCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~--~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ....+||||||++.++++||+.+|..||.|.+|.|++. +    |  ||||||+|.+.  .++.+||..|||.++.|+. 
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE-T----G--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~-   79 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT-K----G--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGR-   79 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc-c----C--CceEEEEecCCcHHHHHHHHHHhcCCeecCce-
Confidence            44579999999999999999999999999999999832 1    4  89999999987  7899999999999999998 


Q ss_pred             CCCceEEEeecC
Q 030012          158 DSPTLKIQFAHF  169 (184)
Q Consensus       158 ~~~~l~V~~a~~  169 (184)
                          |+|+-|+.
T Consensus        80 ----LKVNKAKP   87 (759)
T PLN03213         80 ----LRLEKAKE   87 (759)
T ss_pred             ----eEEeeccH
Confidence                99999986

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.54  E-value=1.5e-15  Score=114.72  Aligned_cols=83  Identities=18%  Similarity=0.412  Sum_probs=76.0

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ..+.-|||||||++.||.||--+|++||+|++|.|++++   .+|+++||||+.|++..+..-|+..|||..|.||.   
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk---~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRt---  106 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDK---KTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRT---  106 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecC---CCCcccceEEEEecCccceEEEEeccCCceeccee---
Confidence            456789999999999999999999999999999999964   34899999999999999999999999999999998   


Q ss_pred             CceEEEeecCC
Q 030012          160 PTLKIQFAHFP  170 (184)
Q Consensus       160 ~~l~V~~a~~~  170 (184)
                        |+|+...+.
T Consensus       107 --irVDHv~~Y  115 (219)
T KOG0126|consen  107 --IRVDHVSNY  115 (219)
T ss_pred             --EEeeecccc
Confidence              999986543

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.53  E-value=6.6e-15  Score=114.34  Aligned_cols=89  Identities=19%  Similarity=0.352  Sum_probs=80.5

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++||||+|..+++|.-|...|-+||.|++|.+..+   ...+++|||+||+|+..++|.+||+.||+.++.||.  
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlD---yesqkHRgFgFVefe~aEDAaaAiDNMnesEL~Grt--   81 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLD---YESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRT--   81 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccc---hhcccccceeEEEeeccchhHHHhhcCchhhhccee--
Confidence            345689999999999999999999999999999999874   334789999999999999999999999999999998  


Q ss_pred             CCceEEEeecCCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~~  175 (184)
                         |+|+||++++-+.+
T Consensus        82 ---irVN~AkP~kikeg   95 (298)
T KOG0111|consen   82 ---IRVNLAKPEKIKEG   95 (298)
T ss_pred             ---EEEeecCCccccCC
Confidence               99999999876654

>smart00362 RRM_2 RNA recognition motif

Probab=99.53  E-value=6.3e-14  Score=89.81  Aligned_cols=71  Identities=30%  Similarity=0.570  Sum_probs=64.3

Q ss_pred             EEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceE
Q 030012           84 LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLK  163 (184)
Q Consensus        84 ~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~  163 (184)
                      +|||+|||..+++++|+++|++||.+..+++...+     +.++|+|||+|.+.++|+.|++.+++..+.++.     |+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-----~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~-----i~   70 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT-----GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRP-----LR   70 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-----CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEE-----Ee
Confidence            58999999999999999999999999999887642     467889999999999999999999999999876     76


Q ss_pred             E
Q 030012          164 I  164 (184)
Q Consensus       164 V  164 (184)
                      |
T Consensus        71 v   71 (72)
T smart00362       71 V   71 (72)
T ss_pred             e
Confidence            5

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.52  E-value=7.3e-14  Score=123.98  Aligned_cols=76  Identities=25%  Similarity=0.400  Sum_probs=69.4

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCC--CCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPF--VGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~--G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ...++|||+||++++++++|+++|++|  |.|++|++++           +||||+|++.++|++|++.|||.+|.|+. 
T Consensus       231 ~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r-----------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~-  298 (578)
T TIGR01648       231 AKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR-----------DYAFVHFEDREDAVKAMDELNGKELEGSE-  298 (578)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec-----------CeEEEEeCCHHHHHHHHHHhCCCEECCEE-
Confidence            345789999999999999999999999  9999997753           39999999999999999999999999998 


Q ss_pred             CCCceEEEeecCCC
Q 030012          158 DSPTLKIQFAHFPF  171 (184)
Q Consensus       158 ~~~~l~V~~a~~~~  171 (184)
                          |+|+|++.+.
T Consensus       299 ----I~V~~Akp~~  308 (578)
T TIGR01648       299 ----IEVTLAKPVD  308 (578)
T ss_pred             ----EEEEEccCCC
Confidence                9999998643

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.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.52  E-value=7.7e-14  Score=121.26  Aligned_cols=82  Identities=21%  Similarity=0.344  Sum_probs=73.7

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||..+++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|+. |+|..+.|+.  
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d---~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~--  159 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKD---RNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRP--  159 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeec---CCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCee--
Confidence            345789999999999999999999999999999999984   3347899999999999999999996 9999999987  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |.|+++..
T Consensus       160 ---i~v~~~~~  167 (457)
T TIGR01622       160 ---IIVQSSQA  167 (457)
T ss_pred             ---eEEeecch
Confidence               99988754

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.

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.50  E-value=1e-13  Score=110.13  Aligned_cols=85  Identities=22%  Similarity=0.416  Sum_probs=77.7

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ++....|.|.-||.++|+||++.+|...|+|++|++++++   ..|.+.||+||.|.++++|++|+..|||..+..++  
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDK---itGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KT--  112 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDK---ITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKT--  112 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeecc---ccccccccceeeecChHHHHHHHhhhcceeeccce--
Confidence            4555689999999999999999999999999999999954   45899999999999999999999999999999887  


Q ss_pred             CCceEEEeecCCC
Q 030012          159 SPTLKIQFAHFPF  171 (184)
Q Consensus       159 ~~~l~V~~a~~~~  171 (184)
                         |+|.||++..
T Consensus       113 ---IKVSyARPSs  122 (360)
T KOG0145|consen  113 ---IKVSYARPSS  122 (360)
T ss_pred             ---EEEEeccCCh
Confidence               9999998643

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.49  E-value=6.5e-14  Score=111.64  Aligned_cols=79  Identities=19%  Similarity=0.364  Sum_probs=73.8

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCc
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPT  161 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~  161 (184)
                      .-.+||+.|..+++.++|++.|.+||+|.+++++++.   .++++|||+||.|.+.++|+.||..|||..|..|.     
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~---~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~-----  133 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDM---NTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRT-----  133 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecc---cCCcccceeEEeccchHHHHHHHHHhCCeeeccce-----
Confidence            4589999999999999999999999999999999964   34899999999999999999999999999999998     


Q ss_pred             eEEEeec
Q 030012          162 LKIQFAH  168 (184)
Q Consensus       162 l~V~~a~  168 (184)
                      |+-+||.
T Consensus       134 IRTNWAT  140 (321)
T KOG0148|consen  134 IRTNWAT  140 (321)
T ss_pred             eeccccc
Confidence            9999984

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.48  E-value=2.4e-13  Score=119.39  Aligned_cols=79  Identities=22%  Similarity=0.346  Sum_probs=71.3

Q ss_pred             CCCCCEEEEcCCCC-CCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           79 KGESNLLFVDGLPT-DCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        79 ~~~~~~lfVgnLp~-~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ..++++|||+||++ .+|+++|+++|+.||.|.+|+++.+        .+|||||+|.+.++|+.|++.|||..+.|+. 
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~--------~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~-  342 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKN--------KKETALIEMADPYQAQLALTHLNGVKLFGKP-  342 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeC--------CCCEEEEEECCHHHHHHHHHHhCCCEECCce-
Confidence            34678999999998 6999999999999999999999863        2469999999999999999999999999997 


Q ss_pred             CCCceEEEeecCC
Q 030012          158 DSPTLKIQFAHFP  170 (184)
Q Consensus       158 ~~~~l~V~~a~~~  170 (184)
                          |+|.+++..
T Consensus       343 ----l~v~~s~~~  351 (481)
T TIGR01649       343 ----LRVCPSKQQ  351 (481)
T ss_pred             ----EEEEEcccc
Confidence                999998653

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).

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.48  E-value=8.2e-14  Score=119.70  Aligned_cols=82  Identities=22%  Similarity=0.417  Sum_probs=76.9

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      +.+||||+|++++|++|.++|+..|.|.+++++.+   +.+|+++||+|++|.+.++++.|++.|||+++.|++     |
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D---~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~-----l   90 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYD---RETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRK-----L   90 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeeccc---ccCCCcCceeeEecCchhhHHHHHHhcCCcccCCce-----E
Confidence            89999999999999999999999999999999984   556999999999999999999999999999999998     9


Q ss_pred             EEEeecCCCC
Q 030012          163 KIQFAHFPFH  172 (184)
Q Consensus       163 ~V~~a~~~~~  172 (184)
                      +|.|+.+...
T Consensus        91 ~v~~~~~~~~  100 (435)
T KOG0108|consen   91 RVNYASNRKN  100 (435)
T ss_pred             Eeecccccch
Confidence            9999976443

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.48  E-value=2.1e-13  Score=108.12  Aligned_cols=80  Identities=29%  Similarity=0.561  Sum_probs=74.1

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCc
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPT  161 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~  161 (184)
                      .++|||+|||..+++++|+++|..||.|..+++..+.   ..++++|||||+|.+.++|..|++.++|..+.|+.     
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~---~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~-----  186 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDR---ETGKSRGFAFVEFESEESAEKAIEELNGKELEGRP-----  186 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeecc---ccCccCceEEEEecCHHHHHHHHHHcCCCeECCce-----
Confidence            5999999999999999999999999999999998853   34789999999999999999999999999999998     


Q ss_pred             eEEEeecC
Q 030012          162 LKIQFAHF  169 (184)
Q Consensus       162 l~V~~a~~  169 (184)
                      |+|.++..
T Consensus       187 ~~v~~~~~  194 (306)
T COG0724         187 LRVQKAQP  194 (306)
T ss_pred             eEeecccc
Confidence            99999753

>smart00360 RRM RNA recognition motif

Probab=99.48  E-value=2.4e-13  Score=86.71  Aligned_cols=70  Identities=31%  Similarity=0.584  Sum_probs=62.7

Q ss_pred             EcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceEE
Q 030012           87 VDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKI  164 (184)
Q Consensus        87 VgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~V  164 (184)
                      |+|||..+++++|+++|++||.|..+.+....   ..++++|+|||+|.+.++|..|++.|++..+.++.     |+|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~---~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~-----~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDK---DTGKSKGFAFVEFESEEDAEKALEALNGKELDGRP-----LKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCC---CCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcE-----EEe
Confidence            57999999999999999999999999987743   23678899999999999999999999999998886     776

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.46  E-value=2.5e-13  Score=119.22  Aligned_cols=75  Identities=16%  Similarity=0.263  Sum_probs=67.9

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHh--cCCeeCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDAL--HGYKFDDKKPD  158 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l--~g~~~~g~~~~  158 (184)
                      ++++|||+|||++++|++|+++|++||.|.+|+++.         +++||||+|++.++|++|++.|  ++..+.|+.  
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~---------~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~--   69 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLP---------GKRQALVEFEDEESAKACVNFATSVPIYIRGQP--   69 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC---------CCCEEEEEeCchHHHHHHHHHhhcCCceEcCeE--
Confidence            468999999999999999999999999999999874         2469999999999999999875  789999997  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |+|+|+..
T Consensus        70 ---l~v~~s~~   77 (481)
T TIGR01649        70 ---AFFNYSTS   77 (481)
T ss_pred             ---EEEEecCC
Confidence               99999864

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=99.46  E-value=7.3e-13  Score=85.23  Aligned_cols=74  Identities=31%  Similarity=0.632  Sum_probs=66.3

Q ss_pred             EEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceE
Q 030012           84 LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLK  163 (184)
Q Consensus        84 ~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~  163 (184)
                      +|||+|||..+++++|+++|+.||.|..+.+.....    ..++|+|||+|.+.++|+.|++.+++..+.+++     +.
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~----~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~-----~~   71 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKD----TKSKGFAFVEFEDEEDAEKALEALNGKELGGRP-----LR   71 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCC----CCcceEEEEEECCHHHHHHHHHHhCCCeECCeE-----EE
Confidence            489999999999999999999999999999886432    256789999999999999999999999999987     88


Q ss_pred             EEe
Q 030012          164 IQF  166 (184)
Q Consensus       164 V~~  166 (184)
                      |.|
T Consensus        72 v~~   74 (74)
T cd00590          72 VEF   74 (74)
T ss_pred             EeC
Confidence            865

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).

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.45  E-value=3.9e-13  Score=113.39  Aligned_cols=82  Identities=22%  Similarity=0.303  Sum_probs=73.2

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ...++.||||.||.++.|+||..+|++.|.|-++||+.+   +.+|.+||||||+|.+.++|++|++.||+++|.-.+  
T Consensus        80 p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD---~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK--  154 (506)
T KOG0117|consen   80 PPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMD---PFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGK--  154 (506)
T ss_pred             CCCCceEEecCCCccccchhhHHHHHhccceeeEEEeec---ccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCC--
Confidence            366889999999999999999999999999999999984   445899999999999999999999999999997554  


Q ss_pred             CCceEEEee
Q 030012          159 SPTLKIQFA  167 (184)
Q Consensus       159 ~~~l~V~~a  167 (184)
                        .|.|..+
T Consensus       155 --~igvc~S  161 (506)
T KOG0117|consen  155 --LLGVCVS  161 (506)
T ss_pred             --EeEEEEe
Confidence              4776654

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.44  E-value=2.3e-12  Score=102.58  Aligned_cols=84  Identities=25%  Similarity=0.422  Sum_probs=76.4

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....+.|||-||.+++.|.-|.++|.+||.|.+|+++++-+   +.+.|||+||+..+.++|..||..|||+.+.++. 
T Consensus       274 ~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~t---tnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rv-  349 (360)
T KOG0145|consen  274 GPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFT---TNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRV-  349 (360)
T ss_pred             CCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCC---cccccceeEEEecchHHHHHHHHHhcCccccceE-
Confidence            445578999999999999999999999999999999999643   3678999999999999999999999999999997 


Q ss_pred             CCCceEEEeecC
Q 030012          158 DSPTLKIQFAHF  169 (184)
Q Consensus       158 ~~~~l~V~~a~~  169 (184)
                          |.|.|..+
T Consensus       350 ----LQVsFKtn  357 (360)
T KOG0145|consen  350 ----LQVSFKTN  357 (360)
T ss_pred             ----EEEEEecC
Confidence                99999754

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.42  E-value=2.7e-13  Score=109.11  Aligned_cols=76  Identities=24%  Similarity=0.459  Sum_probs=69.7

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      .+|||||||.++++.+|+.+|++||.|++|.|++.           |+||..++...|+.||..|||++++|..     |
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN-----------YgFVHiEdktaaedairNLhgYtLhg~n-----I   66 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN-----------YGFVHIEDKTAAEDAIRNLHGYTLHGVN-----I   66 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc-----------cceEEeecccccHHHHhhcccceecceE-----E
Confidence            47999999999999999999999999999999863           9999999999999999999999999997     9


Q ss_pred             EEEeecCCCCCC
Q 030012          163 KIQFAHFPFHLP  174 (184)
Q Consensus       163 ~V~~a~~~~~~~  174 (184)
                      +|+-+++....+
T Consensus        67 nVeaSksKsk~s   78 (346)
T KOG0109|consen   67 NVEASKSKSKAS   78 (346)
T ss_pred             EEEeccccCCCc
Confidence            999888764333

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.42  E-value=2.5e-13  Score=102.70  Aligned_cols=82  Identities=17%  Similarity=0.235  Sum_probs=74.8

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      .+...||||+||+..++++.|.++|-+.|.|+++++.++   +-....+||||++|.++++|+-|++.||..++.|+.  
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkD---rv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrp--   80 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKD---RVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRP--   80 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchh---hhcccccceeEEEEechhhhHHHHHHHHHHHhcCce--
Confidence            456789999999999999999999999999999999885   333578999999999999999999999999999996  


Q ss_pred             CCceEEEeec
Q 030012          159 SPTLKIQFAH  168 (184)
Q Consensus       159 ~~~l~V~~a~  168 (184)
                         |+|.-+.
T Consensus        81 ---Irv~kas   87 (203)
T KOG0131|consen   81 ---IRVNKAS   87 (203)
T ss_pred             ---eEEEecc
Confidence               9999886

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.41  E-value=5.1e-13  Score=112.73  Aligned_cols=79  Identities=20%  Similarity=0.321  Sum_probs=71.2

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      .-+.|||.||+.++|||.|+++|++||.|..|+.+++           ||||.|.++++|-+||+.+||++|+|..    
T Consensus       258 ~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-----------YaFVHf~eR~davkAm~~~ngkeldG~~----  322 (506)
T KOG0117|consen  258 KVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-----------YAFVHFAEREDAVKAMKETNGKELDGSP----  322 (506)
T ss_pred             heeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-----------eeEEeecchHHHHHHHHHhcCceecCce----
Confidence            3478999999999999999999999999999877653           9999999999999999999999999996    


Q ss_pred             ceEEEeecCCCCCCC
Q 030012          161 TLKIQFAHFPFHLPS  175 (184)
Q Consensus       161 ~l~V~~a~~~~~~~~  175 (184)
                       |.|.+|+++-.++.
T Consensus       323 -iEvtLAKP~~k~k~  336 (506)
T KOG0117|consen  323 -IEVTLAKPVDKKKK  336 (506)
T ss_pred             -EEEEecCChhhhcc
Confidence             99999998654443

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.37  E-value=1.8e-12  Score=111.78  Aligned_cols=79  Identities=24%  Similarity=0.454  Sum_probs=72.9

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      +.++|.|.||||.+.+.+|+.+|+.||.|++|.|.+.    .+|+.+|||||.|.+..+|..|++.||+.+|+||.    
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k----~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~----  187 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRK----KDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRP----  187 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccC----CCCCccceEEEEEeeHHHHHHHHHhccCceecCce----
Confidence            4679999999999999999999999999999999853    34677899999999999999999999999999997    


Q ss_pred             ceEEEeec
Q 030012          161 TLKIQFAH  168 (184)
Q Consensus       161 ~l~V~~a~  168 (184)
                       |-|+||-
T Consensus       188 -VAVDWAV  194 (678)
T KOG0127|consen  188 -VAVDWAV  194 (678)
T ss_pred             -eEEeeec
Confidence             9999985

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.37  E-value=1.5e-12  Score=103.93  Aligned_cols=86  Identities=28%  Similarity=0.398  Sum_probs=74.1

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ..++||||-|...-.|||++.+|..||.|.+|.+.+..    +|.+|||+||.|.+..+|+.||..|||.......  +.
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~----dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGA--SS   91 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP----DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGA--SS   91 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC----CCCCCCceEEEeccchHHHHHHHHhcccccCCCC--cc
Confidence            56899999999999999999999999999999998643    3789999999999999999999999995544333  45


Q ss_pred             ceEEEeecCCCC
Q 030012          161 TLKIQFAHFPFH  172 (184)
Q Consensus       161 ~l~V~~a~~~~~  172 (184)
                      .|.|.|+...+.
T Consensus        92 SLVVK~ADTdkE  103 (371)
T KOG0146|consen   92 SLVVKFADTDKE  103 (371)
T ss_pred             ceEEEeccchHH
Confidence            699999976553

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.35  E-value=2e-12  Score=97.84  Aligned_cols=109  Identities=11%  Similarity=0.210  Sum_probs=89.8

Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEE-EEeecCCCCCCCCcceEEEEEECCHHHH
Q 030012           62 INGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREI-RVIHKEPRRTGDRAMVLCFVEFDDPKCA  140 (184)
Q Consensus        62 ~~~~p~~~~~~~~~~~~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v-~l~~~~~~~~~g~~~G~afV~F~~~~~A  140 (184)
                      +-++|+.+..........+.+.+|||+||.++++|..|.+.|+.||.+.+. ++++++   .+|.++||+||.|.+.+.+
T Consensus        76 LYgrpIrv~kas~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~---~tg~~~~~g~i~~~sfeas  152 (203)
T KOG0131|consen   76 LYGRPIRVNKASAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDP---DTGNPKGFGFINYASFEAS  152 (203)
T ss_pred             hcCceeEEEecccccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccc---cCCCCCCCeEEechhHHHH
Confidence            456788777766555567778999999999999999999999999998763 555543   2378899999999999999


Q ss_pred             HHHHHHhcCCeeCCCCCCCCceEEEeecCCCCCCCCCCC
Q 030012          141 RTAMDALHGYKFDDKKPDSPTLKIQFAHFPFHLPSDGDE  179 (184)
Q Consensus       141 ~~Ai~~l~g~~~~g~~~~~~~l~V~~a~~~~~~~~~~~~  179 (184)
                      .+|+..++|+.+..+.     +.|.|+.....+. .+++
T Consensus       153 d~ai~s~ngq~l~nr~-----itv~ya~k~~~kg-~~~g  185 (203)
T KOG0131|consen  153 DAAIGSMNGQYLCNRP-----ITVSYAFKKDTKG-ERHG  185 (203)
T ss_pred             HHHHHHhccchhcCCc-----eEEEEEEecCCCc-ccCC
Confidence            9999999999999997     9999997665555 4543

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.35  E-value=9.1e-13  Score=109.07  Aligned_cols=79  Identities=16%  Similarity=0.364  Sum_probs=73.0

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      ++||||.+.+++.||.|+..|..||.|+++.+.++.   .+++++|||||+|+-++.|+-|++.|||..++||.     |
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp---~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRN-----i  185 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDP---ATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRN-----I  185 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeeccccc---ccccccceEEEEEeCcHHHHHHHHHhccccccCcc-----c
Confidence            789999999999999999999999999999998853   45899999999999999999999999999999998     9


Q ss_pred             EEEeecC
Q 030012          163 KIQFAHF  169 (184)
Q Consensus       163 ~V~~a~~  169 (184)
                      +|....+
T Consensus       186 KVgrPsN  192 (544)
T KOG0124|consen  186 KVGRPSN  192 (544)
T ss_pred             cccCCCC
Confidence            9885544

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.34  E-value=4.5e-12  Score=104.13  Aligned_cols=106  Identities=20%  Similarity=0.322  Sum_probs=85.5

Q ss_pred             CCCCCCCCCCCCccccCCCCCCCCCCCCCCCCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcc
Q 030012           48 RDIAPGINPTIPDVINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAM  127 (184)
Q Consensus        48 ~~~~~g~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~  127 (184)
                      ++...|.+.++...+-.+......  ..|+++....+|||++|-..++|.+|++.|.+||+|+++++...         +
T Consensus       196 ~dryyg~ndPva~kil~ra~~~~~--lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~---------~  264 (377)
T KOG0153|consen  196 KDRYYGLNDPVALKILNRAGSAGT--LEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR---------K  264 (377)
T ss_pred             ccccccccChHHHHHHhhcccccc--cCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc---------c
Confidence            566677777666555455554444  44456677789999999999999999999999999999998752         3


Q ss_pred             eEEEEEECCHHHHHHHHHH-hcCCeeCCCCCCCCceEEEeecC
Q 030012          128 VLCFVEFDDPKCARTAMDA-LHGYKFDDKKPDSPTLKIQFAHF  169 (184)
Q Consensus       128 G~afV~F~~~~~A~~Ai~~-l~g~~~~g~~~~~~~l~V~~a~~  169 (184)
                      +||||+|.+.++|+.|.+. ++-..|+|++     |+|.|++.
T Consensus       265 ~CAFv~ftTR~aAE~Aae~~~n~lvI~G~R-----l~i~Wg~~  302 (377)
T KOG0153|consen  265 GCAFVTFTTREAAEKAAEKSFNKLVINGFR-----LKIKWGRP  302 (377)
T ss_pred             ccceeeehhhHHHHHHHHhhcceeeecceE-----EEEEeCCC
Confidence            4999999999999998764 4778889998     99999987

>PF13893 RRM_5: RNA recognition motif

Probab=99.33  E-value=8.4e-12  Score=77.97  Aligned_cols=56  Identities=30%  Similarity=0.592  Sum_probs=49.7

Q ss_pred             HHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceEEEee
Q 030012           99 VSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA  167 (184)
Q Consensus        99 L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~V~~a  167 (184)
                      |+++|++||.|.++.+..+.        +++|||+|.+.++|+.|++.|||..+.|+.     |+|+||
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--------RGFAFVEFASVEDAQKAIEQLNGRQFNGRP-----LKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS--------TTEEEEEESSHHHHHHHHHHHTTSEETTEE-----EEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC--------CCEEEEEECCHHHHHHHHHHhCCCEECCcE-----EEEEEC
Confidence            67899999999999987532        369999999999999999999999999997     999996

(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 ....

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.31  E-value=9.1e-12  Score=97.15  Aligned_cols=82  Identities=24%  Similarity=0.430  Sum_probs=73.4

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHH----hhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSH----LFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDD  154 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~----~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g  154 (184)
                      ..++.||||.||+..+..++|++    +|++||.|++|.....      .+.+|-|||.|.+.+.|-.|+..|+|+-+.|
T Consensus         6 ~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt------~KmRGQA~VvFk~~~~As~A~r~l~gfpFyg   79 (221)
T KOG4206|consen    6 VNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKT------PKMRGQAFVVFKETEAASAALRALQGFPFYG   79 (221)
T ss_pred             cCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCC------CCccCceEEEecChhHHHHHHHHhcCCcccC
Confidence            34556999999999999999988    9999999999987642      5788999999999999999999999999999


Q ss_pred             CCCCCCceEEEeecCCC
Q 030012          155 KKPDSPTLKIQFAHFPF  171 (184)
Q Consensus       155 ~~~~~~~l~V~~a~~~~  171 (184)
                      ..     ++|+||++..
T Consensus        80 K~-----mriqyA~s~s   91 (221)
T KOG4206|consen   80 KP-----MRIQYAKSDS   91 (221)
T ss_pred             ch-----hheecccCcc
Confidence            86     9999998754

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.31  E-value=1e-11  Score=107.27  Aligned_cols=83  Identities=24%  Similarity=0.390  Sum_probs=73.2

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHh-----cC-Ce
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDAL-----HG-YK  151 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l-----~g-~~  151 (184)
                      ......+|||.|||+++||++|++.|++||.|.++.|+.+   +.+++++|+|||.|.+..+|++||+..     .| +.
T Consensus       288 n~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~---k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~l  364 (678)
T KOG0127|consen  288 NITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKD---KDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVL  364 (678)
T ss_pred             cccccceEEEecCCccccHHHHHHHHHhhccceeEEEEec---cCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEE
Confidence            3455689999999999999999999999999999999884   445899999999999999999999877     34 88


Q ss_pred             eCCCCCCCCceEEEeec
Q 030012          152 FDDKKPDSPTLKIQFAH  168 (184)
Q Consensus       152 ~~g~~~~~~~l~V~~a~  168 (184)
                      ++||.     |+|..|-
T Consensus       365 l~GR~-----Lkv~~Av  376 (678)
T KOG0127|consen  365 LDGRL-----LKVTLAV  376 (678)
T ss_pred             EeccE-----Eeeeecc
Confidence            89987     9998874

>smart00361 RRM_1 RNA recognition motif

Probab=99.27  E-value=2.1e-11  Score=79.82  Aligned_cols=60  Identities=17%  Similarity=0.241  Sum_probs=50.6

Q ss_pred             HHHHHHhhc----CCCCEEEEE-EeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           96 RREVSHLFR----PFVGYREIR-VIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        96 e~~L~~~F~----~~G~i~~v~-l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      +++|+++|+    +||.|.++. ++.+... ..++++||+||+|.+.++|++|++.|||..+.|+.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~-~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~   66 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVG-YENHKRGNVYITFERSEDAARAIVDLNGRYFDGRT   66 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCC-CCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            578999998    999999995 5443221 12678999999999999999999999999999986

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.27  E-value=5.9e-12  Score=100.55  Aligned_cols=84  Identities=29%  Similarity=0.510  Sum_probs=76.6

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      +.+++++|||-.||.+..+.||..+|..||.|++.++..+   +.+..+|.|+||.|++..+|+.||..|||+.|.-++ 
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvD---RATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKR-  356 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVD---RATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKR-  356 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeeh---hccccccceeeEecCCchhHHHHHHHhcchhhhhhh-
Confidence            4567899999999999999999999999999999988774   445788999999999999999999999999999988 


Q ss_pred             CCCceEEEeecC
Q 030012          158 DSPTLKIQFAHF  169 (184)
Q Consensus       158 ~~~~l~V~~a~~  169 (184)
                          |+|+..+.
T Consensus       357 ----LKVQLKRP  364 (371)
T KOG0146|consen  357 ----LKVQLKRP  364 (371)
T ss_pred             ----hhhhhcCc
Confidence                99998765

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.25  E-value=1.9e-11  Score=107.66  Aligned_cols=76  Identities=24%  Similarity=0.425  Sum_probs=62.2

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCC------------CCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHH
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPF------------VGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMD  145 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~------------G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~  145 (184)
                      .....++|||+|||+.+|+++|+++|..+            +.|..+.+         .+.+|||||+|.+.++|+.|| 
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~---------~~~kg~afVeF~~~e~A~~Al-  240 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI---------NKEKNFAFLEFRTVEEATFAM-  240 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE---------CCCCCEEEEEeCCHHHHhhhh-
Confidence            35567899999999999999999999874            23444433         345689999999999999999 


Q ss_pred             HhcCCeeCCCCCCCCceEEEeec
Q 030012          146 ALHGYKFDDKKPDSPTLKIQFAH  168 (184)
Q Consensus       146 ~l~g~~~~g~~~~~~~l~V~~a~  168 (184)
                      .|+|..+.|+.     |+|...+
T Consensus       241 ~l~g~~~~g~~-----l~v~r~~  258 (509)
T TIGR01642       241 ALDSIIYSNVF-----LKIRRPH  258 (509)
T ss_pred             cCCCeEeeCce-----eEecCcc
Confidence            59999999986     9987654

Members of this subfamily are found in plants, metazoa and fungi.

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.24  E-value=2.4e-11  Score=102.65  Aligned_cols=80  Identities=21%  Similarity=0.419  Sum_probs=72.4

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhc-CCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFR-PFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~-~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ..+.+||.|||++..+++|+++|. +-|+|..|.|+.++.    |++||||.|||++++.+++|++.||-+++.||.   
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~----GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~---  115 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDES----GKARGCAVVEFKDPENVQKALEKLNKYEVNGRE---  115 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccC----CCcCCceEEEeeCHHHHHHHHHHhhhccccCce---
Confidence            345699999999999999999996 579999999998765    789999999999999999999999999999997   


Q ss_pred             CceEEEeecC
Q 030012          160 PTLKIQFAHF  169 (184)
Q Consensus       160 ~~l~V~~a~~  169 (184)
                        |+|.-.+.
T Consensus       116 --l~vKEd~d  123 (608)
T KOG4212|consen  116 --LVVKEDHD  123 (608)
T ss_pred             --EEEeccCc
Confidence              98876654

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.23  E-value=1.2e-11  Score=106.65  Aligned_cols=76  Identities=21%  Similarity=0.438  Sum_probs=69.4

Q ss_pred             EEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceE
Q 030012           84 LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLK  163 (184)
Q Consensus        84 ~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~  163 (184)
                      .||||||.++++|++|+.+|+.||.|..|.+..+..   +|.++||+||+|.+.++|.+|++.|||+++.|+.     |+
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~---tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~-----ik  351 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSE---TGRSKGFGFITFVNKEDARKALEQLNGFELAGRL-----IK  351 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccc---cccccCcceEEEecHHHHHHHHHHhccceecCce-----EE
Confidence            399999999999999999999999999999987532   3899999999999999999999999999999997     88


Q ss_pred             EEee
Q 030012          164 IQFA  167 (184)
Q Consensus       164 V~~a  167 (184)
                      |..-
T Consensus       352 V~~v  355 (549)
T KOG0147|consen  352 VSVV  355 (549)
T ss_pred             EEEe
Confidence            7654

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.22  E-value=2.5e-11  Score=108.29  Aligned_cols=79  Identities=27%  Similarity=0.373  Sum_probs=73.2

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCc
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPT  161 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~  161 (184)
                      ++|||||+|+..++|.||+.+|+.||+|.+|.++.         ++|||||......+|++|+..|+.+.+.++.     
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~---------~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~-----  486 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP---------PRGCAFIKMVRRQDAEKALQKLSNVKVADKT-----  486 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeecc---------CCceeEEEEeehhHHHHHHHHHhccccccee-----
Confidence            57999999999999999999999999999999863         4679999999999999999999999999997     


Q ss_pred             eEEEeecCCCCCC
Q 030012          162 LKIQFAHFPFHLP  174 (184)
Q Consensus       162 l~V~~a~~~~~~~  174 (184)
                      |+|.||.+.+-+.
T Consensus       487 Iki~Wa~g~G~ks  499 (894)
T KOG0132|consen  487 IKIAWAVGKGPKS  499 (894)
T ss_pred             eEEeeeccCCcch
Confidence            9999998877665

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.20  E-value=6e-11  Score=100.80  Aligned_cols=74  Identities=20%  Similarity=0.381  Sum_probs=67.9

Q ss_pred             EEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceEE
Q 030012           85 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKI  164 (184)
Q Consensus        85 lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~V  164 (184)
                      |||.||++.++.++|.++|+.||+|++|++..++.    | ++|| ||+|+++++|++|++.+||..+.+.+     |.|
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~----g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kk-----i~v  147 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN----G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKK-----IYV  147 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC----C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCe-----eEE
Confidence            99999999999999999999999999999998654    3 8999 99999999999999999999999987     877


Q ss_pred             EeecC
Q 030012          165 QFAHF  169 (184)
Q Consensus       165 ~~a~~  169 (184)
                      .....
T Consensus       148 g~~~~  152 (369)
T KOG0123|consen  148 GLFER  152 (369)
T ss_pred             eeccc
Confidence            66543

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.17  E-value=9.3e-10  Score=86.03  Aligned_cols=87  Identities=34%  Similarity=0.565  Sum_probs=72.5

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      .+.-+||||.+||.++...||..+|..|-..+.+.|...  .+.+.-.+-++|++|.+..+|+.|+..|||..|+-..  
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~T--sk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~--  106 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYT--SKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPET--  106 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeec--cCCCccccceEEEEecchHHHHHHHHHhcCeeecccc--
Confidence            355789999999999999999999999977777766442  2222234569999999999999999999999999876  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                      ..+|++++||.
T Consensus       107 ~stLhiElAKS  117 (284)
T KOG1457|consen  107 GSTLHIELAKS  117 (284)
T ss_pred             CceeEeeehhc
Confidence            67799999985

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.16  E-value=2.8e-11  Score=107.12  Aligned_cols=81  Identities=27%  Similarity=0.472  Sum_probs=74.2

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ..++|.|.|||+.++..+++++|..||.+++|+|... .++  +.++|||||+|-+..+|.+|+++|.+..+.||+    
T Consensus       612 ~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK-~~k--~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRr----  684 (725)
T KOG0110|consen  612 KGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKK-IGK--GAHRGFGFVDFLTPREAKNAFDALGSTHLYGRR----  684 (725)
T ss_pred             ccceeeeeccchHHHHHHHHHHHhcccceeeeccchh-hcc--hhhccceeeeccCcHHHHHHHHhhcccceechh----
Confidence            3679999999999999999999999999999999875 222  568999999999999999999999999999999    


Q ss_pred             ceEEEeecC
Q 030012          161 TLKIQFAHF  169 (184)
Q Consensus       161 ~l~V~~a~~  169 (184)
                       |.++||+.
T Consensus       685 -LVLEwA~~  692 (725)
T KOG0110|consen  685 -LVLEWAKS  692 (725)
T ss_pred             -hheehhcc
Confidence             99999976

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.16  E-value=5.1e-11  Score=98.39  Aligned_cols=83  Identities=23%  Similarity=0.401  Sum_probs=76.7

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      .++.+.|||-.|.+-++.+||.-+|+.||.|++|.++++   +.+|.+.-||||+|++.++.++|.-.|++..|++++  
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD---~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrR--  310 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRD---RKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRR--  310 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEec---ccccchhheeeeeecchhhHHHHHhhhcceeeccce--
Confidence            456789999999999999999999999999999999995   344789999999999999999999999999999999  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |.|+|+.+
T Consensus       311 ---IHVDFSQS  318 (479)
T KOG0415|consen  311 ---IHVDFSQS  318 (479)
T ss_pred             ---EEeehhhh
Confidence               99999864

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.16  E-value=1.4e-10  Score=89.51  Aligned_cols=85  Identities=19%  Similarity=0.358  Sum_probs=73.6

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCC-CCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPF-VGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~-G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      ......-+||..+|..+.+.++..+|.+| |.+..+++.+   ++.+|.++|||||+|++.+.|+-|.+.||++.+.++-
T Consensus        45 ~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsR---nkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~l  121 (214)
T KOG4208|consen   45 EQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSR---NKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHL  121 (214)
T ss_pred             ccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeec---ccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhhe
Confidence            34556689999999999999999999998 6677777766   4455899999999999999999999999999999997


Q ss_pred             CCCCceEEEeecCC
Q 030012          157 PDSPTLKIQFAHFP  170 (184)
Q Consensus       157 ~~~~~l~V~~a~~~  170 (184)
                           |.|.+-...
T Consensus       122 -----L~c~vmppe  130 (214)
T KOG4208|consen  122 -----LECHVMPPE  130 (214)
T ss_pred             -----eeeEEeCch
Confidence                 999987654

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.12  E-value=9.8e-11  Score=94.48  Aligned_cols=74  Identities=24%  Similarity=0.430  Sum_probs=69.1

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ..+.+|+||||.+.++.+||+..|++||.|++|+|+++           |+||.|+-.++|..|++.||+.++.|++   
T Consensus        76 k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd-----------y~fvh~d~~eda~~air~l~~~~~~gk~---  141 (346)
T KOG0109|consen   76 KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD-----------YAFVHFDRAEDAVEAIRGLDNTEFQGKR---  141 (346)
T ss_pred             CCccccccCCCCccccCHHHhhhhcccCCceeeeeecc-----------eeEEEEeeccchHHHHhcccccccccce---
Confidence            45679999999999999999999999999999999863           9999999999999999999999999998   


Q ss_pred             CceEEEeecC
Q 030012          160 PTLKIQFAHF  169 (184)
Q Consensus       160 ~~l~V~~a~~  169 (184)
                        ++|+.+.+
T Consensus       142 --m~vq~sts  149 (346)
T KOG0109|consen  142 --MHVQLSTS  149 (346)
T ss_pred             --eeeeeecc
Confidence              99999854

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.11  E-value=4.8e-10  Score=94.89  Aligned_cols=76  Identities=18%  Similarity=0.322  Sum_probs=68.9

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||.|||+++|++.|++-|..||.|....|+..      |+++|  .|.|.++++|+.|+..|+|.++.|+.  
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~------GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~--  602 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMEN------GKSKG--VVRFFSPEDAERACALMNGSRLDGRN--  602 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhhcc------CCccc--eEEecCHHHHHHHHHHhccCcccCce--
Confidence            456788999999999999999999999999999988542      67777  89999999999999999999999998  


Q ss_pred             CCceEEEee
Q 030012          159 SPTLKIQFA  167 (184)
Q Consensus       159 ~~~l~V~~a  167 (184)
                         |+|+|.
T Consensus       603 ---I~V~y~  608 (608)
T KOG4212|consen  603 ---IKVTYF  608 (608)
T ss_pred             ---eeeeeC
Confidence               999884

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.07  E-value=2.7e-10  Score=94.59  Aligned_cols=81  Identities=14%  Similarity=0.294  Sum_probs=72.9

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      .-++|||..+.++.+|+||+.+|+.||+|++|.+.+.   .+++.+|||+|++|.+..+...|+..||=+.++|+.    
T Consensus       209 ~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~---pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQy----  281 (544)
T KOG0124|consen  209 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARA---PTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQY----  281 (544)
T ss_pred             hhheEEeeecCCCccHHHHHHHHHhhcceeeEEeecc---CCCCCccceeeEEeccccchHHHhhhcchhhcccce----
Confidence            3479999999999999999999999999999999884   445679999999999999999999999999999997    


Q ss_pred             ceEEEeecC
Q 030012          161 TLKIQFAHF  169 (184)
Q Consensus       161 ~l~V~~a~~  169 (184)
                       |+|--.-.
T Consensus       282 -LRVGk~vT  289 (544)
T KOG0124|consen  282 -LRVGKCVT  289 (544)
T ss_pred             -EecccccC
Confidence             88876543

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.05  E-value=7.2e-10  Score=98.32  Aligned_cols=80  Identities=30%  Similarity=0.429  Sum_probs=70.7

Q ss_pred             EEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceE
Q 030012           84 LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLK  163 (184)
Q Consensus        84 ~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~  163 (184)
                      +|||.||++++|.++|..+|...|.|.++.|.........-.+.||+||+|.+.++|+.|++.|+|..++|+.     |.
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~-----l~  591 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHK-----LE  591 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCce-----EE
Confidence            4999999999999999999999999999988764332212346799999999999999999999999999998     99


Q ss_pred             EEeec
Q 030012          164 IQFAH  168 (184)
Q Consensus       164 V~~a~  168 (184)
                      |.++.
T Consensus       592 lk~S~  596 (725)
T KOG0110|consen  592 LKISE  596 (725)
T ss_pred             EEecc
Confidence            99998

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.93  E-value=3e-09  Score=92.71  Aligned_cols=82  Identities=17%  Similarity=0.276  Sum_probs=72.9

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      -+++|||.+|+..+...||+.+|++||.|+-.+++..-..   .-.+.|+||++.+.++|.+||+.||-.+++|+.    
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRs---PGaRCYGfVTMSts~eAtkCI~hLHrTELHGrm----  476 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARS---PGARCYGFVTMSTSAEATKCIEHLHRTELHGRM----  476 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCC---CCcceeEEEEecchHHHHHHHHHhhhhhhccee----
Confidence            3578999999999999999999999999999999875322   235679999999999999999999999999998    


Q ss_pred             ceEEEeecCC
Q 030012          161 TLKIQFAHFP  170 (184)
Q Consensus       161 ~l~V~~a~~~  170 (184)
                       |.|+-+++.
T Consensus       477 -ISVEkaKNE  485 (940)
T KOG4661|consen  477 -ISVEKAKNE  485 (940)
T ss_pred             -eeeeecccC
Confidence             999999873

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.88  E-value=2e-09  Score=89.21  Aligned_cols=72  Identities=25%  Similarity=0.422  Sum_probs=62.2

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      ...+|||++|+|+++++.|++.|.+||+|.+|.++++.   ..++++||+||+|++.+...+++.. .-.+|+++.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~---~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~   76 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDP---STGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRS   76 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccC---CCCCcccccceecCCCcchheeecc-cccccCCcc
Confidence            67899999999999999999999999999999999854   3489999999999999998888753 345666665

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.88  E-value=2e-09  Score=84.48  Aligned_cols=72  Identities=24%  Similarity=0.439  Sum_probs=66.4

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      ..+||++||+.+.+.+|+++|..||.+.++.+..           ||+||+|++..+|+.|+..||+.++.+.+     +
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~-----------gf~fv~fed~rda~Dav~~l~~~~l~~e~-----~   65 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN-----------GFGFVEFEDPRDADDAVHDLDGKELCGER-----L   65 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec-----------ccceeccCchhhhhcccchhcCceeccee-----e
Confidence            3689999999999999999999999999998753           49999999999999999999999999987     9


Q ss_pred             EEEeecCC
Q 030012          163 KIQFAHFP  170 (184)
Q Consensus       163 ~V~~a~~~  170 (184)
                      .|+|++..
T Consensus        66 vve~~r~~   73 (216)
T KOG0106|consen   66 VVEHARGK   73 (216)
T ss_pred             eeeccccc
Confidence            99999853

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.84  E-value=1e-08  Score=84.57  Aligned_cols=81  Identities=17%  Similarity=0.251  Sum_probs=73.1

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEE--------EEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCe
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYRE--------IRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYK  151 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~--------v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~  151 (184)
                      ..+..|||.|||.++|-+++.++|++||-|..        |+|.+++.    |+.+|=|++.|-..++++-|++.|++..
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~----G~lKGDaLc~y~K~ESVeLA~~ilDe~~  207 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ----GKLKGDALCCYIKRESVELAIKILDEDE  207 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC----CCccCceEEEeecccHHHHHHHHhCccc
Confidence            44667999999999999999999999998864        77877543    7899999999999999999999999999


Q ss_pred             eCCCCCCCCceEEEeecC
Q 030012          152 FDDKKPDSPTLKIQFAHF  169 (184)
Q Consensus       152 ~~g~~~~~~~l~V~~a~~  169 (184)
                      +.|++     |+|+.|+.
T Consensus       208 ~rg~~-----~rVerAkf  220 (382)
T KOG1548|consen  208 LRGKK-----LRVERAKF  220 (382)
T ss_pred             ccCcE-----EEEehhhh
Confidence            99998     99999975

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.83  E-value=1.5e-08  Score=81.20  Aligned_cols=82  Identities=22%  Similarity=0.336  Sum_probs=71.5

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ....+|+|.||+..++++||+++|..||.+..+-+-.++.    |.+.|.|-|.|...++|+.|++.|||..++|+.   
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~----G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~---  153 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRA----GRSLGTADVSFNRRDDAERAVKKYNGVALDGRP---  153 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCC----CCCCccceeeecchHhHHHHHHHhcCcccCCce---
Confidence            3447899999999999999999999999888777766544    788999999999999999999999999999986   


Q ss_pred             CceEEEeecCC
Q 030012          160 PTLKIQFAHFP  170 (184)
Q Consensus       160 ~~l~V~~a~~~  170 (184)
                        +++.....+
T Consensus       154 --mk~~~i~~~  162 (243)
T KOG0533|consen  154 --MKIEIISSP  162 (243)
T ss_pred             --eeeEEecCc
Confidence              887776543

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.79  E-value=1.8e-08  Score=85.80  Aligned_cols=72  Identities=24%  Similarity=0.362  Sum_probs=66.2

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      ..||||   +++||.+|.++|+.+|.++++++.++.    +  +.|||||.|.+..+|++||+.||-..+.|+.     +
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~----t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~-----~   67 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA----T--SLGYAYVNFQQPADAERALDTMNFDVLKGKP-----I   67 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC----C--ccceEEEecCCHHHHHHHHHHcCCcccCCcE-----E
Confidence            468999   899999999999999999999999853    2  7899999999999999999999999999997     9


Q ss_pred             EEEeec
Q 030012          163 KIQFAH  168 (184)
Q Consensus       163 ~V~~a~  168 (184)
                      ++-|+.
T Consensus        68 rim~s~   73 (369)
T KOG0123|consen   68 RIMWSQ   73 (369)
T ss_pred             Eeehhc
Confidence            999974

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.75  E-value=1.1e-08  Score=88.89  Aligned_cols=70  Identities=27%  Similarity=0.365  Sum_probs=62.8

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      .-...+|+|-|||..+++++|.++|+.||+|+.++...        ..+|.+||+|.|..+|++|+++|++.++.|++
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~--------~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~  141 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETP--------NKRGIVFVEFYDVRDAERALKALNRREIAGKR  141 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccc--------ccCceEEEEEeehHhHHHHHHHHHHHHhhhhh
Confidence            44567999999999999999999999999999976543        33569999999999999999999999999987

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.75  E-value=4.1e-08  Score=78.48  Aligned_cols=82  Identities=13%  Similarity=0.220  Sum_probs=72.7

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ......+||+|+.+.+|.++++..|+.||.+..+.+..+   +..++++||+||+|.+.+.++.++. |||..+.++.  
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d---~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~--  171 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKD---KFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPA--  171 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeecc---ccCCCcceeEEEecccHhhhHHHhh-cCCccccccc--
Confidence            445679999999999999999999999999988888774   4457899999999999999999998 9999999998  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         +.|.+.+.
T Consensus       172 ---i~vt~~r~  179 (231)
T KOG4209|consen  172 ---IEVTLKRT  179 (231)
T ss_pred             ---ceeeeeee
Confidence               88888763

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.71  E-value=3.3e-08  Score=84.89  Aligned_cols=80  Identities=24%  Similarity=0.423  Sum_probs=65.9

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ...+|||.|||.++++++|+++|..||.|+..+|....   .+++...|+||+|++.++++.|+++- -..+++++    
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~---~~~~~~~fgFV~f~~~~~~~~~i~As-p~~ig~~k----  358 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRS---PGGKNPCFGFVEFENAAAVQNAIEAS-PLEIGGRK----  358 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEec---cCCCcCceEEEEEeecchhhhhhhcC-ccccCCee----
Confidence            34569999999999999999999999999998887643   22444489999999999999999754 67777777    


Q ss_pred             ceEEEeecC
Q 030012          161 TLKIQFAHF  169 (184)
Q Consensus       161 ~l~V~~a~~  169 (184)
                       |.|+--+.
T Consensus       359 -l~Veek~~  366 (419)
T KOG0116|consen  359 -LNVEEKRP  366 (419)
T ss_pred             -EEEEeccc
Confidence             88876654

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.70  E-value=5.6e-08  Score=86.59  Aligned_cols=86  Identities=16%  Similarity=0.252  Sum_probs=72.6

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ++..++|||+||++.++|+.|...|..||.|.++++++..+....-+.+-|+||-|-+..+|++|++.|+|..+....  
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e--  248 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYE--  248 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeee--
Confidence            345678999999999999999999999999999998873221111234569999999999999999999999999998  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         +++-|++.
T Consensus       249 ---~K~gWgk~  256 (877)
T KOG0151|consen  249 ---MKLGWGKA  256 (877)
T ss_pred             ---eeeccccc
Confidence               99999964

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.68  E-value=7.6e-09  Score=80.72  Aligned_cols=80  Identities=11%  Similarity=0.155  Sum_probs=69.6

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....+||||+|+...++|+-|.++|-+.|.|..|.|...+.    ++.+ ||||+|.++.+..-|++.+||..+.++.  
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d----~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e--   78 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD----QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDE--   78 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc----CCCc-eeeeecccccchhhhhhhcccchhccch--
Confidence            35568999999999999999999999999999999876433    4555 9999999999999999999999999986  


Q ss_pred             CCceEEEeec
Q 030012          159 SPTLKIQFAH  168 (184)
Q Consensus       159 ~~~l~V~~a~  168 (184)
                         ++|++-.
T Consensus        79 ---~q~~~r~   85 (267)
T KOG4454|consen   79 ---EQRTLRC   85 (267)
T ss_pred             ---hhccccc
Confidence               7777643

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.65  E-value=7.3e-08  Score=79.96  Aligned_cols=80  Identities=24%  Similarity=0.370  Sum_probs=67.5

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ..++|||++||.++++++++++|.+||.|..+.++.+.   ...+++||+||+|.+++++++++. ..-..|.++.    
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~---~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~----  167 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDK---TTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKK----  167 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecc---cccccccceeeEeccccccceecc-cceeeecCce----
Confidence            35699999999999999999999999988888887753   336899999999999999999974 5667888876    


Q ss_pred             ceEEEeecC
Q 030012          161 TLKIQFAHF  169 (184)
Q Consensus       161 ~l~V~~a~~  169 (184)
                       +.|.-|.+
T Consensus       168 -vevkrA~p  175 (311)
T KOG4205|consen  168 -VEVKRAIP  175 (311)
T ss_pred             -eeEeeccc
Confidence             77777753

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.52  E-value=8.2e-08  Score=75.24  Aligned_cols=70  Identities=23%  Similarity=0.514  Sum_probs=58.0

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDK  155 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~  155 (184)
                      ...+.||||.||..++|||+|+.+|+.|-...-++|-..    . |  ...||++|++.+.|..||..|+|..+--.
T Consensus       207 ~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~----~-g--~~vaf~~~~~~~~at~am~~lqg~~~s~~  276 (284)
T KOG1457|consen  207 ARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR----G-G--MPVAFADFEEIEQATDAMNHLQGNLLSSS  276 (284)
T ss_pred             chhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC----C-C--cceEeecHHHHHHHHHHHHHhhcceeccc
Confidence            345679999999999999999999999988777777432    1 2  23899999999999999999999887543

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.49  E-value=1.4e-07  Score=82.33  Aligned_cols=85  Identities=28%  Similarity=0.452  Sum_probs=75.8

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....+++||++||...++++++++...||.+...+++.+..   .|.++||||.+|.+......|+..|||..+.+..  
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~---~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~--  360 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSA---TGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKK--  360 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccc---cccccceeeeeeeCCcchhhhhcccchhhhcCce--
Confidence            45568999999999999999999999999999999988533   3789999999999999999999999999999997  


Q ss_pred             CCceEEEeecCCC
Q 030012          159 SPTLKIQFAHFPF  171 (184)
Q Consensus       159 ~~~l~V~~a~~~~  171 (184)
                         |.|+.|-...
T Consensus       361 ---lvvq~A~~g~  370 (500)
T KOG0120|consen  361 ---LVVQRAIVGA  370 (500)
T ss_pred             ---eEeehhhccc
Confidence               9999886433

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.48  E-value=1.7e-06  Score=60.02  Aligned_cols=84  Identities=15%  Similarity=0.278  Sum_probs=66.2

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCC--CCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPF--VGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~--G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      +||.|.|||...|.++|.+++...  |..--+.|..+-   ...-+.|||||.|.+.+.|.+-.+.++|..+.... ...
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf---~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~-s~K   77 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDF---KNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFN-SKK   77 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeec---cCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCC-CCc
Confidence            589999999999999999888653  555555555542   22568999999999999999999999999997653 244


Q ss_pred             ceEEEeecCC
Q 030012          161 TLKIQFAHFP  170 (184)
Q Consensus       161 ~l~V~~a~~~  170 (184)
                      .+.|.||+--
T Consensus        78 vc~i~yAriQ   87 (97)
T PF04059_consen   78 VCEISYARIQ   87 (97)
T ss_pred             EEEEehhHhh
Confidence            6789998743

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.47  E-value=7.5e-07  Score=69.83  Aligned_cols=78  Identities=37%  Similarity=0.663  Sum_probs=67.8

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ..++.++|+.|||.+++.+.|..+|.+|....+++++..   +     .+.|||+|.+...|..|...|+|..+--.   
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~---~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~---  211 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPP---R-----SGIAFVEFLSDRQASAAQQALQGFKITKK---  211 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccC---C-----CceeEEecchhhhhHHHhhhhccceeccC---
Confidence            567789999999999999999999999999999999862   2     34999999999999999999999998742   


Q ss_pred             CCceEEEeec
Q 030012          159 SPTLKIQFAH  168 (184)
Q Consensus       159 ~~~l~V~~a~  168 (184)
                       ++++|.|++
T Consensus       212 -~~m~i~~a~  220 (221)
T KOG4206|consen  212 -NTMQITFAK  220 (221)
T ss_pred             -ceEEecccC
Confidence             248888875

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.45  E-value=3.3e-06  Score=71.38  Aligned_cols=75  Identities=21%  Similarity=0.376  Sum_probs=67.5

Q ss_pred             CCEEEEcCCCC-CCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           82 SNLLFVDGLPT-DCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        82 ~~~lfVgnLp~-~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      +..|.|.||.. .+|.+-|..+|..||+|..|+|...+.   +     -|+|.|.|...|+-|++.|+|..+.|++    
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk---d-----~ALIQmsd~~qAqLA~~hL~g~~l~gk~----  364 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK---D-----NALIQMSDGQQAQLAMEHLEGHKLYGKK----  364 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC---c-----ceeeeecchhHHHHHHHHhhcceecCce----
Confidence            67889999976 579999999999999999999987432   2     7999999999999999999999999998    


Q ss_pred             ceEEEeecC
Q 030012          161 TLKIQFAHF  169 (184)
Q Consensus       161 ~l~V~~a~~  169 (184)
                       |+|.++|-
T Consensus       365 -lrvt~SKH  372 (492)
T KOG1190|consen  365 -LRVTLSKH  372 (492)
T ss_pred             -EEEeeccC
Confidence             99999984

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.43  E-value=1.1e-06  Score=59.00  Aligned_cols=72  Identities=19%  Similarity=0.261  Sum_probs=47.8

Q ss_pred             CEEEEcCCCCCCcHHH----HHHhhcCCCC-EEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           83 NLLFVDGLPTDCTRRE----VSHLFRPFVG-YREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~----L~~~F~~~G~-i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ..|||.|||.+.+...    |++++..||. |.+|  .           .+.|+|.|.+.+.|++|.+.|+|..+.|++ 
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~-----------~~tAilrF~~~~~A~RA~KRmegEdVfG~k-   68 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--S-----------GGTAILRFPNQEFAERAQKRMEGEDVFGNK-   68 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE---------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e-----------CCEEEEEeCCHHHHHHHHHhhcccccccce-
Confidence            4689999999887765    5677778854 4443  1           148999999999999999999999999998 


Q ss_pred             CCCceEEEeecCCCC
Q 030012          158 DSPTLKIQFAHFPFH  172 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~  172 (184)
                          |.|.|....+.
T Consensus        69 ----I~v~~~~~~r~   79 (90)
T PF11608_consen   69 ----ISVSFSPKNRE   79 (90)
T ss_dssp             -----EEESS--S--
T ss_pred             ----EEEEEcCCccc
Confidence                99999855443

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.42  E-value=3e-07  Score=73.27  Aligned_cols=73  Identities=19%  Similarity=0.371  Sum_probs=65.3

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      ...+||.|.|.-+++++.|...|.+|-.....++++++   .+|+++||+||.|.+..++..|++.|+|..++.+-
T Consensus       189 ~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdk---RTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrp  261 (290)
T KOG0226|consen  189 DDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDK---RTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRP  261 (290)
T ss_pred             ccceeecccccccccHHHHHHHHHhccchhhccccccc---cccccccceeeeecCHHHHHHHHHhhcccccccch
Confidence            34689999999999999999999999888888888853   34899999999999999999999999999998874

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.32  E-value=1.9e-06  Score=71.63  Aligned_cols=82  Identities=20%  Similarity=0.370  Sum_probs=69.6

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEE--------EEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYRE--------IRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGY  150 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~--------v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~  150 (184)
                      ...+.+|||-+|+..+++++|.++|.+++.|..        |.|.+   .+.+++.||=|.|.|++..+|+.|+..+++.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~---dkeT~~~KGeatvS~~D~~~akaai~~~agk  139 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYT---DKETGAPKGEATVSYEDPPAAKAAIEWFAGK  139 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccc---cccccCcCCceeeeecChhhhhhhhhhhccc
Confidence            456779999999999999999999999998753        33333   2345899999999999999999999999999


Q ss_pred             eeCCCCCCCCceEEEeec
Q 030012          151 KFDDKKPDSPTLKIQFAH  168 (184)
Q Consensus       151 ~~~g~~~~~~~l~V~~a~  168 (184)
                      .+.+..     |+|.++.
T Consensus       140 df~gn~-----ikvs~a~  152 (351)
T KOG1995|consen  140 DFCGNT-----IKVSLAE  152 (351)
T ss_pred             cccCCC-----chhhhhh
Confidence            999976     8887775

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.19  E-value=6.3e-06  Score=71.08  Aligned_cols=76  Identities=16%  Similarity=0.240  Sum_probs=59.7

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ....-|=+.+|||++|++||.++|+.++ |.++.+.+     ..|+..|=|||+|.+++++++|++ .|-..+..+-   
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r-----~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RY---   77 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR-----RNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRY---   77 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec-----cCCCcCcceEEEeechHHHHHHHH-hhHHHhCCce---
Confidence            3445666789999999999999999984 77766643     337888999999999999999996 5666666665   


Q ss_pred             CceEEEee
Q 030012          160 PTLKIQFA  167 (184)
Q Consensus       160 ~~l~V~~a  167 (184)
                        |.|--+
T Consensus        78 --IEVf~~   83 (510)
T KOG4211|consen   78 --IEVFTA   83 (510)
T ss_pred             --EEEEcc
Confidence              665444

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=98.04  E-value=2e-05  Score=55.63  Aligned_cols=59  Identities=20%  Similarity=0.367  Sum_probs=38.5

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCC
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGY  150 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~  150 (184)
                      ..|+|.++...++.++|+++|+.||.|..|.+....       .  -|+|.|.+.+.|+.|++.+.-.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~-------~--~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD-------T--EGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT--------S--EEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC-------C--EEEEEECCcchHHHHHHHHHhc
Confidence            568899999999999999999999999998886521       1  7899999999999999877433

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=97.98  E-value=7.3e-06  Score=64.57  Aligned_cols=73  Identities=21%  Similarity=0.364  Sum_probs=62.8

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ......++|.+++..+.+++|++.|.++|.+.+..+           ..+++||+|...++|.+|++.|++.++.++.  
T Consensus        96 ~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~-----------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~--  162 (216)
T KOG0106|consen   96 SRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA-----------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRR--  162 (216)
T ss_pred             ccccceeeeccchhhhhHHHHhhhhcccCCCchhhh-----------hccccceeehhhhhhhhcchhccchhhcCce--
Confidence            456778999999999999999999999999855433           1249999999999999999999999999997  


Q ss_pred             CCceEEEee
Q 030012          159 SPTLKIQFA  167 (184)
Q Consensus       159 ~~~l~V~~a  167 (184)
                         |.+.+.
T Consensus       163 ---l~~~~~  168 (216)
T KOG0106|consen  163 ---ISVEKN  168 (216)
T ss_pred             ---eeeccc
Confidence               888443

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.95  E-value=7.4e-06  Score=68.16  Aligned_cols=79  Identities=9%  Similarity=0.190  Sum_probs=64.6

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCC--CEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFV--GYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G--~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      -.+|||||-|++|++||.+.+...|  .+.++++..   ++..|.+||||+|...+..+.++-|+.|--.+|+|+.    
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFE---NR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~----  153 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFE---NRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQS----  153 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhh---cccCCcccceEEEEecchHHHHHHHHhcccceecCCC----
Confidence            4799999999999999988887655  445555554   4555899999999999999999999999999999987    


Q ss_pred             ceEEEeec
Q 030012          161 TLKIQFAH  168 (184)
Q Consensus       161 ~l~V~~a~  168 (184)
                      +..+.|.+
T Consensus       154 P~V~~~NK  161 (498)
T KOG4849|consen  154 PTVLSYNK  161 (498)
T ss_pred             Ceeeccch
Confidence            45555544

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=97.91  E-value=6.4e-05  Score=63.18  Aligned_cols=82  Identities=26%  Similarity=0.234  Sum_probs=67.0

Q ss_pred             CCCCCEEEEcCCC--CCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           79 KGESNLLFVDGLP--TDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        79 ~~~~~~lfVgnLp--~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      ..+++.|.+.=|.  ..+|-|-|..+....|.|..|.|.++        +-.-|.|||++.+.|++|...|||..|.-. 
T Consensus       117 ~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--------ngVQAmVEFdsv~~AqrAk~alNGADIYsG-  187 (494)
T KOG1456|consen  117 ATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--------NGVQAMVEFDSVEVAQRAKAALNGADIYSG-  187 (494)
T ss_pred             CCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--------cceeeEEeechhHHHHHHHhhccccccccc-
Confidence            3445566655444  56899999999999999999988753        224799999999999999999999998875 


Q ss_pred             CCCCceEEEeecCCC
Q 030012          157 PDSPTLKIQFAHFPF  171 (184)
Q Consensus       157 ~~~~~l~V~~a~~~~  171 (184)
                        +++|+|+||++.+
T Consensus       188 --CCTLKIeyAkP~r  200 (494)
T KOG1456|consen  188 --CCTLKIEYAKPTR  200 (494)
T ss_pred             --ceeEEEEecCcce
Confidence              6789999999755

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=97.84  E-value=6.3e-06  Score=71.87  Aligned_cols=81  Identities=22%  Similarity=0.383  Sum_probs=71.0

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....+++|+--|+..+++.+|.++|+.+|.|..|+++.+   +..++++|.|||+|.|.+....|| .|.|..+.|..  
T Consensus       176 ERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~D---r~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~p--  249 (549)
T KOG0147|consen  176 ERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGD---RNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVP--  249 (549)
T ss_pred             HHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeecc---ccchhhcceeEEEEecccchhhHh-hhcCCcccCce--
Confidence            344579999999999999999999999999999999985   344789999999999999999999 79999999975  


Q ss_pred             CCceEEEeec
Q 030012          159 SPTLKIQFAH  168 (184)
Q Consensus       159 ~~~l~V~~a~  168 (184)
                         |.|+...
T Consensus       250 ---v~vq~sE  256 (549)
T KOG0147|consen  250 ---VIVQLSE  256 (549)
T ss_pred             ---eEecccH
Confidence               8887653

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.81  E-value=2.3e-05  Score=64.66  Aligned_cols=82  Identities=16%  Similarity=0.272  Sum_probs=70.0

Q ss_pred             CCCCCEEE-EcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           79 KGESNLLF-VDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        79 ~~~~~~lf-VgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++| |++|++.+++++|+..|..+|.|..+++..   ...++..+||++|+|.+...+..++.. +...+.++. 
T Consensus       181 ~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~---~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~-  255 (285)
T KOG4210|consen  181 SGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPT---DEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRP-  255 (285)
T ss_pred             cCccccceeecccccccchHHHhhhccCcCcceeeccCC---CCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcc-
Confidence            34455666 999999999999999999999999998876   444589999999999999999999877 788888875 


Q ss_pred             CCCceEEEeecC
Q 030012          158 DSPTLKIQFAHF  169 (184)
Q Consensus       158 ~~~~l~V~~a~~  169 (184)
                          +.+.+...
T Consensus       256 ----~~~~~~~~  263 (285)
T KOG4210|consen  256 ----LRLEEDEP  263 (285)
T ss_pred             ----cccccCCC
Confidence                88888764

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=97.71  E-value=0.00021  Score=61.88  Aligned_cols=77  Identities=18%  Similarity=0.345  Sum_probs=56.9

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEE-EEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYRE-IRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~-v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ....|-+.+||+.||++||.++|+..--+.. +.++.+..    +++.|=|||.|++.+.|++|+. -|-..|..|-   
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~r----gR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRY---  173 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQR----GRPTGEAFVQFESQESAEIALG-RHRENIGHRY---  173 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCC----CCcccceEEEecCHHHHHHHHH-HHHHhhccce---
Confidence            4567888999999999999999998643333 33444322    6778899999999999999986 4556666655   


Q ss_pred             CceEEEee
Q 030012          160 PTLKIQFA  167 (184)
Q Consensus       160 ~~l~V~~a  167 (184)
                        |.|.-+
T Consensus       174 --IEvF~S  179 (510)
T KOG4211|consen  174 --IEVFRS  179 (510)
T ss_pred             --EEeehh
Confidence              555443

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.68  E-value=0.00011  Score=64.73  Aligned_cols=80  Identities=20%  Similarity=0.313  Sum_probs=63.4

Q ss_pred             CCCCEEEEcCCCCCCc------HHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeC
Q 030012           80 GESNLLFVDGLPTDCT------RREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFD  153 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~t------e~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~  153 (184)
                      .....|+|.|+|---.      ..-|..+|+++|.++...+.-++.    |..+||.|++|.+..+|+.|++.|||+.++
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~----ggtkG~lf~E~~~~~~A~~aVK~l~G~~ld  131 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE----GGTKGYLFVEYASMRDAKKAVKSLNGKRLD  131 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc----CCeeeEEEEEecChhhHHHHHHhcccceec
Confidence            3456899999985322      234678999999999988876654    458999999999999999999999999998


Q ss_pred             CCCCCCCceEEEee
Q 030012          154 DKKPDSPTLKIQFA  167 (184)
Q Consensus       154 g~~~~~~~l~V~~a  167 (184)
                      ..    +++.|..-
T Consensus       132 kn----Htf~v~~f  141 (698)
T KOG2314|consen  132 KN----HTFFVRLF  141 (698)
T ss_pred             cc----ceEEeehh
Confidence            74    46766544

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.66  E-value=0.00013  Score=63.38  Aligned_cols=67  Identities=24%  Similarity=0.344  Sum_probs=51.0

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcce---EEEEEECCHHHHHHHHHHh
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMV---LCFVEFDDPKCARTAMDAL  147 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G---~afV~F~~~~~A~~Ai~~l  147 (184)
                      .-+++||||+||++++|++|...|..||.+. |.+..+...+..-.++|   |.|+.|+++.+.+.-+.+.
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            3468999999999999999999999999864 44443222222244677   9999999999988866544

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=97.64  E-value=0.00016  Score=61.48  Aligned_cols=79  Identities=15%  Similarity=0.272  Sum_probs=65.2

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      +++.+|.+.|+|..++||+|+..|..-|..++.....       ++.+-++++.+++.++|..|+-.++.+.+.+..   
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff-------~kd~kmal~q~~sveeA~~ali~~hnh~lgen~---  481 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF-------QKDRKMALPQLESVEEAIQALIDLHNHYLGENH---  481 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeeec-------CCCcceeecccCChhHhhhhccccccccCCCCc---
Confidence            4567999999999999999999999888776654433       233449999999999999999999998887753   


Q ss_pred             CceEEEeecC
Q 030012          160 PTLKIQFAHF  169 (184)
Q Consensus       160 ~~l~V~~a~~  169 (184)
                       -|+|.|++.
T Consensus       482 -hlRvSFSks  490 (492)
T KOG1190|consen  482 -HLRVSFSKS  490 (492)
T ss_pred             -eEEEEeecc
Confidence             599999874

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.61  E-value=0.00011  Score=62.67  Aligned_cols=72  Identities=21%  Similarity=0.319  Sum_probs=57.8

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeec---CCCCCCCCc-------ceEEEEEECCHHHHHHHHHHh
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHK---EPRRTGDRA-------MVLCFVEFDDPKCARTAMDAL  147 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~---~~~~~~g~~-------~G~afV~F~~~~~A~~Ai~~l  147 (184)
                      +..++++|.+-|||.+-.-+.|.++|..+|.|+.|+|...   ..+..+...       +-||||+|+..+.|.+|.+.|
T Consensus       227 eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~  306 (484)
T KOG1855|consen  227 EELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELL  306 (484)
T ss_pred             cccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhh
Confidence            3457899999999999888999999999999999999764   222222222       568999999999999999877


Q ss_pred             cC
Q 030012          148 HG  149 (184)
Q Consensus       148 ~g  149 (184)
                      +-
T Consensus       307 ~~  308 (484)
T KOG1855|consen  307 NP  308 (484)
T ss_pred             ch
Confidence            53

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=97.54  E-value=0.0052  Score=51.96  Aligned_cols=81  Identities=17%  Similarity=0.268  Sum_probs=69.0

Q ss_pred             CCCCCCEEEEcCCCCC-CcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           78 KKGESNLLFVDGLPTD-CTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~-~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      ...++..+.|-+|... ++-+.|-.+|..||.|..|++++.++        |-|.|+..|..+.++|+..||+..+-|.+
T Consensus       283 g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~--------gtamVemgd~~aver~v~hLnn~~lfG~k  354 (494)
T KOG1456|consen  283 GGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKP--------GTAMVEMGDAYAVERAVTHLNNIPLFGGK  354 (494)
T ss_pred             CCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeeccc--------ceeEEEcCcHHHHHHHHHHhccCccccce
Confidence            3456788999999864 57788999999999999999987432        48999999999999999999998888887


Q ss_pred             CCCCceEEEeecCCC
Q 030012          157 PDSPTLKIQFAHFPF  171 (184)
Q Consensus       157 ~~~~~l~V~~a~~~~  171 (184)
                           |.|.+++...
T Consensus       355 -----l~v~~SkQ~~  364 (494)
T KOG1456|consen  355 -----LNVCVSKQNF  364 (494)
T ss_pred             -----EEEeeccccc
Confidence                 9999887643

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.43  E-value=0.00038  Score=42.90  Aligned_cols=52  Identities=23%  Similarity=0.351  Sum_probs=39.7

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHH
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM  144 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai  144 (184)
                      +.|-|.+.+.+..+. +...|..||+|.++.+...         .-+.+|+|.++.+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~---------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPES---------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCC---------CcEEEEEECCHHHHHhhC
Confidence            456778877666544 5558889999999887521         128999999999999985

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.42  E-value=0.00056  Score=56.98  Aligned_cols=81  Identities=19%  Similarity=0.383  Sum_probs=61.8

Q ss_pred             CCCEEEEcCCCCCCcHHH----H--HHhhcCCCCEEEEEEeecCCCCCCCCcceE--EEEEECCHHHHHHHHHHhcCCee
Q 030012           81 ESNLLFVDGLPTDCTRRE----V--SHLFRPFVGYREIRVIHKEPRRTGDRAMVL--CFVEFDDPKCARTAMDALHGYKF  152 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~----L--~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~--afV~F~~~~~A~~Ai~~l~g~~~  152 (184)
                      ..+-+||-+|++.+..++    |  .++|.+||.|..|.+-++-..-  ...-+.  .||+|.+.++|.+||...+|..+
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~--nst~~h~gvYITy~~kedAarcIa~vDgs~~  190 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSL--NSTASHAGVYITYSTKEDAARCIAEVDGSLL  190 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEeccccccc--ccccccceEEEEecchHHHHHHHHHhccccc
Confidence            456799999998887666    2  4899999999998764421100  111122  39999999999999999999999


Q ss_pred             CCCCCCCCceEEEeec
Q 030012          153 DDKKPDSPTLKIQFAH  168 (184)
Q Consensus       153 ~g~~~~~~~l~V~~a~  168 (184)
                      +|+-     |+..|..
T Consensus       191 DGr~-----lkatYGT  201 (480)
T COG5175         191 DGRV-----LKATYGT  201 (480)
T ss_pred             cCce-----EeeecCc
Confidence            9997     9998874

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=97.41  E-value=0.00057  Score=60.08  Aligned_cols=65  Identities=23%  Similarity=0.353  Sum_probs=50.3

Q ss_pred             HHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceEEEee
Q 030012           98 EVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA  167 (184)
Q Consensus        98 ~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~V~~a  167 (184)
                      +++.-+.+||.|.+|.+.+.-....-....|.-||+|.+.+++++|+++|+|.++.++.     +...|-
T Consensus       425 dvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRt-----VvtsYy  489 (500)
T KOG0120|consen  425 DVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRT-----VVASYY  489 (500)
T ss_pred             HHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcE-----EEEEec
Confidence            45566778999999998765111111234577899999999999999999999999997     777764

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.40  E-value=9.1e-05  Score=63.19  Aligned_cols=85  Identities=18%  Similarity=0.300  Sum_probs=65.8

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCC--CCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcC-CeeCCCCCCC
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPF--VGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHG-YKFDDKKPDS  159 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~--G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g-~~~~g~~~~~  159 (184)
                      +++|++||.+..+.+||+.+|...  +.-.. .++.          .||+||++.+...|.+|++.++| .++.|.+   
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~-fl~k----------~gyafvd~pdq~wa~kaie~~sgk~elqGkr---   67 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQ-FLVK----------SGYAFVDCPDQQWANKAIETLSGKVELQGKR---   67 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcc-eeee----------cceeeccCCchhhhhhhHHhhchhhhhcCce---
Confidence            579999999999999999999653  21111 2222          25999999999999999999999 5677776   


Q ss_pred             CceEEEeecCCCCCCCCCCCCCCC
Q 030012          160 PTLKIQFAHFPFHLPSDGDEKCTP  183 (184)
Q Consensus       160 ~~l~V~~a~~~~~~~~~~~~~~~~  183 (184)
                        +.|.+.-....+++..+.+.+|
T Consensus        68 --~e~~~sv~kkqrsrk~Qirnip   89 (584)
T KOG2193|consen   68 --QEVEHSVPKKQRSRKIQIRNIP   89 (584)
T ss_pred             --eeccchhhHHHHhhhhhHhcCC
Confidence              8898887777666666666665

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.40  E-value=0.0022  Score=58.04  Aligned_cols=75  Identities=21%  Similarity=0.392  Sum_probs=62.1

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEE-EEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCc
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYR-EIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPT  161 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~-~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~  161 (184)
                      +.|-+.|+|++++-+||.++|..|--+- +|++-..+.    |...|-|.|.|++.++|.+|...|++..|..++     
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~----G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~-----  938 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDD----GVPTGECMVAFESQEEARRASMDLDGQKIRNRV-----  938 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeecCC----CCcccceeEeecCHHHHHhhhhccccCccccee-----
Confidence            4788999999999999999999995543 355544333    677789999999999999999999999999887     


Q ss_pred             eEEEe
Q 030012          162 LKIQF  166 (184)
Q Consensus       162 l~V~~  166 (184)
                      ++|..
T Consensus       939 V~l~i  943 (944)
T KOG4307|consen  939 VSLRI  943 (944)
T ss_pred             EEEEe
Confidence            77653

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.28  E-value=0.00076  Score=58.83  Aligned_cols=68  Identities=19%  Similarity=0.187  Sum_probs=57.1

Q ss_pred             CCCCCCCCEEEEcCCCCCCcHHHHHHhhc-CCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHH
Q 030012           76 PLKKGESNLLFVDGLPTDCTRREVSHLFR-PFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDA  146 (184)
Q Consensus        76 ~~~~~~~~~lfVgnLp~~~te~~L~~~F~-~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~  146 (184)
                      ..+.++.+|||||+||.-++.+||..+|+ -||.|..+-|=.+..   -+-++|-+-|+|.+..+-.+||.+
T Consensus       364 sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k---~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  364 NQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPK---LKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcc---cCCCCCcceeeecccHHHHHHHhh
Confidence            34567889999999999999999999998 699999988855411   145788999999999999999873

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.24  E-value=0.00016  Score=66.19  Aligned_cols=83  Identities=11%  Similarity=0.093  Sum_probs=69.6

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCc
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPT  161 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~  161 (184)
                      ...+||.|+|+..|.++|+.++..+|.+++++++....    |+++|.+||.|.++.++.++....+...+....     
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~----gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~-----  806 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRA----GKPKGKARVDYNTEADASRKVASVDVAGKRENN-----  806 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhc----cccccceeccCCCcchhhhhcccchhhhhhhcC-----
Confidence            45799999999999999999999999999999876433    789999999999999999998888877777665     


Q ss_pred             eEEEeecCCCCC
Q 030012          162 LKIQFAHFPFHL  173 (184)
Q Consensus       162 l~V~~a~~~~~~  173 (184)
                      +.|+.+..+..+
T Consensus       807 ~~v~vsnp~~~K  818 (881)
T KOG0128|consen  807 GEVQVSNPERDK  818 (881)
T ss_pred             ccccccCCcccc
Confidence            777775544333

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.16  E-value=0.00083  Score=61.99  Aligned_cols=85  Identities=19%  Similarity=0.290  Sum_probs=72.9

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ......+++++|..++....|...|..||.|..|.+-.         ...|++|.|++...++.|+..|-|+-+.+..  
T Consensus       452 st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h---------gq~yayi~yes~~~aq~a~~~~rgap~G~P~--  520 (975)
T KOG0112|consen  452 STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH---------GQPYAYIQYESPPAAQAATHDMRGAPLGGPP--  520 (975)
T ss_pred             cccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc---------CCcceeeecccCccchhhHHHHhcCcCCCCC--
Confidence            34567899999999999999999999999999887633         2349999999999999999999999999864  


Q ss_pred             CCceEEEeecCCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~~  175 (184)
                       ..|.|.|++.++..+.
T Consensus       521 -~r~rvdla~~~~~~Pq  536 (975)
T KOG0112|consen  521 -RRLRVDLASPPGATPQ  536 (975)
T ss_pred             -cccccccccCCCCChh
Confidence             4599999998776554

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=97.14  E-value=0.0016  Score=54.42  Aligned_cols=77  Identities=13%  Similarity=0.218  Sum_probs=61.3

Q ss_pred             CCCCCEEEEcCCC----CCCc-------HHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHh
Q 030012           79 KGESNLLFVDGLP----TDCT-------RREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDAL  147 (184)
Q Consensus        79 ~~~~~~lfVgnLp----~~~t-------e~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l  147 (184)
                      ....++|.+.||=    +..+       +++|++-.++||.|.+|.+..       -++.|.+-|.|.+.++|+.||+.|
T Consensus       262 ~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d-------~hPdGvvtV~f~n~eeA~~ciq~m  334 (382)
T KOG1548|consen  262 ARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYD-------RHPDGVVTVSFRNNEEADQCIQTM  334 (382)
T ss_pred             ccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEec-------cCCCceeEEEeCChHHHHHHHHHh
Confidence            3456789999984    2334       345666688999999998864       256689999999999999999999


Q ss_pred             cCCeeCCCCCCCCceEEEee
Q 030012          148 HGYKFDDKKPDSPTLKIQFA  167 (184)
Q Consensus       148 ~g~~~~g~~~~~~~l~V~~a  167 (184)
                      +|..|+||.     |.....
T Consensus       335 ~GR~fdgRq-----l~A~i~  349 (382)
T KOG1548|consen  335 DGRWFDGRQ-----LTASIW  349 (382)
T ss_pred             cCeeecceE-----EEEEEe
Confidence            999999998     876654

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=97.13  E-value=0.00051  Score=60.88  Aligned_cols=80  Identities=21%  Similarity=0.332  Sum_probs=65.4

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhc-CCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFR-PFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~-~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      ....++.|||.||-.-.|.-+|+.++. .+|.|.+. |+.        +-+..|||.|.+.++|.+-..+|||..+....
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-WmD--------kIKShCyV~yss~eEA~atr~AlhnV~WP~sN  510 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WMD--------KIKSHCYVSYSSVEEAAATREALHNVQWPPSN  510 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHH-HHH--------HhhcceeEecccHHHHHHHHHHHhccccCCCC
Confidence            456789999999999999999999998 45666665 432        23448999999999999999999999998776


Q ss_pred             CCCCceEEEeec
Q 030012          157 PDSPTLKIQFAH  168 (184)
Q Consensus       157 ~~~~~l~V~~a~  168 (184)
                        ..-|.+.|+.
T Consensus       511 --PK~L~adf~~  520 (718)
T KOG2416|consen  511 --PKHLIADFVR  520 (718)
T ss_pred             --CceeEeeecc
Confidence              3348888875

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=97.03  E-value=0.0027  Score=48.92  Aligned_cols=66  Identities=18%  Similarity=0.197  Sum_probs=56.8

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDD  154 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g  154 (184)
                      ......|.|.+||...+++||++...+.|+|....+.++          |++.|+|...++.+-|+..|+..++.-
T Consensus       112 rrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD----------g~GvV~~~r~eDMkYAvr~ld~~~~~s  177 (241)
T KOG0105|consen  112 RRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD----------GVGVVEYLRKEDMKYAVRKLDDQKFRS  177 (241)
T ss_pred             cccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc----------cceeeeeeehhhHHHHHHhhccccccC
Confidence            445568999999999999999999999999988877653          388999999999999999998766654

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=96.99  E-value=0.00084  Score=56.85  Aligned_cols=73  Identities=19%  Similarity=0.287  Sum_probs=60.0

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      ..|-|.||.+.+|.++++.+|...|.|.+++|+....+-......-.|||.|.|...+..|. .|..+++-++.
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdra   80 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRA   80 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeee
Confidence            37889999999999999999999999999998764433333445568999999999999986 47777777775

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.94  E-value=0.0006  Score=54.71  Aligned_cols=76  Identities=11%  Similarity=0.238  Sum_probs=59.7

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCC-----CCCCCcceE----EEEEECCHHHHHHHHHHhcCCe
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPR-----RTGDRAMVL----CFVEFDDPKCARTAMDALHGYK  151 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~-----~~~g~~~G~----afV~F~~~~~A~~Ai~~l~g~~  151 (184)
                      ..-.||+++||+.++..-|+++|..||.|=.|.|......     ...|.++..    +.|+|.+...|..+.+.||+..
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            4468999999999999999999999999988887543211     001122222    3589999999999999999999


Q ss_pred             eCCCC
Q 030012          152 FDDKK  156 (184)
Q Consensus       152 ~~g~~  156 (184)
                      |.|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99986

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.90  E-value=0.0049  Score=39.15  Aligned_cols=56  Identities=23%  Similarity=0.402  Sum_probs=45.4

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCC---CCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHh
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPF---VGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDAL  147 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~---G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l  147 (184)
                      ...+|+|.++. +.+.+||+.+|..|   .....|.++.+.          -|-|.|.+.+.|.+|+..|
T Consensus         4 rpeavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt----------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    4 RPEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT----------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eeceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC----------cEEEEECCHHHHHHHHHcC
Confidence            35689999985 68889999999988   235678888752          5889999999999999764

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=96.87  E-value=0.0017  Score=58.18  Aligned_cols=67  Identities=15%  Similarity=0.069  Sum_probs=59.8

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      +.++.-++||+|+...+..+-++.++..+|.|.+++...            |+|++|........|+..++-..+++..
T Consensus        36 ~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~------------fgf~~f~~~~~~~ra~r~~t~~~~~~~k  102 (668)
T KOG2253|consen   36 PLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK------------FGFCEFLKHIGDLRASRLLTELNIDDQK  102 (668)
T ss_pred             CCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh------------hcccchhhHHHHHHHHHHhcccCCCcch
Confidence            355678999999999999999999999999998886543            9999999999999999999999998876

>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=96.71  E-value=0.0039  Score=47.92  Aligned_cols=88  Identities=18%  Similarity=0.268  Sum_probs=56.3

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcC-CCCEE---EEEE-eecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRP-FVGYR---EIRV-IHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDD  154 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~-~G~i~---~v~l-~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g  154 (184)
                      ....+|-|.+||+.+||+++.+.+.. ++...   .+.- ..+...+  .....-|+|.|.+.+++..-++.++|+.+.+
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~--~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D   82 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFK--PPTYSRAYINFKNPEDLLEFRDRFDGHVFVD   82 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSST--TS--EEEEEEESSCHHHHHHHHHCTTEEEE-
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCC--CCcceEEEEEeCCHHHHHHHHHhcCCcEEEC
Confidence            44569999999999999999997776 66652   3321 1111111  1234479999999999999999999999998


Q ss_pred             CCCCCCceEEEeecC
Q 030012          155 KKPDSPTLKIQFAHF  169 (184)
Q Consensus       155 ~~~~~~~l~V~~a~~  169 (184)
                      .++...+-.|+||-.
T Consensus        83 ~kg~~~~~~VE~Apy   97 (176)
T PF03467_consen   83 SKGNEYPAVVEFAPY   97 (176)
T ss_dssp             TTS-EEEEEEEE-SS
T ss_pred             CCCCCcceeEEEcch
Confidence            875555667888855

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.

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=96.68  E-value=0.0024  Score=54.07  Aligned_cols=79  Identities=15%  Similarity=0.278  Sum_probs=61.3

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCC-EEE--EEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVG-YRE--IRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~-i~~--v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      .....|-+.+||++++.+||.++|..|-. |..  |.++....    |++.|=|||+|.+.+.|..|....+.+....|.
T Consensus       278 ~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~q----GrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RY  353 (508)
T KOG1365|consen  278 RSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQ----GRPSGEAFIQMRNAERARAAAQKCHKKLMKSRY  353 (508)
T ss_pred             CCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCC----CCcChhhhhhhhhhHHHHHHHHHHHHhhcccce
Confidence            33568889999999999999999988743 333  56665322    678889999999999999999888877776765


Q ss_pred             CCCCceEEEee
Q 030012          157 PDSPTLKIQFA  167 (184)
Q Consensus       157 ~~~~~l~V~~a  167 (184)
                           |.|--.
T Consensus       354 -----iEvfp~  359 (508)
T KOG1365|consen  354 -----IEVFPC  359 (508)
T ss_pred             -----EEEeec
Confidence                 665433

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=96.64  E-value=0.01  Score=41.35  Aligned_cols=80  Identities=16%  Similarity=0.208  Sum_probs=49.6

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecC-C---CCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKE-P---RRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~-~---~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .+-|.|-+-|.. ..+.+-+.|++||.|++..-.... .   .........+-.|+|.++.+|++|+. .||..+.|.- 
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~-   82 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSL-   82 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCE-
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcE-
Confidence            455778888877 556777899999999887510000 0   00000112389999999999999995 7999999863 


Q ss_pred             CCCceEEEee
Q 030012          158 DSPTLKIQFA  167 (184)
Q Consensus       158 ~~~~l~V~~a  167 (184)
                         .+-|.|.
T Consensus        83 ---mvGV~~~   89 (100)
T PF05172_consen   83 ---MVGVKPC   89 (100)
T ss_dssp             ---EEEEEE-
T ss_pred             ---EEEEEEc
Confidence               2346665

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.

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.45  E-value=0.0088  Score=44.40  Aligned_cols=72  Identities=19%  Similarity=0.296  Sum_probs=50.4

Q ss_pred             CCCCEEEEcCCC------CCCcH---HHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCC
Q 030012           80 GESNLLFVDGLP------TDCTR---REVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGY  150 (184)
Q Consensus        80 ~~~~~lfVgnLp------~~~te---~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~  150 (184)
                      ++..||.|.=+.      ....+   ++|-+.|..||+++-+|++..           .-.|+|.+-.+|.+|+. ++|.
T Consensus        25 PpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~-----------~mwVTF~dg~sALaals-~dg~   92 (146)
T PF08952_consen   25 PPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD-----------TMWVTFRDGQSALAALS-LDGI   92 (146)
T ss_dssp             -TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT-----------CEEEEESSCHHHHHHHH-GCCS
T ss_pred             CCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC-----------eEEEEECccHHHHHHHc-cCCc
Confidence            344566665444      12232   367788889999998888742           56999999999999995 9999


Q ss_pred             eeCCCCCCCCceEEEeec
Q 030012          151 KFDDKKPDSPTLKIQFAH  168 (184)
Q Consensus       151 ~~~g~~~~~~~l~V~~a~  168 (184)
                      ++.|+.     |+|....
T Consensus        93 ~v~g~~-----l~i~LKt  105 (146)
T PF08952_consen   93 QVNGRT-----LKIRLKT  105 (146)
T ss_dssp             EETTEE-----EEEEE--
T ss_pred             EECCEE-----EEEEeCC
Confidence            999997     8887643

; PDB: 1UFW_A 2DNR_A.

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.40  E-value=0.0077  Score=54.61  Aligned_cols=83  Identities=18%  Similarity=0.212  Sum_probs=63.8

Q ss_pred             CCCCCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEE-EEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeC
Q 030012           75 SPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYRE-IRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFD  153 (184)
Q Consensus        75 ~~~~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~-v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~  153 (184)
                      .+.+......|||..||..+++.++.++|...-.|++ |.|....+    ++.++.|||+|..++++..|...-+-+.+.
T Consensus       427 vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~----~~~~~~afv~F~~~~a~~~a~~~~~k~y~G  502 (944)
T KOG4307|consen  427 VPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPT----DLLRPAAFVAFIHPTAPLTASSVKTKFYPG  502 (944)
T ss_pred             CCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCc----ccccchhhheeccccccchhhhcccccccC
Confidence            3445677889999999999999999999998777776 66654332    567789999999999988887655555555


Q ss_pred             CCCCCCCceEEEe
Q 030012          154 DKKPDSPTLKIQF  166 (184)
Q Consensus       154 g~~~~~~~l~V~~  166 (184)
                      .+.     |+|.-
T Consensus       503 ~r~-----irv~s  510 (944)
T KOG4307|consen  503 HRI-----IRVDS  510 (944)
T ss_pred             ceE-----EEeec
Confidence            554     77764

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=96.39  E-value=0.022  Score=48.47  Aligned_cols=59  Identities=25%  Similarity=0.336  Sum_probs=46.8

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCC----CCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHH
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPF----VGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMD  145 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~----G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~  145 (184)
                      -.|-+.+||+++++.|+.++|.+-    |..+.+-+++.    .+|+..|=|||.|..+++|+.|+.
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r----pdgrpTGdAFvlfa~ee~aq~aL~  224 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR----PDGRPTGDAFVLFACEEDAQFALR  224 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC----CCCCcccceEEEecCHHHHHHHHH
Confidence            356678999999999999999632    35556666643    336777899999999999999986

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.37  E-value=0.029  Score=37.74  Aligned_cols=56  Identities=20%  Similarity=0.453  Sum_probs=42.1

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhc
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALH  148 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~  148 (184)
                      ..+..||+ .|.++...||.++|+.||.|. |.++.+ +         -|||...+.+.|..++..+.
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d-T---------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND-T---------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT-T---------EEEEEECCCHHHHHHHHHHT
T ss_pred             cceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC-C---------cEEEEeecHHHHHHHHHHhc
Confidence            34566676 999999999999999999864 555542 1         79999999999999998885

; 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.

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.10  E-value=0.02  Score=47.07  Aligned_cols=66  Identities=18%  Similarity=0.240  Sum_probs=51.6

Q ss_pred             HHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceEEEeec
Q 030012           96 RREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAH  168 (184)
Q Consensus        96 e~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~V~~a~  168 (184)
                      ++++++-.++||.|..|.|...+....  .-..--||+|+..++|.+|+-.|||.-|.|+.     ++..|..
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~--deavRiFveF~r~e~aiKA~VdlnGRyFGGr~-----v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPE--DEAVRIFVEFERVESAIKAVVDLNGRYFGGRV-----VSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCcc--chhheeeeeeccHHHHHHHHHhcCCceeccee-----eeheecc
Confidence            457888899999999988766443221  12235699999999999999999999999997     7766653

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=95.86  E-value=0.15  Score=36.20  Aligned_cols=71  Identities=20%  Similarity=0.313  Sum_probs=53.6

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCC-CCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPF-VGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~-G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ...+.+...|..++.++|..+.+.+ ..|..++++++..     .++--++++|.+.+.|..-.+.+||+.+.--.+
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~-----pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEp   84 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT-----PNRYMVLIKFRDQESADEFYEEFNGKPFNSLEP   84 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC-----CceEEEEEEECCHHHHHHHHHHhCCCccCCCCC
Confidence            3455556666667777887777766 5667889987532     356688999999999999999999998877553

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=95.72  E-value=0.0054  Score=49.31  Aligned_cols=60  Identities=17%  Similarity=0.321  Sum_probs=47.7

Q ss_pred             HHHhhc-CCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceEEEee
Q 030012           99 VSHLFR-PFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA  167 (184)
Q Consensus        99 L~~~F~-~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~V~~a  167 (184)
                      +...|+ +||+|+++.+-..    .+.+..|-.+|.|...++|++|++.||+-.+.|+.     |..++.
T Consensus        85 ~f~E~~~kygEiee~~Vc~N----l~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~p-----i~ae~~  145 (260)
T KOG2202|consen   85 VFTELEDKYGEIEELNVCDN----LGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRP-----IHAELS  145 (260)
T ss_pred             HHHHHHHHhhhhhhhhhhcc----cchhhhhhhhhhcccHHHHHHHHHHHcCccccCCc-----ceeeec
Confidence            333334 8999999866542    23567788999999999999999999999999986     887775

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=95.68  E-value=0.012  Score=47.31  Aligned_cols=62  Identities=19%  Similarity=0.181  Sum_probs=53.0

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhc
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALH  148 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~  148 (184)
                      ..|||.||+..++.|.|.+.|+.||.|....++.+..    ++..+=++|+|...-.|.+|+..+.
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 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDR----GKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeeccc----ccccccchhhhhcchhHHHHHHHhc
Confidence            7899999999999999999999999998765555433    4556678999999999999998774

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=95.60  E-value=0.0037  Score=57.93  Aligned_cols=79  Identities=15%  Similarity=0.174  Sum_probs=64.7

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ..+.+||+|||+..+++.+|+..|..+|.|.+|.|-....    +.---|+||.|.+...+..|+..+.+..|....   
T Consensus       370 ~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~----~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~---  442 (975)
T KOG0112|consen  370 RATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI----KTESAYAFVSLLNTDMTPSAKFEESGPLIGNGT---  442 (975)
T ss_pred             hhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC----CcccchhhhhhhccccCcccchhhcCCccccCc---
Confidence            3568999999999999999999999999999998855322    223349999999999999999999987776654   


Q ss_pred             CceEEEee
Q 030012          160 PTLKIQFA  167 (184)
Q Consensus       160 ~~l~V~~a  167 (184)
                        +++.+.
T Consensus       443 --~r~glG  448 (975)
T KOG0112|consen  443 --HRIGLG  448 (975)
T ss_pred             --cccccc
Confidence              666666

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=95.37  E-value=0.001  Score=61.05  Aligned_cols=69  Identities=20%  Similarity=0.290  Sum_probs=56.1

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeC
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFD  153 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~  153 (184)
                      ..++||.||+..+.+++|...|..+|.+..+++..   ....++.+|.|+++|...+.+.+|+...++..+.
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~---h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVI---HKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHH---HhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            35899999999999999999999999887776652   1222678899999999999999999765554444

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=95.09  E-value=0.011  Score=49.36  Aligned_cols=84  Identities=19%  Similarity=0.410  Sum_probs=61.5

Q ss_pred             CCCEEEEcCCCCCCcHH-HH--HHhhcCCCCEEEEEEeecCC--CCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCC
Q 030012           81 ESNLLFVDGLPTDCTRR-EV--SHLFRPFVGYREIRVIHKEP--RRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDK  155 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~-~L--~~~F~~~G~i~~v~l~~~~~--~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~  155 (184)
                      ..+-+||-+|+.....+ .|  .+.|.+||.|..+.+..+..  ...++ . --++|+|+..++|..||...+|+..+++
T Consensus        76 qknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~-~-~s~yITy~~~eda~rci~~v~g~~~dg~  153 (327)
T KOG2068|consen   76 QKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGG-T-CSVYITYEEEEDADRCIDDVDGFVDDGR  153 (327)
T ss_pred             hhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCC-C-CcccccccchHhhhhHHHHhhhHHhhhh
Confidence            34678899998776444 44  37889999999987765331  11111 1 1379999999999999999999999998


Q ss_pred             CCCCCceEEEeecCCC
Q 030012          156 KPDSPTLKIQFAHFPF  171 (184)
Q Consensus       156 ~~~~~~l~V~~a~~~~  171 (184)
                      .     |+..++-.+.
T Consensus       154 ~-----lka~~gttky  164 (327)
T KOG2068|consen  154 A-----LKASLGTTKY  164 (327)
T ss_pred             h-----hHHhhCCCcc
Confidence            6     7777765543

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=94.81  E-value=0.052  Score=42.04  Aligned_cols=61  Identities=25%  Similarity=0.411  Sum_probs=45.0

Q ss_pred             cHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhc--CCeeCCCCCCCCceEEEeecC
Q 030012           95 TRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALH--GYKFDDKKPDSPTLKIQFAHF  169 (184)
Q Consensus        95 te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~--g~~~~g~~~~~~~l~V~~a~~  169 (184)
                      ..+.|+++|..++.+..+..++.         .+-..|.|.+.+.|.+|...|+  +..+.|..     |+|.|+..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s---------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~-----l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS---------FRRIRVVFESPESAQRARQLLHWDGTSFNGKR-----LRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT---------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE------EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC---------CCEEEEEeCCHHHHHHHHHHhcccccccCCCc-----eEEEEccc
Confidence            45789999999999988877642         2267999999999999999999  99999987     99999843

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.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=94.38  E-value=0.17  Score=45.01  Aligned_cols=78  Identities=13%  Similarity=0.252  Sum_probs=57.7

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcC--CCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHH-------HhcCCee
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRP--FVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMD-------ALHGYKF  152 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~--~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~-------~l~g~~~  152 (184)
                      .+.|.+..||..+.+|+++.+|+.  |-.+++|.+....          -=||+|++..+|+.|.+       .++|+-|
T Consensus       175 RcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~----------nWyITfesd~DAQqAykylreevk~fqgKpI  244 (684)
T KOG2591|consen  175 RCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND----------NWYITFESDTDAQQAYKYLREEVKTFQGKPI  244 (684)
T ss_pred             eeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC----------ceEEEeecchhHHHHHHHHHHHHHhhcCcch
Confidence            356778999999999999999964  7888999886531          23999999999999976       4567777


Q ss_pred             CCCCCCCCceEEEeecCCCC
Q 030012          153 DDKKPDSPTLKIQFAHFPFH  172 (184)
Q Consensus       153 ~g~~~~~~~l~V~~a~~~~~  172 (184)
                      ..|.   ++|.-.++++..+
T Consensus       245 mARI---Kaintf~pkngyr  261 (684)
T KOG2591|consen  245 MARI---KAINTFFPKNGYR  261 (684)
T ss_pred             hhhh---hhhhcccCCCCCC
Confidence            7763   2344344455444

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.35  E-value=0.32  Score=36.12  Aligned_cols=73  Identities=14%  Similarity=0.195  Sum_probs=54.1

Q ss_pred             CCCCEEEEcCCCCCCcH-HHHH---HhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCC
Q 030012           80 GESNLLFVDGLPTDCTR-REVS---HLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDK  155 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te-~~L~---~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~  155 (184)
                      .+=.||.|.=|..++.. +|++   ..++.||.|.+|.+.-    +.      -|.|.|.|..+|=.|+.+++. ...|.
T Consensus        84 pPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG----rq------savVvF~d~~SAC~Av~Af~s-~~pgt  152 (166)
T PF15023_consen   84 PPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG----RQ------SAVVVFKDITSACKAVSAFQS-RAPGT  152 (166)
T ss_pred             CCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC----Cc------eEEEEehhhHHHHHHHHhhcC-CCCCc
Confidence            44468888877666533 4444   4567899999998752    22      699999999999999999987 55566


Q ss_pred             CCCCCceEEEeec
Q 030012          156 KPDSPTLKIQFAH  168 (184)
Q Consensus       156 ~~~~~~l~V~~a~  168 (184)
                      .     +++.|-.
T Consensus       153 m-----~qCsWqq  160 (166)
T PF15023_consen  153 M-----FQCSWQQ  160 (166)
T ss_pred             e-----EEeeccc
Confidence            5     8888853

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=93.87  E-value=0.039  Score=51.17  Aligned_cols=75  Identities=16%  Similarity=0.223  Sum_probs=61.3

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      .+.++.|.+-..+..-|..+|.+||.|.+.+.+++-.         .|.|+|...+.|..|+++|+|+++---   ..|.
T Consensus       299 p~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N---------~alvs~~s~~sai~a~dAl~gkevs~~---g~Ps  366 (1007)
T KOG4574|consen  299 PKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN---------MALVSFSSVESAILALDALQGKEVSVT---GAPS  366 (1007)
T ss_pred             chhhhhcccccchHHHHHHHHHhhcchhhheeccccc---------chhhhhHHHHHHHHhhhhhcCCccccc---CCce
Confidence            3455666667788899999999999999988776422         799999999999999999999876543   3468


Q ss_pred             EEEeecC
Q 030012          163 KIQFAHF  169 (184)
Q Consensus       163 ~V~~a~~  169 (184)
                      +|.||+.
T Consensus       367 ~V~~ak~  373 (1007)
T KOG4574|consen  367 RVSFAKT  373 (1007)
T ss_pred             eEEeccc
Confidence            9999984

>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=92.20  E-value=0.58  Score=30.46  Aligned_cols=67  Identities=27%  Similarity=0.464  Sum_probs=38.6

Q ss_pred             EEEEc-CCCCCCcHHHHHHhhcCCCCE-----EEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           84 LLFVD-GLPTDCTRREVSHLFRPFVGY-----REIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        84 ~lfVg-nLp~~~te~~L~~~F~~~G~i-----~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ++||. +--..++..+|..++...+.+     -.+++...           |+||+-.. +.|+.+++.|++..+.|++ 
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~-----------~S~vev~~-~~a~~v~~~l~~~~~~gk~-   68 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN-----------FSFVEVPE-EVAEKVLEALNGKKIKGKK-   68 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS------------EEEEE-T-T-HHHHHHHHTT--SSS---
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEeee-----------EEEEEECH-HHHHHHHHHhcCCCCCCee-
Confidence            34552 233467888888888776554     45666431           89999764 5889999999999999998 


Q ss_pred             CCCceEEEee
Q 030012          158 DSPTLKIQFA  167 (184)
Q Consensus       158 ~~~~l~V~~a  167 (184)
                          ++|+.|
T Consensus        69 ----v~ve~A   74 (74)
T PF03880_consen   69 ----VRVERA   74 (74)
T ss_dssp             ------EEE-
T ss_pred             ----EEEEEC
Confidence                988764

; PDB: 2G0C_A 3MOJ_B.

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=91.61  E-value=0.79  Score=39.96  Aligned_cols=72  Identities=19%  Similarity=0.400  Sum_probs=60.9

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCC-CCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPF-VGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~-G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      +..|+|=-+|-.++..||-.+...+ -.|.+++++++..     .++-..+|+|.+.++|..-.+.+||..|..-.++
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~-----pnrymvLIkFr~q~da~~Fy~efNGk~Fn~le~e  146 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGM-----PNRYMVLIKFRDQADADTFYEEFNGKQFNSLEPE  146 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCC-----CceEEEEEEeccchhHHHHHHHcCCCcCCCCCcc
Confidence            7899999999999999999988765 6788999998532     3455789999999999999999999999876533

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=91.41  E-value=0.83  Score=29.34  Aligned_cols=52  Identities=25%  Similarity=0.342  Sum_probs=40.1

Q ss_pred             CCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           93 DCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        93 ~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      .++-++++..+..|.- ..|+  .   +++     || ||.|.+..+|++|....+|..+...+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~~I~--~---d~t-----Gf-YIvF~~~~Ea~rC~~~~~~~~~f~y~   62 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-DRIR--D---DRT-----GF-YIVFNDSKEAERCFRAEDGTLFFTYR   62 (66)
T ss_pred             CccHHHHHHHHhcCCc-ceEE--e---cCC-----EE-EEEECChHHHHHHHHhcCCCEEEEEE
Confidence            5778899999999963 3333  2   232     34 89999999999999999998887654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=90.72  E-value=0.49  Score=42.08  Aligned_cols=44  Identities=16%  Similarity=0.323  Sum_probs=35.2

Q ss_pred             CcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceEEEeecC
Q 030012          125 RAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHF  169 (184)
Q Consensus       125 ~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~V~~a~~  169 (184)
                      .+.|||||.|.+.+++....+++||+.+..-. ......+.||+-
T Consensus       429 cNvGYAFINm~sp~ai~~F~kAFnGk~W~~Fn-S~Kia~itYArI  472 (549)
T KOG4660|consen  429 CNVGYAFINMTSPEAIIRFYKAFNGKKWEKFN-SEKIASITYARI  472 (549)
T ss_pred             cccceeEEeecCHHHHHHHHHHHcCCchhhhc-ceeeeeeehhhh
Confidence            46899999999999999999999998776543 233467888864

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=90.43  E-value=0.24  Score=41.03  Aligned_cols=74  Identities=18%  Similarity=0.077  Sum_probs=59.2

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      ....++|++++.+.+.+.+...++..+|....+.+...+   ....++|++.+.|...+.+..|+.....+...++.
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~---~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~  159 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLE---DSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNK  159 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhc---cccccccceeeccccHHHHHHHHHhhhcccccccc
Confidence            357899999999999999999999999988877665522   22578899999999999999999755555665554

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=89.39  E-value=0.2  Score=43.73  Aligned_cols=72  Identities=21%  Similarity=0.236  Sum_probs=55.2

Q ss_pred             CEEEEcCCCCCC-cHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCc
Q 030012           83 NLLFVDGLPTDC-TRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPT  161 (184)
Q Consensus        83 ~~lfVgnLp~~~-te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~  161 (184)
                      +.|-+.-.++.. +..+|...|.+||.|..|.+-..         --.|.|+|.+..+|-+|. ..++..|+++-     
T Consensus       373 s~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~---------~~~a~vTF~t~aeag~a~-~s~~avlnnr~-----  437 (526)
T KOG2135|consen  373 SPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS---------SLHAVVTFKTRAEAGEAY-ASHGAVLNNRF-----  437 (526)
T ss_pred             chhhhhccCCCCchHhhhhhhhhhcCccccccccCc---------hhhheeeeeccccccchh-ccccceecCce-----
Confidence            344444455555 45889999999999999877432         116899999999997765 47999999997     


Q ss_pred             eEEEeecC
Q 030012          162 LKIQFAHF  169 (184)
Q Consensus       162 l~V~~a~~  169 (184)
                      |+|.|-+.
T Consensus       438 iKl~whnp  445 (526)
T KOG2135|consen  438 IKLFWHNP  445 (526)
T ss_pred             eEEEEecC
Confidence            99999765

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=89.03  E-value=0.11  Score=44.47  Aligned_cols=65  Identities=15%  Similarity=0.089  Sum_probs=52.2

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFD  153 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~  153 (184)
                      ..++++|.+|+..+...++-++|..+|+|...++...       ...-+|-++|........|+. ++|.++.
T Consensus       150 irRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~ask-------~~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  150 IRRTREVQSLISAAILPESGESFERKGEVSYAHTASK-------SRSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             HHhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhcc-------CCCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            3479999999999999999999999999998877543       223378899998888888875 5666655

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=86.80  E-value=1.1  Score=37.20  Aligned_cols=58  Identities=17%  Similarity=0.141  Sum_probs=42.5

Q ss_pred             EcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCC
Q 030012           87 VDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDK  155 (184)
Q Consensus        87 VgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~  155 (184)
                      |-+.|+.- -..|...|++||.|++.....         .--|-+|.|.+..+|++||. .||..|+|.
T Consensus       202 VfGFppg~-~s~vL~~F~~cG~Vvkhv~~~---------ngNwMhirYssr~~A~KALs-kng~ii~g~  259 (350)
T KOG4285|consen  202 VFGFPPGQ-VSIVLNLFSRCGEVVKHVTPS---------NGNWMHIRYSSRTHAQKALS-KNGTIIDGD  259 (350)
T ss_pred             EeccCccc-hhHHHHHHHhhCeeeeeecCC---------CCceEEEEecchhHHHHhhh-hcCeeeccc
Confidence            33554433 345677899999998764431         11289999999999999995 788888886

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=85.48  E-value=0.83  Score=37.71  Aligned_cols=50  Identities=16%  Similarity=0.238  Sum_probs=36.8

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHH
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKC  139 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~  139 (184)
                      ..-||++||+.++.-.||+..+.+-+.+ -.++.++       -++|-||+.|.+...
T Consensus       330 ~~di~~~nl~rd~rv~dlk~~lr~~~~~-pm~iswk-------g~~~k~flh~~~~~~  379 (396)
T KOG4410|consen  330 KTDIKLTNLSRDIRVKDLKSELRKRECT-PMSISWK-------GHFGKCFLHFGNRKG  379 (396)
T ss_pred             ccceeeccCccccchHHHHHHHHhcCCC-ceeEeee-------cCCcceeEecCCccC
Confidence            3469999999999999999999887653 2233332       235689999988543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	184
3pgw_A	282	Crystal Structure Of Human U1 Snrnp Length = 282		3e-06
2u1a_A	88	Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20		3e-06
2b0g_A	83	Solution Structure Of Drosophila Melanogaster Snf R		9e-05

>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp Length = 282

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 29/86 (33%), Positives = 44/86 (51%), Gaps = 12/86 (13%)
Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           +++LF+  LP +     +S LF  F G++E+R++   P R       + FVEFD+   A 
Sbjct: 207 NHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV---PGRHD-----IAFVEFDNEVQAG 258
Query: 142 TAMDALHGYKFDDKKPDSPTLKIQFA 167
            A DAL G+K          +KI FA
Sbjct: 259 AARDALQGFKITQNN----AMKISFA 280

>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20 Structures Length = 88

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 29/86 (33%), Positives = 44/86 (51%), Gaps = 12/86 (13%)
Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           +++LF+  LP +     +S LF  F G++E+R++   P R       + FVEFD+   A 
Sbjct: 13  NHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV---PGRHD-----IAFVEFDNEVQAG 64
Query: 142 TAMDALHGYKFDDKKPDSPTLKIQFA 167
            A DAL G+K          +KI FA
Sbjct: 65  AARDALQGFKITQNN----AMKISFA 86

>pdb|2B0G|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2 Length = 83

Iteration: 1
 Score = 43.1 bits (100), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 44/88 (50%), Gaps = 16/88 (18%)
Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           + +LF+  LP +     +S LF  F G++E+R++   P R       + FVEF     + 
Sbjct: 8   NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLV---PNRHD-----IAFVEFTTELQSN 59
Query: 142 TAMDALHGYKFDDKKPDSPT--LKIQFA 167
            A +AL G+K       +PT  +KI FA
Sbjct: 60  AAKEALQGFKI------TPTHAMKITFA 81

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	184
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	9e-13
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-12
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-11
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-06
2dis_A	109	Unnamed protein product; structural genomics, RRM	6e-11
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-11
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-05
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-08
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-10
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-10
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	4e-10
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-10
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-05
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-09
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-09
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-09
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-09
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-09
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-09
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-09
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	4e-09
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	4e-09
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	5e-09
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	5e-09
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	5e-09
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	6e-09
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	7e-09
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-04
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	7e-09
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	8e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	8e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-05
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	8e-09
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	8e-09
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	9e-09
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-08
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-08
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-08
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-08
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-08
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-08
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-08
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	9e-08
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-05
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-08
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-08
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-08
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-08
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-08
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	4e-08
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-08
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	7e-08
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-08
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	7e-08
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	7e-08
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	8e-08
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-07
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-07
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-07
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-07
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-07
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-07
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-07
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-07
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	2e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-07
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-07
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-07
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	3e-07
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-07
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	4e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-07
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	4e-07
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-07
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	5e-07
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	5e-07
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	5e-07
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	5e-07
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-07
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-04
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	5e-07
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	5e-07
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	5e-07
1x4e_A	85	RNA binding motif, single-stranded interacting pro	6e-07
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	6e-07
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	6e-07
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	7e-07
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	7e-07
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	7e-07
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	7e-07
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	8e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	9e-07
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-06
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-06
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-06
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-06
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-06
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-06
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	3e-06
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	3e-06
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-06
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-06
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-06
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	5e-06
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-06
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	5e-06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	5e-06
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	6e-06
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-05
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-05
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-05
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-05
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-05
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-05
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-05
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-05
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-05
2div_A	99	TRNA selenocysteine associated protein; structural	2e-05
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-05
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-05
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-05
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-05
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-05
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	3e-05
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	3e-05
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-05
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	6e-05
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	7e-05
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	7e-05
1x5o_A	114	RNA binding motif, single-stranded interacting pro	8e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	9e-05
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	9e-05
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-04
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-04
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-04
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-04
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	6e-04
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-04
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-04
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-04
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-04
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	3e-04
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	5e-04
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	7e-04
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	8e-04

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 60.5 bits (147), Expect = 9e-13
 Identities = 15/95 (15%), Positives = 32/95 (33%), Gaps = 11/95 (11%)

Query: 73  AGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFV 132
           +GS  K+     L +  +P       +  L   +        ++               V
Sbjct: 6   SGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNT--DSETAVV----NV 59

Query: 133 EFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
            +     AR A+D L+G++ ++       LK+ + 
Sbjct: 60  TYSSKDQARQALDKLNGFQLENFT-----LKVAYI 89

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 58.6 bits (142), Expect = 3e-12
 Identities = 21/86 (24%), Positives = 32/86 (37%), Gaps = 15/86 (17%)

Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           S+ + V  LP D   +EV  L + +   +   V         DR     FV   + + A+
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYV---------DRNKRTAFVTLLNGEQAQ 54

Query: 142 TAMDALHGYKFDDKKPDSPTLKIQFA 167
            A+   H Y F  K      L +Q  
Sbjct: 55  NAIQMFHQYSFRGKD-----LIVQLQ 75

>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 = 57.3 bits (139), Expect = 2e-11
 Identities = 26/117 (22%), Positives = 45/117 (38%), Gaps = 17/117 (14%)

Query: 53  GINPTIPDVINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREI 112
           G + +  + I  +P     N G P     + +L++  L    T R++  LF  F   +  
Sbjct: 1   GSSGSSGEEIRKIPMFSSYNPGEP-----NKVLYLKNLSPRVTERDLVSLFARFQEKKGP 55

Query: 113 RVI--HKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
            +       R  G       F+ F + + A  A+  ++GYK   K      L I+F 
Sbjct: 56  PIQFRMMTGRMRG-----QAFITFPNKEIAWQALHLVNGYKLYGK-----ILVIEFG 102

>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 = 57.0 bits (138), Expect = 2e-11
 Identities = 21/89 (23%), Positives = 40/89 (44%), Gaps = 13/89 (14%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRV-IHKEPRRTGDRAMVLCFVEFDDPKC 139
            + +L++  LP   T  E+  +F  +   R+IRV    E R T        +V ++D   
Sbjct: 7   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTA-------YVVYEDIFD 59

Query: 140 ARTAMDALHGYKFDDKKPDSPTLKIQFAH 168
           A+ A+D L G+   ++      L + + +
Sbjct: 60  AKNAVDHLSGFNVSNRY-----LVVLYYN 83

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 58.6 bits (141), Expect = 3e-11
 Identities = 16/88 (18%), Positives = 31/88 (35%), Gaps = 4/88 (4%)

Query: 80  GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKC 139
             SN+L     P + T      +     G +    +     ++   +     +E+D    
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDEL-GVKRPTSVKVFSGKSERSSS--GLLEWDSKSD 177

Query: 140 ARTAMDALHGYKFDDKKPDSP-TLKIQF 166
           A   +  L+ Y+  +     P TLK+ F
Sbjct: 178 ALETLGFLNHYQMKNPNGPYPYTLKLCF 205

>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 = 44.7 bits (105), Expect = 3e-06
 Identities = 17/101 (16%), Positives = 31/101 (30%), Gaps = 12/101 (11%)

Query: 80  GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKC 139
            +S +L V GL       +   +F  F  Y  +  +     + G        VE  D   
Sbjct: 2   ADSPVLMVYGLDQSKMNCD--RVFNVFCLYGNVEKVKFMKSKPG-----AAMVEMADGYA 54

Query: 140 ARTAMDALHGYKFDDKKPDSPTLKIQFAHFPFHLPSDGDEK 180
              A+  L+      +K     + +  +  P  +P      
Sbjct: 55  VDRAITHLNNNFMFGQK-----MNVCVSKQPAIMPGQSYGL 90

>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 = 56.0 bits (135), Expect = 6e-11
 Identities = 13/87 (14%), Positives = 29/87 (33%), Gaps = 4/87 (4%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCA 140
            +  LF+ G+P    R E+              +++        +     FVE++  + A
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKM-KNRGFAFVEYESHRAA 65

Query: 141 RTAMDALHGYKFDDKKPDSPTLKIQFA 167
             A   L   +    +     + + +A
Sbjct: 66  AMARRKLMPGRI---QLWGHQIAVDWA 89

>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 = 58.0 bits (140), Expect = 6e-11
 Identities = 13/86 (15%), Positives = 31/86 (36%), Gaps = 11/86 (12%)

Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           S  L +  +P   +  ++  LF    G  +     ++ R+          ++    + A 
Sbjct: 120 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMA-------LIQMGSVEEAV 172

Query: 142 TAMDALHGYKFDDKKPDSPTLKIQFA 167
            A+  LH +   +       L++ F+
Sbjct: 173 QALIDLHNHDLGENHH----LRVSFS 194

>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 = 43.3 bits (102), Expect = 1e-05
 Identities = 17/104 (16%), Positives = 38/104 (36%), Gaps = 14/104 (13%)

Query: 82  SNLLFVDGL-PTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCA 140
           +++L V  L P   T + +  LF  +   + ++++  +             V+  D   A
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE--------NALVQMADGNQA 54

Query: 141 RTAMDALHGYKFDDKKPDSPTLKIQFAHFPFHLPSDGDEKCTPR 184
           + AM  L+G+K   K      ++I  +           ++    
Sbjct: 55  QLAMSHLNGHKLHGKP-----IRITLSKHQNVQLPREGQEDQGL 93

>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 = 58.7 bits (141), Expect = 6e-11
 Identities = 42/167 (25%), Positives = 63/167 (37%), Gaps = 12/167 (7%)

Query: 1   MRPGALGLVDTAGVGVHPEPGMVGITAVASVKGYSSPLPDPNLIGQRRDIAPGINPTIPD 60
              GA  +V      V   P M     +        P   P  +     +APG  P    
Sbjct: 126 QGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAM 185

Query: 61  VINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPR 120
               +       A    +   +++LF+  LP +     +S LF  F G++E+R++   P 
Sbjct: 186 PPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV---PG 242

Query: 121 RTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           R       + FVEFD+   A  A DAL G+K          +KI FA
Sbjct: 243 RHD-----IAFVEFDNEVQAGAARDALQGFKITQNNA----MKISFA 280

>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 = 52.2 bits (124), Expect = 1e-08
 Identities = 17/93 (18%), Positives = 40/93 (43%), Gaps = 15/93 (16%)

Query: 82  SNLLFVDGLPTDCT----RREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDP 137
           ++ ++++ L         ++ +  +F  F    +I ++ +  +  G       FV F + 
Sbjct: 9   NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDI-LVSRSLKMRG-----QAFVIFKEV 62

Query: 138 KCARTAMDALHGYKFDDKKPDSPTLKIQFAHFP 170
             A  A+ ++ G+ F DK      ++IQ+A   
Sbjct: 63  SSATNALRSMQGFPFYDK-----PMRIQYAKTD 90

>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 = 54.5 bits (131), Expect = 2e-10
 Identities = 17/88 (19%), Positives = 29/88 (32%), Gaps = 8/88 (9%)

Query: 83  NLLFVDGLPTDCTRREV---SHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKC 139
           NL+FV GL       EV      F  F    ++ + +              +V +   + 
Sbjct: 16  NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75

Query: 140 ARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           A  A+  ++    D +     TLK    
Sbjct: 76  ALRAIQCVNNVVVDGR-----TLKASLG 98

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 54.1 bits (130), Expect = 2e-10
 Identities = 21/105 (20%), Positives = 37/105 (35%), Gaps = 13/105 (12%)

Query: 64  GVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTG 123
           G   S    +        +  ++V  LP D    ++    R   G   +R+  + PRR  
Sbjct: 1   GSSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALREL-GSVPLRLTWQGPRRR- 58

Query: 124 DRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAH 168
                  F+ + D   A+ A+  L G +         TL++  A 
Sbjct: 59  ------AFLHYPDSAAAQQAVSCLQGLRLGTD-----TLRVALAR 92

>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 = 54.9 bits (132), Expect = 3e-10
 Identities = 17/84 (20%), Positives = 35/84 (41%), Gaps = 13/84 (15%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           ++V  L  +  + E+   F  +   R + V  + P           FVEF+DP+ A  A+
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVA-RNPPGFA-------FVEFEDPRDAADAV 127

Query: 145 DALHGYKFDDKKPDSPTLKIQFAH 168
             L G      +     ++++ ++
Sbjct: 128 RELDGRTLCGCR-----VRVELSN 146

>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 = 53.4 bits (129), Expect = 4e-10
 Identities = 19/95 (20%), Positives = 36/95 (37%), Gaps = 16/95 (16%)

Query: 74  GSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVE 133
           GS    G +  +FV  +   CT +E+  LF       E  V+    +          FV 
Sbjct: 1   GSSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV----KDYA-------FVH 49

Query: 134 FDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAH 168
            +    A+ A+  L+G +   K+     + ++ + 
Sbjct: 50  MEKEADAKAAIAQLNGKEVKGKR-----INVELST 79

>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 = 53.0 bits (128), Expect = 5e-10
 Identities = 23/95 (24%), Positives = 36/95 (37%), Gaps = 17/95 (17%)

Query: 74  GSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVE 133
           GS    G   L F+  LP + T +E+  LF  +    E  +I    +  G       FV 
Sbjct: 1   GSSGSSGMVKL-FIGNLPREATEQEIRSLFEQYGKVLECDII----KNYG-------FVH 48

Query: 134 FDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAH 168
            +D   A  A+  LH YK          + ++ + 
Sbjct: 49  IEDKTAAEDAIRNLHHYKLHGVN-----INVEASK 78

>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 = 53.3 bits (128), Expect = 5e-10
 Identities = 18/95 (18%), Positives = 27/95 (28%), Gaps = 14/95 (14%)

Query: 73  AGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFV 132
             S        ++    LP      E+   F  F     +  +                V
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRF---GSLGRVLLPEGGI------TAIV 51

Query: 133 EFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           EF +P  AR A   L   KF         L +++A
Sbjct: 52  EFLEPLEARKAFRHLAYSKFHHV-----PLYLEWA 81

>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 = 55.4 bits (133), Expect = 7e-10
 Identities = 13/86 (15%), Positives = 32/86 (37%), Gaps = 11/86 (12%)

Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           S  L +  +P   +  ++  LF    G  +     ++ R+       +  ++    + A 
Sbjct: 151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK-------MALIQMGSVEEAV 203

Query: 142 TAMDALHGYKFDDKKPDSPTLKIQFA 167
            A+  LH +   +       L++ F+
Sbjct: 204 QALIDLHNHDLGENHH----LRVSFS 225

>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 = 42.7 bits (100), Expect = 2e-05
 Identities = 20/121 (16%), Positives = 42/121 (34%), Gaps = 14/121 (11%)

Query: 65  VPSSLRNNAGSPLKKGESNLLFVDGL-PTDCTRREVSHLFRPFVGYREIRVIHKEPRRTG 123
             S +   A   L    +++L V  L P   T + +  LF  +   + ++++  +     
Sbjct: 17  RGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE--- 73

Query: 124 DRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHFPFHLPSDGDEKCTP 183
                   V+  D   A+ AM  L+G+K   K      ++I  +           ++   
Sbjct: 74  -----NALVQMADGNQAQLAMSHLNGHKLHGKP-----IRITLSKHQNVQLPREGQEDQG 123

Query: 184 R 184
            
Sbjct: 124 L 124

>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 = 52.7 bits (127), Expect = 1e-09
 Identities = 21/99 (21%), Positives = 40/99 (40%), Gaps = 8/99 (8%)

Query: 70  RNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL 129
                 P +  E  +LFV  +  +    E+   F  +   + I +     RRTG  +   
Sbjct: 14  DELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD--RRTG-FSKGY 70

Query: 130 CFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAH 168
             VE++  K A  A +AL+G +   +     T+++ +  
Sbjct: 71  ALVEYETHKQALAAKEALNGAEIMGQ-----TIQVDWCF 104

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 52.3 bits (126), Expect = 1e-09
 Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 5/88 (5%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCA 140
            S+ LF+  L    T   +  +F      +   +  K+ +     +M   FVE+  P+ A
Sbjct: 4   GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63

Query: 141 RTAMDALHGYKFDDKKPDSPTLKIQFAH 168
           + A+  L G+  D  K     L+++ + 
Sbjct: 64  QKALKQLQGHTVDGHK-----LEVRISE 86

>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 = 52.8 bits (127), Expect = 1e-09
 Identities = 21/98 (21%), Positives = 40/98 (40%), Gaps = 8/98 (8%)

Query: 70  RNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL 129
             +   P +  E  +LFV G+  + T  ++   F  +   + I +     RRTG      
Sbjct: 10  DGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD--RRTG-YLKGY 66

Query: 130 CFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
             VE++  K A+ AM+ L+G     +      + + + 
Sbjct: 67  TLVEYETYKEAQAAMEGLNGQDLMGQ-----PISVDWC 99

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 52.6 bits (126), Expect = 2e-09
 Identities = 15/101 (14%), Positives = 33/101 (32%), Gaps = 15/101 (14%)

Query: 71  NNAGSPLKKGESNLLFVDGLPTDCT----RREVSHLFRPFVGYREIRVIHKEPRRTGDRA 126
           +   +P     S ++ +  +  +      +  +  L        +I V       +G   
Sbjct: 18  DLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVV-DLSDDNSG--- 73

Query: 127 MVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
               ++ F   + A+  ++A  GY F         L I F+
Sbjct: 74  --KAYIVFATQESAQAFVEAFQGYPFQGNP-----LVITFS 107

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 51.9 bits (125), Expect = 2e-09
 Identities = 21/99 (21%), Positives = 40/99 (40%), Gaps = 8/99 (8%)

Query: 70  RNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL 129
             +   P +  E  +LFV G+  + T  ++   F  +   + I +     RRTG      
Sbjct: 11  DGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD--RRTG-YLKGY 67

Query: 130 CFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAH 168
             VE++  K A+ AM+ L+G     +      + + +  
Sbjct: 68  TLVEYETYKEAQAAMEGLNGQDLMGQ-----PISVDWCF 101

>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 = 51.6 bits (124), Expect = 2e-09
 Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 11/84 (13%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           ++V  LP D   +++  +F  +   R+I +                FVEF+DP+ A  A+
Sbjct: 25  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLK-NRRGGPP-----FAFVEFEDPRDAEDAV 78

Query: 145 DALHGYKFDDKKPDSPTLKIQFAH 168
               GY +D  +     L+++F  
Sbjct: 79  YGRDGYDYDGYR-----LRVEFPR 97

>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 = 51.5 bits (124), Expect = 3e-09
 Identities = 24/99 (24%), Positives = 44/99 (44%), Gaps = 8/99 (8%)

Query: 70  RNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL 129
             ++G   KK  ++ + V  +P    +RE+  LF  F   + +R+  K+   TG      
Sbjct: 3   SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLP-KKMTGTG-AHRGF 60

Query: 130 CFVEFDDPKCARTAMDAL-HGYKFDDKKPDSPTLKIQFA 167
            FV+F   + A+ A +AL H      +      L +++A
Sbjct: 61  GFVDFITKQDAKKAFNALCHSTHLYGR-----RLVLEWA 94

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 50.8 bits (122), Expect = 4e-09
 Identities = 16/95 (16%), Positives = 31/95 (32%), Gaps = 11/95 (11%)

Query: 64  GVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEP--RR 121
           G   S  +++G P       ++ V  +P   +  E+   F  +        +        
Sbjct: 1   GSSGSSGSSSGKP----GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMP 56

Query: 122 TGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK 156
           TG+       V F+    A  A+  L+      +K
Sbjct: 57  TGE-----AMVAFESRDEATAAVIDLNDRPIGSRK 86

>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 = 50.7 bits (122), Expect = 4e-09
 Identities = 16/84 (19%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 70  RNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL 129
             ++G+      +  L V GL    T R++  +F  +    ++ +++   +++  R+   
Sbjct: 3   SGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYD--QQSR-RSRGF 59

Query: 130 CFVEFDDPKCARTAMDALHGYKFD 153
            FV F++   A+ A +  +G + D
Sbjct: 60  AFVYFENVDDAKEAKERANGMELD 83

>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 = 50.7 bits (122), Expect = 5e-09
 Identities = 18/90 (20%), Positives = 39/90 (43%), Gaps = 15/90 (16%)

Query: 82  SNLLFVDGLPTDCT----RREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDP 137
           ++ ++++ L         ++ +  +F  F    +I V  +  +  G       FV F + 
Sbjct: 8   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV-SRSLKMRG-----QAFVIFKEV 61

Query: 138 KCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
             A  A+ ++ G+ F DK      ++IQ+A
Sbjct: 62  SSATNALRSMQGFPFYDKP-----MRIQYA 86

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 50.4 bits (121), Expect = 5e-09
 Identities = 17/84 (20%), Positives = 33/84 (39%), Gaps = 13/84 (15%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           ++V  L T   + E+   F  +   R + +    P           FVEF+DP+ A  A+
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG--------FAFVEFEDPRDAEDAV 54

Query: 145 DALHGYKFDDKKPDSPTLKIQFAH 168
             L G      +     ++++ + 
Sbjct: 55  RGLDGKVICGSR-----VRVELST 73

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 50.3 bits (121), Expect = 5e-09
 Identities = 16/85 (18%), Positives = 36/85 (42%), Gaps = 17/85 (20%)

Query: 85  LFVDGLPT-DCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTA 143
           LF+  LP  + ++ ++  +F P+    +I +      +         F++FD+P+  R A
Sbjct: 13  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI------KNA-----FGFIQFDNPQSVRDA 61

Query: 144 MDALHGYKFDDKKPDSPTLKIQFAH 168
           ++         KK     L ++ + 
Sbjct: 62  IECESQEMNFGKK-----LILEVSS 81

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 50.4 bits (121), Expect = 6e-09
 Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 16/83 (19%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           LFV   P D    E++ +F PF   +E+++                FVEF++ + A  A+
Sbjct: 34  LFVRPFPLDVQESELNEIFGPFGPMKEVKI----LNGFA-------FVEFEEAESAAKAI 82

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
           + +HG  F ++      L++ ++
Sbjct: 83  EEVHGKSFANQ-----PLEVVYS 100

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 51.8 bits (125), Expect = 7e-09
 Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 1/72 (1%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           +FV  +P   + +++  LF  +    EI V+ ++  +   ++   CFV F   K A  A 
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVL-RDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 145 DALHGYKFDDKK 156
           +ALH  K     
Sbjct: 65  NALHNMKVLPGM 76

>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 = 39.5 bits (93), Expect = 1e-04
 Identities = 20/88 (22%), Positives = 35/88 (39%), Gaps = 16/88 (18%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKE---PRRTGDRAMVLCFVEFDDPKCAR 141
           LF+  +   CT  ++  +F  F    E R++       R          FV F     A+
Sbjct: 98  LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCA-------FVTFTTRAMAQ 150

Query: 142 TAMDALHGYKFDD--KKPDSPTLKIQFA 167
           TA+ A+H  +  +    P    + ++FA
Sbjct: 151 TAIKAMHQAQTMEGCSSP----MVVKFA 174

>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 = 50.0 bits (120), Expect = 7e-09
 Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 17/85 (20%)

Query: 85  LFVDGLPT-DCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTA 143
           LF+  LP  + ++ ++  +F P+    +I  I               F++FD+P+  R A
Sbjct: 25  LFIGNLPLKNVSKEDLFRIFSPYGHIMQIN-IKNA----------FGFIQFDNPQSVRDA 73

Query: 144 MDALHGYKFDDKKPDSPTLKIQFAH 168
           ++         KK     L ++ + 
Sbjct: 74  IEXESQEMNFGKK-----LILEVSS 93

>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 = 50.0 bits (120), Expect = 8e-09
 Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 3/81 (3%)

Query: 71  NNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLC 130
           ++  S +K  ++  LF+  +P +   +++  LF  F    E+ V+  + R TG       
Sbjct: 2   SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVL--KDRFTG-MHKGCA 58

Query: 131 FVEFDDPKCARTAMDALHGYK 151
           F+ + + + A  A  ALH  K
Sbjct: 59  FLTYCERESALKAQSALHEQK 79

>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 = 52.7 bits (127), Expect = 8e-09
 Identities = 11/78 (14%), Positives = 29/78 (37%), Gaps = 3/78 (3%)

Query: 79  KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPK 138
                 L++   P   T+R +  L +       + +  + P    + +    +++    +
Sbjct: 114 HLTECTLWMTNFPPSYTQRNIRDLLQDI-N--VVALSIRLPSLRFNTSRRFAYIDVTSKE 170

Query: 139 CARTAMDALHGYKFDDKK 156
            AR  ++ L+G K +   
Sbjct: 171 DARYCVEKLNGLKIEGYT 188

>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 = 42.7 bits (101), Expect = 2e-05
 Identities = 12/88 (13%), Positives = 26/88 (29%), Gaps = 5/88 (5%)

Query: 68  SLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAM 127
           + +    +  +  E   + V  LP    + +V   F+       + V     +       
Sbjct: 27  TSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR---- 82

Query: 128 VLCFVEFDDPKCARTAMDALHGYKFDDK 155
               +EF     A  A+   H     ++
Sbjct: 83  -FARIEFARYDGALAAITKTHKVVGQNE 109

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 50.0 bits (120), Expect = 8e-09
 Identities = 21/101 (20%), Positives = 44/101 (43%), Gaps = 9/101 (8%)

Query: 67  SSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRA 126
           SS  +         E + LF+ GLP  CT+ E+  + +     +++R++     R G + 
Sbjct: 2   SSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN---RAG-KP 57

Query: 127 MVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
             L +VE+++   A  A+  + G    +       +K+  +
Sbjct: 58  KGLAYVEYENESQASQAVMKMDGMTIKEN-----IIKVAIS 93

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 50.1 bits (120), Expect = 8e-09
 Identities = 18/83 (21%), Positives = 32/83 (38%), Gaps = 5/83 (6%)

Query: 76  PLKKGESNLLFVDGLPTDCTRRE---VSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFV 132
               G  +++ VD +P     R     + + + F  + +I      P   G +     F+
Sbjct: 9   QEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY-PEEDG-KTKGYIFL 66

Query: 133 EFDDPKCARTAMDALHGYKFDDK 155
           E+  P  A  A+    GYK D +
Sbjct: 67  EYASPAHAVDAVKNADGYKLDKQ 89

>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 = 49.6 bits (119), Expect = 9e-09
 Identities = 19/83 (22%), Positives = 29/83 (34%), Gaps = 14/83 (16%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L+V  L    +   +   F         RV  K+ R          FV F + + A  AM
Sbjct: 18  LYVRNLMLSTSEEMIEKEFNNIKPGAVERV--KKIRDYA-------FVHFSNREDAVEAM 68

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
            AL+G   D        +++  A
Sbjct: 69  KALNGKVLDGS-----PIEVTLA 86

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 49.5 bits (119), Expect = 1e-08
 Identities = 17/96 (17%), Positives = 32/96 (33%), Gaps = 16/96 (16%)

Query: 73  AGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFV 132
             S      S  L V  +   CT +E+   F  +    E  ++    +          FV
Sbjct: 1   GSSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV----KDYA-------FV 49

Query: 133 EFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAH 168
             +  + A  A+  L   +F  K+     + +Q + 
Sbjct: 50  HMERAEDAVEAIRGLDNTEFQGKR-----MHVQLST 80

>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 = 49.6 bits (119), Expect = 1e-08
 Identities = 14/88 (15%), Positives = 29/88 (32%), Gaps = 7/88 (7%)

Query: 71  NNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEP--RRTGDRAMV 128
            ++G+   K    ++ V  +P   +  E+   F  +        +        TG+    
Sbjct: 4   GSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGE---- 59

Query: 129 LCFVEFDDPKCARTAMDALHGYKFDDKK 156
              V F+    A  A+  L+      +K
Sbjct: 60  -AMVAFESRDEATAAVIDLNDRPIGSRK 86

>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 = 51.0 bits (123), Expect = 1e-08
 Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 8/83 (9%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L V+ LP + T+ E   LF         +++    + TG +++   FV + DPK A  A+
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRD--KITG-QSLGYGFVNYIDPKDAEKAI 61

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
           + L+G +   K     T+K+ +A
Sbjct: 62  NTLNGLRLQTK-----TIKVSYA 79

>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 = 49.2 bits (118), Expect = 2e-08
 Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 7/84 (8%)

Query: 70  RNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL 129
             ++G+    GES  L +  L    T   +  +F        I+V   +    G ++   
Sbjct: 3   SGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKAT---FIKVPQNQ---NG-KSKGY 55

Query: 130 CFVEFDDPKCARTAMDALHGYKFD 153
            F+EF   + A+ A+++ +  + +
Sbjct: 56  AFIEFASFEDAKEALNSCNKREIE 79

>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 = 50.2 bits (120), Expect = 2e-08
 Identities = 23/128 (17%), Positives = 45/128 (35%), Gaps = 16/128 (12%)

Query: 59  PDVINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVG---YREIRVI 115
            + +  +        G P     +  ++V  L      +++ ++F  +V      +  + 
Sbjct: 27  REEMETLSVFRSYEPGEP-----NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMF 81

Query: 116 HKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHF--PFHL 173
                + G R     F+   + K A  A+   +GY    K      + +QFA    P   
Sbjct: 82  DIRLMKEG-RMKGQAFIGLPNEKAAAKALKEANGYVLFGK-----PMVVQFARSARPKQD 135

Query: 174 PSDGDEKC 181
           P +G  KC
Sbjct: 136 PKEGKRKC 143

>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 = 49.2 bits (118), Expect = 2e-08
 Identities = 20/101 (19%), Positives = 39/101 (38%), Gaps = 17/101 (16%)

Query: 72  NAGSPLKKGE-----SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRA 126
           ++GS  K G      +  L+V GL  + +   ++  F  F G   IR I      +    
Sbjct: 2   SSGSSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRF-G--SIRTIDHVKGDS---- 54

Query: 127 MVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
               +++++    A+ A   + G+           L++ FA
Sbjct: 55  --FAYIQYESLDAAQAACAKMRGFPLG---GPDRRLRVDFA 90

>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 = 51.5 bits (124), Expect = 2e-08
 Identities = 20/113 (17%), Positives = 39/113 (34%), Gaps = 16/113 (14%)

Query: 61  VINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPR 120
           +++      R        +    +  + GLP D T +EV  L   +   +   V     +
Sbjct: 2   MLDPEEIRKRLEHTERQFRNRRKI-LIRGLPGDVTNQEVHDLLSDY-ELKYCFVDKY--K 57

Query: 121 RTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHFPFHL 173
            T        FV   + + A  A++A H  +  +++     L +Q       L
Sbjct: 58  GTA-------FVTLLNGEQAEAAINAFHQSRLRERE-----LSVQLQPTDALL 98

>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 = 49.6 bits (119), Expect = 9e-08
 Identities = 22/87 (25%), Positives = 34/87 (39%), Gaps = 8/87 (9%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCA 140
              LL V  LP   T+++   L RPF       +++ E  RTG ++    F E+     A
Sbjct: 94  TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSE--RTG-QSKGYGFAEYMKKDSA 150

Query: 141 RTAMDALHGYKFDDKKPDSPTLKIQFA 167
             A   L G     +     TL + + 
Sbjct: 151 ARAKSDLLGKPLGPR-----TLYVHWT 172

>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 = 41.9 bits (99), Expect = 3e-05
 Identities = 12/84 (14%), Positives = 24/84 (28%), Gaps = 10/84 (11%)

Query: 85  LFVDGLPTDCTRRE-VSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTA 143
           L VD LP      + +             ++   +  +    A     +E++  + A  A
Sbjct: 187 LCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFA----VLEYETAEMAEEA 242

Query: 144 MDALHGYKFDDKKPDSPTLKIQFA 167
                G            L++ F 
Sbjct: 243 QQQADGLSLGGSH-----LRVSFC 261

>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 = 50.2 bits (120), Expect = 2e-08
 Identities = 21/99 (21%), Positives = 40/99 (40%), Gaps = 8/99 (8%)

Query: 70  RNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL 129
                 P +  E  +LFV  +  +    E+   F  +   + I +     RRTG  +   
Sbjct: 60  DELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD--RRTG-FSKGY 116

Query: 130 CFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAH 168
             VE++  K A  A +AL+G +   +     T+++ +  
Sbjct: 117 ALVEYETHKQALAAKEALNGAEIMGQ-----TIQVDWCF 150

>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 = 50.3 bits (121), Expect = 2e-08
 Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 8/83 (9%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L V+ LP D T RE+  LFR        R++     +TG  +    FV+F     ++ A+
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRD--YKTG-YSYGYAFVDFTSEMDSQRAI 62

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
             L+G    +K      LK+ +A
Sbjct: 63  KVLNGITVRNK-----RLKVSYA 80

>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 = 49.7 bits (119), Expect = 2e-08
 Identities = 22/117 (18%), Positives = 44/117 (37%), Gaps = 9/117 (7%)

Query: 51  APGINPTIPDVINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYR 110
             G    +  +       +     +P      NL  V+ +PT     ++  LF  +    
Sbjct: 12  PYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNL-MVNYIPTTVDEVQLRQLFERYGPIE 70

Query: 111 EIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
            ++++    R T  ++    FV+F     A+ A+  L+G+   +K      LK+  A
Sbjct: 71  SVKIVCD--RETR-QSRGYGFVKFQSGSSAQQAIAGLNGFNILNK-----RLKVALA 119

>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 = 49.8 bits (119), Expect = 3e-08
 Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 3/74 (4%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCA 140
           +S  L+V  L    T  ++  LF      ++I +     +     A   CFVE+     A
Sbjct: 38  KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD--KMKK-TACGFCFVEYYSRADA 94

Query: 141 RTAMDALHGYKFDD 154
             AM  ++G + DD
Sbjct: 95  ENAMRYINGTRLDD 108

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 48.4 bits (116), Expect = 3e-08
 Identities = 17/76 (22%), Positives = 25/76 (32%), Gaps = 3/76 (3%)

Query: 78  KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDP 137
               S  LFV  L    +  ++  LF  +    E+         T  +     FV F  P
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPID--SLTK-KPKGFAFVTFMFP 60

Query: 138 KCARTAMDALHGYKFD 153
           + A  A   + G  F 
Sbjct: 61  EHAVKAYAEVDGQVFQ 76

>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 = 48.6 bits (116), Expect = 4e-08
 Identities = 22/108 (20%), Positives = 43/108 (39%), Gaps = 16/108 (14%)

Query: 70  RNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPF--------VGYREIRVIHKEPRR 121
             ++G P +  +++ ++V GL    T  +++  F+           G   I +     + 
Sbjct: 3   SGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLD--KE 60

Query: 122 TGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHF 169
           TG +      V ++DP  A+ A++   G  F   K     LK+  A  
Sbjct: 61  TG-KPKGDATVSYEDPPTAKAAVEWFDGKDFQGSK-----LKVSLARK 102

>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 = 48.0 bits (115), Expect = 4e-08
 Identities = 21/96 (21%), Positives = 36/96 (37%), Gaps = 14/96 (14%)

Query: 72  NAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCF 131
           ++G      + + LFV  LP D T  E+  LF  +    E+ +   + +  G       F
Sbjct: 5   SSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH--KDKGFG-------F 55

Query: 132 VEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           +  +    A  A   L       K      L+++FA
Sbjct: 56  IRLETRTLAEIAKVELDNMPLRGK-----QLRVRFA 86

>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 = 47.8 bits (114), Expect = 7e-08
 Identities = 16/87 (18%), Positives = 30/87 (34%), Gaps = 17/87 (19%)

Query: 85  LFVDGLPTD-CTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTA 143
           +F+  L T    + +V  +F  +       V     +          FV++ + + AR A
Sbjct: 30  VFIGNLNTALVKKSDVETIFSKYGRVAGCSV----HKGYA-------FVQYSNERHARAA 78

Query: 144 MDALHGYKFDDKKPDSPTLKIQFAHFP 170
           +   +G     +      L I  A  P
Sbjct: 79  VLGENGRVLAGQT-----LDINMAGEP 100

>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 = 49.3 bits (118), Expect = 7e-08
 Identities = 25/113 (22%), Positives = 42/113 (37%), Gaps = 8/113 (7%)

Query: 55  NPTIPDVINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRV 114
           +      ++  PS       S +    ++ LF+ GLP      +V  L   F   +   +
Sbjct: 87  DYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNL 146

Query: 115 IHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           +      TG  +    F E+ D      A+  L+G +  DKK     L +Q A
Sbjct: 147 VK--DSATG-LSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK-----LLVQRA 191

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 47.7 bits (114), Expect = 3e-07
 Identities = 18/86 (20%), Positives = 29/86 (33%), Gaps = 8/86 (9%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEP--RRTGDRAMVLCFVEFDDPKCART 142
           L+V  +P   T   +   F   +    +      P      ++     F+EF        
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 143 AMDALHGYKFDDKKPDSPTLKIQFAH 168
           AM A  G  F  +     +LKI+  H
Sbjct: 67  AM-AFDGIIFQGQ-----SLKIRRPH 86

>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 = 48.0 bits (114), Expect = 7e-08
 Identities = 18/112 (16%), Positives = 35/112 (31%), Gaps = 8/112 (7%)

Query: 45  GQRRDIAPGINPTIPDVINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFR 104
                 + G+ P    + +           +         + + GLP  CT+ E+   F 
Sbjct: 5   HHHHHHSSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFS 64

Query: 105 PFVGYREIRVIHKEP--RRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDD 154
                     +  +P  + TG+      FV+F   + A  A+   H  +   
Sbjct: 65  GLEIVPNGITLPVDPEGKITGE-----AFVQFASQELAEKALG-KHKERIGH 110

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 47.8 bits (114), Expect = 7e-08
 Identities = 25/102 (24%), Positives = 40/102 (39%), Gaps = 20/102 (19%)

Query: 78  KKGESNLLFVDGLPTDCTRREVSHLFRPF--------VGYREIRVIH-KEPRRT-GDRAM 127
              ++N +FV GL  + T   V+  F+           G   I +   +E  +  G+   
Sbjct: 3   DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE--- 59

Query: 128 VLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHF 169
               V FDDP  A+ A+D   G +F         +K+ FA  
Sbjct: 60  --ATVSFDDPPSAKAAIDWFDGKEFSGNP-----IKVSFATR 94

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 47.4 bits (113), Expect = 8e-08
 Identities = 12/85 (14%), Positives = 26/85 (30%), Gaps = 8/85 (9%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           +    L  +     +  + R +    E+ ++     RT  + + L  V F   + A+  +
Sbjct: 9   VTFARLNDNVRETFLKDMCRKYGEVEEVEILLH--PRTR-KHLGLARVLFTSTRGAKETV 65

Query: 145 DALHGYKFDDKKPDSPTLKIQFAHF 169
             LH             +  Q    
Sbjct: 66  KNLHLTSVMGNI-----IHAQLDIK 85

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 47.1 bits (112), Expect = 1e-07
 Identities = 16/104 (15%), Positives = 31/104 (29%), Gaps = 16/104 (15%)

Query: 66  PSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDR 125
                 N   P K   S ++ + GL       ++    + F     + V+ K  +R    
Sbjct: 5   HHHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK--KRQA-- 60

Query: 126 AMVLCFVEFDDPKCARTAMDALHG--YKFDDKKPDSPTLKIQFA 167
                 VEF+D   A  A++                    + ++
Sbjct: 61  -----LVEFEDVLGACNAVNYAADNQIYIAGHP-----AFVNYS 94

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 47.4 bits (113), Expect = 1e-07
 Identities = 12/85 (14%), Positives = 25/85 (29%), Gaps = 8/85 (9%)

Query: 71  NNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEP--RRTGDRAMV 128
            ++G            +  +P   T+ +V               +  +   +  G     
Sbjct: 4   GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQ---- 59

Query: 129 LCFVEFDDPKCARTAMDALHGYKFD 153
              V+F +   AR +   LH  K +
Sbjct: 60  -ALVQFKNEDDARKSE-RLHRKKLN 82

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 46.9 bits (112), Expect = 1e-07
 Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 5/84 (5%)

Query: 73  AGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFV 132
           +G+   K     L V  +P      ++  +F  F    ++ +I  E    G       FV
Sbjct: 6   SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG-----FGFV 60

Query: 133 EFDDPKCARTAMDALHGYKFDDKK 156
            F++   A  A + LHG   + +K
Sbjct: 61  TFENSADADRAREKLHGTVVEGRK 84

>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 = 49.3 bits (118), Expect = 1e-07
 Identities = 29/121 (23%), Positives = 41/121 (33%), Gaps = 22/121 (18%)

Query: 53  GINPTIPDVINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREI 112
           G+  TI      + S L+   G         L FV  LPTD T  +   LF  +    E+
Sbjct: 1   GMGFTID-----IKSFLK--PGEKTYTQRCRL-FVGNLPTDITEEDFKRLFERYGEPSEV 52

Query: 113 RVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHFPFH 172
            +         DR     F+  +    A  A   L G     +      L+I+FA     
Sbjct: 53  FINR-------DRG--FGFIRLESRTLAEIAKAELDGTILKSR-----PLRIRFATHGAA 98

Query: 173 L 173
           L
Sbjct: 99  L 99

>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 = 46.7 bits (111), Expect = 2e-07
 Identities = 21/111 (18%), Positives = 42/111 (37%), Gaps = 17/111 (15%)

Query: 70  RNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL 129
             ++G  +    S +L +  LP + T  EV  L  PF G  ++  I     +        
Sbjct: 3   SGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPF-G--KVTNILMLKGKNQ------ 53

Query: 130 CFVEFDDPKCARTAMD--ALHGYKFDDKKPDSPTLKIQFAHFPFHLPSDGD 178
            F+E    + A T ++  +       ++      + IQ+++    L + G 
Sbjct: 54  AFLELATEEAAITMVNYYSAVTPHLRNQ-----PIYIQYSNHK-ELKTSGP 98

>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 = 46.5 bits (111), Expect = 2e-07
 Identities = 27/99 (27%), Positives = 42/99 (42%), Gaps = 12/99 (12%)

Query: 72  NAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKE---PRRTGDRAMV 128
           ++GS  + G    LFV  L    +  +V  LF+PF    E  V+       +        
Sbjct: 5   SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCA----- 59

Query: 129 LCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
             FV+F     A+ A+ ALHG +       S +L ++FA
Sbjct: 60  --FVKFSSHTEAQAAIHALHGSQTMP--GASSSLVVKFA 94

>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 = 46.8 bits (111), Expect = 2e-07
 Identities = 20/118 (16%), Positives = 39/118 (33%), Gaps = 12/118 (10%)

Query: 63  NGVPSSLRNNAGSPLKKGESNLLFVD--GLPTDCTRREVSHLFRPFVGYREIRVIHKEPR 120
           +G   +L  + G       +  L V   GL    +R ++  +         +  +   P 
Sbjct: 6   SGAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCG---LVDALLMPPN 62

Query: 121 RTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA-HFPFHLPSDG 177
           +         F  +   + ++ A   L+G +  D      TL + F     +  PS G
Sbjct: 63  KP------YSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQWSGPSSG 114

>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 = 46.5 bits (111), Expect = 2e-07
 Identities = 20/96 (20%), Positives = 36/96 (37%), Gaps = 18/96 (18%)

Query: 74  GSPLKKGESNL--LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCF 131
           GS    G + +  LFV  L    T   +   F  F     ++ +    +          F
Sbjct: 1   GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL----KDYA-------F 49

Query: 132 VEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           + FD+   A  AM+ ++G   + +      ++I FA
Sbjct: 50  IHFDERDGAVKAMEEMNGKDLEGE-----NIEIVFA 80

>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 = 46.4 bits (111), Expect = 2e-07
 Identities = 19/96 (19%), Positives = 33/96 (34%), Gaps = 8/96 (8%)

Query: 73  AGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFV 132
             S         L VD L    +   +  +F  +    ++ +       T        FV
Sbjct: 4   GSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPR--EPHTK-APRGFAFV 60

Query: 133 EFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAH 168
            F D + A+ A  A+ G + D +      L++Q A 
Sbjct: 61  RFHDRRDAQDAEAAMDGAELDGR-----ELRVQVAR 91

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 46.9 bits (111), Expect = 2e-07
 Identities = 20/105 (19%), Positives = 39/105 (37%), Gaps = 12/105 (11%)

Query: 65  VPSSLRNNAGSPLKKGESN--LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRT 122
           + +S           G+S    + V+ L    T   +  L + F  +  +  I    +  
Sbjct: 9   LAASAAAVDAGMAMAGQSPVLRIIVENLFYPVT---LDVLHQIFSKFGTVLKIITFTKNN 65

Query: 123 GDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
             +A     +++ DP  A+ A  +L G    +      TL+I F+
Sbjct: 66  QFQA----LLQYADPVSAQHAKLSLDGQNIYN---ACCTLRIDFS 103

>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 = 46.1 bits (110), Expect = 2e-07
 Identities = 25/97 (25%), Positives = 39/97 (40%), Gaps = 20/97 (20%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLF--------RPFVGYREIRVIH-KEPRRT-GDRAMVLC 130
           ++N +FV GL  + T   V+  F            G   I +   +E  +  G+      
Sbjct: 12  DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE-----A 66

Query: 131 FVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
            V FDDP  A+ A+D   G +F         +K+ FA
Sbjct: 67  TVSFDDPPSAKAAIDWFDGKEFSGNP-----IKVSFA 98

>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 = 47.0 bits (112), Expect = 2e-07
 Identities = 16/88 (18%), Positives = 38/88 (43%), Gaps = 3/88 (3%)

Query: 66  PSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDR 125
                 + G+      +  L V GL    T R++  +F  +    ++ +++   +++  R
Sbjct: 30  MGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYD--QQSR-R 86

Query: 126 AMVLCFVEFDDPKCARTAMDALHGYKFD 153
           +    FV F++   A+ A +  +G + D
Sbjct: 87  SRGFAFVYFENVDDAKEAKERANGMELD 114

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 45.6 bits (109), Expect = 2e-07
 Identities = 18/83 (21%), Positives = 31/83 (37%), Gaps = 6/83 (7%)

Query: 74  GSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVE 133
           GS    G   + FV  LP D T + +   F          +        G ++     V+
Sbjct: 1   GSSGSSGACQI-FVRNLPFDFTWKMLKDKFNECGHVLYADIK----MENG-KSKGCGVVK 54

Query: 134 FDDPKCARTAMDALHGYKFDDKK 156
           F+ P+ A  A   ++G K   ++
Sbjct: 55  FESPEVAERACRMMNGMKLSGRE 77

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 45.5 bits (108), Expect = 3e-07
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 83  NLLFVDGLP---TDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKC 139
           +++ VD +P    D   +  + + + F  + +I      P   G +     F+E+  P  
Sbjct: 2   SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY-PEEDG-KTKGYIFLEYASPAH 59

Query: 140 ARTAMDALHGYKFDDK 155
           A  A+    GYK D +
Sbjct: 60  AVDAVKNADGYKLDKQ 75

>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 = 45.7 bits (109), Expect = 3e-07
 Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 10/77 (12%)

Query: 78  KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGD-RAMVLCFVEFDD 136
           K   +  L    L  + T  E+  +F   +   EIR++     + G  + +   ++EF  
Sbjct: 12  KVRAARTLLAKNLSFNITEDELKEVFEDAL---EIRLV----SQDGKSKGI--AYIEFKS 62

Query: 137 PKCARTAMDALHGYKFD 153
              A   ++   G + D
Sbjct: 63  EADAEKNLEEKQGAEID 79

>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 = 45.7 bits (109), Expect = 4e-07
 Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 3/82 (3%)

Query: 72  NAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCF 131
           ++GS     +   LFV GL  D   + +  +F  +    E+ V+    R T  R+    F
Sbjct: 2   SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKD--RETQ-RSRGFGF 58

Query: 132 VEFDDPKCARTAMDALHGYKFD 153
           V F++   A+ AM A++G   D
Sbjct: 59  VTFENIDDAKDAMMAMNGKSVD 80

>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 = 46.1 bits (109), Expect = 4e-07
 Identities = 20/107 (18%), Positives = 38/107 (35%), Gaps = 16/107 (14%)

Query: 63  NGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRT 122
           +G+     +   S      S ++ +  LP D T  EV  L  PF G  ++  +     + 
Sbjct: 12  SGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPF-G--KVTNLLMLKGKN 68

Query: 123 GDRAMVLCFVEFDDPKCARTAMD--ALHGYKFDDKKPDSPTLKIQFA 167
                   F+E +  + A T ++           +      + IQF+
Sbjct: 69  Q------AFIEMNTEEAANTMVNYYTSVTPVLRGQ-----PIYIQFS 104

>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 = 45.2 bits (108), Expect = 4e-07
 Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 3/74 (4%)

Query: 80  GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKC 139
             S+ L+V  L  + T   +  +F PF     I ++      TG R+    F+ F D +C
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKD--SDTG-RSKGYGFITFSDSEC 59

Query: 140 ARTAMDALHGYKFD 153
           AR A++ L+G++  
Sbjct: 60  ARRALEQLNGFELA 73

>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 = 45.6 bits (108), Expect = 4e-07
 Identities = 15/99 (15%), Positives = 30/99 (30%), Gaps = 16/99 (16%)

Query: 71  NNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLC 130
            ++GS  K   S ++ V GL       ++      F G   I  +   P +         
Sbjct: 4   GSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKF-G--TICYVMMMPFKR------QA 54

Query: 131 FVEFDDPKCARTAMDAL--HGYKFDDKKPDSPTLKIQFA 167
            VEF++   A+  +            +          ++
Sbjct: 55  LVEFENIDSAKECVTFAADVPVYIAGQ-----QAFFNYS 88

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 45.3 bits (108), Expect = 4e-07
 Identities = 20/98 (20%), Positives = 38/98 (38%), Gaps = 9/98 (9%)

Query: 70  RNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL 129
             ++GS L K      F+  LP D T   +   FR       +R+  +      +R    
Sbjct: 3   SGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPRE--PSNPERLKGF 59

Query: 130 CFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
            + EF+D     +A+ +L+     +K      +++  A
Sbjct: 60  GYAEFEDLDSLLSAL-SLNEESLGNK-----RIRVDVA 91

>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 = 45.1 bits (107), Expect = 5e-07
 Identities = 20/82 (24%), Positives = 32/82 (39%), Gaps = 6/82 (7%)

Query: 71  NNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLC 130
            ++GS  +    + + + GLP   T  ++ + F P    R    I  + R TG+      
Sbjct: 4   GSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGE-----A 58

Query: 131 FVEFDDPKCARTAMDALHGYKF 152
            VEF   + A  AM A      
Sbjct: 59  DVEFATHEDAVAAM-AKDKANM 79

>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 = 44.8 bits (107), Expect = 5e-07
 Identities = 13/87 (14%), Positives = 32/87 (36%), Gaps = 7/87 (8%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCA 140
           +   + +  L  + T+  +  +F  +   + I +   E       +    +VEF++P  A
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMP-VERMHPH-LSKGYAYVEFENPDEA 60

Query: 141 RTAMDALHGYKFDDKKPDSPTLKIQFA 167
             A+  + G + D +      +     
Sbjct: 61  EKALKHMDGGQIDGQ-----EITATAV 82

>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 = 45.3 bits (108), Expect = 5e-07
 Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 3/81 (3%)

Query: 73  AGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFV 132
           +GS        +L+V GL  +   + +   F PF    +I++       T  +     FV
Sbjct: 3   SGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIP--LDYETE-KHRGFAFV 59

Query: 133 EFDDPKCARTAMDALHGYKFD 153
           EF+  + A  A+D ++  +  
Sbjct: 60  EFELAEDAAAAIDNMNESELF 80

>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 = 44.8 bits (107), Expect = 5e-07
 Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 3/69 (4%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L+V GL  +   + +   F PF    +I++       T  +     FVEF+  + A  A+
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPL--DYETE-KHRGFAFVEFELAEDAAAAI 66

Query: 145 DALHGYKFD 153
           D ++  +  
Sbjct: 67  DNMNESELF 75

>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 = 46.4 bits (111), Expect = 5e-07
 Identities = 14/72 (19%), Positives = 30/72 (41%), Gaps = 8/72 (11%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L    L  + T  E+  +F   +   EIR++ ++ +  G     + ++EF     A   +
Sbjct: 102 LLAKNLSFNITEDELKEVFEDAL---EIRLVSQDGKSKG-----IAYIEFKSEADAEKNL 153

Query: 145 DALHGYKFDDKK 156
           +   G + D + 
Sbjct: 154 EEKQGAEIDGRS 165

>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 = 38.7 bits (91), Expect = 3e-04
 Identities = 12/93 (12%), Positives = 30/93 (32%), Gaps = 12/93 (12%)

Query: 77  LKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRT-GDRAMVLCFVEFD 135
            +      LF+  L  + +  E+           ++ V+                +V+F+
Sbjct: 8   SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK-----FGYVDFE 62

Query: 136 DPKCARTAMDALHGYKFDDKKPDSPTLKIQFAH 168
             +    A++ L G K    +     +K++   
Sbjct: 63  SAEDLEKALE-LTGLKVFGNE-----IKLEKPK 89

>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 = 45.4 bits (108), Expect = 5e-07
 Identities = 21/88 (23%), Positives = 43/88 (48%), Gaps = 9/88 (10%)

Query: 66  PSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDR 125
            ++L+  +  P++      L+V  L  + T   +  +F PF     I+++      TG R
Sbjct: 16  ANNLQKGSAGPMR------LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMD--SETG-R 66

Query: 126 AMVLCFVEFDDPKCARTAMDALHGYKFD 153
           +    F+ F D +CA+ A++ L+G++  
Sbjct: 67  SKGYGFITFSDSECAKKALEQLNGFELA 94

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 46.5 bits (110), Expect = 5e-07
 Identities = 16/118 (13%), Positives = 34/118 (28%), Gaps = 7/118 (5%)

Query: 38  LPDPNLIGQRRDIAPGINPTIPDVINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRR 97
           L   NL  Q  +  P +        N    ++         +     ++V       T +
Sbjct: 13  LGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGL--RNRRAAVYVGSFSWWTTDQ 70

Query: 98  EVSHLFRPF--VGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFD 153
           ++  + R        E++    E R  G ++     V           ++ L G   +
Sbjct: 71  QLIQVIRSIGVYDVVELKFA--ENRANG-QSKGYAEVVVASENSVHKLLELLPGKVLN 125

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 46.2 bits (109), Expect = 5e-07
 Identities = 21/105 (20%), Positives = 40/105 (38%), Gaps = 12/105 (11%)

Query: 65  VPSSLRNNAGSPLKKGESNLLF--VDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRT 122
           + +S           G+S +L   V+ L    T   +  L + F  +  +  I    +  
Sbjct: 27  LAASAAAVDAGMAMAGQSPVLRIIVENLFYPVT---LDVLHQIFSKFGTVLKIITFTKNN 83

Query: 123 GDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
             +A     +++ DP  A+ A  +L G    +      TL+I F+
Sbjct: 84  QFQA----LLQYADPVSAQHAKLSLDGQNIYN---ACCTLRIDFS 121

>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 = 44.4 bits (106), Expect = 6e-07
 Identities = 22/87 (25%), Positives = 35/87 (40%), Gaps = 15/87 (17%)

Query: 74  GSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLC--- 130
           GS    G S L ++ GL    T +++  L +P+      + I        D+    C   
Sbjct: 1   GSS---GSSGL-YIRGLQPGTTDQDLVKLCQPYGKIVSTKAIL-------DKTTNKCKGY 49

Query: 131 -FVEFDDPKCARTAMDALHGYKFDDKK 156
            FV+FD P  A+ A+ AL       + 
Sbjct: 50  GFVDFDSPSAAQKAVTALKASGVQAQM 76

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 45.6 bits (108), Expect = 6e-07
 Identities = 17/87 (19%), Positives = 31/87 (35%), Gaps = 6/87 (6%)

Query: 66  PSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDR 125
                 ++   ++    + + + GLP   T  ++ + F P    R    I  + R TG+ 
Sbjct: 30  MGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGE- 88

Query: 126 AMVLCFVEFDDPKCARTAMDALHGYKF 152
                 VEF   + A  AM +      
Sbjct: 89  ----ADVEFATHEEAVAAM-SKDRANM 110

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 45.9 bits (109), Expect = 6e-07
 Identities = 23/121 (19%), Positives = 45/121 (37%), Gaps = 16/121 (13%)

Query: 42  NLIGQRRDIAPGINPTIPDVINGVPSSLR------NNAGSPLKKGESNL---LFVDGLPT 92
           NL  +  +I   +    P+ +     +         + GS    G +     L+V GL  
Sbjct: 18  NLSDEMYEILSNL----PESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAE 73

Query: 93  DCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKF 152
           +   + +   F PF    +I++       T  +     FVEF+  + A  A+D ++  + 
Sbjct: 74  EVDDKVLHAAFIPFGDITDIQIPL--DYETE-KHRGFAFVEFELAEDAAAAIDNMNESEL 130

Query: 153 D 153
            
Sbjct: 131 F 131

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 45.0 bits (107), Expect = 7e-07
 Identities = 19/91 (20%), Positives = 34/91 (37%), Gaps = 5/91 (5%)

Query: 66  PSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDR 125
               R +  +   K +   L V  +P      ++  +F  F    ++ +I  E    G  
Sbjct: 13  GLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG-- 70

Query: 126 AMVLCFVEFDDPKCARTAMDALHGYKFDDKK 156
                FV F++   A  A + LHG   + +K
Sbjct: 71  ---FGFVTFENSADADRAREKLHGTVVEGRK 98

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 45.1 bits (107), Expect = 7e-07
 Identities = 29/121 (23%), Positives = 50/121 (41%), Gaps = 16/121 (13%)

Query: 51  APGINPTIPDVINGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYR 110
           +     T P     + ++    AG  ++  E   LF+  LP + T  +++  F PF    
Sbjct: 9   SASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVI 68

Query: 111 EIRVIHKEPRRTGDRAMVLC----FVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQF 166
             +V         D+   L     FV FD+P  A+ A+ A++G++   K      LK+Q 
Sbjct: 69  SAKVFI-------DKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTK-----RLKVQL 116

Query: 167 A 167
            
Sbjct: 117 K 117

>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 = 44.5 bits (106), Expect = 7e-07
 Identities = 11/72 (15%), Positives = 31/72 (43%), Gaps = 3/72 (4%)

Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
            + ++V  LP   T  ++  +F  +    ++ ++    + T  ++  + F+ F D   A+
Sbjct: 16  KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKD--KDTR-KSKGVAFILFLDKDSAQ 72

Query: 142 TAMDALHGYKFD 153
               A++  +  
Sbjct: 73  NCTRAINNKQLF 84

>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 = 44.5 bits (106), Expect = 7e-07
 Identities = 18/87 (20%), Positives = 41/87 (47%), Gaps = 8/87 (9%)

Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           S ++++  +P D T  ++  L         ++++     +TG R+    F+EF D + + 
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMF--DPQTG-RSKGYAFIEFRDLESSA 58

Query: 142 TAMDALHGYKFDDKKPDSPTLKIQFAH 168
           +A+  L+GY+   +      LK  ++ 
Sbjct: 59  SAVRNLNGYQLGSR-----FLKCGYSS 80

>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 = 45.0 bits (107), Expect = 8e-07
 Identities = 26/109 (23%), Positives = 47/109 (43%), Gaps = 16/109 (14%)

Query: 63  NGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRT 122
           +G+       AGS  +  E   LF+  LP +   +++  +F PF      +V        
Sbjct: 6   SGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFI------ 59

Query: 123 GDRAMVLC----FVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
            D+   L     FV +D+P  A+ A+ +++G++   K      LK+Q  
Sbjct: 60  -DKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMK-----RLKVQLK 102

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 44.5 bits (105), Expect = 9e-07
 Identities = 19/86 (22%), Positives = 33/86 (38%), Gaps = 12/86 (13%)

Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           S ++ +  LP D T  EV  L  PF G  ++  +     +         F+E +  + A 
Sbjct: 16  SRVIHIRKLPIDVTEGEVISLGLPF-G--KVTNLLMLKGKNQ------AFIEMNTEEAAN 66

Query: 142 TAMDALHGYKFDDKKPDSPTLKIQFA 167
           T ++    Y           + IQF+
Sbjct: 67  TMVNY---YTSVTPVLRGQPIYIQFS 89

>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 = 44.5 bits (106), Expect = 1e-06
 Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 5/71 (7%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L+V  L  D T   +  LF      +  ++I +            CFVEF + + A  A+
Sbjct: 18  LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-----YCFVEFYEHRDAAAAL 72

Query: 145 DALHGYKFDDK 155
            A++G K   K
Sbjct: 73  AAMNGRKILGK 83

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 44.4 bits (105), Expect = 1e-06
 Identities = 16/88 (18%), Positives = 32/88 (36%), Gaps = 8/88 (9%)

Query: 71  NNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEP--RRTGDRAMV 128
            ++G+         + + GLP  C++ E+   F           +  +   R TG+    
Sbjct: 4   GSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGE---- 59

Query: 129 LCFVEFDDPKCARTAMDALHGYKFDDKK 156
             FV+F   + A  A+   H  +   + 
Sbjct: 60  -AFVQFASQEIAEKALK-KHKERIGHRY 85

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 44.8 bits (106), Expect = 1e-06
 Identities = 16/84 (19%), Positives = 30/84 (35%), Gaps = 8/84 (9%)

Query: 73  AGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEP--RRTGDRAMVLC 130
           + S         +++ GLP +   + V   F+      +   I   P  + TG+      
Sbjct: 16  SRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGE-----G 70

Query: 131 FVEFDDPKCARTAMDALHGYKFDD 154
           FVEF +    + A+   H     +
Sbjct: 71  FVEFRNEADYKAAL-CRHKQYMGN 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 = 43.8 bits (104), Expect = 1e-06
 Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 6/84 (7%)

Query: 70  RNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL 129
             ++G   +   S  LFV GL  D T   +   F   V     R++    R TG  +   
Sbjct: 3   SGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTD--RETG-SSKGF 56

Query: 130 CFVEFDDPKCARTAMDALHGYKFD 153
            FV+F+  + A+ A +A+   + D
Sbjct: 57  GFVDFNSEEDAKAAKEAMEDGEID 80

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 43.8 bits (104), Expect = 2e-06
 Identities = 14/84 (16%), Positives = 34/84 (40%), Gaps = 16/84 (19%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGY-REIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTA 143
            ++  +P   T  ++  LF+ F G+  + +          ++    CF+++D  + A   
Sbjct: 30  AYIGNIPHFATEADLIPLFQNF-GFILDFKHYP-------EKG--CCFIKYDTHEQAAVC 79

Query: 144 MDALHGYKFDDKKPDSPTLKIQFA 167
           + AL  + F  +      L+  + 
Sbjct: 80  IVALANFPFQGR-----NLRTGWG 98

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 43.8 bits (104), Expect = 2e-06
 Identities = 20/94 (21%), Positives = 39/94 (41%), Gaps = 8/94 (8%)

Query: 74  GSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVE 133
           G   +  ++  + V  L  D    ++  LFRPF     I +     + TG ++    F+ 
Sbjct: 7   GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKD--KTTG-QSKGFAFIS 63

Query: 134 FDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           F   + A  A+  + G+ +D        L +++A
Sbjct: 64  FHRREDAARAIAGVSGFGYDHL-----ILNVEWA 92

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 43.6 bits (103), Expect = 2e-06
 Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 7/80 (8%)

Query: 78  KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMV-LCFVEFDD 136
              ++  +++ G PTD T  ++            I++     RRT  +A     FV FD 
Sbjct: 7   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQM-----RRTLHKAFKGSIFVVFDS 61

Query: 137 PKCARTAMDALHGYKFDDKK 156
            + A+  +    G K+ +  
Sbjct: 62  IESAKKFV-ETPGQKYKETD 80

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 44.0 bits (104), Expect = 2e-06
 Identities = 19/91 (20%), Positives = 31/91 (34%), Gaps = 3/91 (3%)

Query: 63  NGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRT 122
             +     +    P        L VD L    +   +  +F  +    ++ +     R T
Sbjct: 28  QQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRD--RYT 85

Query: 123 GDRAMVLCFVEFDDPKCARTAMDALHGYKFD 153
              +    FV F D + A  AMDA+ G   D
Sbjct: 86  K-ESRGFAFVRFHDKRDAEDAMDAMDGAVLD 115

>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 = 43.0 bits (102), Expect = 2e-06
 Identities = 12/71 (16%), Positives = 23/71 (32%), Gaps = 5/71 (7%)

Query: 85  LFVDGLPTDCTRREVSHLFRPF--VGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCART 142
           L++  L    T  +++            EI+    E R  G ++     V       ++ 
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFF--ENRANG-QSKGFALVGVGSEASSKK 60

Query: 143 AMDALHGYKFD 153
            MD L   +  
Sbjct: 61  LMDLLPKRELH 71

>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 = 44.8 bits (105), Expect = 3e-06
 Identities = 24/146 (16%), Positives = 50/146 (34%), Gaps = 11/146 (7%)

Query: 16  VHPEPGMVGITAVASVKGYSSPLPDPNLIGQRRDIAPGINPTIPDVINGVPS----SLRN 71
           +  + G V +  +      +    D N+I +    +      I +    +       L  
Sbjct: 39  IKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPE 98

Query: 72  NAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLC- 130
                    ++  +++ G PTD T  ++            I++     RRT  +A     
Sbjct: 99  VTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQM-----RRTLHKAFKGSI 153

Query: 131 FVEFDDPKCARTAMDALHGYKFDDKK 156
           FV FD  + A+  ++   G K+ +  
Sbjct: 154 FVVFDSIESAKKFVETP-GQKYKETD 178

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 43.1 bits (102), Expect = 3e-06
 Identities = 14/89 (15%), Positives = 29/89 (32%), Gaps = 6/89 (6%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPF--VGYREIRVIHKEPRRTGDRAMVLCFVEFDDPK 138
             + + +  +        +     P+  +    IR+I    ++T  +     FV+     
Sbjct: 8   HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKD--KQTQ-QNRGFAFVQLSSAM 64

Query: 139 CARTAMDALHGYKFDDKKPDSPTLKIQFA 167
            A   +  L        K D  T+ + FA
Sbjct: 65  DASQLLQILQS-LHPPLKIDGKTIGVDFA 92

>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 = 42.6 bits (101), Expect = 3e-06
 Identities = 15/83 (18%), Positives = 28/83 (33%), Gaps = 4/83 (4%)

Query: 73  AGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFV 132
              P ++     +FV  L        +  LF       ++ +      R G +     FV
Sbjct: 7   GMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD---REG-KPKSFGFV 62

Query: 133 EFDDPKCARTAMDALHGYKFDDK 155
            F  P+    A+  L+G +   +
Sbjct: 63  CFKHPESVSYAIALLNGIRLYGR 85

>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 = 44.1 bits (104), Expect = 4e-06
 Identities = 21/105 (20%), Positives = 38/105 (36%), Gaps = 8/105 (7%)

Query: 63  NGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRT 122
               +   ++    +       L VD L    +   +  +F  +    ++ +     R T
Sbjct: 51  TFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRD--RYT 108

Query: 123 GDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
              +    FV F D + A  AMDA+ G   D +      L++Q A
Sbjct: 109 K-ESRGFAFVRFHDKRDAEDAMDAMDGAVLDGR-----ELRVQMA 147

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 44.2 bits (105), Expect = 5e-06
 Identities = 14/91 (15%), Positives = 36/91 (39%), Gaps = 8/91 (8%)

Query: 66  PSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDR 125
            ++ R  A + + +     ++V  +  +     +   F PF   + I +       T  +
Sbjct: 17  SAAQRQGALAIMSR-----VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWD--SVTM-K 68

Query: 126 AMVLCFVEFDDPKCARTAMDALHGYKFDDKK 156
                FVE++ P+ A+ A++ ++      + 
Sbjct: 69  HKGFAFVEYEVPEAAQLALEQMNSVMLGGRN 99

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 42.4 bits (100), Expect = 5e-06
 Identities = 15/79 (18%), Positives = 26/79 (32%), Gaps = 3/79 (3%)

Query: 80  GESNLLFVDGLP-TDCTRREV--SHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDD 136
           G    + V+G P     +  V    L   F    ++  +         +     FVE   
Sbjct: 4   GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGS 63

Query: 137 PKCARTAMDALHGYKFDDK 155
              A+  + + HG + D K
Sbjct: 64  MNDAKKIIKSFHGKRLDLK 82

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 42.7 bits (101), Expect = 5e-06
 Identities = 17/91 (18%), Positives = 32/91 (35%), Gaps = 17/91 (18%)

Query: 73  AGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVI-HKE---PRRTGDRAMV 128
           +G P    E   +F+  L  D     +  + + F   + +RV+ H +    +        
Sbjct: 6   SGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCA----- 60

Query: 129 LCFVEFDDPKCARTAMDALH------GYKFD 153
             F +F   + A+  + A        G K D
Sbjct: 61  --FAQFMTQEAAQKCLAAASLEAEGGGLKLD 89

>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 = 42.2 bits (100), Expect = 5e-06
 Identities = 19/101 (18%), Positives = 38/101 (37%), Gaps = 9/101 (8%)

Query: 67  SSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRA 126
           S   ++  S L K      F+  LP D T   +   FR       +R+  +      +R 
Sbjct: 4   SHHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPRE--PSNPERL 60

Query: 127 MVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
               + EF+D     +A+ +L+     ++      +++  A
Sbjct: 61  KGFGYAEFEDLDSLLSAL-SLNEESLGNR-----RIRVDVA 95

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 43.0 bits (101), Expect = 5e-06
 Identities = 21/80 (26%), Positives = 30/80 (37%), Gaps = 10/80 (12%)

Query: 70  RNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPF----VGYREIRVI-HKEPRRTGD 124
            N     L K    ++ + GLP   T  EV   F        G   I  + + + R TGD
Sbjct: 11  SNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGD 70

Query: 125 RAMVLCFVEFDDPKCARTAM 144
                 FV F   + A+ A+
Sbjct: 71  -----AFVLFACEEYAQNAL 85

>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 = 41.9 bits (99), Expect = 6e-06
 Identities = 15/83 (18%), Positives = 32/83 (38%), Gaps = 13/83 (15%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L+V GL    T  ++ + F  F   R I V+ +  ++         F++F   + A  A 
Sbjct: 15  LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR--QQCA-------FIQFATRQAAEVAA 65

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
           +        + +     L +++ 
Sbjct: 66  EKSFNKLIVNGRR----LNVKWG 84

>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 = 42.6 bits (101), Expect = 1e-05
 Identities = 19/88 (21%), Positives = 30/88 (34%), Gaps = 12/88 (13%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEP---RRTG-DRAMVLCFVEFDDPKCA 140
           L+V  +P   T   +   F   +    +      P    +   D+     F+EF      
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNF--AFLEFRSVDET 64

Query: 141 RTAMDALHGYKFDDKKPDSPTLKIQFAH 168
             AM A  G  F  +     +LKI+  H
Sbjct: 65  TQAM-AFDGIIFQGQ-----SLKIRRPH 86

>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 = 41.4 bits (98), Expect = 3e-05
 Identities = 23/83 (27%), Positives = 35/83 (42%), Gaps = 8/83 (9%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           LF+ GLP      +V  L   F   +   ++ K+   TG  +    F E+ D      A+
Sbjct: 97  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLV-KDSA-TG-LSKGYAFCEYVDINVTDQAI 153

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
             L+G +  DKK     L +Q A
Sbjct: 154 AGLNGMQLGDKK-----LLVQRA 171

>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 = 41.1 bits (97), Expect = 1e-05
 Identities = 15/70 (21%), Positives = 25/70 (35%), Gaps = 9/70 (12%)

Query: 80  GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKC 139
              N L++  L    T  ++  LF         +V+ K             FV++ D   
Sbjct: 6   SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK--SGYA-------FVDYPDQNW 56

Query: 140 ARTAMDALHG 149
           A  A++ L G
Sbjct: 57  AIRAIETLSG 66

>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 = 41.5 bits (98), Expect = 1e-05
 Identities = 17/84 (20%), Positives = 33/84 (39%), Gaps = 16/84 (19%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGY-REIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTA 143
           ++  G+ +  T + +   F PF G   EIRV         ++     FV F   + A  A
Sbjct: 28  VYCGGIASGLTDQLMRQTFSPF-GQIMEIRVFP-------EKG--YSFVRFSTHESAAHA 77

Query: 144 MDALHGYKFDDKKPDSPTLKIQFA 167
           + +++G   +        +K  + 
Sbjct: 78  IVSVNGTTIEGH-----VVKCYWG 96

>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 = 42.5 bits (101), Expect = 1e-05
 Identities = 18/94 (19%), Positives = 35/94 (37%), Gaps = 9/94 (9%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L+V  L    T   +   F+       I+++     +   + +   FVE+     A  A+
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMID---KNN-KNVNYAFVEYHQSHDANIAL 58

Query: 145 DALHGYKFDDKKPDSPTLKIQFAHFPFHLPSDGD 178
             L+G + ++       +KI +A       SD  
Sbjct: 59  QTLNGKQIENN-----IVKINWAFQSQQSSSDDT 87

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 41.4 bits (97), Expect = 1e-05
 Identities = 10/72 (13%), Positives = 24/72 (33%), Gaps = 6/72 (8%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           + +  LP  C+ +++  L R          ++               +EF   +    A+
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDG------TGALEFPSEEILVEAL 84

Query: 145 DALHGYKFDDKK 156
           + L+  +F    
Sbjct: 85  ERLNNIEFRGSV 96

>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 = 41.3 bits (97), Expect = 2e-05
 Identities = 11/79 (13%), Positives = 24/79 (30%), Gaps = 8/79 (10%)

Query: 78  KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVI-HKEPRRTGDRAMVLCFVEFDD 136
              +   + V G+P      +V   F        + ++     R  G+       V+F  
Sbjct: 12  INPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGN-----GLVKFLS 65

Query: 137 PKCARTAMDALHGYKFDDK 155
           P+    A+   +      +
Sbjct: 66  PQDTFEALK-RNRMLMIQR 83

>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 = 42.8 bits (100), Expect = 2e-05
 Identities = 19/126 (15%), Positives = 37/126 (29%), Gaps = 6/126 (4%)

Query: 34  YSSPLPDPNLIGQRRDIAPGINPTIPDVINGVPSSLRNNAGSPLKKGESNLLFVDGLPTD 93
           Y   +      G   +    ++   P V + V              G+   L++  L   
Sbjct: 21  YDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKG-AAPNVVYTYTGKRIALYIGNLTWW 79

Query: 94  CTRREVSHLFRPF--VGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYK 151
            T  +++            EI+    E R  G ++     V       ++  MD L   +
Sbjct: 80  TTDEDLTEAVHSLGVNDILEIKFF--ENRANG-QSKGFALVGVGSEASSKKLMDLLPKRE 136

Query: 152 FDDKKP 157
              + P
Sbjct: 137 LHGQNP 142

>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 = 41.1 bits (97), Expect = 2e-05
 Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 3/78 (3%)

Query: 76  PLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFD 135
           P        +FV  +P + T  ++  +F         R+++   R TG +     F E+ 
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYD--RETG-KPKGYGFCEYQ 58

Query: 136 DPKCARTAMDALHGYKFD 153
           D + A +AM  L+G +F 
Sbjct: 59  DQETALSAMRNLNGREFS 76

>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 = 41.2 bits (97), Expect = 2e-05
 Identities = 22/95 (23%), Positives = 34/95 (35%), Gaps = 5/95 (5%)

Query: 74  GSPLKKGESNLLFVDGLPTDCTRREVSHLFRPF-VGYREIRVIHKEPRRTGDRAMVLCFV 132
           GS    G +  L++  L        +S  F         +++I    R TG      CFV
Sbjct: 1   GSSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIR--NRLTG-IPAGYCFV 57

Query: 133 EFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           EF D   A   +  ++G       P     K+ +A
Sbjct: 58  EFADLATAEKCLHKINGKPLPGATPAKR-FKLNYA 91

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 18/95 (18%), Positives = 34/95 (35%), Gaps = 8/95 (8%)

Query: 73  AGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFV 132
           +G   ++ +   ++V GL    +   +  LF          +     R TG +     FV
Sbjct: 6   SGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKD--RVTG-QHQGYGFV 62

Query: 133 EFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           EF   + A  A+  +   K   K      +++  A
Sbjct: 63  EFLSEEDADYAIKIMDMIKLYGK-----PIRVNKA 92

>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 = 40.7 bits (96), Expect = 2e-05
 Identities = 14/81 (17%), Positives = 29/81 (35%), Gaps = 8/81 (9%)

Query: 73  AGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVI-HKEPRRTGDRAMVLCF 131
             S       + + + G P + T + V     P      IR++ +    +TG       F
Sbjct: 1   GSSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGY-----IF 54

Query: 132 VEFDDPKCARTAMDALHGYKF 152
           V+F + +  + A+   +    
Sbjct: 55  VDFSNEEEVKQALK-CNREYM 74

>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 = 40.6 bits (96), Expect = 2e-05
 Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 3/72 (4%)

Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           +  LFV  L  +     + + F+ F  Y    V+     +TG  +    FV F     A+
Sbjct: 1   TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWD--MQTG-SSRGYGFVSFTSQDDAQ 57

Query: 142 TAMDALHGYKFD 153
            AMD++ G   +
Sbjct: 58  NAMDSMQGQDLN 69

>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 = 41.2 bits (97), Expect = 2e-05
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 4/79 (5%)

Query: 78  KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDP 137
           +      LF+ GL  +   + +  +F       E+ +I     RT  ++    F+ F++P
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIK---DRTS-KSRGFAFITFENP 58

Query: 138 KCARTAMDALHGYKFDDKK 156
             A+ A   ++G     K 
Sbjct: 59  ADAKNAAKDMNGKSLHGKA 77

>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 = 41.5 bits (97), Expect = 2e-05
 Identities = 17/85 (20%), Positives = 33/85 (38%), Gaps = 9/85 (10%)

Query: 64  GVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIH----KEP 119
           G     R +     + GE  ++ + GLP  C+  +V +       +     +H    +E 
Sbjct: 26  GGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREG 85

Query: 120 RRTGDRAMVLCFVEFDDPKCARTAM 144
           R++G+      FVE       + A+
Sbjct: 86  RQSGE-----AFVELGSEDDVKMAL 105

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 41.1 bits (96), Expect = 3e-05
 Identities = 17/90 (18%), Positives = 35/90 (38%), Gaps = 10/90 (11%)

Query: 67  SSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIH----KEPRRT 122
           SS  +      + GE  ++ + GLP  C+  +V +       +  +  +H    +E R++
Sbjct: 2   SSGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQS 61

Query: 123 GDRAMVLCFVEFDDPKCARTAMDALHGYKF 152
           G+      FVE +     + A+        
Sbjct: 62  GE-----AFVELESEDDVKLAL-KKDRESM 85

>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 = 40.6 bits (95), Expect = 3e-05
 Identities = 14/64 (21%), Positives = 24/64 (37%), Gaps = 1/64 (1%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCA 140
           +  L+   GLP  CT  +V + F           IH    R G +      +E +  +  
Sbjct: 10  DVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDG-KRRGDALIEMESEQDV 68

Query: 141 RTAM 144
           + A+
Sbjct: 69  QKAL 72

>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 = 40.0 bits (94), Expect = 4e-05
 Identities = 18/97 (18%), Positives = 28/97 (28%), Gaps = 15/97 (15%)

Query: 74  GSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKE---PRRTGDRAMVLC 130
           G          L V  L    +  ++  LF  F   ++  V +        T        
Sbjct: 21  GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTA------- 73

Query: 131 FVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
            V F+    A  AM   +G   D +      + IQ  
Sbjct: 74  DVHFERKADALKAMKQYNGVPLDGR-----PMNIQLV 105

>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 = 39.1 bits (92), Expect = 6e-05
 Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 3/69 (4%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           +FV  L  + T   ++  F PF    + RV+      TG ++    FV F +   A  A+
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPFGRISDARVVKD--MATG-KSKGYGFVSFFNKWDAENAI 65

Query: 145 DALHGYKFD 153
             + G    
Sbjct: 66  QQMGGQWLG 74

>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 = 39.6 bits (93), Expect = 7e-05
 Identities = 18/88 (20%), Positives = 32/88 (36%), Gaps = 9/88 (10%)

Query: 66  PSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDR 125
            S  + +  +         +FV  L  + T  ++   F PF    + RV+      TG +
Sbjct: 5   SSGQKKDTSNHFH------VFVGDLSPEITTEDIKAAFAPFGRISDARVVKD--MATG-K 55

Query: 126 AMVLCFVEFDDPKCARTAMDALHGYKFD 153
           +    FV F +   A  A+  + G    
Sbjct: 56  SKGYGFVSFFNKWDAENAIQQMGGQWLG 83

>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 = 39.5 bits (93), Expect = 7e-05
 Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 6/77 (7%)

Query: 80  GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKC 139
           G  N+ F+  L      + +   F  F      +V+  E    G       FV F+  + 
Sbjct: 4   GSGNI-FIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG-----YGFVHFETQEA 57

Query: 140 ARTAMDALHGYKFDDKK 156
           A  A++ ++G   +D+K
Sbjct: 58  AERAIEKMNGMLLNDRK 74

>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 = 39.2 bits (92), Expect = 8e-05
 Identities = 11/75 (14%), Positives = 24/75 (32%), Gaps = 10/75 (13%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKE---PRRTGDRAMVLCFVEFDDPKCAR 141
           L++  LP     +E+ ++ +PF      R++       R  G       F   +  +   
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVG-------FARMESTEKCE 80

Query: 142 TAMDALHGYKFDDKK 156
             +   +G       
Sbjct: 81  AVIGHFNGKFIKTPP 95

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 39.7 bits (92), Expect = 9e-05
 Identities = 22/99 (22%), Positives = 38/99 (38%), Gaps = 9/99 (9%)

Query: 69  LRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMV 128
           +     +    G + +L +           V  L+       +++ I    +R G +A  
Sbjct: 10  ITRPGNTDDPSGGNKVLLLSIQNPLYPI-TVDVLYTVCNPVGKVQRI-VIFKRNGIQA-- 65

Query: 129 LCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
              VEF+   CA+ A  AL+G           TLKI++A
Sbjct: 66  --MVEFESVLCAQKAKAALNGADIYAG---CCTLKIEYA 99

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 39.0 bits (91), Expect = 9e-05
 Identities = 11/43 (25%), Positives = 15/43 (34%)

Query: 114 VIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK 156
            I +             FVEF      + AM  L G KF ++ 
Sbjct: 46  EIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRV 88

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 39.0 bits (91), Expect = 1e-04
 Identities = 18/87 (20%), Positives = 29/87 (33%), Gaps = 10/87 (11%)

Query: 70  RNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL 129
             ++G P  +   N + V GLP   + +++    R         V       TG      
Sbjct: 3   SGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTG------ 53

Query: 130 CFVEFDDPKCARTAMDALHGYKFDDKK 156
             VEF   +    A+  L   KF   +
Sbjct: 54  -VVEFVRKEDMTYAVRKLDNTKFRSHE 79

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 39.3 bits (92), Expect = 1e-04
 Identities = 18/99 (18%), Positives = 27/99 (27%), Gaps = 15/99 (15%)

Query: 72  NAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKE---PRRTGDRAMV 128
             G          L V  L    +  ++  LF  F   ++  V +        T      
Sbjct: 25  GCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTA----- 79

Query: 129 LCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
              V F+    A  AM    G   D +      + IQ  
Sbjct: 80  --DVHFERRADALKAMKQYKGVPLDGR-----PMDIQLV 111

>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 = 38.2 bits (89), Expect = 1e-04
 Identities = 18/84 (21%), Positives = 28/84 (33%), Gaps = 12/84 (14%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEP----RRTGDRAMVLCFVEFDDPKCA 140
           L+V  +P   T   +   F   +    +      P    +   D+     F+EF      
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNF--AFLEFRSVDET 66

Query: 141 RTAMDALHGYKFDDKKPDSPTLKI 164
             AM A  G  F  +     +LKI
Sbjct: 67  TQAM-AFDGIIFQGQ-----SLKI 84

>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 = 40.0 bits (94), Expect = 1e-04
 Identities = 20/86 (23%), Positives = 32/86 (37%), Gaps = 8/86 (9%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L+V  L  D T   +   F P      IRV       T  R++   +V F  P  A  A+
Sbjct: 18  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRD--MITR-RSLGYAYVNFQQPADAERAL 74

Query: 145 DALHGYKFDDKKPDSPTLKIQFAHFP 170
           D ++      K      ++I ++   
Sbjct: 75  DTMNFDVIKGK-----PVRIMWSQRD 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 = 38.0 bits (89), Expect = 6e-04
 Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 10/84 (11%)

Query: 75  SPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVI--HKEPRRTGDRAMVLCFV 132
           S  K G  N+ F+  L      + +   F  F      +V+      +  G       FV
Sbjct: 97  SLRKSGVGNI-FIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYG-------FV 148

Query: 133 EFDDPKCARTAMDALHGYKFDDKK 156
            F+  + A  A++ ++G   +D+K
Sbjct: 149 HFETQEAAERAIEKMNGMLLNDRK 172

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 37.6 bits (88), Expect = 2e-04
 Identities = 19/98 (19%), Positives = 41/98 (41%), Gaps = 10/98 (10%)

Query: 70  RNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL 129
             ++G  L        +V  LP +  + ++  +F+     R +R++    + T  +    
Sbjct: 3   SGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLV--RDKDTD-KFKGF 58

Query: 130 CFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           C+VEFD+    + A+    G    D+     +L++  A
Sbjct: 59  CYVEFDEVDSLKEAL-TYDGALLGDR-----SLRVDIA 90

>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 = 38.1 bits (89), Expect = 3e-04
 Identities = 16/83 (19%), Positives = 33/83 (39%), Gaps = 9/83 (10%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           +F   L      R++   F      R++R+I    R +  R+  + +VEF + +    A+
Sbjct: 28  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISD--RNSR-RSKGIAYVEFCEIQSVPLAI 84

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
             L G +          + +Q +
Sbjct: 85  -GLTGQRLLGVP-----IIVQAS 101

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 38.7 bits (90), Expect = 3e-04
 Identities = 26/135 (19%), Positives = 41/135 (30%), Gaps = 11/135 (8%)

Query: 33  GYSSPLPDPNLIGQRRDIAPGINPTIPDVINGVPSSLRNNAGSPLKKGESNLLFVDGLPT 92
           G     P     G+ R         +PD          +  G          L V  L  
Sbjct: 41  GPRRNRPAIARGGRNRPAPYSRPKPLPD--KWQHDLFDSGCGGGEGVETGAKLLVSNLDF 98

Query: 93  DCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKF 152
             +  ++  LF  F   ++  V +    R+G R++    V F+    A  AM    G   
Sbjct: 99  GVSDADIQELFAEFGTLKKAAVDY---DRSG-RSLGTADVHFERRADALKAMKQYKGVPL 154

Query: 153 DDKKPDSPTLKIQFA 167
           D +      + IQ  
Sbjct: 155 DGR-----PMDIQLV 164

>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 = 37.3 bits (87), Expect = 3e-04
 Identities = 21/96 (21%), Positives = 37/96 (38%), Gaps = 16/96 (16%)

Query: 72  NAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCF 131
           ++G      + N L+V G   D T   +   F PF    ++ +    PR          F
Sbjct: 5   SSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD--PPRNCA-------F 53

Query: 132 VEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           V ++  + A  A+  L+G + +        LK+  A
Sbjct: 54  VTYEKMESADQAVAELNGTQVESV-----QLKVNIA 84

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 36.5 bits (85), Expect = 5e-04
 Identities = 12/72 (16%), Positives = 22/72 (30%), Gaps = 9/72 (12%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           +FV G P      ++S  F  F     + V+ K+             VE  D       +
Sbjct: 11  VFVSGFPRGVDSAQLSEYFLAFGPVASV-VMDKDKGVFA-------IVEMGDVGAREAVL 62

Query: 145 DALHGYKFDDKK 156
            +   +     +
Sbjct: 63  -SQSQHSLGGHR 73

>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 = 36.4 bits (85), Expect = 7e-04
 Identities = 16/69 (23%), Positives = 26/69 (37%), Gaps = 4/69 (5%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           ++V  L    T  +V  LF  F     +++I+   R T  +     FVE  +      A+
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYD--RETK-KPKGFGFVEMQEES-VSEAI 59

Query: 145 DALHGYKFD 153
             L    F 
Sbjct: 60  AKLDNTDFM 68

>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 = 36.7 bits (85), Expect = 8e-04
 Identities = 20/87 (22%), Positives = 32/87 (36%), Gaps = 11/87 (12%)

Query: 70  RNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL 129
           R   G P ++ E N + V GLP   + +++    R         V + +  R G      
Sbjct: 5   RGRYGPPSRRSE-NRVVVSGLPPSGSWQDLKDHMREA-----GDVCYADVYRDGT----- 53

Query: 130 CFVEFDDPKCARTAMDALHGYKFDDKK 156
             VEF   +    A+  L   KF   +
Sbjct: 54  GVVEFVRKEDMTYAVRKLDNTKFRSHE 80

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	184
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.89
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.87
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.86
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.86
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.86
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.86
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.86
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.86
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.86
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.85
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.85
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.85
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.85
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.85
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.85
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.85
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.85
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.85
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.85
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.85
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.85
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.85
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.85
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.85
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.84
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.84
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.84
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.84
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.84
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.84
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.84
2div_A	99	TRNA selenocysteine associated protein; structural	99.84
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.84
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.84
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.84
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.84
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.84
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.84
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.84
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.84
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.84
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.84
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.84
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.84
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.83
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.83
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.83
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.83
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.83
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.83
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.83
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.83
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.83
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.83
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.83
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.83
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.82
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.82
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.82
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.82
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.82
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.82
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.82
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.82
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.81
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.81
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.81
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.81
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.81
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.81
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.81
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.81
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.81
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.81
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.81
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.81
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.81
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.81
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.81
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.81
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.81
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.81
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.81
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.81
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.81
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.81
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.81
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.81
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.81
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.81
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.8
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.8
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.8
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.8
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.8
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.8
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.8
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.8
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.8
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.8
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.8
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.8
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.8
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.79
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.79
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.79
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.79
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.79
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.79
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.79
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.79
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.79
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.79
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.79
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.79
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.79
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.78
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.78
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.78
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.78
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.78
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.78
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.78
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.78
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.77
1x5p_A	97	Negative elongation factor E; structure genomics,	99.77
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.77
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.77
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.77
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.77
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.77
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.64
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.77
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.76
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.76
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.76
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.76
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.75
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.75
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.75
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.75
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.75
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.75
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.75
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.74
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.74
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.74
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.74
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.74
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.74
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.74
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.73
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.73
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.73
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.73
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.72
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.72
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.72
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.72
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.72
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.71
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.71
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.71
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.71
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.71
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.7
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.7
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.7
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.7
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.7
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.69
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.69
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.69
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.69
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.69
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.69
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.68
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.68
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.67
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.66
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.64
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.64
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.63
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.63
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.62
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.62
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.62
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.61
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.6
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.6
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.59
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.58
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.57
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.57
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.57
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.56
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.55
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.54
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.54
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.53
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.53
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.51
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.38
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.28
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.2
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.04
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.96
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.42
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.0
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.81
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.67
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.45
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.3
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.25
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.61
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.05
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.95
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.89
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	92.87
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	92.12

>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=99.89  E-value=7e-23  Score=142.26  Aligned_cols=82  Identities=23%  Similarity=0.409  Sum_probs=75.8

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ..+++|||+|||+++|+++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+.   
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d---~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~---   90 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRD---KVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKT---   90 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEC---SSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE---
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeec---CCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEE---
Confidence            45689999999999999999999999999999999984   334789999999999999999999999999999997   


Q ss_pred             CceEEEeecC
Q 030012          160 PTLKIQFAHF  169 (184)
Q Consensus       160 ~~l~V~~a~~  169 (184)
                        |+|+||++
T Consensus        91 --l~V~~AkP   98 (99)
T 4fxv_A           91 --IKVSYARP   98 (99)
T ss_dssp             --CEEEECCB
T ss_pred             --EEEEEeeC
Confidence              99999974

>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=99.87  E-value=5.7e-21  Score=133.10  Aligned_cols=88  Identities=27%  Similarity=0.352  Sum_probs=79.1

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCC---C
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDD---K  155 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g---~  155 (184)
                      ...+++|||+|||.++++++|+++|++||.|.+|+++.+.    .++++|||||+|.+.++|++|++.|||..+.+   +
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~----~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~   87 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP----DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASS   87 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS----SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC----CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCc
Confidence            4568999999999999999999999999999999998854    27899999999999999999999999999998   7


Q ss_pred             CCCCCceEEEeecCCCCCCC
Q 030012          156 KPDSPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       156 ~~~~~~l~V~~a~~~~~~~~  175 (184)
                      .     |+|+|++....+..
T Consensus        88 ~-----l~V~~a~~~~~~~~  102 (105)
T 2dnh_A           88 S-----LVVKFADTDKESGP  102 (105)
T ss_dssp             C-----CEEEESCSSCCCSC
T ss_pred             c-----EEEEECccCcccCC
Confidence            6     99999987665443

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.86  E-value=2e-21  Score=137.45  Aligned_cols=83  Identities=12%  Similarity=0.113  Sum_probs=76.3

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      .+.++|||+|||+++++++|+++|++||.|.+|+|+.+.   .+++++|||||+|.+.++|++|++.|||..+.|+.   
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~---~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~---   77 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHP---RTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNI---   77 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE---
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECC---CCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeE---
Confidence            457899999999999999999999999999999999853   34789999999999999999999999999999998   


Q ss_pred             CceEEEeecCC
Q 030012          160 PTLKIQFAHFP  170 (184)
Q Consensus       160 ~~l~V~~a~~~  170 (184)
                        |+|++++..
T Consensus        78 --i~V~~a~~~   86 (110)
T 3s8s_A           78 --IHAQLDIKG   86 (110)
T ss_dssp             --CEEEECSTT
T ss_pred             --EEEEECCCC
Confidence              999999643

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=5.7e-21  Score=130.71  Aligned_cols=88  Identities=23%  Similarity=0.429  Sum_probs=78.9

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ..+++|||+|||.++++++|+++|++||.|.+|+++.+.   .+++++|||||+|.+.++|++|++.|||..+.|+.   
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~---   76 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDS---DTGRSKGYGFITFSDSECARRALEQLNGFELAGRP---   76 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCS---SSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSC---
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecC---CCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcE---
Confidence            467899999999999999999999999999999998743   34788999999999999999999999999999998   


Q ss_pred             CceEEEeecCCCCCCC
Q 030012          160 PTLKIQFAHFPFHLPS  175 (184)
Q Consensus       160 ~~l~V~~a~~~~~~~~  175 (184)
                        |+|+|++......+
T Consensus        77 --l~V~~a~~~~~~~~   90 (95)
T 2dnz_A           77 --MRVGHVTERLDGGS   90 (95)
T ss_dssp             --CEEEESSCCCCCCC
T ss_pred             --EEEEEcccccCCCC
Confidence              99999987554443

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=4.3e-21  Score=133.40  Aligned_cols=90  Identities=20%  Similarity=0.390  Sum_probs=80.4

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|+++.+   +..++++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~---~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~-   86 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKD---KTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLI-   86 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEEC---SSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEE-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeec---CCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcE-
Confidence            3566789999999999999999999999999999999874   334789999999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~~  175 (184)
                          |+|+|++....+..
T Consensus        87 ----l~v~~a~~~~~~~~  100 (103)
T 2cq0_A           87 ----LNVEWAKPSTNSGP  100 (103)
T ss_dssp             ----CEEEESSCCCCSCC
T ss_pred             ----EEEEECCCCCCCCC
Confidence                99999987655443

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=4.9e-21  Score=133.13  Aligned_cols=90  Identities=20%  Similarity=0.278  Sum_probs=80.1

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~---~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~-   84 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPRE---PHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRE-   84 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBC---SSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBC-
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeC---CCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcE-
Confidence            4566799999999999999999999999999999999874   334789999999999999999999999999999998 


Q ss_pred             CCCceEEEeecCCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~~  175 (184)
                          |+|+|++.......
T Consensus        85 ----l~V~~a~~~~~~~~   98 (103)
T 2dnm_A           85 ----LRVQVARYGRRDLS   98 (103)
T ss_dssp             ----CEEEECSSCCSCCC
T ss_pred             ----EEEEECCcCCCCCC
Confidence                99999987654443

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=1.1e-20  Score=130.36  Aligned_cols=89  Identities=25%  Similarity=0.394  Sum_probs=78.9

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||.++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++ ||+..+.|+. 
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~-   80 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYD---AEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKK-   80 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCC---TTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCB-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeC---CCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeE-
Confidence            3466789999999999999999999999999999999874   3337889999999999999999998 9999999997 


Q ss_pred             CCCceEEEeecCCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~~  175 (184)
                          |+|+|++....+.+
T Consensus        81 ----l~V~~a~~~~~~~~   94 (99)
T 2dgs_A           81 ----VEVKRAEPRDSKSS   94 (99)
T ss_dssp             ----CEEEECCCCCCCCC
T ss_pred             ----EEEEECCCCcccCC
Confidence                99999987655443

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.86  E-value=1.2e-20  Score=133.65  Aligned_cols=90  Identities=19%  Similarity=0.304  Sum_probs=80.0

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|+++.+.   ..++++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~-   86 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDM---ATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQ-   86 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEE-
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcC---CCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEE-
Confidence            35667899999999999999999999999999999998853   23789999999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~~  175 (184)
                          |+|.|++.......
T Consensus        87 ----l~V~~a~~~~~~~~  100 (115)
T 2dgo_A           87 ----IRTNWATRKPPAPK  100 (115)
T ss_dssp             ----CEEEESSCCCCCSC
T ss_pred             ----EEEEEccCCCCCCc
Confidence                99999986554443

>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=99.86  E-value=8.5e-21  Score=132.23  Aligned_cols=89  Identities=16%  Similarity=0.139  Sum_probs=79.7

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|+++.+.   .+++++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~-   86 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDR---VTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKP-   86 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCS---SSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCB-
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC---CCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeE-
Confidence            45667899999999999999999999999999999998743   34789999999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~  174 (184)
                          |+|+|++......
T Consensus        87 ----l~v~~a~~~~~~~   99 (105)
T 1x5u_A           87 ----IRVNKASAHNKNL   99 (105)
T ss_dssp             ----CEEEETTTTSCCC
T ss_pred             ----EEEEECCCCCcCC
Confidence                9999998765443

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.85  E-value=1.3e-20  Score=130.28  Aligned_cols=85  Identities=20%  Similarity=0.443  Sum_probs=77.9

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||.++++++|+++|++||.|.+|+++.+.    .++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~----~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~--   87 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR----AGKPKGLAYVEYENESQASQAVMKMDGMTIKENI--   87 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT----TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCE--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC----CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEE--
Confidence            4567899999999999999999999999999999998854    3789999999999999999999999999999997  


Q ss_pred             CCceEEEeecCCCC
Q 030012          159 SPTLKIQFAHFPFH  172 (184)
Q Consensus       159 ~~~l~V~~a~~~~~  172 (184)
                         |+|+|++....
T Consensus        88 ---l~v~~a~~~~~   98 (100)
T 2do4_A           88 ---IKVAISNSGPS   98 (100)
T ss_dssp             ---EEEEECCCCSC
T ss_pred             ---EEEEECCCCCC
Confidence               99999986554

>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=99.85  E-value=7.4e-21  Score=134.81  Aligned_cols=89  Identities=22%  Similarity=0.433  Sum_probs=79.3

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|+++.+.   .+++++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~-   96 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDK---QTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKR-   96 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECS---SSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEE-
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC---CCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEE-
Confidence            34567899999999999999999999999999999998853   33789999999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~  174 (184)
                          |+|+|++....+.
T Consensus        97 ----l~V~~a~~~~~~~  109 (115)
T 2cpz_A           97 ----LKVQLKRSKNDSK  109 (115)
T ss_dssp             ----CEEECCCCSCCCC
T ss_pred             ----EEEEEcCCCCcCC
Confidence                9999998655433

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.85  E-value=1e-20  Score=130.62  Aligned_cols=83  Identities=28%  Similarity=0.472  Sum_probs=76.2

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEE--------EEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYRE--------IRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHG  149 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~--------v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g  149 (184)
                      +....++|||+|||+++++++|+++|++||.|.+        ++++.+   +.+++++|||||+|.+.++|++|++.|||
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~---~~~g~~~G~afV~f~~~~~a~~Ai~~l~g   85 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTD---RETGKLKGEATVSFDDPPSAKAAIDWFDG   85 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEEC---TTTCSEEEEEEEEBSSHHHHHHHHHHHTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEec---CCCCCeeeEEEEEECCHHHHHHHHHHhCC
Confidence            4567899999999999999999999999999999        999874   33478999999999999999999999999


Q ss_pred             CeeCCCCCCCCceEEEeec
Q 030012          150 YKFDDKKPDSPTLKIQFAH  168 (184)
Q Consensus       150 ~~~~g~~~~~~~l~V~~a~  168 (184)
                      ..+.|+.     |+|+||+
T Consensus        86 ~~~~g~~-----l~V~~A~   99 (99)
T 2la6_A           86 KEFSGNP-----IKVSFAT   99 (99)
T ss_dssp             CBSSSSB-----CEEEECC
T ss_pred             CEeCCcE-----EEEEecC
Confidence            9999997     9999985

>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=99.85  E-value=6.8e-21  Score=135.72  Aligned_cols=86  Identities=20%  Similarity=0.387  Sum_probs=78.2

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      .+..++|||+|||.++++++|+++|++||.|.+|+++.+.    +++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~----~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~--   77 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR----TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKA--   77 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST----TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSB--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC----CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEE--
Confidence            4567899999999999999999999999999999998754    3788999999999999999999999999999997  


Q ss_pred             CCceEEEeecCCCCC
Q 030012          159 SPTLKIQFAHFPFHL  173 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~  173 (184)
                         |+|+|++.+...
T Consensus        78 ---l~V~~a~~~~~~   89 (116)
T 2fy1_A           78 ---IKVEQAKKPSFQ   89 (116)
T ss_dssp             ---CEEEECCCSSCS
T ss_pred             ---EEEEECCCCCCC
Confidence               999999865433

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.85  E-value=3.6e-22  Score=136.49  Aligned_cols=85  Identities=20%  Similarity=0.351  Sum_probs=74.5

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCC-CEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHh-cCCeeCCCCCCC
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFV-GYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDAL-HGYKFDDKKPDS  159 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G-~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l-~g~~~~g~~~~~  159 (184)
                      +++|||+|||+++||++|+++|++|| .|.+|+++++   +.+++++|||||+|.+.++|++|++.+ ++..+.|+.   
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d---~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~---   74 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRN---KSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQK---   74 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSC---SSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEE---
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEec---CCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEE---
Confidence            57999999999999999999999999 8999999874   344789999999999999999999987 457899997   


Q ss_pred             CceEEEeecCCCCCC
Q 030012          160 PTLKIQFAHFPFHLP  174 (184)
Q Consensus       160 ~~l~V~~a~~~~~~~  174 (184)
                        |+|+|+++.....
T Consensus        75 --i~V~~a~~~~~~~   87 (91)
T 2lxi_A           75 --VSMHYSDPKPKIN   87 (91)
T ss_dssp             --EEEECCCSCCCCS
T ss_pred             --EEEEEcCCCCCCC
Confidence              9999997654443

>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=99.85  E-value=1.5e-20  Score=132.04  Aligned_cols=87  Identities=24%  Similarity=0.482  Sum_probs=77.4

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|++..+      ++++|||||+|.+.++|++|++.||+..+.|+. 
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~-   90 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR------RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYR-   90 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS------SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEE-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC------CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeE-
Confidence            3456789999999999999999999999999999998542      457899999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~~  175 (184)
                          |+|+|++......+
T Consensus        91 ----l~V~~a~~~~~~~~  104 (109)
T 1x4a_A           91 ----LRVEFPRSGRGTGS  104 (109)
T ss_dssp             ----CEEECCCCCCCCCC
T ss_pred             ----EEEEEcccCCCCCC
Confidence                99999987665444

>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=99.85  E-value=5.2e-21  Score=136.00  Aligned_cols=81  Identities=19%  Similarity=0.314  Sum_probs=73.7

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ...+|||+|||+++++++|+++|++||.|.+|+|+.+.     +.++|||||+|.+.++|++|++.|||..+.|+.    
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~-----~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~----   74 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-----NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRK----   74 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-----TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEE----
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC-----CCCCceEEEEECCHHHHHHHHHHcCCCEECCEE----
Confidence            35689999999999999999999999999999998853     357999999999999999999999999999997    


Q ss_pred             ceEEEeecCCC
Q 030012          161 TLKIQFAHFPF  171 (184)
Q Consensus       161 ~l~V~~a~~~~  171 (184)
                       |+|.|++...
T Consensus        75 -i~V~~a~~~~   84 (115)
T 4f25_A           75 -VFVGRFKSRK   84 (115)
T ss_dssp             -CEEEESSCCC
T ss_pred             -EEEEECCCcc
Confidence             9999997644

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=2.9e-20  Score=129.14  Aligned_cols=87  Identities=22%  Similarity=0.310  Sum_probs=78.7

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|+++.+     .++++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~-   84 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-----GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKP-   84 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-----SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSB-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcE-
Confidence            3457889999999999999999999999999999999874     2789999999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~  174 (184)
                          |+|.|++....+.
T Consensus        85 ----l~V~~a~~~~~~~   97 (103)
T 2d9p_A           85 ----LYVALAQRKEERQ   97 (103)
T ss_dssp             ----CEEEECSSCCCCC
T ss_pred             ----EEEEEecccccCC
Confidence                9999998755443

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=9.4e-21  Score=131.36  Aligned_cols=89  Identities=24%  Similarity=0.384  Sum_probs=79.5

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ..+.++|||+|||+++++++|+++|++||.|.+|+++.+.   .+++++|||||+|.+.++|++|++.||+..+.|+.  
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~--   83 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDR---ETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQ--   83 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCS---SSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCC--
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCC---CCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeE--
Confidence            4567899999999999999999999999999999998743   34788999999999999999999999999999998  


Q ss_pred             CCceEEEeecCCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~~  175 (184)
                         |+|+|++.....++
T Consensus        84 ---l~v~~a~~~~~~~~   97 (102)
T 1x5s_A           84 ---IRVDQAGKSSDNRS   97 (102)
T ss_dssp             ---CEEEEEECCCCCCC
T ss_pred             ---EEEEECCCCCCCCC
Confidence               99999987655443

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.85  E-value=1.3e-20  Score=128.22  Aligned_cols=87  Identities=17%  Similarity=0.256  Sum_probs=78.9

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ...+++|||+|||+++++++|+++|++||.|.++++..+     .++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-----~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~--   77 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-----NGKSKGCGVVKFESPEVAERACRMMNGMKLSGRE--   77 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-----SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBC--
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-----CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcE--
Confidence            466789999999999999999999999999999999862     2688999999999999999999999999999998  


Q ss_pred             CCceEEEeecCCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~~  175 (184)
                         |+|+|++.....++
T Consensus        78 ---l~v~~a~~~~~~~~   91 (92)
T 2dgv_A           78 ---IDVRIDRNASGPSS   91 (92)
T ss_dssp             ---CCCEECSCCSSCCC
T ss_pred             ---EEEEEcCCCCCCCC
Confidence               99999988665543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.85  E-value=1.2e-21  Score=135.14  Aligned_cols=82  Identities=16%  Similarity=0.338  Sum_probs=73.0

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCC--EEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCC----eeC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVG--YREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGY----KFD  153 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~--i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~----~~~  153 (184)
                      ..=++|||+|||+++|+++|+++|++||.  +.+|+++++   +.++++||||||+|.+.++|++|++.|||.    .++
T Consensus         7 ~~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            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKD---KQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKID   83 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCC---SSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEET
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEec---CCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceEC
Confidence            34579999999999999999999999995  678988874   344789999999999999999999999997    589


Q ss_pred             CCCCCCCceEEEeecC
Q 030012          154 DKKPDSPTLKIQFAHF  169 (184)
Q Consensus       154 g~~~~~~~l~V~~a~~  169 (184)
                      |+.     |+|+||++
T Consensus        84 Gr~-----i~V~~Aks   94 (95)
T 2lkz_A           84 GKT-----IGVDFAKS   94 (95)
T ss_dssp             TEE-----EEEEECCC
T ss_pred             CEE-----EEEEEccC
Confidence            997     99999985

>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=99.85  E-value=8.3e-21  Score=127.76  Aligned_cols=82  Identities=21%  Similarity=0.340  Sum_probs=74.0

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      .+.++|||+|||.++++++|+++|++||.|.+++++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+.   
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~---   77 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKD---MATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQ---   77 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---TTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE---
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEec---CCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeE---
Confidence            45789999999999999999999999999999999884   234789999999999999999999999999999997   


Q ss_pred             CceEEEeecC
Q 030012          160 PTLKIQFAHF  169 (184)
Q Consensus       160 ~~l~V~~a~~  169 (184)
                        |+|+|++.
T Consensus        78 --l~v~~a~~   85 (87)
T 3bs9_A           78 --IRTNWATR   85 (87)
T ss_dssp             --CEEEEEC-
T ss_pred             --EEEEecCC
Confidence              99999975

>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=99.85  E-value=1.3e-20  Score=129.90  Aligned_cols=87  Identities=20%  Similarity=0.271  Sum_probs=78.4

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ..++++|||+|||+++++++|+++|++||.|.+|+++.+.   ..++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~--   79 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDS---LTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRM--   79 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCT---TTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCE--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecC---CCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcE--
Confidence            4567899999999999999999999999999999998743   33788999999999999999999999999999997  


Q ss_pred             CCceEEEeecCCCCC
Q 030012          159 SPTLKIQFAHFPFHL  173 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~  173 (184)
                         |+|+|++.....
T Consensus        80 ---l~V~~a~~~~~~   91 (99)
T 1whw_A           80 ---LHVLPSTIKKEA   91 (99)
T ss_dssp             ---EEEEECCCCSTT
T ss_pred             ---EEEEEcCCCccc
Confidence               999999876544

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=2.3e-20  Score=130.31  Aligned_cols=90  Identities=23%  Similarity=0.396  Sum_probs=79.1

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHh-cCCeeCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDAL-HGYKFDDKK  156 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l-~g~~~~g~~  156 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|+++.+.  +..++++|||||+|.+.++|++|++.| |+..+.|+.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~--~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~   88 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKM--TGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRR   88 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCC--SSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCB
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCC--CCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCE
Confidence            35667899999999999999999999999999999998641  224788999999999999999999999 999999997


Q ss_pred             CCCCceEEEeecCCCCCC
Q 030012          157 PDSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       157 ~~~~~l~V~~a~~~~~~~  174 (184)
                           |+|+|++......
T Consensus        89 -----l~v~~a~~~~~~~  101 (107)
T 2cph_A           89 -----LVLEWADSEVTVQ  101 (107)
T ss_dssp             -----CEEEECCCCCCCC
T ss_pred             -----EEEEeCCCCCCCC
Confidence                 9999998754433

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=4.8e-21  Score=131.31  Aligned_cols=88  Identities=14%  Similarity=0.254  Sum_probs=78.7

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEE-EEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREI-RVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v-~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      .++++|||+|||+++++++|+++|++||.|.++ +++.+   +..++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~---~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~--   77 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRD---PDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRP--   77 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCC---TTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEE--
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEc---CCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEE--
Confidence            457899999999999999999999999999999 88874   234788999999999999999999999999999997  


Q ss_pred             CCceEEEeecCCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~~  175 (184)
                         |+|+|++....+..
T Consensus        78 ---l~v~~a~~~~~~~~   91 (96)
T 1x5t_A           78 ---ITVSYAFKKDSKGS   91 (96)
T ss_dssp             ---CEEEESCCCCCCCC
T ss_pred             ---EEEEEecccCCCCC
Confidence               99999987665544

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.84  E-value=2.4e-20  Score=136.31  Aligned_cols=90  Identities=20%  Similarity=0.371  Sum_probs=80.4

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|+.||.|.+|+++.+.   .+++++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~-  113 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDR---ETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKR-  113 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEET---TTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCE-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcC---CCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeE-
Confidence            45667899999999999999999999999999999998853   23789999999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~~  175 (184)
                          |+|.|++....+.+
T Consensus       114 ----l~v~~a~~~~~~~~  127 (139)
T 1u6f_A          114 ----LKVALAASGHQRPG  127 (139)
T ss_dssp             ----EEEEESSCCCCCCC
T ss_pred             ----EEEEECCCCCCCCC
Confidence                99999987554443

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.84  E-value=2e-20  Score=133.01  Aligned_cols=83  Identities=28%  Similarity=0.513  Sum_probs=75.1

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~---~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~-  111 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFID---KQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKR-  111 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCC---SSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEE-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeC---CCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEE-
Confidence            3556789999999999999999999999999999999874   234788999999999999999999999999999997 


Q ss_pred             CCCceEEEeec
Q 030012          158 DSPTLKIQFAH  168 (184)
Q Consensus       158 ~~~~l~V~~a~  168 (184)
                          |+|+|++
T Consensus       112 ----l~V~~ak  118 (118)
T 2khc_A          112 ----LKVQLKK  118 (118)
T ss_dssp             ----CCEEEC-
T ss_pred             ----EEEEecC
Confidence                9999985

>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=99.84  E-value=7.2e-21  Score=127.51  Aligned_cols=82  Identities=20%  Similarity=0.385  Sum_probs=75.2

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ..+.++|||+|||+++++++|+++|++||.|.+++++.+.   .+++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~--   78 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY---ETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRT--   78 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEET---TTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEE--
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECC---CCCccccEEEEEECCHHHHHHHHHHhCCCEECCcE--
Confidence            4567899999999999999999999999999999998752   23788999999999999999999999999999997  


Q ss_pred             CCceEEEeec
Q 030012          159 SPTLKIQFAH  168 (184)
Q Consensus       159 ~~~l~V~~a~  168 (184)
                         |+|+|++
T Consensus        79 ---l~v~~ak   85 (85)
T 3mdf_A           79 ---IRVNLAK   85 (85)
T ss_dssp             ---CEEEECC
T ss_pred             ---EEEEEcC
Confidence               9999985

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.84  E-value=1.4e-20  Score=131.29  Aligned_cols=90  Identities=21%  Similarity=0.284  Sum_probs=79.1

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCee---CC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKF---DD  154 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~---~g  154 (184)
                      .....++|||+|||.++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.|||..+   .+
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g   85 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKD---RFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMN   85 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCC---SSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEec---CCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCC
Confidence            3466789999999999999999999999999999999874   33478899999999999999999999999987   77


Q ss_pred             CCCCCCceEEEeecCCCCCCC
Q 030012          155 KKPDSPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       155 ~~~~~~~l~V~~a~~~~~~~~  175 (184)
                      +.     |+|.|++....+.+
T Consensus        86 ~~-----l~v~~a~~~~~~~~  101 (106)
T 2dgp_A           86 RP-----IQVKPADSESRGGS  101 (106)
T ss_dssp             SC-----CEEEECCCCSCCCC
T ss_pred             ce-----EEEEECCcccccCC
Confidence            87     99999987665443

>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=99.84  E-value=3.1e-20  Score=130.50  Aligned_cols=89  Identities=19%  Similarity=0.341  Sum_probs=79.0

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhc------CCe
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALH------GYK  151 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~------g~~  151 (184)
                      ...+.++|||+|||+++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.||      +..
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~---~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~   87 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLH---PDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLK   87 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBC---SSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEE
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEec---CCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcE
Confidence            3566789999999999999999999999999999999874   3347889999999999999999999999      999


Q ss_pred             eCCCCCCCCceEEEeecCCCCCC
Q 030012          152 FDDKKPDSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       152 ~~g~~~~~~~l~V~~a~~~~~~~  174 (184)
                      +.|+.     |+|+|++......
T Consensus        88 ~~g~~-----l~v~~a~~~~~~~  105 (111)
T 1x4h_A           88 LDGRQ-----LKVDLAVTRDEAA  105 (111)
T ss_dssp             SSSCE-----EEEECCCCCCCCC
T ss_pred             EcCEE-----EEEEECCCCccCC
Confidence            99997     9999998654433

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.6e-20  Score=128.29  Aligned_cols=83  Identities=18%  Similarity=0.318  Sum_probs=76.3

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ..++++|||+|||+++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~---~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~--   86 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYD---QQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR--   86 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEEC---SSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEE--
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEc---CCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEE--
Confidence            456789999999999999999999999999999999874   333789999999999999999999999999999997  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |+|+|++.
T Consensus        87 ---l~v~~a~~   94 (95)
T 2cqc_A           87 ---IRVSGPSS   94 (95)
T ss_dssp             ---EEEECCSC
T ss_pred             ---EEEEecCC
Confidence               99999975

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.84  E-value=1.5e-20  Score=129.35  Aligned_cols=90  Identities=21%  Similarity=0.310  Sum_probs=78.4

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      .++++|||+|||+++++++|+++|++||.|.+|+++.+.....+++++|||||+|.+.++|++|++.|||..+.|+.   
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~---   79 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHK---   79 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEE---
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeE---
Confidence            45789999999999999999999999999999999875432212488999999999999999999999999999997   


Q ss_pred             CceEEEeecCCCCCC
Q 030012          160 PTLKIQFAHFPFHLP  174 (184)
Q Consensus       160 ~~l~V~~a~~~~~~~  174 (184)
                        |+|+|++......
T Consensus        80 --l~V~~a~~~~~~~   92 (98)
T 2cpf_A           80 --LEVRISERATKPA   92 (98)
T ss_dssp             --CEEECSSCSSCCC
T ss_pred             --EEEEEccCCCCCC
Confidence              9999998655433

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=1.6e-20  Score=129.50  Aligned_cols=91  Identities=19%  Similarity=0.333  Sum_probs=78.7

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEE-EEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYR-EIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ...+++|||+|||+++++++|+++|++||.|. +|+++.+.   ..++++|||||+|.+.++|++|++.|||..+.|+..
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~---~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~   82 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNR---LTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATP   82 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECS---SSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSS
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecC---CCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCc
Confidence            45679999999999999999999999999999 99998853   347899999999999999999999999999999730


Q ss_pred             CCCceEEEeecCCCCC
Q 030012          158 DSPTLKIQFAHFPFHL  173 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~  173 (184)
                       ...|+|+|++..+..
T Consensus        83 -~~~l~v~~a~~~~~~   97 (99)
T 2div_A           83 -AKRFKLNYATYSGPS   97 (99)
T ss_dssp             -CEECCEEETTCCSSS
T ss_pred             -ceeEEEeecCCCCCC
Confidence             112899999876544

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1e-20  Score=131.14  Aligned_cols=89  Identities=19%  Similarity=0.313  Sum_probs=79.6

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ..+.++|||+|||+++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~---~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~--   83 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD---YETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRT--   83 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCC---SSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEE--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEec---CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcE--
Confidence            356789999999999999999999999999999999874   233788999999999999999999999999999997  


Q ss_pred             CCceEEEeecCCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~~  175 (184)
                         |+|+|++....+.+
T Consensus        84 ---l~V~~a~~~~~~~~   97 (102)
T 2cqb_A           84 ---IRVNLAKPMRIKES   97 (102)
T ss_dssp             ---EEEEECCCCCCCCC
T ss_pred             ---EEEEeCCCCCCCCC
Confidence               99999987665544

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=1.9e-20  Score=127.84  Aligned_cols=82  Identities=15%  Similarity=0.297  Sum_probs=75.1

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||.++++++|+++|++||.|.+|+++.+.   .+++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~---~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~--   87 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDK---DTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRV--   87 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCS---SSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEE--
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCC---CCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcE--
Confidence            4567899999999999999999999999999999998743   33688999999999999999999999999999997  


Q ss_pred             CCceEEEeec
Q 030012          159 SPTLKIQFAH  168 (184)
Q Consensus       159 ~~~l~V~~a~  168 (184)
                         |+|+||+
T Consensus        88 ---l~v~~ak   94 (94)
T 2e5h_A           88 ---IKASIAI   94 (94)
T ss_dssp             ---EEEEECC
T ss_pred             ---EEEEecC
Confidence               9999985

>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=99.84  E-value=2.5e-20  Score=124.34  Aligned_cols=80  Identities=24%  Similarity=0.366  Sum_probs=73.8

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      .+|||+|||.++++++|+++|++||.|.+++++.+   +..++++|||||+|.+.++|++|++.|||..+.|+.     |
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~---~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~-----l   73 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWD---MQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRP-----L   73 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEEC---TTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEE-----C
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEc---CCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcE-----E
Confidence            58999999999999999999999999999999874   234789999999999999999999999999999997     9


Q ss_pred             EEEeecCC
Q 030012          163 KIQFAHFP  170 (184)
Q Consensus       163 ~V~~a~~~  170 (184)
                      +|+|++..
T Consensus        74 ~v~~a~~~   81 (83)
T 3md1_A           74 RINWAAKL   81 (83)
T ss_dssp             EEEECCCC
T ss_pred             EEEecCcC
Confidence            99999753

>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=99.84  E-value=1.3e-20  Score=129.42  Aligned_cols=83  Identities=19%  Similarity=0.367  Sum_probs=76.0

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ++++|||+|||.++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+.    
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~---~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~----   73 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFD---PQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRF----   73 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBC---TTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEE----
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeC---CCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeE----
Confidence            3689999999999999999999999999999999874   334788999999999999999999999999999997    


Q ss_pred             ceEEEeecCCC
Q 030012          161 TLKIQFAHFPF  171 (184)
Q Consensus       161 ~l~V~~a~~~~  171 (184)
                       |+|+|++...
T Consensus        74 -l~V~~a~~~~   83 (96)
T 2x1f_A           74 -LKCGYSSNSD   83 (96)
T ss_dssp             -CEEEECSCSS
T ss_pred             -EEEEEcCCCC
Confidence             9999998754

>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=99.84  E-value=3.4e-20  Score=128.79  Aligned_cols=88  Identities=27%  Similarity=0.433  Sum_probs=78.1

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|+++.+.     ..++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~-   84 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH-----TSNDPYCFVEFYEHRDAAAALAAMNGRKILGKE-   84 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCC-----CSSCCEEEEEESSHHHHHHHHHHHTTEEETTEE-
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecC-----CCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCe-
Confidence            35667999999999999999999999999999999998752     236899999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~~  175 (184)
                          |+|+|++.+..+..
T Consensus        85 ----l~V~~a~~~~~~~~   98 (103)
T 2cqi_A           85 ----VKVNWATTPSSQKS   98 (103)
T ss_dssp             ----EEEEECCCTTCCCC
T ss_pred             ----EEEEECCCCccccc
Confidence                99999987665443

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=7.1e-20  Score=129.34  Aligned_cols=84  Identities=12%  Similarity=0.179  Sum_probs=77.0

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ...+++|||+|||+++++++|+++|++||.|.+|+++.+.+    ++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~----g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~--   85 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD----GKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRP--   85 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTT----CSEEEEEEEEESSHHHHHHHHHHHTTCEETTEE--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC----CCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCE--
Confidence            45678999999999999999999999999999999988532    789999999999999999999999999999997  


Q ss_pred             CCceEEEeecCCC
Q 030012          159 SPTLKIQFAHFPF  171 (184)
Q Consensus       159 ~~~l~V~~a~~~~  171 (184)
                         |+|+|++...
T Consensus        86 ---l~v~~a~~~~   95 (114)
T 2do0_A           86 ---MHVKMDERAL   95 (114)
T ss_dssp             ---CEEEECSCCC
T ss_pred             ---EEEEEcccCC
Confidence               9999997543

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.84  E-value=4.5e-20  Score=128.29  Aligned_cols=87  Identities=20%  Similarity=0.431  Sum_probs=77.2

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      +....++|||+|||+++++++|+++|++|| |.+|+++.+.   .+++++|||||+|.+.++|++|+ .|||..+.|+. 
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~---~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~-   84 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDK---DTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRS-   84 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECS---SSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEE-
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecC---CCCccceEEEEEECCHHHHHHHH-hhCCCeECCeE-
Confidence            456678999999999999999999999996 9999998853   34789999999999999999999 89999999997 


Q ss_pred             CCCceEEEeecCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~  174 (184)
                          |+|+|++......
T Consensus        85 ----l~V~~a~~~~~~~   97 (103)
T 2dng_A           85 ----LRVDIAEGRKQDK   97 (103)
T ss_dssp             ----CEEEECCCCCCCC
T ss_pred             ----EEEEEecCCCCCC
Confidence                9999998755443

>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=99.84  E-value=3.3e-21  Score=131.09  Aligned_cols=83  Identities=13%  Similarity=0.164  Sum_probs=70.0

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCC--CEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFV--GYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G--~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      .+|||+|||+++++++|+++|++||  .|.+++++.+   +.+|+++|||||+|.+.++|++|++.|||..+.|+.    
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~---~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~----   74 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFEN---RANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQN----   74 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEEC---TTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCC----
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEec---CCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEE----
Confidence            4799999999999999999999999  9999999884   334799999999999999999999999999999998    


Q ss_pred             ceEEEeecCCCCC
Q 030012          161 TLKIQFAHFPFHL  173 (184)
Q Consensus       161 ~l~V~~a~~~~~~  173 (184)
                       |+|.++..+...
T Consensus        75 -i~V~~~~~~~~~   86 (90)
T 3p5t_L           75 -PVVTPSNKLEHH   86 (90)
T ss_dssp             -CEECCC------
T ss_pred             -EEEEECCCCccc
Confidence             999999875543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=2.2e-20  Score=130.36  Aligned_cols=84  Identities=20%  Similarity=0.352  Sum_probs=76.6

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ...+++|||+|||.++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~---~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~--   94 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD---RRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQP--   94 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEEC---TTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSB--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEec---CCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcE--
Confidence            456789999999999999999999999999999999874   334789999999999999999999999999999997  


Q ss_pred             CCceEEEeecCC
Q 030012          159 SPTLKIQFAHFP  170 (184)
Q Consensus       159 ~~~l~V~~a~~~  170 (184)
                         |+|+|++..
T Consensus        95 ---l~V~~a~~~  103 (106)
T 1p27_B           95 ---ISVDWCFVR  103 (106)
T ss_dssp             ---CEEEESEES
T ss_pred             ---EEEEeecCC
Confidence               999999754

>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=99.84  E-value=1.2e-20  Score=129.00  Aligned_cols=83  Identities=14%  Similarity=0.262  Sum_probs=76.4

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|++..+..    ++++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~----g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~-   86 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE----GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRP-   86 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT----SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEE-
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC----CCCceEEEEEECCHHHHHHHHHHhCCCEECCCE-
Confidence            345678999999999999999999999999999999988532    689999999999999999999999999999997 


Q ss_pred             CCCceEEEeecC
Q 030012          158 DSPTLKIQFAHF  169 (184)
Q Consensus       158 ~~~~l~V~~a~~  169 (184)
                          |+|+|+++
T Consensus        87 ----l~V~~a~~   94 (95)
T 2ywk_A           87 ----INVSGPSS   94 (95)
T ss_dssp             ----CEEECCCC
T ss_pred             ----EEEEEcCC
Confidence                99999975

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=3.7e-20  Score=128.96  Aligned_cols=88  Identities=19%  Similarity=0.353  Sum_probs=77.0

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      +..+.++|||+|||+++++++|+++|++|| |.+|+++.+..  +.++++|||||+|.+.++|++|+ .||+..+.|+. 
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~--~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~-   85 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPS--NPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKR-   85 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSS--CTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEE-
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCC--CCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcE-
Confidence            345678999999999999999999999999 99999987532  12688999999999999999999 99999999997 


Q ss_pred             CCCceEEEeecCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~  174 (184)
                          |+|+|++....+.
T Consensus        86 ----l~V~~a~~~~~~~   98 (104)
T 1wi8_A           86 ----IRVDVADQAQDKD   98 (104)
T ss_dssp             ----CEEEECCCCCCCC
T ss_pred             ----EEEEEccCCCCCC
Confidence                9999998755443

>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=99.84  E-value=4.3e-20  Score=129.95  Aligned_cols=85  Identities=21%  Similarity=0.437  Sum_probs=77.4

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ....+++|||+|||..+++++|+++|++||.|.+|+++.+.   .+++++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        22 ~~~~~~~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           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDS---ETGRSKGYGFITFSDSECAKKALEQLNGFELAGRP-   97 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEET---TTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSC-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcC---CCCccceEEEEEECCHHHHHHHHHHcCCCEECCEE-
Confidence            45667899999999999999999999999999999998753   33789999999999999999999999999999998 


Q ss_pred             CCCceEEEeecCC
Q 030012          158 DSPTLKIQFAHFP  170 (184)
Q Consensus       158 ~~~~l~V~~a~~~  170 (184)
                          |+|+|++..
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                999999753

>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=99.83  E-value=1.7e-20  Score=134.88  Aligned_cols=85  Identities=19%  Similarity=0.341  Sum_probs=76.8

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ....+++|||+|||+++++++|+++|++||.|.+|+|+.+.   .+++++|||||+|.+.++|++|++.|||..|.|+. 
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~-   93 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR---RTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQP-   93 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCT---TTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSB-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC---CCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeE-
Confidence            34567899999999999999999999999999999998743   34788999999999999999999999999999997 


Q ss_pred             CCCceEEEeecCC
Q 030012          158 DSPTLKIQFAHFP  170 (184)
Q Consensus       158 ~~~~l~V~~a~~~  170 (184)
                          |+|+|++..
T Consensus        94 ----l~v~~a~~~  102 (126)
T 3ex7_B           94 ----ISVDWCFVR  102 (126)
T ss_dssp             ----CEEEESEES
T ss_pred             ----EEEEEecCC
Confidence                999999753

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=9.8e-20  Score=126.48  Aligned_cols=87  Identities=21%  Similarity=0.342  Sum_probs=77.5

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|+++.+.     ..++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~-----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~-   84 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-----RGSKGFGFVTFENSADADRAREKLHGTVVEGRK-   84 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT-----TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEE-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-----CCCcEEEEEEECCHHHHHHHHHHhCCCEECCEE-
Confidence            35667999999999999999999999999999999998753     237899999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~  174 (184)
                          |+|+|++......
T Consensus        85 ----l~v~~a~~~~~~~   97 (103)
T 2cq3_A           85 ----IEVNNATARVMTN   97 (103)
T ss_dssp             ----CEEEECCSSCCCC
T ss_pred             ----EEEEEcccCCCCC
Confidence                9999998755444

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=3.5e-20  Score=130.85  Aligned_cols=89  Identities=19%  Similarity=0.361  Sum_probs=78.7

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEE--------EEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYR--------EIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHG  149 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~--------~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g  149 (184)
                      .....++|||+|||+++++++|+++|++||.|.        .|+++.+   +.+++++|||||+|.+.++|++|++.|||
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~---~~~g~~~g~afV~f~~~~~A~~Ai~~l~g   87 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLD---KETGKPKGDATVSYEDPPTAKAAVEWFDG   87 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBC---TTTCSBCSEEEEEBSSHHHHHHHHHHHTT
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEe---CCCCCeeeEEEEEECCHHHHHHHHHHcCC
Confidence            346678999999999999999999999999998        5888774   33478999999999999999999999999


Q ss_pred             CeeCCCCCCCCceEEEeecCCCCCC
Q 030012          150 YKFDDKKPDSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       150 ~~~~g~~~~~~~l~V~~a~~~~~~~  174 (184)
                      ..+.|+.     |+|+|++......
T Consensus        88 ~~~~g~~-----l~V~~a~~~~~~~  107 (113)
T 2cpe_A           88 KDFQGSK-----LKVSLARKKPPMN  107 (113)
T ss_dssp             CEETTEE-----CEEECSSCCCCST
T ss_pred             CccCCCE-----EEEEECCCCCCCC
Confidence            9999997     9999998755443

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.83  E-value=1.6e-20  Score=126.45  Aligned_cols=85  Identities=15%  Similarity=0.313  Sum_probs=75.7

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      .+++|||+|||.++++++|+++|++||.|.+++++.+..  .+++++|||||+|.+.++|++|++.|||..+.|+.    
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~--~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~----   76 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERM--HPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQE----   76 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETT--EEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEE----
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCC--CCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeE----
Confidence            468999999999999999999999999999999987532  12348899999999999999999999999999997    


Q ss_pred             ceEEEeecCCCC
Q 030012          161 TLKIQFAHFPFH  172 (184)
Q Consensus       161 ~l~V~~a~~~~~  172 (184)
                       |+|+|++.+..
T Consensus        77 -l~v~~a~~~~~   87 (88)
T 4a8x_A           77 -ITATAVLAPWP   87 (88)
T ss_dssp             -CEEEEECCCCC
T ss_pred             -EEEEECCCCCC
Confidence             99999987653

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=5.7e-20  Score=130.40  Aligned_cols=85  Identities=25%  Similarity=0.316  Sum_probs=76.2

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|+|+.+   +.+++++|||||+|.+.++|++|++.|++ .+.|+. 
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~-   87 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITD---RQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRK-   87 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCC---SSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEE-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEc---CCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEE-
Confidence            3456789999999999999999999999999999999874   33478999999999999999999999998 899997 


Q ss_pred             CCCceEEEeecCCC
Q 030012          158 DSPTLKIQFAHFPF  171 (184)
Q Consensus       158 ~~~~l~V~~a~~~~  171 (184)
                          |+|+|++...
T Consensus        88 ----l~V~~a~~~~   97 (116)
T 2cqd_A           88 ----ANVNLAYLGA   97 (116)
T ss_dssp             ----CEEEESTTTC
T ss_pred             ----EEEEEcccCC
Confidence                9999997543

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=4.2e-20  Score=128.47  Aligned_cols=87  Identities=20%  Similarity=0.250  Sum_probs=78.2

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcC-CCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCe-eCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRP-FVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYK-FDDK  155 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~-~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~-~~g~  155 (184)
                      ...++++|||+|||+++++++|+++|++ ||.|.+|+++.+.    .++++|||||+|.+.++|++|++.|||.. +.|+
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~----~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~   80 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ----TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSK   80 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT----TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSS
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC----CCCccceEEEEECCHHHHHHHHHHccCCcccCCE
Confidence            3466789999999999999999999999 9999999999853    37899999999999999999999999999 9999


Q ss_pred             CCCCCceEEEeecCCCCC
Q 030012          156 KPDSPTLKIQFAHFPFHL  173 (184)
Q Consensus       156 ~~~~~~l~V~~a~~~~~~  173 (184)
                      .     |+|+|++....+
T Consensus        81 ~-----l~v~~a~~~~~~   93 (104)
T 2dhg_A           81 P-----VRLSVAIPKASR   93 (104)
T ss_dssp             C-----CCCCBCCCCCSC
T ss_pred             e-----EEEEEccCCCcC
Confidence            7     999999764433

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.83  E-value=1.5e-20  Score=136.45  Aligned_cols=89  Identities=15%  Similarity=0.262  Sum_probs=78.6

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEE--EEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCC----e
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYRE--IRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGY----K  151 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~--v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~----~  151 (184)
                      ....+++|||+|||+++|+++|+++|++||.|..  |+|+.+   +.+++++|||||+|.+. +|++|++.|||.    .
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d---~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~   94 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKD---KQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLT   94 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBC---SSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEc---CCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCcc
Confidence            3466789999999999999999999999999977  999885   33478999999999999 999999999999    9


Q ss_pred             eCCCCCCCCceEEEeecCCCCCCC
Q 030012          152 FDDKKPDSPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       152 ~~g~~~~~~~l~V~~a~~~~~~~~  175 (184)
                      +.|+.     |+|+|++.......
T Consensus        95 ~~gr~-----l~V~~a~~~~~~~~  113 (131)
T 2m2b_A           95 IDGKT-----INVEFAKGSKRDMA  113 (131)
T ss_dssp             GGGCC-----CCCEECCCSCCCCC
T ss_pred             CCCEE-----EEEEECCCCCCCCC
Confidence            99998     99999987654443

>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=5.5e-20  Score=137.03  Aligned_cols=87  Identities=22%  Similarity=0.267  Sum_probs=78.3

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||.++++++|+++|++||.|.+|+|+.+.   .+++++|||||+|.+.++|++|++.||+..|.++. 
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~-  110 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK---MKKTACGFCFVEYYSRADAENAMRYINGTRLDDRI-  110 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEE-
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC---CCCccceEEEEEECCHHHHHHHHHHhCCCEECCeE-
Confidence            34567899999999999999999999999999999998843   34789999999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCC
Q 030012          158 DSPTLKIQFAHFPFH  172 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~  172 (184)
                          |+|+|++....
T Consensus       111 ----l~V~~a~~~~~  121 (156)
T 1h2v_Z          111 ----IRTDWDAGFKE  121 (156)
T ss_dssp             ----CEEEEESCCCT
T ss_pred             ----EEEEECCCCCC
Confidence                99999986443

>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=99.83  E-value=2.2e-20  Score=131.21  Aligned_cols=87  Identities=18%  Similarity=0.287  Sum_probs=77.7

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ....+++|||+|||.++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~-   97 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD---RRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQT-   97 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBC---TTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEE-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEec---CCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcE-
Confidence            3456789999999999999999999999999999999874   334789999999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCC
Q 030012          158 DSPTLKIQFAHFPFH  172 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~  172 (184)
                          |+|.|++....
T Consensus        98 ----l~V~~a~~~~~  108 (110)
T 1oo0_B           98 ----IQVDWCFVKGP  108 (110)
T ss_dssp             ----CEEEESEESSC
T ss_pred             ----EEEEEcccCCC
Confidence                99999976443

>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=99.83  E-value=5e-20  Score=130.05  Aligned_cols=88  Identities=18%  Similarity=0.258  Sum_probs=77.0

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHH---HhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVS---HLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDK  155 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~---~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~  155 (184)
                      ....++|||+|||+++++++|+   ++|++||.|.+|+++.+......++++|||||+|.+.++|++|++.|||..+.|+
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            3457899999999999999999   9999999999999987543222246779999999999999999999999999999


Q ss_pred             CCCCCceEEEeecCCC
Q 030012          156 KPDSPTLKIQFAHFPF  171 (184)
Q Consensus       156 ~~~~~~l~V~~a~~~~  171 (184)
                      .     |+|+|++...
T Consensus        92 ~-----l~V~~a~~k~  102 (111)
T 2cpi_A           92 T-----LKASLGTTKY  102 (111)
T ss_dssp             E-----EEEESCCCCS
T ss_pred             E-----EEEEeccccc
Confidence            7     9999998654

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.83  E-value=4.1e-20  Score=134.16  Aligned_cols=86  Identities=19%  Similarity=0.344  Sum_probs=77.8

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ...++++|||+|||+++++++|+++|++||.|.+|+++.+.   .+++++|||||+|.+.++|++|++.|||..|.|+. 
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~---~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~-  117 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ---QSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR-  117 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCS---SSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSC-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC---CCCccceEEEEEECCHHHHHHHHHHhCCCEECCEE-
Confidence            35667899999999999999999999999999999998743   34788999999999999999999999999999998 


Q ss_pred             CCCceEEEeecCCC
Q 030012          158 DSPTLKIQFAHFPF  171 (184)
Q Consensus       158 ~~~~l~V~~a~~~~  171 (184)
                          |+|+|++..+
T Consensus       118 ----l~V~~a~~~~  127 (129)
T 2kxn_B          118 ----IRVDFSITKR  127 (129)
T ss_dssp             ----CEESCCSSSS
T ss_pred             ----EEEEEecCCC
Confidence                9999997644

>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=99.83  E-value=5.1e-20  Score=128.67  Aligned_cols=82  Identities=21%  Similarity=0.295  Sum_probs=76.0

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ....+++|||+|||+++++++|+++|++||.|.+|+++.+.    .++++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~----~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~-   99 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR----SGRSLGTADVHFERKADALKAMKQYNGVPLDGRP-   99 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT----TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC----CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcE-
Confidence            34667899999999999999999999999999999999854    3789999999999999999999999999999997 


Q ss_pred             CCCceEEEeec
Q 030012          158 DSPTLKIQFAH  168 (184)
Q Consensus       158 ~~~~l~V~~a~  168 (184)
                          |+|+|+.
T Consensus       100 ----l~V~~a~  106 (107)
T 3ulh_A          100 ----MNIQLVT  106 (107)
T ss_dssp             ----CEEEEEC
T ss_pred             ----EEEEEeC
Confidence                9999986

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.82  E-value=1.1e-20  Score=131.17  Aligned_cols=82  Identities=18%  Similarity=0.294  Sum_probs=74.9

Q ss_pred             CCCCEEEEcCCCC------CCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeC
Q 030012           80 GESNLLFVDGLPT------DCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFD  153 (184)
Q Consensus        80 ~~~~~lfVgnLp~------~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~  153 (184)
                      ..+++|||+|||.      ++++++|+++|++||.|.+|+|+.+.   .+++++|||||+|.+.++|++|++.|||..+.
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~---~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~   80 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDE---ATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD   80 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEET---TTTEECSEEEEEESSHHHHHHHHHHHTTCBSS
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcC---CCCccceEEEEEECCHHHHHHHHHHhCCcccC
Confidence            4468999999999      99999999999999999999998853   34789999999999999999999999999999


Q ss_pred             C-CCCCCCceEEEeecC
Q 030012          154 D-KKPDSPTLKIQFAHF  169 (184)
Q Consensus       154 g-~~~~~~~l~V~~a~~  169 (184)
                      | +.     |+|.|+..
T Consensus        81 g~r~-----l~V~~a~~   92 (100)
T 3ns6_A           81 LKHR-----LFLYTMKD   92 (100)
T ss_dssp             SSCB-----CEEEESHH
T ss_pred             CCeE-----EEEEECch
Confidence            9 86     99999864

>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=99.82  E-value=2.5e-20  Score=128.29  Aligned_cols=85  Identities=15%  Similarity=0.184  Sum_probs=75.8

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++++++|+++|++||.|.+++++.+   +..++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~--   86 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKY---NEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRK--   86 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEE---CSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEE--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEE---CCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeE--
Confidence            355689999999999999999999999999988777764   233789999999999999999999999999999997  


Q ss_pred             CCceEEEeecCCC
Q 030012          159 SPTLKIQFAHFPF  171 (184)
Q Consensus       159 ~~~l~V~~a~~~~  171 (184)
                         |+|+|++.+.
T Consensus        87 ---l~V~~a~~~~   96 (98)
T 2cqp_A           87 ---VKLVLGSGPS   96 (98)
T ss_dssp             ---CEEEESSCSS
T ss_pred             ---EEEEEcCCCC
Confidence               9999997654

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=1.2e-20  Score=126.62  Aligned_cols=82  Identities=23%  Similarity=0.349  Sum_probs=74.0

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      .++++|||+|||+++++++|+++|++||.|.+++++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+.   
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~---~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~---   76 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILD---KTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQM---   76 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECC---SSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEES---
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEec---CCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEE---
Confidence            56789999999999999999999999999999999874   234788999999999999999999999999999997   


Q ss_pred             CceEEEeecC
Q 030012          160 PTLKIQFAHF  169 (184)
Q Consensus       160 ~~l~V~~a~~  169 (184)
                        |+++|++.
T Consensus        77 --~~~~~~~s   84 (85)
T 1x4e_A           77 --AKQSGPSS   84 (85)
T ss_dssp             --CCSSCCCC
T ss_pred             --EeecCCCC
Confidence              88877653

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=3.5e-20  Score=129.93  Aligned_cols=82  Identities=21%  Similarity=0.254  Sum_probs=72.5

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhc--CCeeCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALH--GYKFDDKK  156 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~--g~~~~g~~  156 (184)
                      ..+.++|||+|||+++||++|+++|++||.|.+|+++.+         ||||||+|++.++|++|++.|+  +.++.|+.
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~---------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~   83 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG---------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQP   83 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT---------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC---------CCEEEEEECCHHHHHHHHHHhccCCceECCEE
Confidence            456899999999999999999999999999999999752         5799999999999999999886  47899997


Q ss_pred             CCCCceEEEeecCCCCCC
Q 030012          157 PDSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       157 ~~~~~l~V~~a~~~~~~~  174 (184)
                           |+|+|++......
T Consensus        84 -----l~V~~A~~~~~~~   96 (105)
T 1sjq_A           84 -----IYIQFSNHKELKT   96 (105)
T ss_dssp             -----CCBCCCSSSSCCC
T ss_pred             -----EEEEEcCCCCCCc
Confidence                 9999998654433

>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=99.82  E-value=5.6e-19  Score=124.79  Aligned_cols=89  Identities=12%  Similarity=0.282  Sum_probs=76.6

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC-
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP-  157 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~-  157 (184)
                      ....++|||+|||+++++++|+++|++||.|.+|+++.+.    .++++|||||+|.+.++|++|++.|||..+.++.. 
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~----~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~   97 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS----SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGV   97 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS----SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC----CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccc
Confidence            4567899999999999999999999999999999998853    37899999999999999999999999999954321 


Q ss_pred             --CCCceEEEeecCCC
Q 030012          158 --DSPTLKIQFAHFPF  171 (184)
Q Consensus       158 --~~~~l~V~~a~~~~  171 (184)
                        ...+|+|.|++++.
T Consensus        98 ~~~~~~l~v~~a~p~~  113 (114)
T 1x5o_A           98 SAPTEPLLCKFSGPSS  113 (114)
T ss_dssp             CCCSSCBEEEECCCSC
T ss_pred             cCCCCceeEEccCCCC
Confidence              23359999998543

>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=99.82  E-value=7e-20  Score=125.99  Aligned_cols=84  Identities=18%  Similarity=0.237  Sum_probs=74.7

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHH----HhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVS----HLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDD  154 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~----~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g  154 (184)
                      ....++|||+|||+++++++|+    ++|++||.|.+|+++.+..    .  +|||||+|.+.++|++|++.|||..+.|
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~----~--rg~afV~f~~~~~A~~Ai~~l~g~~~~g   79 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTD----Y--QLKAVVQMENLQDAIGAVNSLHRYKIGS   79 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCS----T--TCCEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCC----C--CeEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            3456899999999999999999    9999999999999987432    1  7899999999999999999999999999


Q ss_pred             CCCCCCceEEEeecCCCCC
Q 030012          155 KKPDSPTLKIQFAHFPFHL  173 (184)
Q Consensus       155 ~~~~~~~l~V~~a~~~~~~  173 (184)
                      +.     |+|+|++....+
T Consensus        80 r~-----l~V~~a~~~~~~   93 (96)
T 2dgx_A           80 KK-----ILVSLATGASGP   93 (96)
T ss_dssp             EE-----EEEEECCCSSCC
T ss_pred             eE-----EEEEEcCCCCCC
Confidence            97     999999765543

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=1.9e-19  Score=122.15  Aligned_cols=81  Identities=25%  Similarity=0.400  Sum_probs=73.4

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++++++|+++|++||.|.+|++.           +|||||+|.+.++|++|++.|||..+.|+.  
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-----------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~--   71 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-----------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVN--   71 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-----------TTEEEEEESSHHHHHHHHHHHTTCBCSSCB--
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-----------CCEEEEEECCHHHHHHHHHHhcCCccCCcE--
Confidence            4567899999999999999999999999999999986           259999999999999999999999999998  


Q ss_pred             CCceEEEeecCCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~~  175 (184)
                         |+|+|++.......
T Consensus        72 ---l~v~~a~~~~~~~~   85 (90)
T 2dnq_A           72 ---INVEASKNKSKASS   85 (90)
T ss_dssp             ---CEEECSSCCCCCCS
T ss_pred             ---EEEEECCCCCCCCC
Confidence               99999987655443

>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=99.82  E-value=2.1e-20  Score=129.91  Aligned_cols=85  Identities=20%  Similarity=0.341  Sum_probs=77.2

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++++++|+++|++||.|.+++++.+.   .+++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus         5 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~---~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~--   79 (104)
T 1p1t_A            5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDR---ETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRA--   79 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEET---TTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSC--
T ss_pred             CCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCC---CCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcE--
Confidence            3456899999999999999999999999999999998753   23789999999999999999999999999999998  


Q ss_pred             CCceEEEeecCCC
Q 030012          159 SPTLKIQFAHFPF  171 (184)
Q Consensus       159 ~~~l~V~~a~~~~  171 (184)
                         |+|+|++...
T Consensus        80 ---l~v~~a~~~~   89 (104)
T 1p1t_A           80 ---LRVDNAASEK   89 (104)
T ss_dssp             ---BEEEETTCTT
T ss_pred             ---EEEEeCCCcc
Confidence               9999998654

>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=99.81  E-value=1e-19  Score=127.06  Aligned_cols=79  Identities=14%  Similarity=0.180  Sum_probs=70.7

Q ss_pred             CCCCCEEEEcCCCC-CCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcC--CeeCCC
Q 030012           79 KGESNLLFVDGLPT-DCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHG--YKFDDK  155 (184)
Q Consensus        79 ~~~~~~lfVgnLp~-~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g--~~~~g~  155 (184)
                      .+++++|||+|||+ +++++||+++|++||.|.+|+++.+         +|||||+|++.++|++|++.||+  ..+.|+
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~---------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr   82 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK---------INEAFIEMATTEDAQAAVDYYTTTPALVFGK   82 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS---------SSCEEEEESSHHHHHHHHHHHHHSCCEETTE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC---------CCEEEEEECCHHHHHHHHHHHcCCCceECCc
Confidence            45689999999999 9999999999999999999999752         46999999999999999999986  459999


Q ss_pred             CCCCCceEEEeecCCC
Q 030012          156 KPDSPTLKIQFAHFPF  171 (184)
Q Consensus       156 ~~~~~~l~V~~a~~~~  171 (184)
                      .     |+|+|++...
T Consensus        83 ~-----l~V~~a~~~~   93 (102)
T 1x4d_A           83 P-----VRVHLSQKYK   93 (102)
T ss_dssp             E-----CEEEEECCCT
T ss_pred             E-----EEEEECCCCC
Confidence            7     9999998644

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=5.2e-20  Score=128.32  Aligned_cols=88  Identities=20%  Similarity=0.341  Sum_probs=78.3

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++. ++..+.|+. 
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~-   86 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKD---KTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRN-   86 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEEC---SSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEE-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEE-
Confidence            3566789999999999999999999999999999999884   33478999999999999999999998 999999997 


Q ss_pred             CCCceEEEeecCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~  174 (184)
                          |+|+|++.....+
T Consensus        87 ----l~V~~a~~~~~~~   99 (105)
T 2dh8_A           87 ----IDPKPCTPRGMQP   99 (105)
T ss_dssp             ----EBCCCSCCSSCCT
T ss_pred             ----EEEEEccCCCCCC
Confidence                9999998655443

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=6e-20  Score=128.37  Aligned_cols=81  Identities=20%  Similarity=0.286  Sum_probs=74.0

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++|+++|+++|++||.|.+|+++.+.   . ++++|||||+|.+.++|++|++ +++..+.|+.  
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~---~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~--   80 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL---H-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETD--   80 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCC---T-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTT--
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECC---C-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEE--
Confidence            3456899999999999999999999999999999998753   3 7899999999999999999998 9999999998  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |.|.|+..
T Consensus        81 ---l~V~~~~~   88 (103)
T 1s79_A           81 ---LLILFKDD   88 (103)
T ss_dssp             ---CEEEEHHH
T ss_pred             ---EEEEEchH
Confidence               99999864

>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=99.81  E-value=8.4e-20  Score=123.27  Aligned_cols=80  Identities=16%  Similarity=0.308  Sum_probs=73.7

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCc
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPT  161 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~  161 (184)
                      .++|||+|||+++++++|+++|++||.|.+++++.+.   ..++++|||||+|.+.++|++|+ .|||..+.|+.     
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~-----   76 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDK---FSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQ-----   76 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESC---SSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEE-----
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecC---CCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcE-----
Confidence            5799999999999999999999999999999998743   23788999999999999999999 99999999997     


Q ss_pred             eEEEeecCC
Q 030012          162 LKIQFAHFP  170 (184)
Q Consensus       162 l~V~~a~~~  170 (184)
                      |+|++++..
T Consensus        77 l~V~~a~~~   85 (89)
T 3ucg_A           77 IKVIPKRTN   85 (89)
T ss_dssp             CEEEETTTT
T ss_pred             EEEEEccCC
Confidence            999999764

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.81  E-value=8.4e-20  Score=132.31  Aligned_cols=82  Identities=18%  Similarity=0.329  Sum_probs=73.3

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHH----HhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVS----HLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDD  154 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~----~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g  154 (184)
                      ..++++|||+|||+.+++++|+    ++|++||.|.+|.+..      +++++|||||+|.+.++|+.|++.|||..+.|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~------~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~g   99 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL------SDDNSGKAYIVFATQESAQAFVEAFQGYPFQG   99 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC------CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc------CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCC
Confidence            4567899999999999999876    6999999999988743      26789999999999999999999999999999


Q ss_pred             CCCCCCceEEEeecCCC
Q 030012          155 KKPDSPTLKIQFAHFPF  171 (184)
Q Consensus       155 ~~~~~~~l~V~~a~~~~  171 (184)
                      +.     |+|+|++...
T Consensus       100 r~-----l~V~~a~~~~  111 (127)
T 2a3j_A          100 NP-----LVITFSETPQ  111 (127)
T ss_dssp             SC-----CEEEECCCCC
T ss_pred             CE-----EEEEEccCcc
Confidence            97     9999998654

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=1.6e-19  Score=124.30  Aligned_cols=80  Identities=18%  Similarity=0.337  Sum_probs=71.8

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++++++|+++|++||.|. ++++.       ++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~-------~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~--   85 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW-------QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDT--   85 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE-------ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSC--
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc-------CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcE--
Confidence            45578999999999999999999999999997 66665       356789999999999999999999999999998  


Q ss_pred             CCceEEEeecCCC
Q 030012          159 SPTLKIQFAHFPF  171 (184)
Q Consensus       159 ~~~l~V~~a~~~~  171 (184)
                         |+|+|++...
T Consensus        86 ---l~V~~a~~~~   95 (97)
T 2e5j_A           86 ---LRVALARQQR   95 (97)
T ss_dssp             ---CEEEECCCCC
T ss_pred             ---EEEEEcCCCC
Confidence               9999997654

>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=99.81  E-value=4e-19  Score=123.83  Aligned_cols=82  Identities=21%  Similarity=0.256  Sum_probs=72.1

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhc--CCeeCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALH--GYKFDDKK  156 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~--g~~~~g~~  156 (184)
                      ..++++|||+|||+++++++|+++|++||.|.+|+++.+         ||||||+|++.++|++|++.|+  +..+.|+.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~---------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~   82 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG---------KNQAFLELATEEAAITMVNYYSAVTPHLRNQP   82 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT---------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC---------CCEEEEEECCHHHHHHHHHHhccCCceECCcE
Confidence            456789999999999999999999999999999988642         5799999999999999999874  68899997


Q ss_pred             CCCCceEEEeecCCCCCC
Q 030012          157 PDSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       157 ~~~~~l~V~~a~~~~~~~  174 (184)
                           |+|+|++....+.
T Consensus        83 -----l~V~~a~~~~~~~   95 (101)
T 2cq1_A           83 -----IYIQYSNHKELKT   95 (101)
T ss_dssp             -----CEEEECSCSSCCC
T ss_pred             -----EEEEEcCcccCcC
Confidence                 9999998654443

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.81  E-value=7.6e-20  Score=136.91  Aligned_cols=82  Identities=12%  Similarity=0.184  Sum_probs=73.9

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCC--CEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFV--GYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G--~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ...++|||+|||+++++++|+++|++||  .|.+|+++.+   +.+|+++|||||+|.+.++|++||+.|||..|.|+. 
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d---~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~-  128 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAEN---RANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEK-  128 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEEC---TTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEE-
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEec---CCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeE-
Confidence            3568999999999999999999999999  9999999885   334899999999999999999999999999999997 


Q ss_pred             CCCceEEEeecC
Q 030012          158 DSPTLKIQFAHF  169 (184)
Q Consensus       158 ~~~~l~V~~a~~  169 (184)
                          |+|+|+..
T Consensus       129 ----l~V~~a~~  136 (156)
T 3n9u_C          129 ----VDVRPATR  136 (156)
T ss_dssp             ----CEEEECCH
T ss_pred             ----eEEEEcCC
Confidence                99999963

>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=99.81  E-value=1.6e-19  Score=127.73  Aligned_cols=85  Identities=25%  Similarity=0.400  Sum_probs=74.5

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCE----EEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGY----REIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDD  154 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i----~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g  154 (184)
                      ..++++|||+|||+++++++|+++|++||.|    +.+++..       ++++|||||+|.+.++|++|++.|||..+.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~-------g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   94 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMT-------GRMRGQAFITFPNKEIAWQALHLVNGYKLYG   94 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEEC-------SSSCSEEEEECSSHHHHHHHHHHSTTCBCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCC-------CccceEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            4567899999999999999999999999998    5555542       6788999999999999999999999999999


Q ss_pred             CCCCCCceEEEeecCCCCCCC
Q 030012          155 KKPDSPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       155 ~~~~~~~l~V~~a~~~~~~~~  175 (184)
                      +.     |+|+|++....+..
T Consensus        95 ~~-----l~v~~a~~~~~~~~  110 (115)
T 2cpx_A           95 KI-----LVIEFGKNKKQRSS  110 (115)
T ss_dssp             CB-----CEEEECCCCSCCCC
T ss_pred             cE-----EEEEEccCCCCCCC
Confidence            97     99999987654443

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=2e-19  Score=124.48  Aligned_cols=84  Identities=15%  Similarity=0.261  Sum_probs=73.4

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++++++|+++|++||.|   +++.+.    .++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~----~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~--   82 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQ----NGKSKGYAFIEFASFEDAKEALNSCNKREIEGRA--   82 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCS----SSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEE--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECC----CCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeE--
Confidence            4568999999999999999999999999976   455432    2688999999999999999999999999999997  


Q ss_pred             CCceEEEeecCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLP  174 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~  174 (184)
                         |+|+|++......
T Consensus        83 ---l~v~~a~~~~~~~   95 (101)
T 2fc9_A           83 ---IRLELQGPRGSPN   95 (101)
T ss_dssp             ---EEEEECSSCCCCC
T ss_pred             ---EEEEEcCCCCCCC
Confidence               9999998765444

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=2e-19  Score=122.16  Aligned_cols=81  Identities=14%  Similarity=0.245  Sum_probs=74.6

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++++++|+++|+.| .|.+|+++.+.    .++++|||||+|.+.++|++|++ |||..+.|+.  
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~----~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~--   78 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNA----HGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRY--   78 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECT----TSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEE--
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECC----CCCCceEEEEEECCHHHHHHHHH-hCCceeCCcE--
Confidence            4567899999999999999999999999 99999998853    27899999999999999999999 9999999997  


Q ss_pred             CCceEEEeecCC
Q 030012          159 SPTLKIQFAHFP  170 (184)
Q Consensus       159 ~~~l~V~~a~~~  170 (184)
                         |+|.+++..
T Consensus        79 ---i~v~~a~~~   87 (91)
T 2dgw_A           79 ---IEVFREKSG   87 (91)
T ss_dssp             ---EEEEEESSC
T ss_pred             ---EEEEECCcC
Confidence               999999764

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.6e-19  Score=125.83  Aligned_cols=86  Identities=16%  Similarity=0.181  Sum_probs=75.4

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++|++||+++|++|| +++|+|+.++    +++++|||||+|.+.++|++|++ +|+..+.++.  
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G-~~~v~i~~d~----~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~--   83 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP----DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRY--   83 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS----SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSC--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECC----CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcE--
Confidence            35568999999999999999999999999 5599998864    27999999999999999999995 7999999998  


Q ss_pred             CCceEEEeecCCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~~  175 (184)
                         |+|.++.......+
T Consensus        84 ---i~V~~~~~~~~~~~   97 (102)
T 1wez_A           84 ---VELFLNSTAGTSGS   97 (102)
T ss_dssp             ---CEEEEECCCCCCCC
T ss_pred             ---EEEEECCCCCCCCC
Confidence               99999987665444

>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=99.81  E-value=3.7e-19  Score=124.63  Aligned_cols=82  Identities=11%  Similarity=0.108  Sum_probs=71.6

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCC--eeCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGY--KFDDKK  156 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~--~~~g~~  156 (184)
                      ..++++|||+|||+++++++|+++|++||.|.+|+++.         .||||||+|++.++|++|++.|++.  .+.|+.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~---------~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~   82 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP---------FKRQALVEFENIDSAKECVTFAADVPVYIAGQQ   82 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET---------TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEC---------CCCEEEEEECCHHHHHHHHHHhccCCceECCEE
Confidence            45678999999999999999999999999999999864         2579999999999999999999764  589987


Q ss_pred             CCCCceEEEeecCCCCCC
Q 030012          157 PDSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       157 ~~~~~l~V~~a~~~~~~~  174 (184)
                           |+|+|++....+.
T Consensus        83 -----l~V~~a~~~~~~~   95 (104)
T 1wex_A           83 -----AFFNYSTSKRITR   95 (104)
T ss_dssp             -----CEEEECSSSSCCC
T ss_pred             -----EEEEEccCccccC
Confidence                 9999998654433

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.81  E-value=1e-19  Score=130.44  Aligned_cols=86  Identities=13%  Similarity=0.227  Sum_probs=76.7

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ..++|||+|||.++++++|+++|++||.|.+|+++.+.   .+++++|||||+|.+.++|++|+ .|||..+.|+.    
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~----  106 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDK---FSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRT----  106 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEEC---TTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEE----
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC---CCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeE----
Confidence            46899999999999999999999999999999998853   23789999999999999999999 79999999997    


Q ss_pred             ceEEEeecCCCCCCC
Q 030012          161 TLKIQFAHFPFHLPS  175 (184)
Q Consensus       161 ~l~V~~a~~~~~~~~  175 (184)
                       |+|+|++.......
T Consensus       107 -l~V~~a~~~~~~~~  120 (124)
T 2jwn_A          107 -IKVLPKRTNMPGIS  120 (124)
T ss_dssp             -CEEEESSCCCSSCC
T ss_pred             -EEEEECCCCCCCCC
Confidence             99999986554433

>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=99.81  E-value=1.3e-19  Score=136.40  Aligned_cols=88  Identities=18%  Similarity=0.275  Sum_probs=77.1

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ....+++|||+|||+++++++|+++|++||.|.+|+|+.+   +.+++++|||||+|.+.++|++||+.|||..|.|+. 
T Consensus        68 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~---~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~-  143 (165)
T 1rk8_A           68 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD---RRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQT-  143 (165)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---TTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEE-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEec---CCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEE-
Confidence            3456789999999999999999999999999999999874   334789999999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCCC
Q 030012          158 DSPTLKIQFAHFPFHL  173 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~  173 (184)
                          |+|.|++....+
T Consensus       144 ----l~V~~a~~~~~~  155 (165)
T 1rk8_A          144 ----IQVDWCFVKGPK  155 (165)
T ss_dssp             ----CEEEESEECC--
T ss_pred             ----EEEEEecCCCCC
Confidence                999999764433

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.81  E-value=4.7e-20  Score=134.80  Aligned_cols=90  Identities=23%  Similarity=0.341  Sum_probs=79.9

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        43 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~---~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~-  118 (135)
T 2lea_A           43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRD---RYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRE-  118 (135)
T ss_dssp             SGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCC---SSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSC-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEec---CCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEE-
Confidence            4556789999999999999999999999999999999874   234789999999999999999999999999999998 


Q ss_pred             CCCceEEEeecCCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~~  175 (184)
                          |+|+|++......+
T Consensus       119 ----l~V~~a~~~~~~~~  132 (135)
T 2lea_A          119 ----LRVQMARYGRPPDS  132 (135)
T ss_dssp             ----CEEEECCCCCCCTT
T ss_pred             ----EEEEECCCCCCCcc
Confidence                99999987655443

>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=99.81  E-value=1.6e-19  Score=121.55  Aligned_cols=81  Identities=17%  Similarity=0.342  Sum_probs=72.8

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++ +++..+.|+. 
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~-   81 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMD---PNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRV-   81 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEEC---TTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEE-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeec---CCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEE-
Confidence            3567789999999999999999999999999999999874   3347899999999999999999996 5888999997 


Q ss_pred             CCCceEEEee
Q 030012          158 DSPTLKIQFA  167 (184)
Q Consensus       158 ~~~~l~V~~a  167 (184)
                          |+|++|
T Consensus        82 ----i~v~~A   87 (87)
T 3s7r_A           82 ----IDPKKA   87 (87)
T ss_dssp             ----EEEEEC
T ss_pred             ----EEEEeC
Confidence                999986

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.81  E-value=1.2e-19  Score=126.09  Aligned_cols=78  Identities=14%  Similarity=0.184  Sum_probs=70.4

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCe--eCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYK--FDDKK  156 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~--~~g~~  156 (184)
                      ..++++|||+|||+++|+++|+++|++||.|.++++++         +||||||+|++.++|++|++.|++..  +.|+.
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~---------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~   88 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP---------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHP   88 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET---------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc---------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcE
Confidence            45789999999999999999999999999999999874         35799999999999999999999875  77987


Q ss_pred             CCCCceEEEeecCC
Q 030012          157 PDSPTLKIQFAHFP  170 (184)
Q Consensus       157 ~~~~~l~V~~a~~~  170 (184)
                           |+|+|++..
T Consensus        89 -----i~V~~S~~k   97 (100)
T 3r27_A           89 -----AFVNYSTSQ   97 (100)
T ss_dssp             -----EEEEECSCS
T ss_pred             -----EEEEecccc
Confidence                 999999753

>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=99.81  E-value=2.6e-19  Score=125.71  Aligned_cols=83  Identities=17%  Similarity=0.191  Sum_probs=71.5

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++++++|+++|++||.|.+|+++.+          |||||+|.+.++|++||+.|||.++.|....
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~----------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~   81 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD----------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGE   81 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT----------TEEEEEESSHHHHHHHHHHSSSEEEECTTSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC----------CEEEEEECCHHHHHHHHHHHCcCCccCCcCc
Confidence            456789999999999999999999999999999999752          5999999999999999999999999991111


Q ss_pred             CCceEEEeecCCC
Q 030012          159 SPTLKIQFAHFPF  171 (184)
Q Consensus       159 ~~~l~V~~a~~~~  171 (184)
                      ...|+|+|++...
T Consensus        82 ~~~i~V~~a~~~~   94 (108)
T 1x4c_A           82 TAYIRVKVDGPRS   94 (108)
T ss_dssp             EEEEEEEESSCCS
T ss_pred             ceEEEEEeCCCCC
Confidence            1139999998644

>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=99.81  E-value=4.8e-19  Score=122.95  Aligned_cols=86  Identities=16%  Similarity=0.188  Sum_probs=75.9

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++  ++..+.|+. 
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~-   84 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKD---LKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRW-   84 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEEC---SSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEE-
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEec---CCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeE-
Confidence            4566789999999999999999999999999999999884   3347899999999999999999998  578999997 


Q ss_pred             CCCceEEEeecCCCCC
Q 030012          158 DSPTLKIQFAHFPFHL  173 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~  173 (184)
                          |+|+|++.....
T Consensus        85 ----l~v~~a~~~~~~   96 (103)
T 2cqg_A           85 ----CDCKLPNSKQSQ   96 (103)
T ss_dssp             ----EEEECCCTTCCC
T ss_pred             ----EEEEecCCCCcC
Confidence                999999865433

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=7.1e-20  Score=129.90  Aligned_cols=87  Identities=18%  Similarity=0.222  Sum_probs=77.0

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++. ++..+.|+.  
T Consensus        24 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~---~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~--   97 (116)
T 1x4b_A           24 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRD---PASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRV--   97 (116)
T ss_dssp             HHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECC---TTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEE--
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEEC---CCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEE--
Confidence            345689999999999999999999999999999999874   33478899999999999999999987 999999997  


Q ss_pred             CCceEEEeecCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLP  174 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~  174 (184)
                         |+|+|++......
T Consensus        98 ---l~V~~a~~~~~~~  110 (116)
T 1x4b_A           98 ---VEPKRAVAREESG  110 (116)
T ss_dssp             ---EEEECCSSCCCCC
T ss_pred             ---EEEEECCCCccCC
Confidence               9999998655443

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=4.1e-19  Score=123.00  Aligned_cols=86  Identities=24%  Similarity=0.358  Sum_probs=73.7

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|+.|+   +++++.+   +..++++|||||+|.+.++|++|++.|||..|.|+. 
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~---~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~-   83 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTD---RETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNK-   83 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEEC---SSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEE-
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEec---CCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeE-
Confidence            346679999999999999999999999874   5666663   233789999999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~  174 (184)
                          |+|+|++......
T Consensus        84 ----l~V~~a~~~~~~~   96 (102)
T 2fc8_A           84 ----VTLDWAKPKGEGG   96 (102)
T ss_dssp             ----CEEEECCCCCSSS
T ss_pred             ----EEEEEecCCCCCC
Confidence                9999998755443

>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=99.81  E-value=4.9e-20  Score=127.70  Aligned_cols=83  Identities=19%  Similarity=0.391  Sum_probs=71.7

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++|| |.+|+++.+..  ..++++|||||+|.+.++|++|+ .|||..+.|+. 
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~--~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~-   89 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPS--NPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRR-   89 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTT--TTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBC-
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCC--cCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeE-
Confidence            456779999999999999999999999999 99999987531  23789999999999999999999 89999999998 


Q ss_pred             CCCceEEEeecC
Q 030012          158 DSPTLKIQFAHF  169 (184)
Q Consensus       158 ~~~~l~V~~a~~  169 (184)
                          |+|+|++.
T Consensus        90 ----l~V~~a~~   97 (100)
T 2j76_E           90 ----IRVDVADQ   97 (100)
T ss_dssp             ----CCCEECCC
T ss_pred             ----EEEEeccC
Confidence                99999975

>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=99.81  E-value=2.6e-19  Score=128.25  Aligned_cols=83  Identities=20%  Similarity=0.253  Sum_probs=73.4

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhc--CCeeCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALH--GYKFDDKK  156 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~--g~~~~g~~  156 (184)
                      ..++++|||+|||++++|++|+++|++||.|++|+++.+         ||||||+|++.++|++|++.|+  +..+.|+.
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~---------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~   98 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG---------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQP   98 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG---------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC---------CCEEEEEECCHHHHHHHHHHhccCCceECCeE
Confidence            456789999999999999999999999999999999752         5799999999999999999997  47899997


Q ss_pred             CCCCceEEEeecCCCCCCC
Q 030012          157 PDSPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       157 ~~~~~l~V~~a~~~~~~~~  175 (184)
                           |+|+|++....+..
T Consensus        99 -----l~V~~a~~k~~~~~  112 (119)
T 2ad9_A           99 -----IYIQFSNHKELKTD  112 (119)
T ss_dssp             -----CEEEECSSSSCCCC
T ss_pred             -----EEEEEccCCCCCcc
Confidence                 99999986554443

>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=99.81  E-value=2e-19  Score=133.92  Aligned_cols=88  Identities=23%  Similarity=0.339  Sum_probs=78.8

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~---~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~--  141 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRD---RYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRE--  141 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCC---SSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSE--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeec---CCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeE--
Confidence            455789999999999999999999999999999999874   234789999999999999999999999999999997  


Q ss_pred             CCceEEEeecCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLP  174 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~  174 (184)
                         |+|+|++....+.
T Consensus       142 ---l~v~~a~~~~~~~  154 (158)
T 2kn4_A          142 ---LRVQMARYGRPPD  154 (158)
T ss_dssp             ---EEEEEECCSSCCC
T ss_pred             ---EEEEECCCCCCCC
Confidence               9999998765443

>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=99.81  E-value=4.5e-19  Score=121.88  Aligned_cols=80  Identities=19%  Similarity=0.411  Sum_probs=72.0

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeC--CCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFD--DKK  156 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~--g~~  156 (184)
                      ..++++|||+|||+++++++|+++|++||.|.+|++...         +|||||+|.+.++|++|++.|||..+.  ++.
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~---------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~   84 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG---------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRR   84 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS---------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC---------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcE
Confidence            355789999999999999999999999999999988641         579999999999999999999999999  887


Q ss_pred             CCCCceEEEeecCCCC
Q 030012          157 PDSPTLKIQFAHFPFH  172 (184)
Q Consensus       157 ~~~~~l~V~~a~~~~~  172 (184)
                           |+|+|++....
T Consensus        85 -----l~V~~a~~~~~   95 (97)
T 1why_A           85 -----LRVDFAKSGPS   95 (97)
T ss_dssp             -----CEEEECCCCCC
T ss_pred             -----EEEEECCCCCC
Confidence                 99999987543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.80  E-value=1.2e-18  Score=125.03  Aligned_cols=86  Identities=20%  Similarity=0.260  Sum_probs=78.0

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ....+++|||+|||+++++++|+++|++||.|.+|++..+.    .++++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~----~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~-  105 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR----SGRSLGTADVHFERRADALKAMKQYKGVPLDGRP-  105 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS----SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCE-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC----CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcE-
Confidence            34667899999999999999999999999999999998753    3788999999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCC
Q 030012          158 DSPTLKIQFAHFPFH  172 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~  172 (184)
                          |+|+|+.....
T Consensus       106 ----l~V~~a~~~~~  116 (124)
T 2kt5_A          106 ----MDIQLVASQID  116 (124)
T ss_dssp             ----EEEEEECCTTC
T ss_pred             ----EEEEEeCCCCC
Confidence                99999986543

>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=99.80  E-value=6.8e-20  Score=129.62  Aligned_cols=82  Identities=20%  Similarity=0.360  Sum_probs=74.5

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|+ .|||..|.|+.  
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~--   95 (114)
T 2cq4_A           22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISD---RNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVP--   95 (114)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCS---CCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEE--
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEec---CCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeE--
Confidence            345689999999999999999999999999999999874   333788999999999999999999 99999999997  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |+|+|++.
T Consensus        96 ---l~V~~a~~  103 (114)
T 2cq4_A           96 ---IIVQASQA  103 (114)
T ss_dssp             ---EEEEEHHH
T ss_pred             ---EEEEecCC
Confidence               99999875

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.80  E-value=4.3e-20  Score=130.88  Aligned_cols=80  Identities=15%  Similarity=0.174  Sum_probs=71.5

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCC-CEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFV-GYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G-~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....+|||+|||+++++++|+++|++|| .|..+++..       .+++|||||+|.+.++|++|++.|||.++.|+.  
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~-------~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~--   96 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT-------RDFDGTGALEFPSEEILVEALERLNNIEFRGSV--   96 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS-------CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEE--
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc-------CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeE--
Confidence            4568999999999999999999999999 899998853       246789999999999999999999999999998  


Q ss_pred             CCceEEEeecCCC
Q 030012          159 SPTLKIQFAHFPF  171 (184)
Q Consensus       159 ~~~l~V~~a~~~~  171 (184)
                         |+|++++.+.
T Consensus        97 ---i~V~~a~~~p  106 (111)
T 2jvr_A           97 ---ITVERDDNPP  106 (111)
T ss_dssp             ---EEEEESCC--
T ss_pred             ---EEEEECCCCC
Confidence               9999998654

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.80  E-value=1.6e-19  Score=127.22  Aligned_cols=86  Identities=19%  Similarity=0.225  Sum_probs=72.9

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.+ +..+.|+. 
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~---~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~-   95 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRD---PLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKT-   95 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCC---TTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEE-
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEEC---CCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEE-
Confidence            4566789999999999999999999999999999999874   334789999999999999999999976 59999997 


Q ss_pred             CCCceEEEeecCCCC
Q 030012          158 DSPTLKIQFAHFPFH  172 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~  172 (184)
                          |+|+|+.....
T Consensus        96 ----l~V~~a~~~~~  106 (109)
T 2rs2_A           96 ----IDPKVAFPRRA  106 (109)
T ss_dssp             ----EEEEECCCCCC
T ss_pred             ----EEEEEccCCCC
Confidence                99999976443

>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=99.80  E-value=5.7e-20  Score=125.69  Aligned_cols=82  Identities=13%  Similarity=0.143  Sum_probs=72.6

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ...++|||+|||+++++++|+++|++||.|.+++++.+.   ..++++|||||+|.+.++|++|++.|||..+.|+.   
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~---~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~---   86 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN---EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRK---   86 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEEC---TTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE---
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeC---CCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcE---
Confidence            346899999999999999999999999999888877742   33789999999999999999999999999999997   


Q ss_pred             CceEEEeecC
Q 030012          160 PTLKIQFAHF  169 (184)
Q Consensus       160 ~~l~V~~a~~  169 (184)
                        |+|+++..
T Consensus        87 --l~v~~a~s   94 (95)
T 2ek1_A           87 --VKLSGPSS   94 (95)
T ss_dssp             --CEEECCC-
T ss_pred             --EEEEeccC
Confidence              99999864

>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=99.80  E-value=3.3e-19  Score=126.12  Aligned_cols=81  Identities=22%  Similarity=0.386  Sum_probs=74.2

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ...+++|||+|||+++++++|+++|++||.|.+|+++.+      +.++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~------~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~--   76 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT------PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRY--   76 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS------TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCB--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC------CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeE--
Confidence            466789999999999999999999999999999999863      455889999999999999999999999999997  


Q ss_pred             CCceEEEeecCC
Q 030012          159 SPTLKIQFAHFP  170 (184)
Q Consensus       159 ~~~l~V~~a~~~  170 (184)
                         |+|+|++..
T Consensus        77 ---l~v~~a~~~   85 (115)
T 3lqv_A           77 ---LVVLYYNAN   85 (115)
T ss_dssp             ---CEEEECCHH
T ss_pred             ---EEEEEecCC
Confidence               999999753

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=4.5e-19  Score=120.77  Aligned_cols=82  Identities=21%  Similarity=0.353  Sum_probs=73.5

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|++++           +||||+|.+.++|++|++.|||..+.|+. 
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~-----------~~afV~f~~~~~a~~A~~~l~g~~~~g~~-   73 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK-----------DYAFVHMERAEDAVEAIRGLDNTEFQGKR-   73 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS-----------SEEEEEESCHHHHHHHHHHHTTEEETTEE-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC-----------CEEEEEECCHHHHHHHHHHhCCCeeCCcE-
Confidence            345678999999999999999999999999999999863           39999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~~  175 (184)
                          |+|+|++.......
T Consensus        74 ----l~V~~a~~~~~~~~   87 (92)
T 2dgt_A           74 ----MHVQLSTSRLRTAS   87 (92)
T ss_dssp             ----EEEEESSCCCSCCC
T ss_pred             ----EEEEEccCCCCCCC
Confidence                99999987655443

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.80  E-value=1.7e-19  Score=126.02  Aligned_cols=81  Identities=20%  Similarity=0.358  Sum_probs=73.3

Q ss_pred             CCCCCEEEEcCCCCCC------cHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCee
Q 030012           79 KGESNLLFVDGLPTDC------TRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKF  152 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~------te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~  152 (184)
                      ...+++|||+|||+.+      ++++|+++|++||.|.+|+++. +    .|+++|||||+|.+.++|++|++.|||..+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~-~----~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~   86 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE-E----DGKTKGYIFLEYASPAHAVDAVKNADGYKL   86 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC-B----TTBSCCEEEEEECSSSHHHHHHHHCSSEEC
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC-C----CCCeeeEEEEEECCHHHHHHHHHHhCCccc
Confidence            4557899999999999      8899999999999999999872 2    278999999999999999999999999999


Q ss_pred             CCC-CCCCCceEEEeecC
Q 030012          153 DDK-KPDSPTLKIQFAHF  169 (184)
Q Consensus       153 ~g~-~~~~~~l~V~~a~~  169 (184)
                      .|+ .     |+|+|+..
T Consensus        87 ~g~~~-----l~V~~a~~   99 (105)
T 2nlw_A           87 DKQHT-----FRVNLFTD   99 (105)
T ss_dssp             STTCE-----EEEECSCC
T ss_pred             CCCce-----EEEEEcch
Confidence            998 7     99999964

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.80  E-value=7.7e-20  Score=119.84  Aligned_cols=75  Identities=23%  Similarity=0.393  Sum_probs=69.0

Q ss_pred             EEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceE
Q 030012           84 LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLK  163 (184)
Q Consensus        84 ~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~  163 (184)
                      +|||+|||+++++++|+++|++||.|.+++++.+.   .+++++|||||+|.+.++|++|++ |||..+.|+.     |+
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~-----l~   71 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDK---TTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKM-----VE   71 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCS---SSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCC-----CE
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecC---CCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEE-----EE
Confidence            58999999999999999999999999999988743   237899999999999999999998 9999999998     99


Q ss_pred             EEee
Q 030012          164 IQFA  167 (184)
Q Consensus       164 V~~a  167 (184)
                      |+||
T Consensus        72 v~~A   75 (75)
T 2mss_A           72 CKKA   75 (75)
T ss_dssp             EECC
T ss_pred             EEeC
Confidence            9986

>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=99.80  E-value=2.9e-19  Score=119.71  Aligned_cols=77  Identities=19%  Similarity=0.383  Sum_probs=70.8

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHh-cCCeeCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDAL-HGYKFDDKK  156 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l-~g~~~~g~~  156 (184)
                      .....++|||+|||.++++++|+++|++||.|.++++..         ++|||||+|.+.++|++|++.| +|..+.|+.
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~---------~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~   78 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ---------RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRR   78 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG---------GGTEEEEEESSHHHHHHHHHTTTTTCEETTEE
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC---------CCCEEEEEECCHHHHHHHHHHhcCCeeECCCE
Confidence            346678999999999999999999999999999999974         3579999999999999999999 999999997


Q ss_pred             CCCCceEEEeec
Q 030012          157 PDSPTLKIQFAH  168 (184)
Q Consensus       157 ~~~~~l~V~~a~  168 (184)
                           |+|+|++
T Consensus        79 -----l~v~~ak   85 (85)
T 2ytc_A           79 -----LNVKWGR   85 (85)
T ss_dssp             -----CCEEECC
T ss_pred             -----EEEEecC
Confidence                 9999985

>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=99.80  E-value=4e-19  Score=124.94  Aligned_cols=80  Identities=21%  Similarity=0.299  Sum_probs=72.0

Q ss_pred             CCCCCEEEEcCCCCC-CcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           79 KGESNLLFVDGLPTD-CTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~-~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ...+++|||+|||++ +++++|+++|++||.|.+|++           ++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-----------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~-   91 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-----------HKGYAFVQYSNERHARAAVLGENGRVLAGQT-   91 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-----------ETTEEEEECSSSHHHHHHHHHHTTCEETTEE-
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-----------eCCEEEEEECCHHHHHHHHHHcCCCEECCeE-
Confidence            445689999999999 999999999999999999988           2469999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~  174 (184)
                          |+|+|++.+....
T Consensus        92 ----l~V~~a~~~~~~~  104 (110)
T 1wf1_A           92 ----LDINMAGEPKPDR  104 (110)
T ss_dssp             ----CCEEESCCCCSCC
T ss_pred             ----EEEEECCCCCCCC
Confidence                9999998655443

>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=99.80  E-value=6.3e-19  Score=121.61  Aligned_cols=81  Identities=25%  Similarity=0.364  Sum_probs=73.2

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ..+.++|||+|||+++++++|+++|++||.|.+|++..         ++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~---------~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~--   80 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK---------DKGFGFIRLETRTLAEIAKVELDNMPLRGKQ--   80 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET---------TTTEEEEECSSSHHHHHHHHHHTTCCBTTBC--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEec---------CCCEEEEEECCHHHHHHHHHHhCCCEeCCce--
Confidence            45678999999999999999999999999999999864         2579999999999999999999999999998  


Q ss_pred             CCceEEEeecCCCCC
Q 030012          159 SPTLKIQFAHFPFHL  173 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~  173 (184)
                         |+|+|++.....
T Consensus        81 ---l~v~~a~~~~~~   92 (99)
T 2cpj_A           81 ---LRVRFACHSASL   92 (99)
T ss_dssp             ---CEEEESSCCSCC
T ss_pred             ---EEEEEcCCCCCC
Confidence               999999875443

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.9e-19  Score=126.66  Aligned_cols=82  Identities=22%  Similarity=0.390  Sum_probs=74.8

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||.++++++|+++|++||.|.+|+++.+.     +.++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-----~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~-   98 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-----RGSKGFGFVTFENSADADRAREKLHGTVVEGRK-   98 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT-----TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEE-
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC-----CCCceEEEEEECCHHHHHHHHHHcCCCEECCEE-
Confidence            34567899999999999999999999999999999998752     347899999999999999999999999999997 


Q ss_pred             CCCceEEEeecC
Q 030012          158 DSPTLKIQFAHF  169 (184)
Q Consensus       158 ~~~~l~V~~a~~  169 (184)
                          |+|+|++.
T Consensus        99 ----l~V~~a~~  106 (109)
T 2err_A           99 ----IEVNNATA  106 (109)
T ss_dssp             ----CEEEECCC
T ss_pred             ----EEEEECCC
Confidence                99999975

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.79  E-value=1.5e-19  Score=122.36  Aligned_cols=75  Identities=11%  Similarity=0.069  Sum_probs=69.5

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ..+.-|||+||++.+||++|+++|.+||.|.++++..         +||||||+|.+.++|++|++.||+.++.|+.   
T Consensus         5 ~~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~---------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~---   72 (89)
T 2wbr_A            5 WGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL---------NQGIALCKYTTREEANKAQMALNNCVLANTT---   72 (89)
T ss_dssp             CCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET---------TTTEEEEEESSHHHHHHHHHHHTTEEETTEE---
T ss_pred             CccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC---------CCcEEEEEECCHHHHHHHHHHhcCCEECCcE---
Confidence            3467899999999999999999999999999999853         5789999999999999999999999999997   


Q ss_pred             CceEEEeec
Q 030012          160 PTLKIQFAH  168 (184)
Q Consensus       160 ~~l~V~~a~  168 (184)
                        |+|++|.
T Consensus        73 --I~V~~A~   79 (89)
T 2wbr_A           73 --IFAESPS   79 (89)
T ss_dssp             --EEEECCC
T ss_pred             --EEEEECC
Confidence              9999984

>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=99.79  E-value=1.4e-19  Score=124.20  Aligned_cols=83  Identities=22%  Similarity=0.388  Sum_probs=74.8

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHH----HhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVS----HLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDD  154 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~----~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g  154 (184)
                      ..++++|||+|||.++++++|+    ++|++||.|.+|++...      ++++|||||+|.+.++|++|++.|||..+.|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~------~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   78 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS------LKMRGQAFVIFKEVSSATNALRSMQGFPFYD   78 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHH------HHHTTCEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcC------CCcCcEEEEEeCCHHHHHHHHHHhCCCEECC
Confidence            4668899999999999999999    99999999999988642      5778999999999999999999999999999


Q ss_pred             CCCCCCceEEEeecCCCC
Q 030012          155 KKPDSPTLKIQFAHFPFH  172 (184)
Q Consensus       155 ~~~~~~~l~V~~a~~~~~  172 (184)
                      +.     |+|+|++....
T Consensus        79 ~~-----l~v~~a~~~~~   91 (97)
T 1nu4_A           79 KP-----MRIQYAKTDSD   91 (97)
T ss_dssp             EE-----CEEEECSSCCT
T ss_pred             cE-----EEEEEccCCCc
Confidence            87     99999987543

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.79  E-value=3.2e-19  Score=125.52  Aligned_cols=80  Identities=26%  Similarity=0.583  Sum_probs=71.8

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ....+++|||+|||+++++++|+++|++||.|.+|++.           +|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-----------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~-   94 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-----------NGFAFVEFEEAESAAKAIEEVHGKSFANQP-   94 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-----------TTEEEEECSSHHHHHHHHHHHTTCEETTEE-
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-----------CCEEEEEECCHHHHHHHHHHcCCCEECCeE-
Confidence            45667899999999999999999999999999999986           359999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCCC
Q 030012          158 DSPTLKIQFAHFPFHL  173 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~  173 (184)
                          |+|+|++....+
T Consensus        95 ----l~V~~a~~~~~r  106 (108)
T 2jvo_A           95 ----LEVVYSKLPAKR  106 (108)
T ss_dssp             ----CEEESCSCCC--
T ss_pred             ----EEEEEecCCCCC
Confidence                999999876544

>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=99.79  E-value=3.5e-19  Score=124.78  Aligned_cols=86  Identities=16%  Similarity=0.243  Sum_probs=75.2

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCC-EEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhc--CCeeCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVG-YREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALH--GYKFDDKK  156 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~-i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~--g~~~~g~~  156 (184)
                      .+.++|||+|||+++++++|+++|++||. |.+|+++..  .+.+++++|||||+|.+.++|++|++.||  +..+.|+.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~--~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~   83 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYAS--AADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQ   83 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSS--SCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBC
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEcc--CCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCe
Confidence            45789999999999999999999999998 999988732  23346889999999999999999999996  59999998


Q ss_pred             CCCCceEEEeecCCCC
Q 030012          157 PDSPTLKIQFAHFPFH  172 (184)
Q Consensus       157 ~~~~~l~V~~a~~~~~  172 (184)
                           |+|+|++....
T Consensus        84 -----l~V~~a~~~~~   94 (109)
T 2dis_A           84 -----IAVDWAEPEID   94 (109)
T ss_dssp             -----CEEEESCSSCS
T ss_pred             -----EEEEEcCCCCC
Confidence                 99999986443

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=5.3e-19  Score=119.93  Aligned_cols=80  Identities=21%  Similarity=0.368  Sum_probs=72.7

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++++++|+++|++||.|.+|++++           +||||+|.+.++|++|++.|||..+.|+.  
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~-----------~~afV~f~~~~~a~~A~~~l~g~~~~g~~--   72 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK-----------DYAFVHMEKEADAKAAIAQLNGKEVKGKR--   72 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS-----------SCEEEEESCHHHHHHHHHHHTTCEETTEE--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC-----------CEEEEEECCHHHHHHHHHHhCCCEECCcE--
Confidence            45678999999999999999999999999999999863           39999999999999999999999999997  


Q ss_pred             CCceEEEeecCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLP  174 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~  174 (184)
                         |+|+|++....+.
T Consensus        73 ---l~v~~a~~~~~~~   85 (90)
T 2dnp_A           73 ---INVELSTKGQKKS   85 (90)
T ss_dssp             ---CEEEESCCCCCCC
T ss_pred             ---EEEEECCCCCCCC
Confidence               9999998765444

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=1.4e-18  Score=119.87  Aligned_cols=80  Identities=20%  Similarity=0.273  Sum_probs=71.8

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCC--CCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPF--VGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~--G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      ....++|||+|||+++++++|+++|++|  |.|.+|++.           +|||||+|.+.++|++|++.|||..+.|+.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-----------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-----------RDYAFVHFSNREDAVEAMKALNGKVLDGSP   80 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-----------SSEEEEEESSHHHHHHHHHHHSSEEETTEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-----------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            4567899999999999999999999999  999998764           359999999999999999999999999997


Q ss_pred             CCCCceEEEeecCCCCCC
Q 030012          157 PDSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       157 ~~~~~l~V~~a~~~~~~~  174 (184)
                           |+|+|++......
T Consensus        81 -----l~v~~a~~~~~~~   93 (99)
T 2cpd_A           81 -----IEVTLAKPVDKDS   93 (99)
T ss_dssp             -----EEEECCCCCCCCC
T ss_pred             -----EEEEECCCCCCCC
Confidence                 9999998755433

>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=99.79  E-value=2.3e-19  Score=128.94  Aligned_cols=83  Identities=16%  Similarity=0.214  Sum_probs=72.5

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      +....++|||+|||+++|+++|+++|+.||.|.++.++.+.   ..++++|||||+|.+.++|++||+ |||..|.|+. 
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~---~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~-   95 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG---PNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRF-   95 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEEC---TTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSC-
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEEC---CCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcE-
Confidence            34567899999999999999999999999999885444432   237899999999999999999999 9999999998 


Q ss_pred             CCCceEEEeecC
Q 030012          158 DSPTLKIQFAHF  169 (184)
Q Consensus       158 ~~~~l~V~~a~~  169 (184)
                          |+|.++..
T Consensus        96 ----i~V~~a~~  103 (124)
T 1wel_A           96 ----IQVHPITK  103 (124)
T ss_dssp             ----BEEEEECH
T ss_pred             ----EEEEECCH
Confidence                99999863

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.79  E-value=4.9e-19  Score=121.64  Aligned_cols=83  Identities=20%  Similarity=0.352  Sum_probs=70.8

Q ss_pred             CCCCCEEEEcCCCC-CCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           79 KGESNLLFVDGLPT-DCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        79 ~~~~~~lfVgnLp~-~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ..++++|||+|||+ ++++++|+++|++||.|.+|++.           +|||||+|.+.++|++|++.|||..+.|+. 
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-----------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~-   74 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-----------NAFGFIQFDNPQSVRDAIECESQEMNFGKK-   74 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-----------TTEEEEEESCHHHHHHHHHHHTCSSCBTTT-
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-----------CCEEEEEECCHHHHHHHHHHcCCCeeCCcE-
Confidence            45678999999998 99999999999999999999884           359999999999999999999999999998 


Q ss_pred             CCCceEEEeecCCCCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLPSDG  177 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~~~~  177 (184)
                          |+|+|++........+
T Consensus        75 ----l~V~~a~~~~~~~~~~   90 (96)
T 2kvi_A           75 ----LILEVSSSNARPQFDH   90 (96)
T ss_dssp             ----BCEEEEECCCC-----
T ss_pred             ----EEEEEcCcCCCCCCCC
Confidence                9999998765544433

>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=99.79  E-value=7.1e-19  Score=122.25  Aligned_cols=80  Identities=23%  Similarity=0.420  Sum_probs=72.1

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ..+.++|||+|||+++++++|+++|++||.|.+|++++           +||||+|.+.++|++|++.|||..+.|+.  
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~-----------~~afV~f~~~~~a~~A~~~l~g~~~~g~~--   74 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK-----------DYAFIHFDERDGAVKAMEEMNGKDLEGEN--   74 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS-----------SCEEEEESSHHHHHHHHHHHTTEEETTEE--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC-----------CEEEEEeCCHHHHHHHHHHHCCCccCCCE--
Confidence            35578999999999999999999999999999998853           49999999999999999999999999997  


Q ss_pred             CCceEEEeecCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLP  174 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~  174 (184)
                         |+|+|++....+.
T Consensus        75 ---l~v~~a~~~~~~~   87 (103)
T 2dgu_A           75 ---IEIVFAKPPDQKR   87 (103)
T ss_dssp             ---EEEEECCCCCCCC
T ss_pred             ---EEEEEcCCCcccc
Confidence               9999998755444

>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=99.79  E-value=6.7e-19  Score=123.59  Aligned_cols=82  Identities=20%  Similarity=0.326  Sum_probs=73.9

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||.++++++|+++|++||.|.+|+++.+         +|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~---------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~--   90 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE---------KGYSFVRFSTHESAAHAIVSVNGTTIEGHV--   90 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT---------TTEEEEEESSHHHHHHHHHHHTTCEETTEE--
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC---------CCEEEEEECCHHHHHHHHHHcCCCEECCcE--
Confidence            456789999999999999999999999999999999752         569999999999999999999999999997  


Q ss_pred             CCceEEEeecCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLP  174 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~  174 (184)
                         |+|.|++......
T Consensus        91 ---l~v~~a~~~~~~~  103 (109)
T 1x4g_A           91 ---VKCYWGKESPDMT  103 (109)
T ss_dssp             ---CEEECCCCCCSSC
T ss_pred             ---EEEEecCCCCCCC
Confidence               9999998755433

>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=99.79  E-value=1.1e-18  Score=121.82  Aligned_cols=81  Identities=17%  Similarity=0.307  Sum_probs=72.9

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEE-EEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYRE-IRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~-v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ....++|||+|||+++++++|+++|++||.|.+ |+|+.++    .++++|||||+|.+.++|++|++. ++..+.++. 
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~----~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~-   85 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDF----QGRSTGEAFVQFASQEIAEKALKK-HKERIGHRY-   85 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCS----SSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSC-
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECC----CCCcceEEEEEECCHHHHHHHHHh-CcchhCCcE-
Confidence            456789999999999999999999999999987 8887653    278999999999999999999997 999999998 


Q ss_pred             CCCceEEEeecC
Q 030012          158 DSPTLKIQFAHF  169 (184)
Q Consensus       158 ~~~~l~V~~a~~  169 (184)
                          |+|.++..
T Consensus        86 ----i~v~~~~~   93 (104)
T 1wg5_A           86 ----IEIFKSSR   93 (104)
T ss_dssp             ----CEEEEECT
T ss_pred             ----EEEEECCH
Confidence                99999864

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.79  E-value=6.4e-19  Score=128.37  Aligned_cols=81  Identities=20%  Similarity=0.390  Sum_probs=73.6

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||.++++++|+++|++||.|.+++++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~---~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~--  134 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD---YETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRT--  134 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCC---TTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEE--
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeec---CCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEE--
Confidence            456789999999999999999999999999999999874   334788999999999999999999999999999997  


Q ss_pred             CCceEEEee
Q 030012          159 SPTLKIQFA  167 (184)
Q Consensus       159 ~~~l~V~~a  167 (184)
                         |+|+||
T Consensus       135 ---l~v~~A  140 (140)
T 2ku7_A          135 ---IRVNLA  140 (140)
T ss_dssp             ---EEEEC-
T ss_pred             ---EEEEeC
Confidence               999986

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=1.6e-19  Score=118.73  Aligned_cols=76  Identities=21%  Similarity=0.307  Sum_probs=70.1

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      ++|||+|||+++++++|+++|++||.|.+++++.+   +.+++++|||||+|.+.++|++|++.++ ..+.|+.     |
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~-----l   71 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRD---PLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKT-----I   71 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECC---CCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCC-----C
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecC---CCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEE-----E
Confidence            47999999999999999999999999999999874   3347889999999999999999999999 9999998     9


Q ss_pred             EEEee
Q 030012          163 KIQFA  167 (184)
Q Consensus       163 ~V~~a  167 (184)
                      +|+||
T Consensus        72 ~v~~a   76 (77)
T 1uaw_A           72 DPKVA   76 (77)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            99987

>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=99.78  E-value=8.5e-19  Score=120.93  Aligned_cols=78  Identities=21%  Similarity=0.375  Sum_probs=71.0

Q ss_pred             CCCCCCEEEEcCCCC-CCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           78 KKGESNLLFVDGLPT-DCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~-~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      ....+++|||+|||+ ++++++|+++|++||.|.++++.           +|||||+|.+.++|++|++.|||..+.|+.
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-----------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~   86 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-----------NAFGFIQFDNPQSVRDAIEXESQEMNFGKK   86 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-----------SSEEEEEESSHHHHHHHHHHHTTSEETTEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-----------CCEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            456789999999998 99999999999999999999883           469999999999999999999999999997


Q ss_pred             CCCCceEEEeecCCC
Q 030012          157 PDSPTLKIQFAHFPF  171 (184)
Q Consensus       157 ~~~~~l~V~~a~~~~  171 (184)
                           |+|+|++...
T Consensus        87 -----l~V~~a~~~~   96 (97)
T 2xnq_A           87 -----LILEVSSSNA   96 (97)
T ss_dssp             -----CEEEECCCCC
T ss_pred             -----EEEEecCCCC
Confidence                 9999997643

>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=99.78  E-value=7.1e-19  Score=124.71  Aligned_cols=80  Identities=14%  Similarity=0.233  Sum_probs=70.6

Q ss_pred             CCCCCEEEEcCCCCC-CcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcC--CeeCCC
Q 030012           79 KGESNLLFVDGLPTD-CTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHG--YKFDDK  155 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~-~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g--~~~~g~  155 (184)
                      ..++++|||+|||++ +++++|+++|++||.|.+|+|++         ++|||||+|++.++|++|++.|++  ..+.|+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~---------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr   92 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR---------MKSQAFIEMETREDAMAMVDHCLKKALWFQGR   92 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET---------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSS
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec---------CCCEEEEEECCHHHHHHHHHHhccCCceECCE
Confidence            456889999999998 99999999999999999999963         357999999999999999998864  569999


Q ss_pred             CCCCCceEEEeecCCCC
Q 030012          156 KPDSPTLKIQFAHFPFH  172 (184)
Q Consensus       156 ~~~~~~l~V~~a~~~~~  172 (184)
                      .     |+|+|++....
T Consensus        93 ~-----l~V~~a~~~~~  104 (112)
T 1x4f_A           93 C-----VKVDLSEKYKK  104 (112)
T ss_dssp             C-----CEEEEECSCSS
T ss_pred             E-----EEEEECccccc
Confidence            7     99999975443

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.78  E-value=4.5e-19  Score=122.66  Aligned_cols=76  Identities=21%  Similarity=0.350  Sum_probs=70.5

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      ++|||+|||+++++++|+++|++||.|.+|+++.+        ++|||||+|.+.++|++|++.|||..+.|+.     |
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~--------~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~-----l   67 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN--------PPGFAFVEFEDPRDAEDAVRGLDGKVICGSR-----V   67 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS--------SSSEEEEECSSHHHHHHHHHHHHHSCSSSCC-----C
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--------CCCEEEEEECCHHHHHHHHHHHCCCeECCcE-----E
Confidence            48999999999999999999999999999999763        4679999999999999999999999999998     9


Q ss_pred             EEEeecCCC
Q 030012          163 KIQFAHFPF  171 (184)
Q Consensus       163 ~V~~a~~~~  171 (184)
                      +|+|++...
T Consensus        68 ~V~~a~~~~   76 (101)
T 2hvz_A           68 RVELSTGMP   76 (101)
T ss_dssp             EEEESSSCC
T ss_pred             EEEEccCCC
Confidence            999998654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.78  E-value=3.7e-19  Score=127.06  Aligned_cols=80  Identities=18%  Similarity=0.297  Sum_probs=73.5

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCC---EEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVG---YREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDK  155 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~---i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~  155 (184)
                      ....++|||+|||+++|+++|+++|+.||.   |.+|+|+.+..    ++++|||||+|.+.++|++|++ +|+..+.|+
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~----g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr   88 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE----GRQSGEAFVELESEDDVKLALK-KDRESMGHR   88 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS----SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC----CCCCeEEEEEECCHHHHHHHHh-cCCCeECCe
Confidence            456789999999999999999999999999   89999988532    7899999999999999999999 999999999


Q ss_pred             CCCCCceEEEeec
Q 030012          156 KPDSPTLKIQFAH  168 (184)
Q Consensus       156 ~~~~~~l~V~~a~  168 (184)
                      .     |+|.++.
T Consensus        89 ~-----i~V~~a~   96 (118)
T 2db1_A           89 Y-----IEVFKSH   96 (118)
T ss_dssp             E-----EEEEEEC
T ss_pred             E-----EEEEECC
Confidence            7     9999985

>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=99.78  E-value=6.9e-20  Score=124.17  Aligned_cols=81  Identities=20%  Similarity=0.307  Sum_probs=70.8

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      ++|||+|||.++++++|+++|++||.|.+++++.+   +.+++++|||||+|.+.+ |++|++.|||..+.|+.     |
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~---~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~-----l   72 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYD---RETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRT-----I   72 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCC---SSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSS-----C
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEc---CCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeE-----E
Confidence            58999999999999999999999999999999874   333788999999999999 99999999999999998     9


Q ss_pred             EEEeecCCCC
Q 030012          163 KIQFAHFPFH  172 (184)
Q Consensus       163 ~V~~a~~~~~  172 (184)
                      +|+||.....
T Consensus        73 ~V~~a~~~~~   82 (90)
T 2ki2_A           73 RVTEANPKKS   82 (90)
T ss_dssp             SEEEC-----
T ss_pred             EEEEcCCCCC
Confidence            9999976543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.78  E-value=2.2e-19  Score=119.62  Aligned_cols=73  Identities=21%  Similarity=0.397  Sum_probs=66.1

Q ss_pred             CCEEEEcCCCCCC------cHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCC
Q 030012           82 SNLLFVDGLPTDC------TRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDK  155 (184)
Q Consensus        82 ~~~lfVgnLp~~~------te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~  155 (184)
                      +++|||+|||..+      ++++|+++|++||.|.++++.. +    .|+++|||||+|.+.++|++|++.|||..+.|+
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~-~----~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~   75 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE-E----DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   75 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC-B----TTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSS
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC-C----CCcEeEEEEEEECCHHHHHHHHHHhcCcccCCc
Confidence            4789999999999      7899999999999999999862 2    278899999999999999999999999999998


Q ss_pred             -CCCCCceEE
Q 030012          156 -KPDSPTLKI  164 (184)
Q Consensus       156 -~~~~~~l~V  164 (184)
                       .     |+|
T Consensus        76 ~~-----l~V   80 (81)
T 2krb_A           76 HT-----FRV   80 (81)
T ss_dssp             SC-----CCC
T ss_pred             ee-----EEe
Confidence             6     765

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.78  E-value=2.7e-19  Score=123.81  Aligned_cols=77  Identities=17%  Similarity=0.337  Sum_probs=70.6

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ...+++|||+|||.++++++|+++|++||.|.++++..         ++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~---------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~--   92 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP---------EKGCCFIKYDTHEQAAVCIVALANFPFQGRN--   92 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET---------TTTEEEEECSSHHHHHHHHHHHTTCEETTEE--
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec---------CCCEEEEEECCHHHHHHHHHHhCCCeECCeE--
Confidence            34568999999999999999999999999999999862         4579999999999999999999999999997  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |+|.|++.
T Consensus        93 ---l~V~~a~~  100 (101)
T 2la4_A           93 ---LRTGWGKE  100 (101)
T ss_dssp             ---CCCCBCCC
T ss_pred             ---EEEEeccC
Confidence               99999874

>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=4.5e-19  Score=140.45  Aligned_cols=80  Identities=13%  Similarity=0.193  Sum_probs=73.3

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCC--CEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFV--GYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G--~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ..++|||+||++++|+++|+++|++||  .|++|+|+.+   +.+++++|||||+|.+.++|++||+.|||..|.|+.  
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d---~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~--  141 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFEN---RANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQN--  141 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEEC---TTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBC--
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEec---CCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEE--
Confidence            567999999999999999999999999  9999999985   334899999999999999999999999999999998  


Q ss_pred             CCceEEEeec
Q 030012          159 SPTLKIQFAH  168 (184)
Q Consensus       159 ~~~l~V~~a~  168 (184)
                         |+|+|++
T Consensus       142 ---l~V~~a~  148 (229)
T 3q2s_C          142 ---PVVTPVN  148 (229)
T ss_dssp             ---CEEEECC
T ss_pred             ---eEEEECC
Confidence               9999985

>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=99.78  E-value=4.7e-19  Score=125.56  Aligned_cols=81  Identities=12%  Similarity=0.236  Sum_probs=73.6

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCE-EEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGY-REIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i-~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ....++|||+|||+++|+++|+++|+.||.| .+|+|+.+.    .++++|||||+|.+.++|++|++. |+..|.|+. 
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~----~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~-   85 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN----NGQGLGQALVQFKNEDDARKSERL-HRKKLNGRE-   85 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT----TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEE-
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC----CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeE-
Confidence            4567899999999999999999999999999 889998753    378999999999999999999987 999999997 


Q ss_pred             CCCceEEEeecC
Q 030012          158 DSPTLKIQFAHF  169 (184)
Q Consensus       158 ~~~~l~V~~a~~  169 (184)
                          |+|.++..
T Consensus        86 ----i~v~~a~~   93 (114)
T 2cpy_A           86 ----AFVHVVTL   93 (114)
T ss_dssp             ----EEEEEECH
T ss_pred             ----EEEEECCH
Confidence                99999864

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.77  E-value=8e-19  Score=120.23  Aligned_cols=82  Identities=13%  Similarity=0.261  Sum_probs=72.3

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++++++|+++|++||.|..+   . .    .++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~---~-~----~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~--   82 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV---S-Q----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRS--   82 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE---E-E----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEE--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe---C-C----CCCcceEEEEEECCHHHHHHHHHHhCCCEECCeE--
Confidence            4567899999999999999999999999988766   1 1    1688999999999999999999999999999997  


Q ss_pred             CCceEEEeecCCCCC
Q 030012          159 SPTLKIQFAHFPFHL  173 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~  173 (184)
                         |+|+|++...+.
T Consensus        83 ---l~v~~a~~~~~~   94 (96)
T 1fjc_A           83 ---VSLYYTGEKGGT   94 (96)
T ss_dssp             ---EEEEECSSSCCC
T ss_pred             ---EEEEEcCCCCCC
Confidence               999999765543

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=3.4e-18  Score=117.52  Aligned_cols=80  Identities=24%  Similarity=0.326  Sum_probs=71.1

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+||  ++++++|+++|++||.|.+|++.         +++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~---------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~--   78 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD---------PPRNCAFVTYEKMESADQAVAELNGTQVESVQ--   78 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE---------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEE--
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec---------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeE--
Confidence            456789999996  89999999999999999999984         34679999999999999999999999999997  


Q ss_pred             CCceEEEeecCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLP  174 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~  174 (184)
                         |+|+|++......
T Consensus        79 ---l~v~~a~~~~~~~   91 (97)
T 1x5p_A           79 ---LKVNIARKQPMLD   91 (97)
T ss_dssp             ---EEEECCSSCCCCC
T ss_pred             ---EEEEECCCCCCCC
Confidence               9999998755433

>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=99.77  E-value=7.4e-19  Score=119.81  Aligned_cols=81  Identities=17%  Similarity=0.267  Sum_probs=70.3

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCC-EEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcC-CeeCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVG-YREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHG-YKFDDKK  156 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~-i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g-~~~~g~~  156 (184)
                      ....++|||+|||+++++++|+++|++||. |..+.+.          ++|||||+|.+.++|++|++.||| ..+.|+.
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~----------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~   74 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL----------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKI   74 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE----------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc----------CCCEEEEEECCHHHHHHHHHHccCCeeECCEE
Confidence            356789999999999999999999999999 5555552          356999999999999999999999 9999997


Q ss_pred             CCCCceEEEeecCCCCCC
Q 030012          157 PDSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       157 ~~~~~l~V~~a~~~~~~~  174 (184)
                           |+|+|++....+.
T Consensus        75 -----l~v~~a~~~~~~~   87 (93)
T 2cqh_A           75 -----MEVDYSVSKKLRS   87 (93)
T ss_dssp             -----CEEEECCCCCCCC
T ss_pred             -----EEEEEccCccccC
Confidence                 9999998755443

>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=99.77  E-value=5.3e-19  Score=129.51  Aligned_cols=80  Identities=18%  Similarity=0.281  Sum_probs=73.4

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCC---EEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVG---YREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDK  155 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~---i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~  155 (184)
                      ....++|||+|||+++|+++|+++|++||.   |.+|+|+.+.   . |+++|||||+|.+.++|++|++ ||+..+.|+
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~---~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr  115 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR---E-GRQSGEAFVELGSEDDVKMALK-KDRESMGHR  115 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECS---S-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECC---C-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCE
Confidence            456789999999999999999999999999   8899998853   3 7899999999999999999999 999999999


Q ss_pred             CCCCCceEEEeec
Q 030012          156 KPDSPTLKIQFAH  168 (184)
Q Consensus       156 ~~~~~~l~V~~a~  168 (184)
                      .     |+|.++.
T Consensus       116 ~-----i~V~~a~  123 (136)
T 2hgl_A          116 Y-----IEVFKSH  123 (136)
T ss_dssp             E-----EEEEECC
T ss_pred             E-----EEEEECC
Confidence            7     9999985

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.77  E-value=9.2e-20  Score=126.18  Aligned_cols=86  Identities=13%  Similarity=0.156  Sum_probs=72.9

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++++++|+++|++||.|.+ .++.+   +..++++|||||+|.+.++|++|++ |||..+.|+.  
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~---~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~--   86 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVD---VRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNE--   86 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCE---EEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBC--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEec---CCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcE--
Confidence            345789999999999999999999999999877 34332   1226789999999999999999998 9999999998  


Q ss_pred             CCceEEEeecCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLP  174 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~  174 (184)
                         |+|+|++....++
T Consensus        87 ---l~V~~a~~~~~~~   99 (101)
T 1fj7_A           87 ---IKLEKPKGRDGTR   99 (101)
T ss_dssp             ---CEEECCSCCCCSS
T ss_pred             ---EEEEEcCCCCCCC
Confidence               9999998654443

>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=99.77  E-value=2.5e-18  Score=129.26  Aligned_cols=79  Identities=20%  Similarity=0.277  Sum_probs=70.3

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCC--CCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDD--KKPD  158 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g--~~~~  158 (184)
                      ...+|||+||++.+|+++|+++|++||.|++|++..+       +++|||||+|++.++|++|++.|||..|.+  +.  
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k-------~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~--  115 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-------NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCT--  115 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES-------SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSC--
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-------CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcE--
Confidence            3457999999999999999999999999999998752       246899999999999999999999999976  66  


Q ss_pred             CCceEEEeecCCC
Q 030012          159 SPTLKIQFAHFPF  171 (184)
Q Consensus       159 ~~~l~V~~a~~~~  171 (184)
                         |+|+|++...
T Consensus       116 ---L~V~~Ak~~~  125 (164)
T 1sjr_A          116 ---LRIDFSKLTS  125 (164)
T ss_dssp             ---EEEEECSSSS
T ss_pred             ---EEEEEecCCc
Confidence               9999998643

>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=99.77  E-value=9.7e-19  Score=123.56  Aligned_cols=77  Identities=22%  Similarity=0.326  Sum_probs=70.3

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ...++|||+|||+++++++|+++|++||.|.+|++..         ++|||||+|.+.++|++|++.|||..+.|+.   
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~---------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~---   75 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE---------GGITAIVEFLEPLEARKAFRHLAYSKFHHVP---   75 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS---------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSB---
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC---------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeE---
Confidence            3467999999999999999999999999999998853         4579999999999999999999999999997   


Q ss_pred             CceEEEeecCC
Q 030012          160 PTLKIQFAHFP  170 (184)
Q Consensus       160 ~~l~V~~a~~~  170 (184)
                        |+|+|++..
T Consensus        76 --l~V~~a~~~   84 (111)
T 1whx_A           76 --LYLEWAPIG   84 (111)
T ss_dssp             --CEEEEEETT
T ss_pred             --EEEEECCCC
Confidence              999999753

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.64  E-value=2.4e-20  Score=132.47  Aligned_cols=87  Identities=26%  Similarity=0.435  Sum_probs=76.9

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEE--------EEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYRE--------IRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGY  150 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~--------v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~  150 (184)
                      ..+.++|||+|||.++++++|+++|++||.|.+        |+++.+   +.+++++|||||+|.+.++|++|++.|||.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~---~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   80 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTD---RETGKLKGEATVSFDDPPSAKAAIDWFDGK   80 (116)
Confidence            456789999999999999999999999999998        888764   233788999999999999999999999999


Q ss_pred             eeCCCCCCCCceEEEeecCCCCC
Q 030012          151 KFDDKKPDSPTLKIQFAHFPFHL  173 (184)
Q Consensus       151 ~~~g~~~~~~~l~V~~a~~~~~~  173 (184)
                      .+.|+.     |+|+|++.....
T Consensus        81 ~~~g~~-----l~V~~a~~~~~~   98 (116)
T 2lcw_A           81 EFSGNP-----IKVSFATRRADF   98 (116)
Confidence            999998     999999764433

>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=99.77  E-value=1.8e-18  Score=127.93  Aligned_cols=81  Identities=20%  Similarity=0.313  Sum_probs=73.9

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++++++|+++|++||.|.+|+++.+        ++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        69 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~--------~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~-  139 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN--------PPGFAFVEFEDPRDAADAVRELDGRTLCGCR-  139 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS--------SCSEEEEEESSHHHHHHHHHHHSSSCSSSSC-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC--------CCcEEEEEECCHHHHHHHHHHcCCCEECCeE-
Confidence            3456789999999999999999999999999999999753        4679999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCC
Q 030012          158 DSPTLKIQFAHFPF  171 (184)
Q Consensus       158 ~~~~l~V~~a~~~~  171 (184)
                          |+|+|++..+
T Consensus       140 ----l~v~~a~~~~  149 (150)
T 2i2y_A          140 ----VRVELSNGEK  149 (150)
T ss_dssp             ----CEEEECCCCC
T ss_pred             ----EEEEEcCCCC
Confidence                9999998754

>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=99.76  E-value=1.2e-18  Score=127.98  Aligned_cols=85  Identities=20%  Similarity=0.370  Sum_probs=72.9

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEE--------EEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYRE--------IRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGY  150 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~--------v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~  150 (184)
                      ..++++|||+|||+++|+++|+++|++||.|.+        +++..      +++++|||||+|.+.++|++|++.|||.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~------~g~~~g~afV~f~~~~~A~~Ai~~lng~  115 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMK------EGRMKGQAFIGLPNEKAAAKALKEANGY  115 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEE------ETTTEEEEEEECSSHHHHHHHHHHHTTB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEecc------CCCcccEEEEEeCCHHHHHHHHHHhCCC
Confidence            456789999999999999999999999999876        33332      2688999999999999999999999999


Q ss_pred             eeCCCCCCCCceEEEeecCCCCCC
Q 030012          151 KFDDKKPDSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       151 ~~~g~~~~~~~l~V~~a~~~~~~~  174 (184)
                      .+.|+.     |+|+|++....+.
T Consensus       116 ~~~g~~-----l~V~~a~~~~~~~  134 (143)
T 3egn_A          116 VLFGKP-----MVVQFARSARPKQ  134 (143)
T ss_dssp             EETTEE-----CEEEECCCSCC--
T ss_pred             EeCCcE-----EEEEECCCCCCcc
Confidence            999997     9999998754433

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=1.4e-18  Score=122.60  Aligned_cols=78  Identities=14%  Similarity=0.227  Sum_probs=70.8

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ....+|||+|||++++++||+++|+.| .|.+|+|+.+.   . |+++|||||+|.+.++|++|+ .+|+..+.|+.   
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~---~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~---   84 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH---V-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRY---   84 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT---T-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEE---
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC---C-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeE---
Confidence            445799999999999999999999999 89999998753   2 788999999999999999999 69999999997   


Q ss_pred             CceEEEeec
Q 030012          160 PTLKIQFAH  168 (184)
Q Consensus       160 ~~l~V~~a~  168 (184)
                        |.|..+.
T Consensus        85 --i~V~~a~   91 (109)
T 2dnn_A           85 --VEVSPAT   91 (109)
T ss_dssp             --EEEEECC
T ss_pred             --EEEEECC
Confidence              9998875

>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=99.76  E-value=8e-19  Score=123.02  Aligned_cols=82  Identities=15%  Similarity=0.231  Sum_probs=73.8

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCC---EEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVG---YREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDD  154 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~---i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g  154 (184)
                      .....++|||+|||+++|+++|+++|+.||.   |.+|+|+.+.   . |+++|||||+|.+.++|++|++ +|+..+.|
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~---~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~g   81 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNR---D-GKRRGDALIEMESEQDVQKALE-KHRMYMGQ   81 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCT---T-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSS
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECC---C-CCEeeEEEEEECCHHHHHHHHH-hCcceeCC
Confidence            3466789999999999999999999999988   8999998743   3 7899999999999999999999 99999999


Q ss_pred             CCCCCCceEEEeecC
Q 030012          155 KKPDSPTLKIQFAHF  169 (184)
Q Consensus       155 ~~~~~~~l~V~~a~~  169 (184)
                      +.     |+|.++..
T Consensus        82 r~-----i~V~~a~~   91 (107)
T 2lmi_A           82 RY-----VEVYEINN   91 (107)
T ss_dssp             SC-----CCCEECCH
T ss_pred             eE-----EEEEECCH
Confidence            98     99999863

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.76  E-value=6.3e-18  Score=122.69  Aligned_cols=76  Identities=21%  Similarity=0.296  Sum_probs=68.4

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceE-EEEEECCHHHHHHHHHHhcCCeeCC--CCCCC
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL-CFVEFDDPKCARTAMDALHGYKFDD--KKPDS  159 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~-afV~F~~~~~A~~Ai~~l~g~~~~g--~~~~~  159 (184)
                      -.|||+||++.+|+++|+++|++||.|.+|++..+        .+|| |||+|.+.++|++|++.|||..|.+  +.   
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~--------~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~---   97 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK--------NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCT---   97 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE--------TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEE---
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC--------CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcE---
Confidence            47889999999999999999999999999988753        2467 9999999999999999999999998  54   


Q ss_pred             CceEEEeecCCC
Q 030012          160 PTLKIQFAHFPF  171 (184)
Q Consensus       160 ~~l~V~~a~~~~  171 (184)
                        |+|+|++...
T Consensus        98 --LrI~~ak~~~  107 (130)
T 3zzy_A           98 --LRIDFSKLTS  107 (130)
T ss_dssp             --EEEEECSCSS
T ss_pred             --EEEEecCCCc
Confidence              9999998654

>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=4.3e-19  Score=130.48  Aligned_cols=86  Identities=15%  Similarity=0.186  Sum_probs=73.3

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++||+||+++|++|| |++|+|+.++   . ++++|||||+|.+.++|++|| .+|+..+.++.  
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~---~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~--  114 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP---D-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRY--  114 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSS---S-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCC--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECC---C-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEE--
Confidence            45578999999999999999999999999 7799998753   2 789999999999999999999 78999999998  


Q ss_pred             CCceEEEeecCCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~~  175 (184)
                         |+|.++.......+
T Consensus       115 ---i~V~~a~~~~~~~~  128 (139)
T 2hgn_A          115 ---IELFLNSTTGASNG  128 (139)
T ss_dssp             ---CCCEECCCSCC---
T ss_pred             ---EEEEECCCCCCCCC
Confidence               99999876554433

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.75  E-value=5.2e-18  Score=132.23  Aligned_cols=84  Identities=23%  Similarity=0.290  Sum_probs=74.7

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ..+.++|||+|||+++||++|+++|++||.|++|+|+.+   +.+++++|||||+|.+.++|++|++.+++..+.|+.  
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d---~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~--   86 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRD---MITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKP--   86 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---TTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE--
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecc---cCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcc--
Confidence            345689999999999999999999999999999999984   334789999999999999999999999999999997  


Q ss_pred             CCceEEEeecCC
Q 030012          159 SPTLKIQFAHFP  170 (184)
Q Consensus       159 ~~~l~V~~a~~~  170 (184)
                         |++.++...
T Consensus        87 ---i~~~~~~~~   95 (213)
T 4f02_A           87 ---VRIMWSQRD   95 (213)
T ss_dssp             ---CEEEECCCC
T ss_pred             ---ccccccccc
Confidence               999998653

>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=99.75  E-value=4.8e-18  Score=120.65  Aligned_cols=80  Identities=18%  Similarity=0.202  Sum_probs=67.5

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ...++|||+|||+++++++|+++|++||.|.+|+|+.+          |||||+|.+.++|++||+.|||.+|.|+....
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~----------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~   83 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD----------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGET   83 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT----------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC----------CEEEEEECCHHHHHHHHHHhCCCEECCcEeee
Confidence            45789999999999999999999999999999998642          69999999999999999999999999986333


Q ss_pred             CceEEEeecC
Q 030012          160 PTLKIQFAHF  169 (184)
Q Consensus       160 ~~l~V~~a~~  169 (184)
                      .-|+|..++.
T Consensus        84 ~~i~v~~~~~   93 (115)
T 3beg_B           84 AYIRVKVDGP   93 (115)
T ss_dssp             CBCEEEECC-
T ss_pred             EEEEeccCCC
Confidence            4467777654

>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=99.75  E-value=4.8e-19  Score=115.91  Aligned_cols=75  Identities=20%  Similarity=0.360  Sum_probs=68.1

Q ss_pred             EEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceE
Q 030012           84 LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLK  163 (184)
Q Consensus        84 ~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~  163 (184)
                      +|||+|||+++++++|+++|++||.|.+++++.+   +.+++++|||||+|.+.++|++|++ +++..+.|+.     |+
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~---~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~-----l~   71 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMD---NKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSK-----CE   71 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCS---CCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBC-----CC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEec---CCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEE-----EE
Confidence            6899999999999999999999999999998764   3347889999999999999999998 4999999998     99


Q ss_pred             EEee
Q 030012          164 IQFA  167 (184)
Q Consensus       164 V~~a  167 (184)
                      |++|
T Consensus        72 v~~a   75 (75)
T 1iqt_A           72 IKVA   75 (75)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            9885

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.75  E-value=3.3e-18  Score=130.44  Aligned_cols=84  Identities=20%  Similarity=0.261  Sum_probs=76.6

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ....+++|||+|||+++++++|+++|++||.|++|+|+.+.    .++++|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~----~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~-  158 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR----SGRSLGTADVHFERRADALKAMKQYKGVPLDGRP-  158 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT----TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSB-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC----CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEE-
Confidence            34567899999999999999999999999999999998753    3788999999999999999999999999999997 


Q ss_pred             CCCceEEEeecCC
Q 030012          158 DSPTLKIQFAHFP  170 (184)
Q Consensus       158 ~~~~l~V~~a~~~  170 (184)
                          |+|+|+...
T Consensus       159 ----l~V~~a~~~  167 (177)
T 2f3j_A          159 ----MDIQLVASQ  167 (177)
T ss_dssp             ----CEEEEESSG
T ss_pred             ----EEEEEecCC
Confidence                999999753

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.75  E-value=3.7e-18  Score=115.40  Aligned_cols=76  Identities=26%  Similarity=0.392  Sum_probs=69.6

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ..+++|||+|||+++++++|+++|++| .|.++++.         +++|||||+|.+.++|++|++.|||..+.|+.   
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~---------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~---   69 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD---------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKD---   69 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE---------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEE---
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe---------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcE---
Confidence            346899999999999999999999999 99999883         45789999999999999999999999999997   


Q ss_pred             CceEEEeecCC
Q 030012          160 PTLKIQFAHFP  170 (184)
Q Consensus       160 ~~l~V~~a~~~  170 (184)
                        |+|+|+...
T Consensus        70 --l~V~~a~~~   78 (88)
T 1wg1_A           70 --LIVQLQPTD   78 (88)
T ss_dssp             --EEEEECCCC
T ss_pred             --EEEEEcCCC
Confidence              999999653

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.74  E-value=2.3e-17  Score=122.18  Aligned_cols=82  Identities=23%  Similarity=0.397  Sum_probs=75.5

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||.++++++|+++|++||.|.+++++.+.   .+++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        84 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~---~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~--  158 (166)
T 3md3_A           84 SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDM---QTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRP--  158 (166)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECT---TTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEE--
T ss_pred             CCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecC---CCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcE--
Confidence            4567899999999999999999999999999999998753   33789999999999999999999999999999997  


Q ss_pred             CCceEEEeec
Q 030012          159 SPTLKIQFAH  168 (184)
Q Consensus       159 ~~~l~V~~a~  168 (184)
                         |+|+||+
T Consensus       159 ---i~v~~a~  165 (166)
T 3md3_A          159 ---LRINWAA  165 (166)
T ss_dssp             ---CEEEESC
T ss_pred             ---EEEEecC
Confidence               9999986

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.74  E-value=1.6e-18  Score=120.13  Aligned_cols=80  Identities=23%  Similarity=0.323  Sum_probs=73.2

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ...+++|||+|||+++++++|+++|++||.|.+|+++.+.    .++++|||||+|.+.++|++|++  ++..+.|+.  
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~----~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~--   77 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR----TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKK--   77 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT----TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEE--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC----CCCccceEEEEECCHHHHHHHHh--CCCeECCEE--
Confidence            4456899999999999999999999999999999999853    37899999999999999999998  999999997  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |.|.++..
T Consensus        78 ---l~v~~a~~   85 (102)
T 2xs2_A           78 ---LKLGPAIR   85 (102)
T ss_dssp             ---CEEEEEEE
T ss_pred             ---EEEEECCc
Confidence               99999864

>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=99.74  E-value=1.7e-17  Score=123.00  Aligned_cols=82  Identities=24%  Similarity=0.435  Sum_probs=75.2

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCc
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPT  161 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~  161 (184)
                      +++|||+|||+++++++|+++|+.||.|.+++++.+.   ..++++|||||+|.+.++|++|++.|+|..+.|+.     
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~---~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~-----   73 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDK---ITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKT-----   73 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE-----
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC---CCCcceeEEEEEECCHHHHHHHHHHcCCCccCCce-----
Confidence            5899999999999999999999999999999998853   23789999999999999999999999999999997     


Q ss_pred             eEEEeecCCC
Q 030012          162 LKIQFAHFPF  171 (184)
Q Consensus       162 l~V~~a~~~~  171 (184)
                      |+|.|++...
T Consensus        74 l~v~~~~~~~   83 (167)
T 1fxl_A           74 IKVSYARPSS   83 (167)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEecCCCc
Confidence            9999997543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.74  E-value=3.4e-17  Score=118.06  Aligned_cols=80  Identities=25%  Similarity=0.307  Sum_probs=68.3

Q ss_pred             CCCC--EEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceE-EEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           80 GESN--LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL-CFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        80 ~~~~--~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~-afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      .+++  .|||+||++.+++++|+++|++||.|.+|++...         .|| |||+|.+.++|+.|++.|||..|.|+ 
T Consensus        21 ~ps~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~---------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~-   90 (124)
T 2e5i_A           21 GGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR---------NGIQAMVEFESVLCAQKAKAALNGADIYAG-   90 (124)
T ss_dssp             CCCSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES---------SSEEEEEEESSHHHHHHHHHHHTTCCCBTT-
T ss_pred             CCCcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC---------CCCEEEEEECCHHHHHHHHHHhCCCEecCC-
Confidence            3444  4689999999999999999999999999998641         166 99999999999999999999999883 


Q ss_pred             CCCCceEEEeecCCC
Q 030012          157 PDSPTLKIQFAHFPF  171 (184)
Q Consensus       157 ~~~~~l~V~~a~~~~  171 (184)
                        .++|+|+||+...
T Consensus        91 --~~~l~V~~Ak~~~  103 (124)
T 2e5i_A           91 --CCTLKIEYARPTR  103 (124)
T ss_dssp             --BSEEEEECCSCSC
T ss_pred             --CeEEEEEEecCCc
Confidence              1249999998654

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.74  E-value=2.4e-17  Score=127.45  Aligned_cols=86  Identities=14%  Similarity=0.289  Sum_probs=77.7

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ...++|||+|||.++++++|+++|++||.|.+++++.+.   .+++++|||||+|.+.++|++|++.|||..|.|+.   
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~---~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~---  196 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDP---TTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQY---  196 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSB---
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecC---CCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcE---
Confidence            456899999999999999999999999999999998853   23789999999999999999999999999999997   


Q ss_pred             CceEEEeecCCCCC
Q 030012          160 PTLKIQFAHFPFHL  173 (184)
Q Consensus       160 ~~l~V~~a~~~~~~  173 (184)
                        |+|.|++.+...
T Consensus       197 --i~V~~a~~~~~~  208 (216)
T 2qfj_A          197 --LRVGKAVTPPMP  208 (216)
T ss_dssp             --CEEEECSSCSST
T ss_pred             --EEEEEecCCCCC
Confidence              999999876433

>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=99.74  E-value=1.1e-17  Score=124.34  Aligned_cols=84  Identities=26%  Similarity=0.381  Sum_probs=76.1

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ++++|||+|||+++++++|+++|++||.|.+++++.+.   .+++++|||||+|.+.++|++|++.|+|..+.|+.    
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~----   74 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDY---KTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKR----   74 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEET---TTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEE----
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeC---CCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcE----
Confidence            46899999999999999999999999999999998753   23789999999999999999999999999999997    


Q ss_pred             ceEEEeecCCCC
Q 030012          161 TLKIQFAHFPFH  172 (184)
Q Consensus       161 ~l~V~~a~~~~~  172 (184)
                       |+|.|++....
T Consensus        75 -l~v~~~~~~~~   85 (168)
T 1b7f_A           75 -LKVSYARPGGE   85 (168)
T ss_dssp             -CEEEECCCCSS
T ss_pred             -EEEEecCCCcc
Confidence             99999976543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=1.5e-17  Score=113.88  Aligned_cols=80  Identities=16%  Similarity=0.275  Sum_probs=70.2

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEE-EeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIR-VIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~-l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ...+++|||+|||+++++++|+++|++||.|.+|+ ++.+.       ..|.|||+|.+.++|++|++.|||..+.|+. 
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~-------~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~-   83 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS-------ETAVVNVTYSSKDQARQALDKLNGFQLENFT-   83 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSS-------SSEEEEEEESSHHHHHHHHHHHTTCBCSSCB-
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCC-------CCCEEEEEECCHHHHHHHHHHhCCCEECCcE-
Confidence            34578999999999999999999999999999995 65531       2235999999999999999999999999997 


Q ss_pred             CCCceEEEeecCC
Q 030012          158 DSPTLKIQFAHFP  170 (184)
Q Consensus       158 ~~~~l~V~~a~~~  170 (184)
                          |+|+|++..
T Consensus        84 ----l~V~~a~~~   92 (96)
T 2e44_A           84 ----LKVAYIPDE   92 (96)
T ss_dssp             ----CEEEECCCC
T ss_pred             ----EEEEEcCcc
Confidence                999999764

>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=99.73  E-value=8.2e-18  Score=119.49  Aligned_cols=77  Identities=16%  Similarity=0.199  Sum_probs=67.9

Q ss_pred             CCCCCEEEE--cCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCee----
Q 030012           79 KGESNLLFV--DGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKF----  152 (184)
Q Consensus        79 ~~~~~~lfV--gnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~----  152 (184)
                      ..++++|||  +||++++++++|+++|++||.|.+|.+..         .||||||+|.+.++|++|++.|||.++    
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~---------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~l   92 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP---------NKPYSFARYRTTEESKRAYVTLNGKEVVDDL   92 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT---------TCSCEEEEESSHHHHHHHHHHTTTCEEECTT
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC---------CCCEEEEEECCHHHHHHHHHHhCCCEEcccc
Confidence            456789999  78999999999999999999999988752         257999999999999999999999988    


Q ss_pred             -CCCCCCCCceEEEeecC
Q 030012          153 -DDKKPDSPTLKIQFAHF  169 (184)
Q Consensus       153 -~g~~~~~~~l~V~~a~~  169 (184)
                       .++     +|.|.|++.
T Consensus        93 g~g~-----~l~v~~a~~  105 (114)
T 2cq2_A           93 GQKI-----TLYLNFVEK  105 (114)
T ss_dssp             SCEE-----ECEEEEESC
T ss_pred             CCCc-----EEEEEeccc
Confidence             444     499999975

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.73  E-value=4.2e-17  Score=124.49  Aligned_cols=86  Identities=23%  Similarity=0.380  Sum_probs=78.0

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||.++++++|+++|++||.|.++++..+.   ..++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus       111 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~--  185 (198)
T 2yh0_A          111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS---ATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK--  185 (198)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECT---TTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEE--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecC---CCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEE--
Confidence            3567899999999999999999999999999999998753   23789999999999999999999999999999997  


Q ss_pred             CCceEEEeecCCCC
Q 030012          159 SPTLKIQFAHFPFH  172 (184)
Q Consensus       159 ~~~l~V~~a~~~~~  172 (184)
                         |+|+|++...+
T Consensus       186 ---l~v~~a~~~~~  196 (198)
T 2yh0_A          186 ---LLVQRASVGAK  196 (198)
T ss_dssp             ---CEEEESCCCCC
T ss_pred             ---EEEEECCCCCC
Confidence               99999987554

>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=99.73  E-value=2.4e-17  Score=141.72  Aligned_cols=83  Identities=16%  Similarity=0.298  Sum_probs=76.0

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ..+.++|||+|||+.+|+++|+++|++||.|+.|.|+.+   +.+++++|||||+|.+.++|++||+.|||..|.|+.  
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d---~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~--  173 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYS---KRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRR--  173 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeecc---CCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEE--
Confidence            355689999999999999999999999999999999874   234789999999999999999999999999999997  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |+|.|++.
T Consensus       174 ---i~V~~a~~  181 (437)
T 3pgw_S          174 ---VLVDVERG  181 (437)
T ss_pred             ---EEEEEeCC
Confidence               99999975

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=4.3e-18  Score=122.63  Aligned_cols=79  Identities=19%  Similarity=0.233  Sum_probs=70.4

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCE----EEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGY----REIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDK  155 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i----~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~  155 (184)
                      ....+|||+|||+++|++||+++|++||.|    .+|+|+.++    +|+++|||||+|.+.++|++|++. |+..+.++
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~----~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR   95 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP----DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKR   95 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT----TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC----CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCe
Confidence            457899999999999999999999999875    688888753    278999999999999999999986 99999998


Q ss_pred             CCCCCceEEEeec
Q 030012          156 KPDSPTLKIQFAH  168 (184)
Q Consensus       156 ~~~~~~l~V~~a~  168 (184)
                      .     |+|..+.
T Consensus        96 ~-----i~V~~a~  103 (123)
T 2dha_A           96 Y-----IELFRST  103 (123)
T ss_dssp             E-----ECCEEEC
T ss_pred             E-----EEEEECC
Confidence            7     9988874

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.72  E-value=2.6e-17  Score=128.16  Aligned_cols=77  Identities=18%  Similarity=0.268  Sum_probs=70.9

Q ss_pred             CCCEEEEcCCC-CCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           81 ESNLLFVDGLP-TDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        81 ~~~~lfVgnLp-~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ++++|||+||| +.+++++|+++|++||.|.+|+++.+        .+|||||+|.+.++|++|++.|||..+.|+.   
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~--------~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~---   71 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS--------KPGAAMVEMADGYAVDRAITHLNNNFMFGQK---   71 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT--------STTCEEEEESSHHHHHHHHHHHTTCEETTEE---
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC--------CCCEEEEEECCHHHHHHHHHHhCCCEECCce---
Confidence            57899999999 89999999999999999999999752        3579999999999999999999999999997   


Q ss_pred             CceEEEeecCC
Q 030012          160 PTLKIQFAHFP  170 (184)
Q Consensus       160 ~~l~V~~a~~~  170 (184)
                        |+|.|++..
T Consensus        72 --l~v~~s~~~   80 (205)
T 3tyt_A           72 --MNVCVSKQP   80 (205)
T ss_dssp             --CEEEECSCS
T ss_pred             --EEEEEccCC
Confidence              999999753

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=2.9e-17  Score=112.22  Aligned_cols=78  Identities=17%  Similarity=0.276  Sum_probs=67.3

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ...++|||+|||+++++++|+++|++||.|.+| +...    ..++   ||||+|.+.++|++|++ |||..+.|+.   
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v-~~~~----~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~---   73 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV-VMDK----DKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHR---   73 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE-EECS----SSCC---EEEEEESSHHHHHHHHT-CSCCEETTEE---
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE-EEcC----CCCc---EEEEEECCHHHHHHHHh-cCCeEECCEE---
Confidence            456799999999999999999999999999998 3322    1233   99999999999999999 9999999997   


Q ss_pred             CceEEEeecCCC
Q 030012          160 PTLKIQFAHFPF  171 (184)
Q Consensus       160 ~~l~V~~a~~~~  171 (184)
                        |+|+++....
T Consensus        74 --l~V~~a~~~~   83 (94)
T 2e5g_A           74 --LRVRPREQKE   83 (94)
T ss_dssp             --CCCBCSCCSC
T ss_pred             --EEEEECCcCC
Confidence              9999986533

>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=99.72  E-value=1e-17  Score=121.07  Aligned_cols=79  Identities=18%  Similarity=0.340  Sum_probs=69.8

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEE--EEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYR--EIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~--~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      ....++|||+|||+++|+++|+++|++| .|+  +|+|+.+.   . |+++|||||+|.+.++|++|++ +++..+.|+.
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~---~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~  112 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDP---E-GKITGEAFVQFASQELAEKALG-KHKERIGHRY  112 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCS---S-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECC---C-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEE
Confidence            3456899999999999999999999999 787  89888743   3 7899999999999999999998 4789999997


Q ss_pred             CCCCceEEEeec
Q 030012          157 PDSPTLKIQFAH  168 (184)
Q Consensus       157 ~~~~~l~V~~a~  168 (184)
                           |+|.++.
T Consensus       113 -----I~V~~a~  119 (126)
T 2hgm_A          113 -----IEVFKSS  119 (126)
T ss_dssp             -----CCCEEEC
T ss_pred             -----EEEEECC
Confidence                 9998874

>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=2.6e-17  Score=128.22  Aligned_cols=79  Identities=18%  Similarity=0.326  Sum_probs=73.1

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ..++|||+|||+++++++|+++|++||.|.+|+|+.++     +.++|||||+|.+.++|++|++.|||..|.|+.    
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~-----~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~----  172 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-----NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRK----  172 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-----TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEE----
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC-----CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEE----
Confidence            45799999999999999999999999999999998753     357999999999999999999999999999997    


Q ss_pred             ceEEEeecC
Q 030012          161 TLKIQFAHF  169 (184)
Q Consensus       161 ~l~V~~a~~  169 (184)
                       |+|.|++.
T Consensus       173 -i~V~~a~~  180 (213)
T 4f02_A          173 -VFVGRFKS  180 (213)
T ss_dssp             -CEEEECCC
T ss_pred             -EEEEEcCC
Confidence             99999964

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.72  E-value=2.8e-17  Score=121.68  Aligned_cols=81  Identities=20%  Similarity=0.357  Sum_probs=73.6

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      ++|||+|||.++|+++|+++|++||.|.+++++.+..    ++++|||||+|.+.++|++|++.|+|..+.|+.     |
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~-----i   71 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN----NKNVNYAFVEYHQSHDANIALQTLNGKQIENNI-----V   71 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-----CCEEEEEEEESSHHHHHHHHHHHTTCEETTEE-----C
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC----CCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCe-----e
Confidence            5899999999999999999999999999999987543    578999999999999999999999999999997     9


Q ss_pred             EEEeecCCCC
Q 030012          163 KIQFAHFPFH  172 (184)
Q Consensus       163 ~V~~a~~~~~  172 (184)
                      +|.|+.....
T Consensus        72 ~v~~~~~~~~   81 (166)
T 3md3_A           72 KINWAFQSQQ   81 (166)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEcCCCCC
Confidence            9999976543

>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=99.71  E-value=2.7e-17  Score=122.98  Aligned_cols=84  Identities=24%  Similarity=0.384  Sum_probs=72.8

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||..+|+++|+++|++||.|.++++..+..    ++++|||||+|.+.++|++|++.|||..+.+..  
T Consensus        92 ~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~----g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~--  165 (175)
T 3nmr_A           92 AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD----GLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGC--  165 (175)
T ss_dssp             CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT----SCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTC--
T ss_pred             cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCC----CCEEEEEEEEECCHHHHHHHHHHhcCCcccCCC--
Confidence            34678999999999999999999999999999999988532    789999999999999999999999998887510  


Q ss_pred             CCceEEEeec
Q 030012          159 SPTLKIQFAH  168 (184)
Q Consensus       159 ~~~l~V~~a~  168 (184)
                      ..+|+|.||.
T Consensus       166 ~~~l~V~~ad  175 (175)
T 3nmr_A          166 SSPMVVKFAD  175 (175)
T ss_dssp             SSCCEEEECC
T ss_pred             CCCeEEEecC
Confidence            1149999983

>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=99.71  E-value=5.6e-17  Score=130.79  Aligned_cols=82  Identities=22%  Similarity=0.395  Sum_probs=74.6

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHH----HhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVS----HLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDD  154 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~----~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g  154 (184)
                      ..++++|||+|||+++++++|+    ++|++||.|.+|++.+      .++++|||||+|.+.++|++|++.|||..+.|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~------~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   79 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR------SLKMRGQAFVIFKEVSSATNALRSMQGFPFYD   79 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC------CCCcceEEEEEECCHHHHHHHHHHhcCCeeCC
Confidence            4668999999999999999977    8999999999999865      26789999999999999999999999999999


Q ss_pred             CCCCCCceEEEeecCCC
Q 030012          155 KKPDSPTLKIQFAHFPF  171 (184)
Q Consensus       155 ~~~~~~~l~V~~a~~~~  171 (184)
                      +.     |+|+|++...
T Consensus        80 ~~-----l~v~~a~~~~   91 (282)
T 3pgw_A           80 KP-----MRIQYAKTDS   91 (282)
T ss_pred             cE-----EEEEEeccCc
Confidence            97     9999997644

>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=99.71  E-value=4.6e-17  Score=121.61  Aligned_cols=81  Identities=25%  Similarity=0.408  Sum_probs=74.4

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ...++|||+|||.++++++|+++|++||.|.++++..+.   ..++++|||||+|.+.++|++|++.|||..+.|+.   
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~---~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~---  165 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS---ATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK---  165 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECT---TTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEE---
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecC---CCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeE---
Confidence            447899999999999999999999999999999998853   23789999999999999999999999999999997   


Q ss_pred             CceEEEeec
Q 030012          160 PTLKIQFAH  168 (184)
Q Consensus       160 ~~l~V~~a~  168 (184)
                        |+|+||.
T Consensus       166 --l~V~~As  172 (172)
T 2g4b_A          166 --LLVQRAS  172 (172)
T ss_dssp             --CEEEECC
T ss_pred             --EEEEeCC
Confidence              9999973

>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=99.71  E-value=2.9e-17  Score=111.54  Aligned_cols=76  Identities=21%  Similarity=0.277  Sum_probs=61.1

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeC--CC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFD--DK  155 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~--g~  155 (184)
                      .....++|||+|||+++||++|+++|++||.|.+|+++.        .++|||||+|.+.++|++    +++..+.  ++
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~--------~srGfaFV~F~~~~~A~~----~~~~~~~~~g~   74 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK--------PFRAFAFVTFADDKVAQS----LCGEDLIIKGI   74 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCS--------SCCSEEEEEESCHHHHHH----HTTCEEEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEee--------CCCCEEEEEECCHHHHHH----HcCCCcccCCE
Confidence            346678999999999999999999999999999999875        257899999999999983    5666554  66


Q ss_pred             CCCCCceEEEeecCC
Q 030012          156 KPDSPTLKIQFAHFP  170 (184)
Q Consensus       156 ~~~~~~l~V~~a~~~  170 (184)
                      .     |.|.+++..
T Consensus        75 ~-----v~v~~a~~k   84 (89)
T 3d2w_A           75 S-----VHISNAEPK   84 (89)
T ss_dssp             E-----EEEEECC--
T ss_pred             E-----EEEEEcCCC
Confidence            5     889988753

>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=99.71  E-value=1.6e-16  Score=118.16  Aligned_cols=81  Identities=19%  Similarity=0.340  Sum_probs=73.3

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCC--CC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDD--KK  156 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g--~~  156 (184)
                      ....++|||+|||..+++++|+++|++||.|.++++..+.   ..++++|||||+|.+.++|++|++.|||..+.|  +.
T Consensus        86 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~---~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~  162 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK---LTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQP  162 (168)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSC
T ss_pred             cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcC---CCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeE
Confidence            3457899999999999999999999999999999998853   237889999999999999999999999999988  65


Q ss_pred             CCCCceEEEee
Q 030012          157 PDSPTLKIQFA  167 (184)
Q Consensus       157 ~~~~~l~V~~a  167 (184)
                           |+|.||
T Consensus       163 -----l~V~~A  168 (168)
T 1b7f_A          163 -----LSVRLA  168 (168)
T ss_dssp             -----CEEEEC
T ss_pred             -----EEEEeC
Confidence                 999986

>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=99.70  E-value=6.4e-17  Score=123.25  Aligned_cols=84  Identities=14%  Similarity=0.221  Sum_probs=72.7

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ...++|||+|||+++++++|+++|++||.|.+|+++.+.   .+++++|||||+|.+.++|++|++. +|..+.|+.   
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~---  174 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR---GSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHN---  174 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEE---
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecC---CCCCccceEEEEECCHHHHHHHHHh-CCcEECCEE---
Confidence            456899999999999999999999999999999998853   3378999999999999999999986 899999997   


Q ss_pred             CceEEEeecCCCC
Q 030012          160 PTLKIQFAHFPFH  172 (184)
Q Consensus       160 ~~l~V~~a~~~~~  172 (184)
                        |.|.|+.....
T Consensus       175 --i~v~~a~~k~~  185 (196)
T 1l3k_A          175 --CEVRKALSKQE  185 (196)
T ss_dssp             --CEEEECC----
T ss_pred             --EEEEecCChhH
Confidence              99999976443

>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=99.70  E-value=4.8e-17  Score=123.98  Aligned_cols=84  Identities=19%  Similarity=0.249  Sum_probs=74.8

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||+++|+++|+++|+.||.|.+|+++.+   +.+++++|||||+|.+.++|++|++. ++..+.|+. 
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~---~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~-   83 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRD---PNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRV-   83 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---TTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEE-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEc---CCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEE-
Confidence            3456789999999999999999999999999999999884   33478999999999999999999975 999999997 


Q ss_pred             CCCceEEEeecCC
Q 030012          158 DSPTLKIQFAHFP  170 (184)
Q Consensus       158 ~~~~l~V~~a~~~  170 (184)
                          |.|.++...
T Consensus        84 ----l~v~~~~~~   92 (196)
T 1l3k_A           84 ----VEPKRAVSR   92 (196)
T ss_dssp             ----CEEEECCC-
T ss_pred             ----eeeecccCc
Confidence                999998653

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=6e-17  Score=110.64  Aligned_cols=74  Identities=14%  Similarity=0.164  Sum_probs=65.2

Q ss_pred             CCCCE-EEEcCCCCCCcHHH----HHHhhcCC-CCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeC
Q 030012           80 GESNL-LFVDGLPTDCTRRE----VSHLFRPF-VGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFD  153 (184)
Q Consensus        80 ~~~~~-lfVgnLp~~~te~~----L~~~F~~~-G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~  153 (184)
                      .++.+ |||+|||+.+++++    |+++|++| |.|.+|   .       +   |+|||+|.+.++|++|++.|||+.+.
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V---t-------g---G~AfV~F~~~esA~~A~~~l~G~~l~   72 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI---T-------G---CSAILRFINQDSAERAQKRMENEDVF   72 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC---C-------T---TCEEEEESSHHHHHHHHHHHTTCCSS
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE---e-------c---CEEEEEECCHHHHHHHHHHhcCCccC
Confidence            34666 99999999999988    55899999 599987   1       2   79999999999999999999999999


Q ss_pred             CCCCCCCceEEEeecCCC
Q 030012          154 DKKPDSPTLKIQFAHFPF  171 (184)
Q Consensus       154 g~~~~~~~l~V~~a~~~~  171 (184)
                      |+.     |+|+||+..+
T Consensus        73 gr~-----i~v~~A~~~s   85 (96)
T 2diu_A           73 GNR-----IIVSFTPKNR   85 (96)
T ss_dssp             SSC-----CEEESSCCSC
T ss_pred             Cce-----EEEEecCCCc
Confidence            997     9999998644

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=2.4e-17  Score=116.70  Aligned_cols=67  Identities=25%  Similarity=0.364  Sum_probs=58.3

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHh
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDAL  147 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l  147 (184)
                      ...++|||+|||+++++++|+++|++||.|. +.++.+...+..|+++|||||+|.+.++|++|++.|
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~   72 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDAC   72 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHS
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhh
Confidence            4578999999999999999999999999999 777664332222688999999999999999999998

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.70  E-value=1.9e-17  Score=119.30  Aligned_cols=80  Identities=9%  Similarity=0.135  Sum_probs=70.6

Q ss_pred             CEEEEcCC----CCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECC----HHH----HHHHHH--Hhc
Q 030012           83 NLLFVDGL----PTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDD----PKC----ARTAMD--ALH  148 (184)
Q Consensus        83 ~~lfVgnL----p~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~----~~~----A~~Ai~--~l~  148 (184)
                      .+|||+||    |+.+++++|+++|+.||+|.+|+++.+   +.+|+++|||||+|.+    .++    |.+|++  .|+
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~D---p~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~ln   79 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFND---PNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESS   79 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEEC---TTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTT
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEec---CCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhc
Confidence            68999999    999999999999999999999999984   5568999999999996    333    788888  789


Q ss_pred             CCeeCCCCCCCCceEEEeecCC
Q 030012          149 GYKFDDKKPDSPTLKIQFAHFP  170 (184)
Q Consensus       149 g~~~~g~~~~~~~l~V~~a~~~  170 (184)
                      |..|+|+.     |+|.+.++.
T Consensus        80 g~~I~Gr~-----irV~ln~~g   96 (136)
T 2j8a_A           80 GCFIMGFK-----FEVILNKHS   96 (136)
T ss_dssp             CEEETTEE-----EEEEECCTT
T ss_pred             CCeecCcE-----EEEEECccc
Confidence            99999998     999998764

>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=99.69  E-value=2.7e-17  Score=110.36  Aligned_cols=72  Identities=24%  Similarity=0.389  Sum_probs=65.5

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCC----C-------CEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhc
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPF----V-------GYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALH  148 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~----G-------~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~  148 (184)
                      ...++|||+|||+++++++|+++|++|    |       .|.++++..         ++|||||+|.+.++|++|+ .||
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~---------~kg~afV~f~~~~~a~~A~-~l~   73 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ---------DKNFAFLEFRSVDETTQAM-AFD   73 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECS---------SSSEEEEEESSHHHHHHHG-GGT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecC---------CCcEEEEEcCCHHHHHHHH-hcC
Confidence            457899999999999999999999999    8       899998853         3679999999999999999 999


Q ss_pred             CCeeCCCCCCCCceEEEe
Q 030012          149 GYKFDDKKPDSPTLKIQF  166 (184)
Q Consensus       149 g~~~~g~~~~~~~l~V~~  166 (184)
                      |..+.|+.     |+|+.
T Consensus        74 g~~~~g~~-----l~V~r   86 (87)
T 2hzc_A           74 GIIFQGQS-----LKIRR   86 (87)
T ss_dssp             TCEETTEE-----CEEEC
T ss_pred             CCEECCeE-----EEEeC
Confidence            99999997     88874

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=2e-17  Score=111.62  Aligned_cols=80  Identities=18%  Similarity=0.214  Sum_probs=64.4

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ..+++|||+|||+++++++|+++|++||.|.+|+++.+        ++|||||+|.+.++|++++..  ...+.++.   
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~--------~~g~afV~f~~~~~a~~~~~~--~~~~~g~~---   69 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP--------FRAFAFVTFADDQIAQSLCGE--DLIIKGIS---   69 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS--------CCSCCEEECSCHHHHHHTTTC--EEEETTEE---
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC--------CCCEEEEEECCHHHHHHHhcC--CceeCCEE---
Confidence            45789999999999999999999999999999998742        568999999999999754221  23447766   


Q ss_pred             CceEEEeecCCCCCC
Q 030012          160 PTLKIQFAHFPFHLP  174 (184)
Q Consensus       160 ~~l~V~~a~~~~~~~  174 (184)
                        |+|.|++......
T Consensus        70 --l~v~~a~~~~~~~   82 (88)
T 1wf0_A           70 --VHISNAEPKHNSN   82 (88)
T ss_dssp             --EEEECCCCCCCCC
T ss_pred             --EEEEecCCCCCCC
Confidence              9999987654433

>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=99.69  E-value=2e-16  Score=117.11  Aligned_cols=82  Identities=24%  Similarity=0.402  Sum_probs=73.5

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ...++|||+|||..+++++|+++|++||.|.++++..+.   .+++++|||||+|.+.++|++|++.|||..+.|+.   
T Consensus        86 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~---~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~---  159 (167)
T 1fxl_A           86 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ---VTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGAT---  159 (167)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCS---
T ss_pred             CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecC---CCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCc---
Confidence            456899999999999999999999999999999998753   23788999999999999999999999999999973   


Q ss_pred             CceEEEee
Q 030012          160 PTLKIQFA  167 (184)
Q Consensus       160 ~~l~V~~a  167 (184)
                      .+|+|+||
T Consensus       160 ~~i~v~~A  167 (167)
T 1fxl_A          160 EPITVKFA  167 (167)
T ss_dssp             SCCEEEEC
T ss_pred             cceEEEeC
Confidence            35899886

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.69  E-value=1.8e-16  Score=118.37  Aligned_cols=88  Identities=23%  Similarity=0.356  Sum_probs=73.9

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      .+++|||+|||+++|+++|+++|++||.|.+|+++.+..... ++++|||||+|.+.++|++|++.|+|..+.+..  ..
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~-~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~--~~   78 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNP-PQSKGCCFVTFYTRKAALEAQNALHNMKVLPGM--HH   78 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSS-CEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTC--SS
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCC-CCcceEEEEEECCHHHHHHHHHHhcCcEEccCC--cc
Confidence            467999999999999999999999999999999988543210 278999999999999999999999998887443  34


Q ss_pred             ceEEEeecCCC
Q 030012          161 TLKIQFAHFPF  171 (184)
Q Consensus       161 ~l~V~~a~~~~  171 (184)
                      ++.+.++....
T Consensus        79 ~~~~~~~~~~~   89 (175)
T 3nmr_A           79 PIQMKPADSEK   89 (175)
T ss_dssp             CCEEEECGGGC
T ss_pred             ceEEccccccc
Confidence            58888886544

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.69  E-value=1.3e-16  Score=123.39  Aligned_cols=83  Identities=14%  Similarity=0.280  Sum_probs=73.0

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ...++|||+|||.++|+++|+++|++||.|.+|+++.+.   .+++++|||||+|.+.++|++|++.|||..+.|+.   
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~---   99 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDS---VTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRN---   99 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC----CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CC---
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecC---CCCccCceEEEEeCCHHHHHHHHHHccCCeeCCee---
Confidence            346899999999999999999999999999999998743   23788999999999999999999999999999998   


Q ss_pred             CceEEEeecCC
Q 030012          160 PTLKIQFAHFP  170 (184)
Q Consensus       160 ~~l~V~~a~~~  170 (184)
                        |+|.++...
T Consensus       100 --l~v~~~~~~  108 (216)
T 2qfj_A          100 --IKVGRPSNI  108 (216)
T ss_dssp             --CEEECCSCC
T ss_pred             --EEEecCCCc
Confidence              999988654

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.69  E-value=1.6e-15  Score=122.23  Aligned_cols=77  Identities=36%  Similarity=0.673  Sum_probs=70.5

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeC-CCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFD-DKKP  157 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~-g~~~  157 (184)
                      ...+++|||+|||.++++++|+++|++||.|.+|+++.+   +     +|||||+|.+.++|++|++.|||..+. |+. 
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~---~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~-  274 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG---R-----HDIAFVEFDNEVQAGAARDALQGFKITQNNA-  274 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecC---C-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCE-
Confidence            456789999999999999999999999999999999852   1     469999999999999999999999999 887 


Q ss_pred             CCCceEEEeec
Q 030012          158 DSPTLKIQFAH  168 (184)
Q Consensus       158 ~~~~l~V~~a~  168 (184)
                          |+|+|++
T Consensus       275 ----l~v~~ak  281 (282)
T 3pgw_A          275 ----MKISFAK  281 (282)
T ss_pred             ----EEEEEec
Confidence                9999996

>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=5.4e-17  Score=120.71  Aligned_cols=80  Identities=18%  Similarity=0.330  Sum_probs=73.0

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ..++|||+|||.++++++|+++|++||.|.+++++.+.   .+++++|||||+|.+.++|++|++ ++|..+.|+.    
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~---~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~----  157 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK---DTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRK----  157 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSS---SSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSC----
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcC---CCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeE----
Confidence            46799999999999999999999999999999998743   237899999999999999999998 8999999998    


Q ss_pred             ceEEEeecC
Q 030012          161 TLKIQFAHF  169 (184)
Q Consensus       161 ~l~V~~a~~  169 (184)
                       |+|.|+.+
T Consensus       158 -i~V~~a~p  165 (167)
T 2cjk_A          158 -IEIKRAEP  165 (167)
T ss_dssp             -EEEEECCC
T ss_pred             -EEEeecCC
Confidence             99999964

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.68  E-value=1.2e-16  Score=127.10  Aligned_cols=80  Identities=18%  Similarity=0.265  Sum_probs=70.2

Q ss_pred             CCCCCCEEEEcCCCCCC---------cHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhc
Q 030012           78 KKGESNLLFVDGLPTDC---------TRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALH  148 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~---------te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~  148 (184)
                      ....+++|||+||+..+         +|++|+++|++||.|.+|+++.         ++|||||+|.+.++|+.|++.|+
T Consensus       130 ~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~---------~kG~AFV~F~~~~~Ae~A~~am~  200 (240)
T 3u1l_A          130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE---------SKNCGFVKFKYQANAEFAKEAMS  200 (240)
T ss_dssp             -CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG---------GGTEEEEEESSHHHHHHHHHHHT
T ss_pred             cccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC---------CCCEEEEEeCCHHHHHHHHHHhC
Confidence            34568899999999998         7999999999999999999974         36799999999999999999999


Q ss_pred             CCee------------CCCCCCCCceEEEeecCCC
Q 030012          149 GYKF------------DDKKPDSPTLKIQFAHFPF  171 (184)
Q Consensus       149 g~~~------------~g~~~~~~~l~V~~a~~~~  171 (184)
                      |..+            .|+.     |.|.||+...
T Consensus       201 g~~l~~~~~~e~~~~~~gr~-----L~V~wA~~~p  230 (240)
T 3u1l_A          201 NQTLLLPSDKEWDDRREGTG-----LLVKWANEDP  230 (240)
T ss_dssp             TCCCCCTTSTTGGGGGGSCC-----CEEEECC---
T ss_pred             CCEEeccccccccccCCCCE-----EEEEEccCCC
Confidence            9999            7776     9999998643

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.67  E-value=5.1e-16  Score=108.72  Aligned_cols=83  Identities=16%  Similarity=0.211  Sum_probs=71.5

Q ss_pred             CCCCEEEEcCCCC-----CCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCC
Q 030012           80 GESNLLFVDGLPT-----DCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDD  154 (184)
Q Consensus        80 ~~~~~lfVgnLp~-----~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g  154 (184)
                      .++++|+|.||..     +-++++|++.|++||.|.+|+++.+..  .+++++||+||+|.+.++|++|++.|||..+.|
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~--~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~G   83 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPG--APDDEAVRIFLEFERVESAIKAVVDLNGRYFGG   83 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSS--CCTTTSEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCC--CCCCCcEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            4578999999963     237899999999999999999987531  235789999999999999999999999999999


Q ss_pred             CCCCCCceEEEeecC
Q 030012          155 KKPDSPTLKIQFAHF  169 (184)
Q Consensus       155 ~~~~~~~l~V~~a~~  169 (184)
                      +.     |+|.|+..
T Consensus        84 r~-----i~v~~a~~   93 (105)
T 2pe8_A           84 RV-----VKACFYNL   93 (105)
T ss_dssp             EE-----CEEEECCH
T ss_pred             cE-----EEEEEcCH
Confidence            97     99999964

>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=3.6e-16  Score=120.63  Aligned_cols=80  Identities=20%  Similarity=0.288  Sum_probs=71.6

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ..++|||+|||+++++++|+++|++||.|.+|++..+..    ++++|||||+|++.++|++|++.+ +..+.|+.    
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~----~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~----  178 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH----KAFKGSIFVVFDSIESAKKFVETP-GQKYKETD----  178 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTT----CCEEEEEEEEESSHHHHHHHHHCT-TCEETTEE----
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCC----CCcccEEEEEECCHHHHHHHHHhC-CCeECCEE----
Confidence            358999999999999999999999999999999988532    789999999999999999999765 45999997    


Q ss_pred             ceEEEeecCC
Q 030012          161 TLKIQFAHFP  170 (184)
Q Consensus       161 ~l~V~~a~~~  170 (184)
                       |.|.|++..
T Consensus       179 -l~V~~~~~y  187 (193)
T 2voo_A          179 -LLILFKDDY  187 (193)
T ss_dssp             -CEEEETTTC
T ss_pred             -EEEEEhHHH
Confidence             999998754

>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=99.64  E-value=5e-16  Score=122.23  Aligned_cols=79  Identities=20%  Similarity=0.355  Sum_probs=72.4

Q ss_pred             CCCCCEEEEcCCCC-CCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           79 KGESNLLFVDGLPT-DCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        79 ~~~~~~lfVgnLp~-~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ..++++|||+|||+ ++++++|+++|++||.|.+|+++.+.        +|||||+|.+.++|++|++.|||..+.|+. 
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~--------~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~-  101 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--------KENALVQMADGNQAQLAMSHLNGHKLHGKP-  101 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT--------SCCEEEEESCHHHHHHHHHHHTTCBCSSSB-
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC--------CCEEEEEECCHHHHHHHHHHhCCCeECCeE-
Confidence            45689999999999 99999999999999999999998632        579999999999999999999999999997 


Q ss_pred             CCCceEEEeecCC
Q 030012          158 DSPTLKIQFAHFP  170 (184)
Q Consensus       158 ~~~~l~V~~a~~~  170 (184)
                          |+|.|++..
T Consensus       102 ----l~v~~a~~~  110 (229)
T 2adc_A          102 ----IRITLSKHQ  110 (229)
T ss_dssp             ----CEEECCSCC
T ss_pred             ----EEEEEecCc
Confidence                999999754

>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=99.64  E-value=4.4e-16  Score=116.84  Aligned_cols=78  Identities=14%  Similarity=0.312  Sum_probs=69.7

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||..+++++|+++|++||.|..+    ..    .++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        96 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~----~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~--  165 (175)
T 1fje_B           96 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQ----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRS--  165 (175)
T ss_dssp             TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CS----SSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEE--
T ss_pred             cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cC----CCCCceEEEEEECCHHHHHHHHHHhCCCEECCeE--
Confidence            3456899999999999999999999999987766    21    2678999999999999999999999999999997  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |+|+|++.
T Consensus       166 ---i~v~~a~~  173 (175)
T 1fje_B          166 ---VSLYYTGE  173 (175)
T ss_dssp             ---EEEEECSS
T ss_pred             ---EEEEecCC
Confidence               99999964

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.63  E-value=3.7e-16  Score=116.10  Aligned_cols=79  Identities=19%  Similarity=0.326  Sum_probs=69.5

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ++++|||+|||+++|+++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++  ++..+.|+.    
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~---~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~----   72 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKD---PATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKV----   72 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCC---TTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEE----
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEC---CCCCCccceEEEEEccHHHHHHHHh--cccccCCeE----
Confidence            4689999999999999999999999999999999874   3347899999999999999999998  467888886    


Q ss_pred             ceEEEeecC
Q 030012          161 TLKIQFAHF  169 (184)
Q Consensus       161 ~l~V~~a~~  169 (184)
                       |.|.++..
T Consensus        73 -i~v~~~~~   80 (167)
T 2cjk_A           73 -IDPKRAIP   80 (167)
T ss_dssp             -CCCEECCC
T ss_pred             -cccccccc
Confidence             88888753

>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=99.63  E-value=1.4e-15  Score=122.62  Aligned_cols=85  Identities=14%  Similarity=0.162  Sum_probs=76.7

Q ss_pred             CCCCCEEEEcCCCCCC-cHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           79 KGESNLLFVDGLPTDC-TRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~-te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ....++|||+|||+.+ ++++|+++|+.||.|.++++..+..    |+++|||||+|.+.++|.+|++.|||..+.|+. 
T Consensus       181 ~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~----g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~-  255 (284)
T 3smz_A          181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQD----GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSH-  255 (284)
T ss_dssp             TTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSS----CCEEEEEEEECSSHHHHHHHHHHHTTCEETTEE-
T ss_pred             cCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCC----CCcccEEEEEeCCHHHHHHHHHHhCCCccCCeE-
Confidence            4567899999999995 9999999999999999999988543    789999999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCC
Q 030012          158 DSPTLKIQFAHFPFH  172 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~  172 (184)
                          |+|.|++....
T Consensus       256 ----l~v~~a~~~~~  266 (284)
T 3smz_A          256 ----LRVSFCAPGPP  266 (284)
T ss_dssp             ----CEEEECCSSSC
T ss_pred             ----EEEEEecCCCc
Confidence                99999976443

>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=99.62  E-value=6.7e-16  Score=120.11  Aligned_cols=82  Identities=13%  Similarity=0.204  Sum_probs=71.6

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCE--EEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGY--REIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i--~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .++++|||+|||+++|+++|+++|++||.|  .+++++.+.     +.++|||||+|.+.++|.+|+..|||+++.++. 
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~-----~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~-  194 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK-----SERSSSGLLEWDSKSDALETLGFLNHYQMKNPN-  194 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC-----SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSS-
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC-----CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCC-
Confidence            457899999999999999999999999999  899887642     345699999999999999999999999999974 


Q ss_pred             CCCceEEEee
Q 030012          158 DSPTLKIQFA  167 (184)
Q Consensus       158 ~~~~l~V~~a  167 (184)
                      .+.|+.|.|+
T Consensus       195 ~~~p~~vk~~  204 (205)
T 3tyt_A          195 GPYPYTLKLC  204 (205)
T ss_dssp             SSSCEECEEE
T ss_pred             CCcceEEEec
Confidence            3557888775

>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=99.62  E-value=2e-15  Score=121.76  Aligned_cols=85  Identities=21%  Similarity=0.294  Sum_probs=76.5

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ...++|||+|||+++++++|+++|+.||.|.+++++.+.   .+++++|||||+|.+.++|++|++.|+|..+.|+.   
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~---~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~---  166 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSE---RTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRT---  166 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE---
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeC---CCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcE---
Confidence            346799999999999999999999999999999998743   33789999999999999999999999999999997   


Q ss_pred             CceEEEeecCCCC
Q 030012          160 PTLKIQFAHFPFH  172 (184)
Q Consensus       160 ~~l~V~~a~~~~~  172 (184)
                        |+|.|+.....
T Consensus       167 --i~v~~a~~~~~  177 (284)
T 3smz_A          167 --LYVHWTDAGQL  177 (284)
T ss_dssp             --CEEEECCGGGC
T ss_pred             --EEEEECCCCCC
Confidence              99999976443

>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=99.62  E-value=2e-15  Score=118.71  Aligned_cols=78  Identities=15%  Similarity=0.297  Sum_probs=70.9

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCC-CEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeC-CCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFV-GYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFD-DKKP  157 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G-~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~-g~~~  157 (184)
                      .++++|||+|||.++++++|+++|++|| .|.+++++.+        ++|||||+|.+.++|++|++.|||..+. |+. 
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~--------~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~-  219 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK--------DRKMALIQMGSVEEAVQALIDLHNHDLGENHH-  219 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS--------STTCEEEEESSHHHHHHHHHHHTTCBSSSSCB-
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC--------CCcEEEEEECCHHHHHHHHHHHCCCccCCCCe-
Confidence            4578999999999999999999999999 9999998642        3579999999999999999999999999 886 


Q ss_pred             CCCceEEEeecCC
Q 030012          158 DSPTLKIQFAHFP  170 (184)
Q Consensus       158 ~~~~l~V~~a~~~  170 (184)
                          |+|.|++.+
T Consensus       220 ----l~v~~a~~~  228 (229)
T 2adc_A          220 ----LRVSFSKST  228 (229)
T ss_dssp             ----CEEEECSSC
T ss_pred             ----EEEEEecCC
Confidence                999999763

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.61  E-value=1.3e-15  Score=116.61  Aligned_cols=78  Identities=15%  Similarity=0.297  Sum_probs=71.0

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCC-CEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeC-CCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFV-GYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFD-DKKP  157 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G-~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~-g~~~  157 (184)
                      .++++|||+|||..+++++|+++|++|| .|.+++++.+        .+|||||+|.+.++|++|++.|||..+. |+. 
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~--------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~-  188 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK--------DRKMALIQMGSVEEAVQALIDLHNHDLGENHH-  188 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST--------TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCS-
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC--------CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCe-
Confidence            4578999999999999999999999999 9999998652        2579999999999999999999999999 887 


Q ss_pred             CCCceEEEeecCC
Q 030012          158 DSPTLKIQFAHFP  170 (184)
Q Consensus       158 ~~~~l~V~~a~~~  170 (184)
                          |+|.|++.+
T Consensus       189 ----l~v~~a~~~  197 (198)
T 1qm9_A          189 ----LRVSFSKST  197 (198)
T ss_dssp             ----CCEEEECCC
T ss_pred             ----EEEEeeccc
Confidence                999999764

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.60  E-value=1e-15  Score=117.17  Aligned_cols=77  Identities=21%  Similarity=0.367  Sum_probs=70.5

Q ss_pred             CCCEEEEcCCCC-CCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           81 ESNLLFVDGLPT-DCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        81 ~~~~lfVgnLp~-~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      .+++|||+|||+ ++++++|+++|++||.|.+|+++.+.        +|||||+|.+.++|++|++.|||..+.|+.   
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~--------~g~afV~f~~~~~a~~A~~~l~~~~~~g~~---   70 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--------KENALVQMADGNQAQLAMSHLNGHKLHGKP---   70 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC--------SSCCEEECTTTHHHHHHHHHHTTCCCSSCC---
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC--------CCEEEEEECCHHHHHHHHHHhCCCeecCeE---
Confidence            368999999999 99999999999999999999987631        579999999999999999999999999997   


Q ss_pred             CceEEEeecCC
Q 030012          160 PTLKIQFAHFP  170 (184)
Q Consensus       160 ~~l~V~~a~~~  170 (184)
                        |+|.|++..
T Consensus        71 --l~v~~a~~~   79 (198)
T 1qm9_A           71 --IRITLSKHQ   79 (198)
T ss_dssp             --CEEEECCCC
T ss_pred             --EEEEEecCC
Confidence              999999754

>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=99.60  E-value=7.4e-15  Score=103.51  Aligned_cols=79  Identities=15%  Similarity=0.203  Sum_probs=67.5

Q ss_pred             CCCCCEEEEcCCCCCC-----------cHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHh
Q 030012           79 KGESNLLFVDGLPTDC-----------TRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDAL  147 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~-----------te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l  147 (184)
                      ..++++|+|.||....           ++++|+++|++||.|.+|.| .+      ..++|||||+|.+.++|++|++.|
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~------~~~~G~afV~f~~~~~A~~Ai~~l   84 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FD------RHPDGVASVSFRDPEEADYCIQTL   84 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ET------TCTTCEEEEECSCHHHHHHHHHHS
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ec------CCCCEEEEEEECCHHHHHHHHHHc
Confidence            3567899999995433           26899999999999999966 32      136889999999999999999999


Q ss_pred             cCCeeCCCCCCCCceEEEeecC
Q 030012          148 HGYKFDDKKPDSPTLKIQFAHF  169 (184)
Q Consensus       148 ~g~~~~g~~~~~~~l~V~~a~~  169 (184)
                      ||..+.|+.     |+|+|+..
T Consensus        85 ng~~~~gr~-----l~v~~a~~  101 (112)
T 2dit_A           85 DGRWFGGRQ-----ITAQAWDG  101 (112)
T ss_dssp             TTCEETTEE-----CEEEECCS
T ss_pred             CCCEECCcE-----EEEEEeCC
Confidence            999999997     99999865

>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=99.59  E-value=3.1e-15  Score=119.89  Aligned_cols=77  Identities=26%  Similarity=0.393  Sum_probs=70.4

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++|+++|+++|++||.|.+|++.+         ++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~---------~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~--   87 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR---------DRGFGFIRLESRTLAEIAKAELDGTILKSRP--   87 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET---------TTTEEEEECSSHHHHHHHHHHHTTCEETTEE--
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC---------CCcEEEEEECCHHHHHHHHHHcCCcEECCce--
Confidence            35567999999999999999999999999999999853         3679999999999999999999999999987  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |+|.|+..
T Consensus        88 ---l~v~~a~~   95 (261)
T 3sde_A           88 ---LRIRFATH   95 (261)
T ss_dssp             ---CEEEECCC
T ss_pred             ---eEeeeccc
Confidence               99999864

>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=99.58  E-value=2.9e-15  Score=121.28  Aligned_cols=83  Identities=13%  Similarity=0.238  Sum_probs=73.4

Q ss_pred             CCCCCEEEEcCCCCC-CcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           79 KGESNLLFVDGLPTD-CTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~-~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ....++|||+|||+. +++++|+++|++||.|.+|+++.+..  .+++++|||||+|.+.++|++|+ .|||..+.|+. 
T Consensus       207 ~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~--~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~-  282 (292)
T 2ghp_A          207 TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQK--EHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNRE-  282 (292)
T ss_dssp             CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC-----CCCEEEEEEESSHHHHHHHG-GGTTEEETTEE-
T ss_pred             CCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCC--cCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcE-
Confidence            456789999999999 99999999999999999999987432  12678999999999999999999 99999999997 


Q ss_pred             CCCceEEEeecC
Q 030012          158 DSPTLKIQFAHF  169 (184)
Q Consensus       158 ~~~~l~V~~a~~  169 (184)
                          |+|.|++.
T Consensus       283 ----i~V~~a~~  290 (292)
T 2ghp_A          283 ----ISVSLADK  290 (292)
T ss_dssp             ----EEEEECCC
T ss_pred             ----EEEEEecC
Confidence                99999975

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.57  E-value=3.1e-15  Score=111.62  Aligned_cols=76  Identities=22%  Similarity=0.324  Sum_probs=67.5

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCC----C-------CEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPF----V-------GYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHG  149 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~----G-------~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g  149 (184)
                      +.++|||+|||+++|+++|+++|++|    |       .|.++++.         +++|||||+|.+.++|++|+ .|||
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~---------~~~g~afV~f~~~~~A~~A~-~~~~   72 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN---------QDKNFAFLEFRSVDETTQAM-AFDG   72 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE---------TTTTEEEEEESSHHHHHHHG-GGTT
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec---------CCCCEEEEEeCCHHHHHHHH-HhCC
Confidence            46899999999999999999999999    6       77777763         34689999999999999999 8999


Q ss_pred             CeeCCCCCCCCceEEEeecCCC
Q 030012          150 YKFDDKKPDSPTLKIQFAHFPF  171 (184)
Q Consensus       150 ~~~~g~~~~~~~l~V~~a~~~~  171 (184)
                      ..+.|+.     |+|.+++...
T Consensus        73 ~~~~g~~-----i~v~~~~~~~   89 (172)
T 2g4b_A           73 IIFQGQS-----LKIRRPHDYQ   89 (172)
T ss_dssp             CEETTEE-----CEEECCSSCC
T ss_pred             cEecCce-----eeecCCcccC
Confidence            9999997     9999987543

>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=99.57  E-value=4.1e-16  Score=116.96  Aligned_cols=83  Identities=14%  Similarity=0.205  Sum_probs=69.7

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++++++|+++|+.||.+..+.+...    ..++++|||||+|.+.++|++|+ .|||..+.|+.  
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~----~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~--   82 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV----RTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNE--   82 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE----EEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEE--
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEEC----CCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeE--
Confidence            466789999999999999999999999987665322221    12678899999999999999999 59999999997  


Q ss_pred             CCceEEEeecCCC
Q 030012          159 SPTLKIQFAHFPF  171 (184)
Q Consensus       159 ~~~l~V~~a~~~~  171 (184)
                         |+|.|+....
T Consensus        83 ---l~v~~~~~~~   92 (175)
T 1fje_B           83 ---IKLEKPKGRD   92 (175)
T ss_dssp             ---EEEECCCCSS
T ss_pred             ---EEEecCCCcc
Confidence               9999997643

>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=99.57  E-value=8.8e-15  Score=122.01  Aligned_cols=82  Identities=15%  Similarity=0.157  Sum_probs=68.3

Q ss_pred             CCCCCCEEEEcC--CCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCC
Q 030012           78 KKGESNLLFVDG--LPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDK  155 (184)
Q Consensus        78 ~~~~~~~lfVgn--Lp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~  155 (184)
                      ...++++|||+|  |+..+||++|+++|++||.|.+|.+..         +||||||+|.+.++|++|++.|||.++.+.
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~---------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~   84 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP---------NKPYSFARYRTTEESKRAYVTLNGKEVVDD   84 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT---------TCSEEEEEESSHHHHHHHHHHTTTCEEECT
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC---------CCCEEEEEECCHHHHHHHHHHhCCCccccc
Confidence            457789999999  689999999999999999999987642         368999999999999999999999999644


Q ss_pred             CCCCCceEEEeec
Q 030012          156 KPDSPTLKIQFAH  168 (184)
Q Consensus       156 ~~~~~~l~V~~a~  168 (184)
                      .+.+.+|.|.|+.
T Consensus        85 ~g~~~~ly~~~~~   97 (345)
T 3tht_A           85 LGQKITLYLNFVE   97 (345)
T ss_dssp             TSCEEECEEEECS
T ss_pred             cCCceEEEEEEee
Confidence            2223357888874

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.56  E-value=4e-15  Score=113.39  Aligned_cols=75  Identities=23%  Similarity=0.352  Sum_probs=66.1

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCC----C-------CEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPF----V-------GYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHG  149 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~----G-------~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g  149 (184)
                      .+++|||+|||+++++++|+++|++|    |       .|.++++         ++++|||||+|.+.++|++|+ .|||
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~---------~~~~g~afV~F~~~~~A~~Al-~l~g   72 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI---------NQDKNFAFLEFRSVDETTQAM-AFDG   72 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE---------ETTTTEEEEEESCSHHHHHHG-GGTT
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe---------cCCCCEEEEEeCCHHHHHHHH-HhcC
Confidence            46899999999999999999999999    5       6666665         345789999999999999999 8999


Q ss_pred             CeeCCCCCCCCceEEEeecCC
Q 030012          150 YKFDDKKPDSPTLKIQFAHFP  170 (184)
Q Consensus       150 ~~~~g~~~~~~~l~V~~a~~~  170 (184)
                      ..+.|+.     |+|.|++..
T Consensus        73 ~~~~g~~-----i~v~~~~~~   88 (198)
T 2yh0_A           73 IIFQGQS-----LKIRRPHDY   88 (198)
T ss_dssp             EEETTEE-----EEEECCCCC
T ss_pred             CEEcCce-----EEEeCCCCC
Confidence            9999997     999998754

>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=99.55  E-value=2.8e-14  Score=114.31  Aligned_cols=80  Identities=20%  Similarity=0.197  Sum_probs=70.8

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhc-CCeeC---CCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALH-GYKFD---DKK  156 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~-g~~~~---g~~  156 (184)
                      .+++|||+|||..+|+++|+++|+.||.|.+|+++.+++    |+++|||||+|.+.++|.+|++.|| +..+.   ++.
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~----g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~  170 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDR----GRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRP  170 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT----SCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCB
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCC----CCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCce
Confidence            467999999999999999999999999999999998643    7899999999999999999999995 45544   554


Q ss_pred             CCCCceEEEeecC
Q 030012          157 PDSPTLKIQFAHF  169 (184)
Q Consensus       157 ~~~~~l~V~~a~~  169 (184)
                           |.|.++..
T Consensus       171 -----i~v~~~~~  178 (261)
T 3sde_A          171 -----VIVEPMEQ  178 (261)
T ss_dssp             -----CEEEECCC
T ss_pred             -----EEEeeccc
Confidence                 99999875

>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=99.54  E-value=2.1e-15  Score=105.39  Aligned_cols=72  Identities=18%  Similarity=0.294  Sum_probs=63.3

Q ss_pred             EcCCCCCCcHHHHHHhh------------cCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCC
Q 030012           87 VDGLPTDCTRREVSHLF------------RPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDD  154 (184)
Q Consensus        87 VgnLp~~~te~~L~~~F------------~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g  154 (184)
                      +.+|++.+++++|++.|            ++||.|.+|++..+..    ++++|||||+|.+.++|++|++.|||..+.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~----~~~~G~~fV~f~~~~~A~~A~~~lng~~~~G   95 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG----DHLVGNVYVKFRREEDAEKAVIDLNNRWFNG   95 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS----SSSEEEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC----CCccEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            56788888888887766            9999999999987432    6889999999999999999999999999999


Q ss_pred             CCCCCCceEEEee
Q 030012          155 KKPDSPTLKIQFA  167 (184)
Q Consensus       155 ~~~~~~~l~V~~a  167 (184)
                      +.     |+|+|+
T Consensus        96 r~-----i~v~~s  103 (104)
T 1jmt_A           96 QP-----IHAELS  103 (104)
T ss_dssp             EE-----CCEEEC
T ss_pred             EE-----EEEEEc
Confidence            97     999986

>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=99.54  E-value=8.9e-15  Score=118.40  Aligned_cols=82  Identities=16%  Similarity=0.255  Sum_probs=70.4

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCC-CEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFV-GYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G-~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ..++|||+|||+++++++|+++|+.|| .|.+|+++.+..    ++++|||||+|.+.++|++|++.|+|..+.|+.   
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~---  188 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF----NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYT---  188 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-----------CCEEEEECSSHHHHHHHHHHHTTCEETTEE---
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC----CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcE---
Confidence            578999999999999999999999999 999999987533    578899999999999999999999999999987   


Q ss_pred             CceEEEeecCCC
Q 030012          160 PTLKIQFAHFPF  171 (184)
Q Consensus       160 ~~l~V~~a~~~~  171 (184)
                        |+|.|+....
T Consensus       189 --l~v~~a~~~~  198 (292)
T 2ghp_A          189 --LVTKVSNPLE  198 (292)
T ss_dssp             --CEEEECCCC-
T ss_pred             --EEEEECCCCc
Confidence              9999997544

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=1.2e-13  Score=95.88  Aligned_cols=68  Identities=18%  Similarity=0.166  Sum_probs=57.6

Q ss_pred             CCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceEEEeecCCC
Q 030012           92 TDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHFPF  171 (184)
Q Consensus        92 ~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~V~~a~~~~  171 (184)
                      ..+++++|+++|++||.|.+|+|+        ++++|||||+|++.++|+.|++.+++  +.++.     |+|+|++...
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~--------~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~-----l~V~~a~~~~   91 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS--------SKKPGTAVVEFATVKAAELAVQNEVG--LVDNP-----LKISWLEGQP   91 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE--------SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSB-----CEEECSSCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc--------cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCe-----EEEEEccCCC
Confidence            568999999999999999999987        25678999999999999999998555  55765     9999998765


Q ss_pred             CCC
Q 030012          172 HLP  174 (184)
Q Consensus       172 ~~~  174 (184)
                      ...
T Consensus        92 ~~~   94 (100)
T 2d9o_A           92 QDA   94 (100)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            433

>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=99.53  E-value=2.4e-14  Score=100.08  Aligned_cols=82  Identities=17%  Similarity=0.231  Sum_probs=68.3

Q ss_pred             CCCEEEEcCC--CCCC--------cHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCC
Q 030012           81 ESNLLFVDGL--PTDC--------TRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGY  150 (184)
Q Consensus        81 ~~~~lfVgnL--p~~~--------te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~  150 (184)
                      +++.|.+.|+  +.++        .++||++.|++||.|.+|+|.++.... .++++||+||+|.+.++|++|++.|||.
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGV-EVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTB-CCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCC-CcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            5688999998  3333        347899999999999999998753221 1367899999999999999999999999


Q ss_pred             eeCCCCCCCCceEEEeec
Q 030012          151 KFDDKKPDSPTLKIQFAH  168 (184)
Q Consensus       151 ~~~g~~~~~~~l~V~~a~  168 (184)
                      .+.|+.     |+|.|+.
T Consensus        83 ~f~GR~-----i~v~~~~   95 (105)
T 3v4m_A           83 KFANRV-----VVTKYCD   95 (105)
T ss_dssp             EETTEE-----CEEEEEC
T ss_pred             EeCCCE-----EEEEEeC
Confidence            999997     9999985

>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=99.51  E-value=8.5e-14  Score=99.35  Aligned_cols=84  Identities=20%  Similarity=0.277  Sum_probs=70.5

Q ss_pred             CCCEEEEcCCCC--C---CcHHHHHHhhcCCCCEEEEEEeecCCC-CCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCC
Q 030012           81 ESNLLFVDGLPT--D---CTRREVSHLFRPFVGYREIRVIHKEPR-RTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDD  154 (184)
Q Consensus        81 ~~~~lfVgnLp~--~---~te~~L~~~F~~~G~i~~v~l~~~~~~-~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g  154 (184)
                      ++++|++.|+-.  +   --++||++.|++||.|.+|+|+.+... ...++++||+||+|.+.++|++|++.|||..+.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            578999999842  2   246899999999999999999885421 1125788999999999999999999999999999


Q ss_pred             CCCCCCceEEEeecC
Q 030012          155 KKPDSPTLKIQFAHF  169 (184)
Q Consensus       155 ~~~~~~~l~V~~a~~  169 (184)
                      +.     |+|.|+..
T Consensus        99 R~-----i~v~~~~~  108 (118)
T 3ue2_A           99 RK-----VVAEVYDQ  108 (118)
T ss_dssp             EE-----CEEEEECH
T ss_pred             cE-----EEEEEcCh
Confidence            97     99999853

>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=99.38  E-value=2e-12  Score=91.65  Aligned_cols=77  Identities=18%  Similarity=0.159  Sum_probs=64.1

Q ss_pred             CCCCEEEEcCCCCC----------CcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcC
Q 030012           80 GESNLLFVDGLPTD----------CTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHG  149 (184)
Q Consensus        80 ~~~~~lfVgnLp~~----------~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g  149 (184)
                      .+++.|.+.|+=..          --++||++.|++||.|.+|.+.++       .++||+||+|.+.++|++|++.|||
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~-------~~~G~~fV~f~~~e~A~~Ai~~lnG   77 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKN-------SAQGNVYVKCPSIAAAIAAVNALHG   77 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTT-------CTTCCEEEECSSHHHHHHHHHHHTT
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecC-------CCcEEEEEEECCHHHHHHHHHHhCC
Confidence            45678888887321          123588999999999999988542       2478999999999999999999999


Q ss_pred             CeeCCCCCCCCceEEEeec
Q 030012          150 YKFDDKKPDSPTLKIQFAH  168 (184)
Q Consensus       150 ~~~~g~~~~~~~l~V~~a~  168 (184)
                      ..+.|+.     |+|+|+.
T Consensus        78 ~~f~GR~-----i~v~~~~   91 (114)
T 3s6e_A           78 RWFAGKM-----ITAAYVP   91 (114)
T ss_dssp             CEETTEE-----CEEEEEC
T ss_pred             CEECCEE-----EEEEEEc
Confidence            9999998     9999985

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.28  E-value=2e-11  Score=87.21  Aligned_cols=76  Identities=16%  Similarity=0.174  Sum_probs=65.9

Q ss_pred             CCCCCCEEEEcCCCCC-CcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECC-HHHHHHHHHHhc--CCeeC
Q 030012           78 KKGESNLLFVDGLPTD-CTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDD-PKCARTAMDALH--GYKFD  153 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~-~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~-~~~A~~Ai~~l~--g~~~~  153 (184)
                      .-..+..|||+||+.. +++++|+++|++||.|.+|.++.+..         .|||+|.+ .++|..|++.|+  +.+|.
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~---------tgfVrf~~~~~~A~~av~~ln~~~~~i~   84 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK---------EGIILFKEKAKEALGKAKDANNGNLQLR   84 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS---------EEEEEESSCHHHHHHHHHHTTTSCBCTT
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC---------EEEEEECCChHHHHHHHHHhhcCCcEEe
Confidence            3567899999999999 99999999999999999999976422         69999999 899999999994  78888


Q ss_pred             CCCCCCCceEEEee
Q 030012          154 DKKPDSPTLKIQFA  167 (184)
Q Consensus       154 g~~~~~~~l~V~~a  167 (184)
                      +..     ++++.-
T Consensus        85 g~~-----~~~evL   93 (121)
T 1owx_A           85 NKE-----VTWEVL   93 (121)
T ss_dssp             SSS-----EEEEEC
T ss_pred             CcE-----EEEEEC
Confidence            876     777654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.20  E-value=2.4e-11  Score=82.10  Aligned_cols=73  Identities=16%  Similarity=0.236  Sum_probs=61.3

Q ss_pred             CCCCEEEEcCCCC----CCcH----HHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCe
Q 030012           80 GESNLLFVDGLPT----DCTR----REVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYK  151 (184)
Q Consensus        80 ~~~~~lfVgnLp~----~~te----~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~  151 (184)
                      ++..||+|.-++.    +.-.    .+|.+.|.+||.|..++++.+           .+||+|.+.++|.+|++ |||++
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d-----------~~fVtF~d~~sAlaAi~-mnG~~   72 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED-----------KMWVTFLEGSSALNVLS-LNGKE   72 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS-----------SEEEEESSHHHHHHGGG-GTTCE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC-----------CEEEEECChHHHHHHHh-cCCeE
Confidence            4467888877662    2323    579999999999999999863           48999999999999998 99999


Q ss_pred             eCCCCCCCCceEEEeecC
Q 030012          152 FDDKKPDSPTLKIQFAHF  169 (184)
Q Consensus       152 ~~g~~~~~~~l~V~~a~~  169 (184)
                      +.|++     |+|++++.
T Consensus        73 v~Gr~-----LkV~lkt~   85 (91)
T 2dnr_A           73 LLNRT-----ITIALKSP   85 (91)
T ss_dssp             ETTEE-----EEEEECCC
T ss_pred             eCCeE-----EEEEeCCC
Confidence            99998     99999875

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=99.04  E-value=9e-10  Score=85.84  Aligned_cols=71  Identities=21%  Similarity=0.274  Sum_probs=61.5

Q ss_pred             CCcHHHHHHhhcCCCCEEEEEEeecC-CCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceEEEeec
Q 030012           93 DCTRREVSHLFRPFVGYREIRVIHKE-PRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAH  168 (184)
Q Consensus        93 ~~te~~L~~~F~~~G~i~~v~l~~~~-~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~V~~a~  168 (184)
                      +-.+++|++.|++||.|.++.+..+. ..+..++++|++||+|.+.++|++|++.|||..+.||.     |++.|..
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~-----i~~~~~~  211 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRK-----VVAEVYD  211 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSB-----CEEEECC
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeE-----EEEEEcC
Confidence            34668899999999999999997643 23344689999999999999999999999999999997     9999975

>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=98.96  E-value=7.8e-10  Score=75.12  Aligned_cols=73  Identities=16%  Similarity=0.217  Sum_probs=61.0

Q ss_pred             CCCCCEEEEcCCCCC------CcH---HHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcC
Q 030012           79 KGESNLLFVDGLPTD------CTR---REVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHG  149 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~------~te---~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g  149 (184)
                      -++..||+|.-++..      ..+   .+|.+.|.+||+|..++++.+           -+||+|.+.++|.+||+ |||
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d-----------~~fVtF~d~~sAl~AI~-ldG   79 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG-----------QMLVTFADSHSALSVLD-VDG   79 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT-----------EEEEECSCSHHHHHHHH-GGG
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC-----------cEEEEEcChHHHHHHHh-cCC
Confidence            355689999888643      222   468999999999999999863           38999999999999998 999


Q ss_pred             CeeCCCCCCCCceEEEeec
Q 030012          150 YKFDDKKPDSPTLKIQFAH  168 (184)
Q Consensus       150 ~~~~g~~~~~~~l~V~~a~  168 (184)
                      +++.|+.     |+|++-.
T Consensus        80 ~~v~Gr~-----L~V~~k~   93 (95)
T 1ufw_A           80 MKVKGRA-----VKISGPS   93 (95)
T ss_dssp             SEETTEE-----EEEECCC
T ss_pred             eeeCCeE-----EEEeccC
Confidence            9999998     9998753

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.42  E-value=7.2e-07  Score=61.94  Aligned_cols=73  Identities=18%  Similarity=0.233  Sum_probs=64.8

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCC-----CCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPF-----VGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFD  153 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~-----G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~  153 (184)
                      .+..++|-+=|||..+++..|+.+.+.+     |.++.+.+..+   .      +-|+|+|.|...|-+|.-+|+|.+|.
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD---H------~GAivef~d~~~AgKasLaL~G~ef~   88 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD---F------NGAIIIFRDSKFAAKMLMILNGSQFQ   88 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT---T------TEEEEECSCHHHHHHHHHHHSSEEET
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC---C------CceEEEEccchhhHHHHhhcCCeeec
Confidence            4557889999999999999999999999     99999988753   1      26999999999999999999999999


Q ss_pred             CCCCCCCceEEE
Q 030012          154 DKKPDSPTLKIQ  165 (184)
Q Consensus       154 g~~~~~~~l~V~  165 (184)
                      |++     |++.
T Consensus        89 gr~-----Lr~g   95 (117)
T 2l9w_A           89 GKV-----IRSG   95 (117)
T ss_dssp             TEE-----EEEE
T ss_pred             CeE-----EEec
Confidence            997     8875

>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=98.00  E-value=6.6e-05  Score=50.57  Aligned_cols=86  Identities=16%  Similarity=0.291  Sum_probs=67.6

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      .+|-|.+||+.+||+++.+.+.....+.....+..+... ....-.-|+|.|.+.+++..-.+.++|+.+.+.++...+-
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~-~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a   80 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSL-YPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPA   80 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSS-TTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCC-CCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeee
Confidence            478899999999999999999998877666655422111 1233457999999999999999999999999988666666


Q ss_pred             EEEeecC
Q 030012          163 KIQFAHF  169 (184)
Q Consensus       163 ~V~~a~~  169 (184)
                      .|+||-.
T Consensus        81 ~VE~AP~   87 (91)
T 1uw4_A           81 IVEFAPF   87 (91)
T ss_dssp             EEEECSS
T ss_pred             EEEEcCC
Confidence            7888743

>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=97.81  E-value=3.2e-05  Score=53.16  Aligned_cols=75  Identities=24%  Similarity=0.270  Sum_probs=62.5

Q ss_pred             CCCEEEEcCCCCCC-c----HHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCC
Q 030012           81 ESNLLFVDGLPTDC-T----RREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDK  155 (184)
Q Consensus        81 ~~~~lfVgnLp~~~-t----e~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~  155 (184)
                      -.++|+|.||+.++ .    .+.++++|..|+.+......+.-         .-..|.|.+.++|.+|-..||+..+.|.
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF---------RRirv~F~~~~~A~~AR~~Lh~~~f~g~   74 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF---------KRVRINFSNPLSAADARLRLHKTEFLGK   74 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT---------TEEEEECSSTTHHHHHHHTSTTSEETTE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc---------eEEEEEeCChHHHHHHHHHhccceecCc
Confidence            45789999998765 2    25679999999999887776531         1468999999999999999999999999


Q ss_pred             CCCCCceEEEeecC
Q 030012          156 KPDSPTLKIQFAHF  169 (184)
Q Consensus       156 ~~~~~~l~V~~a~~  169 (184)
                      +     |+|-|+..
T Consensus        75 ~-----~r~YFgq~   83 (104)
T 1wey_A           75 E-----MKLYFAQT   83 (104)
T ss_dssp             E-----CEEECCCC
T ss_pred             e-----eEEEecCC
Confidence            8     99999973

>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=97.67  E-value=0.00031  Score=47.66  Aligned_cols=58  Identities=21%  Similarity=0.397  Sum_probs=48.3

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhc
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALH  148 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~  148 (184)
                      ....+.++| +.|.++...||.++|+.||. ..|+++.+   .       .|||.|.+++.|..|+..+.
T Consensus        13 p~r~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidD---T-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           13 PKRDHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDD---T-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEET---T-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcC---C-------eEEEEecCHHHHHHHHHhcc
Confidence            345567778 99999999999999999995 45777763   1       79999999999999998763

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.45  E-value=0.00045  Score=46.89  Aligned_cols=87  Identities=20%  Similarity=0.321  Sum_probs=63.4

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCc
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPT  161 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~  161 (184)
                      +-+|-|..||+.+||+++.+.+...-++.....+.-+.. .....-.-|+|.|.+.++...-.+.++|+.+.+.++...+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s-~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~   87 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLS-LYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYP   87 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSS-SCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccC-CCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEee
Confidence            468999999999999999988877644322222211100 0111224689999999999999999999999999877777


Q ss_pred             eEEEeecC
Q 030012          162 LKIQFAHF  169 (184)
Q Consensus       162 l~V~~a~~  169 (184)
                      -.|+||-.
T Consensus        88 a~VE~APy   95 (97)
T 2l08_A           88 AVVEFAPF   95 (97)
T ss_dssp             EEEEECCC
T ss_pred             eEEEecCC
Confidence            78888843

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.30  E-value=0.002  Score=44.12  Aligned_cols=69  Identities=13%  Similarity=0.151  Sum_probs=53.5

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcC----C-CCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRP----F-VGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDD  154 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~----~-G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g  154 (184)
                      ...++|.|.|||..+.++.|+-+|+.    . |.|.+++...           +-|+|+|.+.+.|++.++. .-+.+.+
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-----------~~AvItF~d~~va~rVL~k-~~H~L~~   73 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-----------CGGVLTFREPADAERVLAQ-ADHELHG   73 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-----------TEEEEEESSHHHHHHHHTC-SCCBSSS
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-----------CcEEEEEcChHHHHHHhcC-CcceecC
Confidence            34679999999999999999999986    2 6777776642           2789999999999998753 2466666


Q ss_pred             CCCCCCceEEE
Q 030012          155 KKPDSPTLKIQ  165 (184)
Q Consensus       155 ~~~~~~~l~V~  165 (184)
                      ..     |.|.
T Consensus        74 ~~-----LsV~   79 (104)
T 2dhx_A           74 AQ-----LSLR   79 (104)
T ss_dssp             SB-----CEEE
T ss_pred             eE-----EEEE
Confidence            54     7763

>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=97.25  E-value=0.00051  Score=46.70  Aligned_cols=55  Identities=22%  Similarity=0.422  Sum_probs=46.4

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhc
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALH  148 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~  148 (184)
                      .+.++| +.|.++...||.++|+.|| -..|+++.+   .       .|||.|.+++.|..|+..+.
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidD---T-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDD---T-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEET---T-------EEEEEEEEECHHHHHHHHHT
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcC---C-------eEEEEecCHHHHHHHHHhcc
Confidence            345667 9999999999999999999 456777763   1       79999999999999999774

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.61  E-value=0.01  Score=41.63  Aligned_cols=65  Identities=14%  Similarity=0.169  Sum_probs=51.6

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDK  155 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~  155 (184)
                      ....-|.|-+.|... .+.+.+.|++||.|++.....         ...+-.|.|.+..+|++|+. .||..+.+.
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~---------~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~   86 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN---------TGNWMHIRYQSKLQARKALS-KDGRIFGES   86 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS---------SSSEEEEEESSHHHHHHHHT-TTTCEETTT
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC---------CCCeEEEEeCCHHHHHHHHH-hCCeEecCC
Confidence            345678888988775 566777899999999887621         11399999999999999996 699999864

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=96.05  E-value=0.0059  Score=44.14  Aligned_cols=34  Identities=12%  Similarity=0.037  Sum_probs=27.3

Q ss_pred             EEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcC
Q 030012          111 EIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHG  149 (184)
Q Consensus       111 ~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g  149 (184)
                      +++|+.+.     .+++|||||+|.+.++|++|++.+++
T Consensus         2 ~~kl~ln~-----~~~~G~~fV~f~~~~~A~~al~~~~~   35 (158)
T 2kn4_A            2 QYKLILNG-----KTLKGETTTEAVDAATAEKVFKQYAN   35 (158)
T ss_dssp             EEEEEEEC-----SSCEEEEEEECSSHHHHHHHHHHHHH
T ss_pred             cEEEEecC-----ccccchhHHHHHHHHhHHHHHHhhcc
Confidence            45555531     36899999999999999999998875

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.95  E-value=0.0029  Score=54.46  Aligned_cols=56  Identities=9%  Similarity=0.145  Sum_probs=40.9

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHH
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMD  145 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~  145 (184)
                      ..+.|||. .+..+++.+|.++|++||.|.++.+-.+   +  |   -|+.|||.+.++++.++.
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~---~--g---~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES---F--G---LYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS---S--S---EEEEEECC---CCHHHHS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc---C--C---eEEEEEeCCHHHHHHHHh
Confidence            35789997 7999999999999999999999877542   1  2   499999999999886653

>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=95.89  E-value=0.0025  Score=45.95  Aligned_cols=40  Identities=13%  Similarity=-0.038  Sum_probs=36.6

Q ss_pred             CCcceEEEEEECCHHHHHHHHHHh-cCCeeCCCCCCCCceEEEeecC
Q 030012          124 DRAMVLCFVEFDDPKCARTAMDAL-HGYKFDDKKPDSPTLKIQFAHF  169 (184)
Q Consensus       124 g~~~G~afV~F~~~~~A~~Ai~~l-~g~~~~g~~~~~~~l~V~~a~~  169 (184)
                      .+.+|+++|+|.+.++|++|++.+ ||..++| .     +.++++..
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~-----~~~~~a~~   50 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-E-----WTYDDATK   50 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-E-----EEEETTTT
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-c-----eecccccC
Confidence            467899999999999999999999 9999999 6     99999864

>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=92.87  E-value=0.3  Score=42.34  Aligned_cols=56  Identities=21%  Similarity=0.428  Sum_probs=46.0

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhc
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALH  148 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~  148 (184)
                      ..+.++|+ .|..+...+|.++|+.||. .+|+++.+          -.|||.|.+.+.|..+++.+.
T Consensus       439 R~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widd----------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          439 RDHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDD----------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSS----------SEEEEECSCHHHHHHHHHHHT
T ss_pred             cCcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcC----------CeEEEEECCHHHHHHHHHHHH
Confidence            34577777 8888999999999999995 45666542          179999999999999999884

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=92.12  E-value=0.092  Score=37.36  Aligned_cols=79  Identities=20%  Similarity=0.173  Sum_probs=50.2

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEE-EEeecC----------CCCCCCCcceEEEEEECCHHHHHHHHHHhcCC
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREI-RVIHKE----------PRRTGDRAMVLCFVEFDDPKCARTAMDALHGY  150 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v-~l~~~~----------~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~  150 (184)
                      ...|.|-+-|++.+ ..+-+.|++||.|.+- ...+..          .....-....+-.|+|++..+|++|+. .||.
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            45566777766554 4566689999998762 111100          000000123588999999999999995 8999


Q ss_pred             eeCCCCCCCCceEEEee
Q 030012          151 KFDDKKPDSPTLKIQFA  167 (184)
Q Consensus       151 ~~~g~~~~~~~l~V~~a  167 (184)
                      .|.|..     |-|..-
T Consensus        85 ii~G~m-----IGV~Py   96 (132)
T 3p3d_A           85 VFNGVL-----LGVIPY   96 (132)
T ss_dssp             EETTEE-----CEEEEC
T ss_pred             EeCcEE-----EEEEEC
Confidence            998864     555543

---

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	184
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-14
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-13
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	4e-13
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-12
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-12
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	7e-12
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-11
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	4e-11
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	9e-11
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	9e-11
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	3e-10
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	4e-10
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	5e-10
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	5e-10
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-10
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	6e-10
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	7e-10
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-09
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-09
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-09
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-09
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-09
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	8e-09
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	9e-09
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	3e-08
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	3e-08
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-08
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	4e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	5e-08
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	5e-08
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-08
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	7e-08
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	7e-08
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-07
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-07
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-07
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-07
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-07
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-07
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-07
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-07
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	4e-07
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-07
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	6e-07
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-07
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	8e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	1e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-06
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-06
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:) 3e-06
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	4e-06
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	4e-06
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	4e-06
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	7e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	8e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	1e-05
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-05
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	3e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-05
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	4e-05
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-04
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-04
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	2e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	3e-04
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	4e-04
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	4e-04
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-04
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	5e-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-04
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	0.002
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	0.002

>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 = 63.0 bits (153), Expect = 3e-14
 Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 8/92 (8%)

Query: 78  KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDP 137
           KK  ++ + V  +P    +RE+  LF  F G  +   + K+   TG       FV+F   
Sbjct: 4   KKQTTSKILVRNIPFQANQREIRELFSTF-GELKTVRLPKKMTGTG-AHRGFGFVDFITK 61

Query: 138 KCARTAMDAL-HGYKFDDKKPDSPTLKIQFAH 168
           + A+ A +AL H      ++     L +++A 
Sbjct: 62  QDAKKAFNALCHSTHLYGRR-----LVLEWAD 88

>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 = 61.1 bits (148), Expect = 2e-13
 Identities = 20/87 (22%), Positives = 35/87 (40%), Gaps = 8/87 (9%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCA 140
           +S  L+V  L    T  ++  LF       +I+ I     +    A   CFVE+     A
Sbjct: 6   KSCTLYVGNLSFYTTEEQIYELFSKSG---DIKKIIMGLDKMKKTACGFCFVEYYSRADA 62

Query: 141 RTAMDALHGYKFDDKKPDSPTLKIQFA 167
             AM  ++G + DD+      ++  + 
Sbjct: 63  ENAMRYINGTRLDDRI-----IRTDWD 84

>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 = 59.6 bits (144), Expect = 4e-13
 Identities = 17/83 (20%), Positives = 29/83 (34%), Gaps = 9/83 (10%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L V  L    +  ++  LF  F   ++  V +    R+    +    V F+    A  AM
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRS----LGTADVHFERKADALKAM 58

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
              +G   D +      + IQ  
Sbjct: 59  KQYNGVPLDGRP-----MNIQLV 76

>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 = 58.8 bits (142), Expect = 1e-12
 Identities = 19/84 (22%), Positives = 31/84 (36%), Gaps = 8/84 (9%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L+V  L  D T   +   F P      IRV          R++   +V F  P  A  A+
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCR---DMITRRSLGYAYVNFQQPADAERAL 59

Query: 145 DALHGYKFDDKKPDSPTLKIQFAH 168
           D ++      K      ++I ++ 
Sbjct: 60  DTMNFDVIKGKP-----VRIMWSQ 78

>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 = 58.5 bits (141), Expect = 1e-12
 Identities = 18/84 (21%), Positives = 35/84 (41%), Gaps = 5/84 (5%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           LF+  L    T   +  +F      +   +  K+ +     +M   FVE+  P+ A+ A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 145 DALHGYKFDDKKPDSPTLKIQFAH 168
             L G+  D  K     L+++ + 
Sbjct: 61  KQLQGHTVDGHK-----LEVRISE 79

>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 = 56.5 bits (136), Expect = 7e-12
 Identities = 16/83 (19%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L+V  LP   T  ++  +F  +     I   +    +   R   + FV ++  + A+ A+
Sbjct: 9   LYVTNLPRTITDDQLDTIFGKY---GSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 65

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
            AL+    +        L ++ A
Sbjct: 66  SALNNVIPEGGS---QPLSVRLA 85

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 2e-11
 Identities = 20/83 (24%), Positives = 31/83 (37%), Gaps = 8/83 (9%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           LF+ GLP      +V  L   F   +   ++          +    F E+ D      A+
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK---DSATGLSKGYAFCEYVDINVTDQAI 60

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
             L+G +  DKK     L +Q A
Sbjct: 61  AGLNGMQLGDKK-----LLVQRA 78

>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 = 54.7 bits (131), Expect = 3e-11
 Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 6/83 (7%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L+V GLP   T++E+  LF  +              +    +  + F+ FD    A  A+
Sbjct: 9   LYVSGLPKTMTQKELEQLFSQYGRIITS---RILVDQVTGVSRGVGFIRFDKRIEAEEAI 65

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
             L+G K       +  + ++FA
Sbjct: 66  KGLNGQKPSGA---TEPITVKFA 85

>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 = 54.7 bits (131), Expect = 4e-11
 Identities = 21/93 (22%), Positives = 38/93 (40%), Gaps = 8/93 (8%)

Query: 76  PLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFD 135
           P +  E  +LFV  +  +    E+   F     Y EI+ IH    R    +     VE++
Sbjct: 1   PQRSVEGWILFVTSIHEEAQEDEIQEKFCD---YGEIKNIHLNLDRRTGFSKGYALVEYE 57

Query: 136 DPKCARTAMDALHGYKFDDKKPDSPTLKIQFAH 168
             K A  A +AL+G +   +      +++ +  
Sbjct: 58  THKQALAAKEALNGAEIMGQT-----IQVDWCF 85

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 4e-11
 Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 11/87 (12%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCA 140
            + +L++  LP   T  E+  +F  +   R+IRV +    R         +V ++D   A
Sbjct: 6   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRG------TAYVVYEDIFDA 59

Query: 141 RTAMDALHGYKFDDKKPDSPTLKIQFA 167
           + A D L G+   ++      L + + 
Sbjct: 60  KNACDHLSGFNVCNRY-----LVVLYY 81

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 53.5 bits (128), Expect = 9e-11
 Identities = 22/83 (26%), Positives = 35/83 (42%), Gaps = 8/83 (9%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L V+ LP D T RE+  LFR        R++               FV+F     ++ A+
Sbjct: 5   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYS---YGYAFVDFTSEMDSQRAI 61

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
             L+G    +K+     LK+ +A
Sbjct: 62  KVLNGITVRNKR-----LKVSYA 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 = 53.9 bits (129), Expect = 9e-11
 Identities = 18/90 (20%), Positives = 37/90 (41%), Gaps = 8/90 (8%)

Query: 78  KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDP 137
           +  ++  + V  L  D    ++  LFRPF        I+    +T  ++    F+ F   
Sbjct: 4   RADDNATIRVTNLSEDTRETDLQELFRPFGSISR---IYLAKDKTTGQSKGFAFISFHRR 60

Query: 138 KCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           + A  A+  + G+ +D        L +++A
Sbjct: 61  EDAARAIAGVSGFGYDHLI-----LNVEWA 85

>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 = 52.8 bits (126), Expect = 3e-10
 Identities = 23/95 (24%), Positives = 45/95 (47%), Gaps = 8/95 (8%)

Query: 73  AGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFV 132
           AGS  +  E   LF+  LP +   +++  +F PF      +V   +     + +    FV
Sbjct: 9   AGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQT---NLSKCFGFV 65

Query: 133 EFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
            +D+P  A+ A+ +++G++   K+     LK+Q  
Sbjct: 66  SYDNPVSAQAAIQSMNGFQIGMKR-----LKVQLK 95

>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 = 52.3 bits (125), Expect = 4e-10
 Identities = 15/94 (15%), Positives = 29/94 (30%), Gaps = 8/94 (8%)

Query: 74  GSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVE 133
           G   ++ +   ++V GL    +   +  LF          +                FVE
Sbjct: 1   GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQH---QGYGFVE 57

Query: 134 FDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           F   + A  A+  +   K   K      +++  A
Sbjct: 58  FLSEEDADYAIKIMDMIKLYGKP-----IRVNKA 86

>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 = 52.0 bits (124), Expect = 5e-10
 Identities = 19/96 (19%), Positives = 37/96 (38%), Gaps = 10/96 (10%)

Query: 72  NAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCF 131
           ++G+   K     L V  +P      ++  +F  F    ++ +I  E            F
Sbjct: 1   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS-----KGFGF 55

Query: 132 VEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           V F++   A  A + LHG   + +K     +++  A
Sbjct: 56  VTFENSADADRAREKLHGTVVEGRK-----IEVNNA 86

>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 = 51.6 bits (123), Expect = 5e-10
 Identities = 16/83 (19%), Positives = 37/83 (44%), Gaps = 3/83 (3%)

Query: 74  GSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVE 133
           G+      +  L V GL    T R++  +F  +    ++ +++    +   R+    FV 
Sbjct: 1   GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYD---QQSRRSRGFAFVY 57

Query: 134 FDDPKCARTAMDALHGYKFDDKK 156
           F++   A+ A +  +G + D ++
Sbjct: 58  FENVDDAKEAKERANGMELDGRR 80

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.0 bits (124), Expect = 5e-10
 Identities = 23/91 (25%), Positives = 39/91 (42%), Gaps = 10/91 (10%)

Query: 80  GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKC 139
           G+   L+V  L  D T   +  LF      +  ++I +            CFVEF + + 
Sbjct: 6   GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH-----TSNDPYCFVEFYEHRD 60

Query: 140 ARTAMDALHGYKFDDKKPDSPTLKIQFAHFP 170
           A  A+ A++G K   K+     +K+ +A  P
Sbjct: 61  AAAALAAMNGRKILGKE-----VKVNWATTP 86

>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 = 51.5 bits (123), Expect = 6e-10
 Identities = 19/87 (21%), Positives = 31/87 (35%), Gaps = 14/87 (16%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCA 140
           + + LFV  LP D T  E+  LF  +    E+ +                F+  +    A
Sbjct: 7   QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD---------KGFGFIRLETRTLA 57

Query: 141 RTAMDALHGYKFDDKKPDSPTLKIQFA 167
             A   L       K+     L+++FA
Sbjct: 58  EIAKVELDNMPLRGKQ-----LRVRFA 79

>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 = 51.5 bits (123), Expect = 7e-10
 Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 14/83 (16%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           ++  G+ +  T + +   F PF    EIRV                FV F   + A  A+
Sbjct: 21  VYCGGIASGLTDQLMRQTFSPFGQIMEIRVF---------PEKGYSFVRFSTHESAAHAI 71

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
            +++G   +        +K  + 
Sbjct: 72  VSVNGTTIEGHV-----VKCYWG 89

>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 = 51.2 bits (122), Expect = 1e-09
 Identities = 18/91 (19%), Positives = 37/91 (40%), Gaps = 15/91 (16%)

Query: 82  SNLLFVDGLPTDCT----RREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDP 137
           ++ ++++ L         ++ +  +F  F    +I V      R         FV F + 
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRG------QAFVIFKEV 56

Query: 138 KCARTAMDALHGYKFDDKKPDSPTLKIQFAH 168
             A  A+ ++ G+ F DK      ++IQ+A 
Sbjct: 57  SSATNALRSMQGFPFYDKP-----MRIQYAK 82

>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 = 50.8 bits (121), Expect = 1e-09
 Identities = 18/93 (19%), Positives = 34/93 (36%), Gaps = 11/93 (11%)

Query: 75  SPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEF 134
           S  K G  N+ F+  L      + +   F  F      +V+  E            FV F
Sbjct: 2   SLRKSGVGNI-FIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-----KGYGFVHF 55

Query: 135 DDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           +  + A  A++ ++G   +D+K     + +   
Sbjct: 56  ETQEAAERAIEKMNGMLLNDRK-----VFVGRF 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 = 50.1 bits (119), Expect = 2e-09
 Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 8/83 (9%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L V+ LP + T+ E   LF       EI        +   +++   FV + DPK A  A+
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSI---GEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
           + L+G +   K      +K+ +A
Sbjct: 62  NTLNGLRLQTKT-----IKVSYA 79

>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 = 49.3 bits (117), Expect = 4e-09
 Identities = 17/83 (20%), Positives = 34/83 (40%), Gaps = 8/83 (9%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L+V GL  +   + +   F PF    +I  I        ++     FVEF+  + A  A+
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPF---GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
           D ++  +   +      +++  A
Sbjct: 65  DNMNESELFGRT-----IRVNLA 82

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 4e-09
 Identities = 12/83 (14%), Positives = 32/83 (38%), Gaps = 7/83 (8%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           +F+  L  +   + +   F  F    +   I ++P      +    F+ F     +  A+
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDT--GNSKGYAFINFASFDASDAAI 58

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
           +A++G    ++      + + +A
Sbjct: 59  EAMNGQYLCNRP-----ITVSYA 76

>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 = 49.3 bits (117), Expect = 5e-09
 Identities = 17/87 (19%), Positives = 28/87 (32%), Gaps = 8/87 (9%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCA 140
            S  LFV  L    +  ++  LF  +    E+            +     FV F  P+ A
Sbjct: 7   GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPI---DSLTKKPKGFAFVTFMFPEHA 63

Query: 141 RTAMDALHGYKFDDKKPDSPTLKIQFA 167
             A   + G  F  +      L +  +
Sbjct: 64  VKAYAEVDGQVFQGRM-----LHVLPS 85

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 48.9 bits (116), Expect = 8e-09
 Identities = 14/102 (13%), Positives = 32/102 (31%), Gaps = 13/102 (12%)

Query: 67  SSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRA 126
           S +  +  +  K   +  L    L  + T  E+  +F   +  R +    K         
Sbjct: 1   SHMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGI----- 55

Query: 127 MVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAH 168
               ++EF     A   ++   G + D +      + + +  
Sbjct: 56  ---AYIEFKSEADAEKNLEEKQGAEIDGRS-----VSLYYTG 89

>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 = 48.6 bits (115), Expect = 9e-09
 Identities = 12/86 (13%), Positives = 30/86 (34%), Gaps = 11/86 (12%)

Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           S  L +  +P   +  ++  LF    G  +     ++          +  ++    + A 
Sbjct: 10  SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD-------RKMALIQMGSVEEAV 62

Query: 142 TAMDALHGYKFDDKKPDSPTLKIQFA 167
            A+  LH +   +       L++ F+
Sbjct: 63  QALIDLHNHDLGENHH----LRVSFS 84

>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 = 47.5 bits (112), Expect = 3e-08
 Identities = 25/106 (23%), Positives = 41/106 (38%), Gaps = 13/106 (12%)

Query: 62  INGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRR 121
           I  +P     N G P     + +L++  L    T R++  LF  F   +   +     R 
Sbjct: 3   IRKIPMFSSYNPGEP-----NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQF---RM 54

Query: 122 TGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
              R     F+ F + + A  A+  ++GYK   K      L I+F 
Sbjct: 55  MTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKI-----LVIEFG 95

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 46.8 bits (110), Expect = 3e-08
 Identities = 24/86 (27%), Positives = 39/86 (45%), Gaps = 12/86 (13%)

Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           + +LF+  LP +     +S LF  F G++E+R++             + FVEF     + 
Sbjct: 8   NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR--------HDIAFVEFTTELQSN 59

Query: 142 TAMDALHGYKFDDKKPDSPTLKIQFA 167
            A +AL G+K          +KI FA
Sbjct: 60  AAKEALQGFKITPTHA----MKITFA 81

>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 = 46.7 bits (110), Expect = 3e-08
 Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 3/72 (4%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L++ GL    T +++  L +P+              +T ++     FV+FD P  A+ A+
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVST---KAILDKTTNKCKGYGFVDFDSPSAAQKAV 57

Query: 145 DALHGYKFDDKK 156
            AL       + 
Sbjct: 58  TALKASGVQAQM 69

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (111), Expect = 4e-08
 Identities = 15/83 (18%), Positives = 28/83 (33%), Gaps = 4/83 (4%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           LF+ G+P    R E+            + VI         +     FVE++  + A  A 
Sbjct: 4   LFIGGIPKMKKREEILEEIAKV-TEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
             L   +    +     + + +A
Sbjct: 63  RKLMPGRI---QLWGHQIAVDWA 82

>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 = 46.5 bits (110), Expect = 5e-08
 Identities = 15/87 (17%), Positives = 28/87 (32%), Gaps = 10/87 (11%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCA 140
           +++ L V GLP   T +++   F  F     ++V           +    FV F + +  
Sbjct: 7   KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKD---LKTGHSKGFGFVRFTEYETQ 63

Query: 141 RTAMDALHGYKFDDKKPDSPTLKIQFA 167
              M   H    D +         +  
Sbjct: 64  VKVMSQRH--MIDGRW-----CDCKLP 83

>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 = 46.7 bits (110), Expect = 5e-08
 Identities = 19/86 (22%), Positives = 31/86 (36%), Gaps = 15/86 (17%)

Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           S+ + V  LP D   +EV  L + +   +   V   +            FV   + + A+
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDRNKRT---------AFVTLLNGEQAQ 54

Query: 142 TAMDALHGYKFDDKKPDSPTLKIQFA 167
            A+   H Y F  K      L +Q  
Sbjct: 55  NAIQMFHQYSFRGKD-----LIVQLQ 75

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.4 bits (110), Expect = 6e-08
 Identities = 16/98 (16%), Positives = 33/98 (33%), Gaps = 17/98 (17%)

Query: 71  NNAGSPLKKGESNLLFVDGLPTD-CTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL 129
            ++G    +  ++ +F+  L T    + +V  +F  +       V               
Sbjct: 4   GSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKG-----------F 52

Query: 130 CFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
            FV++ + + AR A+    G     +      L I  A
Sbjct: 53  AFVQYVNERNARAAVAGEDGRMIAGQV-----LDINLA 85

>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 = 46.3 bits (109), Expect = 7e-08
 Identities = 14/88 (15%), Positives = 29/88 (32%), Gaps = 11/88 (12%)

Query: 82  SNLLFV--DGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKC 139
           +  L V   GL    +R ++  +         + +   +P           F  +   + 
Sbjct: 18  TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPY---------SFARYRTTEE 68

Query: 140 ARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           ++ A   L+G +  D      TL + F 
Sbjct: 69  SKRAYVTLNGKEVVDDLGQKITLYLNFV 96

>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 = 45.8 bits (108), Expect = 7e-08
 Identities = 17/83 (20%), Positives = 27/83 (32%), Gaps = 14/83 (16%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L+V  L    +   +   F         RV          +     FV F + + A  AM
Sbjct: 11  LYVRNLMLSTSEEMIEKEFNNIKPGAVERV---------KKIRDYAFVHFSNREDAVEAM 61

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
            AL+G   D        +++  A
Sbjct: 62  KALNGKVLDGSP-----IEVTLA 79

>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 = 45.1 bits (106), Expect = 1e-07
 Identities = 17/83 (20%), Positives = 34/83 (40%), Gaps = 9/83 (10%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           +FV GL  + T  +V H F  F G  +  ++  +     +R     FV F+         
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQF-GKVDDAMLMFDKTT--NRHRGFGFVTFESEDIVEKVC 58

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
             +H ++ ++K      ++ + A
Sbjct: 59  -EIHFHEINNKM-----VECKKA 75

>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 = 45.2 bits (106), Expect = 1e-07
 Identities = 12/83 (14%), Positives = 32/83 (38%), Gaps = 8/83 (9%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L++   P   T+R +  L +       + +  + P    + +    +++    + AR  +
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQD---INVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
           + L+G K +        L  + +
Sbjct: 61  EKLNGLKIEGYT-----LVTKVS 78

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 1e-07
 Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 8/87 (9%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCA 140
           +   LFV GL  D   +    L + F  Y +I  +     R   R+    FV F++   A
Sbjct: 4   DEGKLFVGGLSFDTNEQS---LEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 60

Query: 141 RTAMDALHGYKFDDKKPDSPTLKIQFA 167
           + AM A++G   D ++     +++  A
Sbjct: 61  KDAMMAMNGKSVDGRQ-----IRVDQA 82

>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 = 45.5 bits (107), Expect = 2e-07
 Identities = 19/98 (19%), Positives = 39/98 (39%), Gaps = 10/98 (10%)

Query: 76  PLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRV-----IHKEPRRTGDRAMVLC 130
           P +  +++ ++V GL    T  +++  F+     +  +      IH    +   +     
Sbjct: 2   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 61

Query: 131 FVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAH 168
            V ++DP  A+ A++   G  F   K     LK+  A 
Sbjct: 62  TVSYEDPPTAKAAVEWFDGKDFQGSK-----LKVSLAR 94

>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 = 45.2 bits (106), Expect = 2e-07
 Identities = 14/93 (15%), Positives = 28/93 (30%), Gaps = 4/93 (4%)

Query: 76  PLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFD 135
           P    E   +F+  L  D     +  + + F   +    +        + +    F +F 
Sbjct: 2   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKY---VRVVLHPDTEHSKGCAFAQFM 58

Query: 136 DPKCARTAMDALHGYKFDDKKP-DSPTLKIQFA 167
             + A+  + A            D   LK+  A
Sbjct: 59  TQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLA 91

>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 = 45.1 bits (106), Expect = 2e-07
 Identities = 20/84 (23%), Positives = 39/84 (46%), Gaps = 11/84 (13%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           ++V  LP D   +++  +F  +   R+I + ++             FVEF+DP+ A  A+
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPF------AFVEFEDPRDAEDAV 70

Query: 145 DALHGYKFDDKKPDSPTLKIQFAH 168
               GY +D  +     L+++F  
Sbjct: 71  YGRDGYDYDGYR-----LRVEFPR 89

>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 = 44.7 bits (105), Expect = 2e-07
 Identities = 14/94 (14%), Positives = 28/94 (29%), Gaps = 8/94 (8%)

Query: 74  GSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVE 133
           G+   K    ++ V  +P   +  E+   F  +        +       G        V 
Sbjct: 1   GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKY--NEKGMPTGE-AMVA 57

Query: 134 FDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           F+    A  A+  L+      +K     +K+   
Sbjct: 58  FESRDEATAAVIDLNDRPIGSRK-----VKLVLG 86

>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 = 44.6 bits (105), Expect = 2e-07
 Identities = 15/72 (20%), Positives = 23/72 (31%), Gaps = 4/72 (5%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           +F+ GL    T+  +   F  F   +E          T        FV F D       +
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECL--VMRDPLTKRS-RGFGFVTFMDQAGVDKVL 59

Query: 145 DALHGYKFDDKK 156
            A   ++ D K 
Sbjct: 60  -AQSRHELDSKT 70

>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 = 44.3 bits (104), Expect = 3e-07
 Identities = 14/72 (19%), Positives = 24/72 (33%), Gaps = 4/72 (5%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           LF+ GL  + T   +   F  +    +          T        FV +   +    AM
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCV--VMRDPNTKRSRGF-GFVTYATVEEVDAAM 65

Query: 145 DALHGYKFDDKK 156
           +A   +K D + 
Sbjct: 66  NA-RPHKVDGRV 76

>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 = 44.0 bits (103), Expect = 4e-07
 Identities = 16/83 (19%), Positives = 29/83 (34%), Gaps = 10/83 (12%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           +++ G PTD T  ++            I++     +          FV FD  + A+  +
Sbjct: 9   VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAF----KGSIFVVFDSIESAKKFV 64

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
               G K+ +       L I F 
Sbjct: 65  -ETPGQKYKETD-----LLILFK 81

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.4 bits (102), Expect = 5e-07
 Identities = 15/72 (20%), Positives = 28/72 (38%), Gaps = 4/72 (5%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           +F+ GL  D T++++   F  F    +      +      R+    FV F + +     M
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDC---TLKLDPITGRSRGFGFVLFKESESVDKVM 58

Query: 145 DALHGYKFDDKK 156
           D    +K + K 
Sbjct: 59  D-QKEHKLNGKV 69

>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 = 43.0 bits (101), Expect = 6e-07
 Identities = 14/72 (19%), Positives = 26/72 (36%), Gaps = 4/72 (5%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           +FV GL  D    ++   F  F    E+  I        ++    CF+ F + +  +  M
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGF---GEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58

Query: 145 DALHGYKFDDKK 156
           +    +     K
Sbjct: 59  EK-KYHNVGLSK 69

>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 = 43.6 bits (102), Expect = 8e-07
 Identities = 12/97 (12%), Positives = 27/97 (27%), Gaps = 12/97 (12%)

Query: 71  NNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLC 130
            ++GS  K   S ++ V GL       ++      F     + ++               
Sbjct: 4   GSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF---------KRQA 54

Query: 131 FVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
            VEF++   A+  +                     ++
Sbjct: 55  LVEFENIDSAKECVTFAADVPV---YIAGQQAFFNYS 88

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 44.5 bits (104), Expect = 8e-07
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 8/83 (9%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           L V+ +PT     ++  LF  +     ++++     R   ++    FV+F     A+ A+
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETR---QSRGYGFVKFQSGSSAQQAI 101

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
             L+G+   +K+     LK+  A
Sbjct: 102 AGLNGFNILNKR-----LKVALA 119

>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 = 43.1 bits (101), Expect = 1e-06
 Identities = 18/101 (17%), Positives = 37/101 (36%), Gaps = 17/101 (16%)

Query: 72  NAGSPLKKG-----ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRA 126
           ++GS  K G      +  L+V GL  + +   ++  F  F   R I  +           
Sbjct: 2   SSGSSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG--------- 52

Query: 127 MVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
               +++++    A+ A   + G+           L++ FA
Sbjct: 53  DSFAYIQYESLDAAQAACAKMRGFPLGGP---DRRLRVDFA 90

>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 = 42.8 bits (100), Expect = 2e-06
 Identities = 18/83 (21%), Positives = 32/83 (38%), Gaps = 8/83 (9%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           +FV  +P + T  +   L   F     +        R   +     F E+ D + A +AM
Sbjct: 11  VFVGNIPYEATEEQ---LKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
             L+G +F  +      L++  A
Sbjct: 68  RNLNGREFSGRA-----LRVDNA 85

>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 = 42.4 bits (99), Expect = 2e-06
 Identities = 20/106 (18%), Positives = 37/106 (34%), Gaps = 14/106 (13%)

Query: 62  INGVPSSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRR 121
           +  VP   +       +K     LF+ GL  + T   + + +  + G     V+ ++P  
Sbjct: 5   LETVPLERKKREKEQFRK-----LFIGGLSFETTEESLRNYYEQW-GKLTDCVVMRDPAS 58

Query: 122 TGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
              R     FV F        AM A   +  D +      ++ + A
Sbjct: 59  KRSRGF--GFVTFSSMAEVDAAM-AARPHSIDGRV-----VEPKRA 96

>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 = 41.9 bits (98), Expect = 3e-06
 Identities = 9/82 (10%), Positives = 26/82 (31%), Gaps = 9/82 (10%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           + +     +      + +   +    E+          GD  +   +V+F   + A  A+
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMN----VCDNLGDHLVGNVYVKFRREEDAEKAV 85

Query: 145 DALHGYKFDDKKPDSPTLKIQF 166
             L+   F+ +      +  + 
Sbjct: 86  IDLNNRWFNGQP-----IHAEL 102

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.3 bits (96), Expect = 4e-06
 Identities = 13/79 (16%), Positives = 26/79 (32%), Gaps = 3/79 (3%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFV---EFDDP 137
           + NL+FV GL       EV      F  + +I  +      +   +          +   
Sbjct: 7   QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 66

Query: 138 KCARTAMDALHGYKFDDKK 156
           + A  A+  ++    D + 
Sbjct: 67  EDALRAIQCVNNVVVDGRT 85

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.7 bits (97), Expect = 4e-06
 Identities = 21/101 (20%), Positives = 41/101 (40%), Gaps = 15/101 (14%)

Query: 82  SNLLFVDGL-PTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCA 140
           +++L V  L P   T + +  LF  +   + ++++  +             V+  D   A
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN--------ALVQMADGNQA 53

Query: 141 RTAMDALHGYKFDDKKPDSPTLKIQFAHFPF-HLPSDGDEK 180
           + AM  L+G+K   K      ++I  +      LP +G E 
Sbjct: 54  QLAMSHLNGHKLHGKP-----IRITLSKHQNVQLPREGQED 89

>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 = 41.5 bits (97), Expect = 4e-06
 Identities = 17/84 (20%), Positives = 30/84 (35%), Gaps = 10/84 (11%)

Query: 84  LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTA 143
            + V+ L    T   +  +F  F    +I    K  +           +++ DP  A+ A
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQA-------LLQYADPVSAQHA 61

Query: 144 MDALHGYKFDDKKPDSPTLKIQFA 167
             +L G           TL+I F+
Sbjct: 62  KLSLDGQNIY---NACCTLRIDFS 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 = 40.5 bits (94), Expect = 7e-06
 Identities = 13/83 (15%), Positives = 26/83 (31%), Gaps = 9/83 (10%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           +FV G+  D     +   F  +     I ++     R   +     FV FDD       +
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD---RGSGKKRGFAFVTFDDHDSVDKIV 61

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
                +  +         +++ A
Sbjct: 62  -IQKYHTVNGHN-----CEVRKA 78

>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 = 40.5 bits (94), Expect = 8e-06
 Identities = 10/88 (11%), Positives = 29/88 (32%), Gaps = 9/88 (10%)

Query: 81  ESNLLFVDGLPTDCTRRE-VSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKC 139
           E   + +  L T+      +   F  F      ++     ++         F+ F++   
Sbjct: 3   EGREIMIRNLSTELLDENLLRESFEGF--GSIEKINIPAGQKEHSFNNCCAFMVFENKDS 60

Query: 140 ARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           A  A+  ++     +++     + +  A
Sbjct: 61  AERAL-QMNRSLLGNRE-----ISVSLA 82

>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 = 40.2 bits (93), Expect = 1e-05
 Identities = 7/79 (8%), Positives = 24/79 (30%), Gaps = 4/79 (5%)

Query: 78  KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDP 137
           ++ +   L++  LP     +E+       +      +  +  R +   +  + F   +  
Sbjct: 14  QEQDPTNLYISNLPLSMDEQEL----ENMLKPFGQVISTRILRDSSGTSRGVGFARMEST 69

Query: 138 KCARTAMDALHGYKFDDKK 156
           +     +   +G       
Sbjct: 70  EKCEAVIGHFNGKFIKTPP 88

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.0 bits (93), Expect = 2e-05
 Identities = 15/87 (17%), Positives = 32/87 (36%), Gaps = 9/87 (10%)

Query: 81  ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCA 140
           ++  +F   L      R++   F      R++R+I     R   R+  + +VEF + +  
Sbjct: 17  DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISD---RNSRRSKGIAYVEFCEIQSV 73

Query: 141 RTAMDALHGYKFDDKKPDSPTLKIQFA 167
                 L G +          + +Q +
Sbjct: 74  P-LAIGLTGQRLLGVP-----IIVQAS 94

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.7 bits (89), Expect = 3e-05
 Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 15/83 (18%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           + + GLP D T +EV  L             ++      D+     FV   + + A  A+
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSD----------YELKYCFVDKYKGTAFVTLLNGEQAEAAI 50

Query: 145 DALHGYKFDDKKPDSPTLKIQFA 167
           +  H  +  +++     L +Q  
Sbjct: 51  NTFHQSRLRERE-----LSVQLQ 68

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.5 bits (91), Expect = 3e-05
 Identities = 21/95 (22%), Positives = 31/95 (32%), Gaps = 15/95 (15%)

Query: 74  GSPLKKGESN-LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFV 132
           GS    G S  ++    LP      E+   F  F     + +             +   V
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG---------GITAIV 51

Query: 133 EFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           EF +P  AR A   L   KF         L +++A
Sbjct: 52  EFLEPLEARKAFRHLAYSKFHHVP-----LYLEWA 81

>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 = 38.5 bits (89), Expect = 4e-05
 Identities = 14/86 (16%), Positives = 25/86 (29%), Gaps = 15/86 (17%)

Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           S+ +FV     D T  E+   F  +    ++ +                FV F D + A+
Sbjct: 5   SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF--------RAFAFVTFADDQIAQ 56

Query: 142 TAMDALHGYKFDDKKPDSPTLKIQFA 167
           +                   + I  A
Sbjct: 57  SLCG--EDLIIKGIS-----VHISNA 75

>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 = 37.8 bits (87), Expect = 1e-04
 Identities = 18/96 (18%), Positives = 33/96 (34%), Gaps = 9/96 (9%)

Query: 72  NAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCF 131
           ++GS L K      F+  LP D T   +   FR                          +
Sbjct: 5   SSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERL---KGFGY 61

Query: 132 VEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
            EF+D     +A+ +L+     +K+     +++  A
Sbjct: 62  AEFEDLDSLLSAL-SLNEESLGNKR-----IRVDVA 91

>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 = 37.0 bits (85), Expect = 1e-04
 Identities = 16/86 (18%), Positives = 32/86 (37%), Gaps = 15/86 (17%)

Query: 83  NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCART 142
           N L++  L    T  ++  LF         +V+ K             FV++ D   A  
Sbjct: 2   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGY---------AFVDYPDQNWAIR 52

Query: 143 AMDALHG-YKFDDKKPDSPTLKIQFA 167
           A++ L G  +   K      +++ ++
Sbjct: 53  AIETLSGKVELHGKI-----MEVDYS 73

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.4 bits (83), Expect = 2e-04
 Identities = 17/87 (19%), Positives = 31/87 (35%), Gaps = 12/87 (13%)

Query: 82  SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 141
           S +L +  LP + T  EV  L  PF     I ++               F+E    + A 
Sbjct: 8   SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG---------KNQAFLELATEEAAI 58

Query: 142 TAMDALHGYKFDDKKPDSPTLKIQFAH 168
           T ++             +  + IQ+++
Sbjct: 59  TMVNYYSAVTPH---LRNQPIYIQYSN 82

>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 = 36.1 bits (83), Expect = 3e-04
 Identities = 9/39 (23%), Positives = 14/39 (35%), Gaps = 5/39 (12%)

Query: 130 CFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAH 168
             V F DP+ A   +  L G  F  ++     +  Q   
Sbjct: 60  ASVSFRDPEEADYCIQTLDGRWFGGRQ-----ITAQAWD 93

>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 = 36.3 bits (83), Expect = 4e-04
 Identities = 11/79 (13%), Positives = 21/79 (26%), Gaps = 9/79 (11%)

Query: 78  KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDP 137
           K G   L F   L     R ++  LF      + I  +           ++L   +  + 
Sbjct: 8   KIG-CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEG-----IILFKEKAKE- 60

Query: 138 KCARTAMDALHGYKFDDKK 156
             A       +      + 
Sbjct: 61  --ALGKAKDANNGNLQLRN 77

>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 = 35.9 bits (82), Expect = 4e-04
 Identities = 14/95 (14%), Positives = 28/95 (29%), Gaps = 15/95 (15%)

Query: 73  AGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFV 132
           +G P  +     + V GLP   + +++    R         V              +  V
Sbjct: 6   SGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK----------DGMGMV 55

Query: 133 EFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           E+   +    A+  L   KF   +      +  + 
Sbjct: 56  EYLRKEDMEYALRKLDDTKFRSHE-----GETSYI 85

>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 = 35.9 bits (82), Expect = 5e-04
 Identities = 20/86 (23%), Positives = 33/86 (38%), Gaps = 6/86 (6%)

Query: 71  NNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLC 130
            ++GS  +    + + + GLP   T  ++ + F P    R    I  + R TG+      
Sbjct: 4   GSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGE-----A 58

Query: 131 FVEFDDPKCARTAMDALHGYKFDDKK 156
            VEF   + A  AM A        + 
Sbjct: 59  DVEFATHEDAVAAM-AKDKANMQHRY 83

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.9 bits (82), Expect = 5e-04
 Identities = 17/84 (20%), Positives = 27/84 (32%), Gaps = 9/84 (10%)

Query: 85  LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 144
           +FV GLP   T   +   F     + +I        R   ++    FV   D   A  A 
Sbjct: 13  IFVGGLPYHTTDASLRKYFEG---FGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 69

Query: 145 DALHGYKFDDKKPDSPTLKIQFAH 168
              +    D +K       +  A+
Sbjct: 70  KDPNPI-IDGRK-----ANVNLAY 87

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.3 bits (81), Expect = 7e-04
 Identities = 16/89 (17%), Positives = 29/89 (32%), Gaps = 8/89 (8%)

Query: 82  SNLLFVDGLPTDCTRREV-SHLFRPFVGYREI--RVIHKEPRRTGDRAMVLCFVEFDDPK 138
            N++  + L  D    E+   +      Y  +    I +             FVEF    
Sbjct: 10  MNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVF 69

Query: 139 CARTAMDALHGYKFDDKKPDSPTLKIQFA 167
             + AM  L G KF ++      +  ++ 
Sbjct: 70  DCQKAMQGLTGRKFANR-----VVVTKYC 93

>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 = 34.2 bits (77), Expect = 0.002
 Identities = 14/97 (14%), Positives = 32/97 (32%), Gaps = 10/97 (10%)

Query: 71  NNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLC 130
           ++     +      LF+  L  + +  E+               +     RTG       
Sbjct: 2   SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISE---LFAKNDLAVVDVRTG-TNRKFG 57

Query: 131 FVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFA 167
           +V+F+  +    A++ L G K    +     +K++  
Sbjct: 58  YVDFESAEDLEKALE-LTGLKVFGNE-----IKLEKP 88

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.7 bits (76), Expect = 0.002
 Identities = 14/73 (19%), Positives = 21/73 (28%), Gaps = 10/73 (13%)

Query: 83  NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCART 142
           N + V GLP   + +++    R         V                 VEF   +    
Sbjct: 1   NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR----------DGTGVVEFVRKEDMTY 50

Query: 143 AMDALHGYKFDDK 155
           A+  L   KF   
Sbjct: 51  AVRKLDNTKFRSH 63

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	184
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.89
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.89
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.89
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.88
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.88
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.88
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.88
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.87
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.87
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.87
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.87
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.87
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.87
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.87
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.87
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.86
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.86
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.85
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.85
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.85
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.85
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.85
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.84
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.84
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.84
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.84
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.84
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.84
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.84
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.84
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.84
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.84
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.83
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.83
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.83
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.83
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.83
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.83
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.82
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.82
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.82
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.82
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.82
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.82
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.82
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.81
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.81
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.81
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.81
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.81
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.8
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.8
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.8
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.8
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.8
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.8
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.8
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.8
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.8
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.79
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.79
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.79
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.78
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.78
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.78
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.77
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.77
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.77
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.74
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.74
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.72
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.71
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.71
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.68
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.68
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.65
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.64
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	99.62
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.59
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.52
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.48
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.46
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.43
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.88
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.28
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.22
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.37

>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=99.89  E-value=4.5e-23  Score=138.74  Aligned_cols=84  Identities=19%  Similarity=0.311  Sum_probs=76.3

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ..++++|||+|||.++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d---~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~--   78 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD---RRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQT--   78 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---TTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEE--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccccccccc---ccccccccceeEEECCHHHHHHHHHHcCCCEECCEE--
Confidence            456789999999999999999999999999999999884   334799999999999999999999999999999997  


Q ss_pred             CCceEEEeecCC
Q 030012          159 SPTLKIQFAHFP  170 (184)
Q Consensus       159 ~~~l~V~~a~~~  170 (184)
                         |+|+||...
T Consensus        79 ---l~V~~a~~k   87 (88)
T d1rk8a_          79 ---IQVDWCFVK   87 (88)
T ss_dssp             ---CEEEESEEC
T ss_pred             ---EEEEEecCC
Confidence               999999754

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=8.2e-23  Score=138.85  Aligned_cols=84  Identities=23%  Similarity=0.302  Sum_probs=76.8

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ...+++|||+|||+++|+++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|+.|++.|||..+.|+.  
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~---~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~--   78 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD---KMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRI--   78 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---TTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEE--
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccc---cccccccceEEEEECCHHHHHHHHHHhCCCEECCEE--
Confidence            356789999999999999999999999999999999884   334789999999999999999999999999999997  


Q ss_pred             CCceEEEeecCC
Q 030012          159 SPTLKIQFAHFP  170 (184)
Q Consensus       159 ~~~l~V~~a~~~  170 (184)
                         |+|+|+...
T Consensus        79 ---i~V~~a~~~   87 (93)
T d1h2vz_          79 ---IRTDWDAGF   87 (93)
T ss_dssp             ---CEEEEESCC
T ss_pred             ---EEEEEcCCC
Confidence               999999754

>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=99.89  E-value=3.7e-23  Score=137.14  Aligned_cols=80  Identities=28%  Similarity=0.426  Sum_probs=74.2

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCc
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPT  161 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~  161 (184)
                      +++|||+|||+++++++|+++|++||.|.+++++.+.   ..++++|||||+|.+.++|++|++.|||..+.|+.     
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~---~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~-----   73 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDY---KTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKR-----   73 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEET---TTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEE-----
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeec---ccCCccccceEEECCHHHHHHHHHHhCCCEECCEE-----
Confidence            5789999999999999999999999999999998753   33789999999999999999999999999999997     


Q ss_pred             eEEEeecC
Q 030012          162 LKIQFAHF  169 (184)
Q Consensus       162 l~V~~a~~  169 (184)
                      |+|+||++
T Consensus        74 l~v~~a~p   81 (82)
T d1b7fa1          74 LKVSYARP   81 (82)
T ss_dssp             CEEEECCC
T ss_pred             EEEEEcCC
Confidence            99999975

>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=99.88  E-value=9.2e-23  Score=138.58  Aligned_cols=85  Identities=18%  Similarity=0.176  Sum_probs=76.9

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||.++|+++|+++|++||.|++++++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d---~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~--   80 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKD---RVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKP--   80 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBC---SSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCB--
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeec---ccccccccceEEEECCHHHHHHHHHHcCCCEECCEE--
Confidence            345679999999999999999999999999999999874   344789999999999999999999999999999997  


Q ss_pred             CCceEEEeecCCC
Q 030012          159 SPTLKIQFAHFPF  171 (184)
Q Consensus       159 ~~~l~V~~a~~~~  171 (184)
                         |+|+||+...
T Consensus        81 ---l~V~~A~~~~   90 (93)
T d1x5ua1          81 ---IRVNKASAHN   90 (93)
T ss_dssp             ---CEEEETTTTS
T ss_pred             ---EEEEEcCCCC
Confidence               9999997543

>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=99.88  E-value=1.2e-22  Score=137.16  Aligned_cols=83  Identities=22%  Similarity=0.422  Sum_probs=76.4

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      .+..++|||+|||.++++++|+++|++||.|.+|+++.+.   .+++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~---~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~--   79 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDK---TTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLI--   79 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECS---SSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEE--
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccc---cccccccceeEEECCHHHHHHHHHHhCCCEECCEE--
Confidence            4567899999999999999999999999999999998843   34789999999999999999999999999999997  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |+|+||++
T Consensus        80 ---i~v~~akp   87 (90)
T d2cq0a1          80 ---LNVEWAKP   87 (90)
T ss_dssp             ---CEEEESSC
T ss_pred             ---EEEEeeeC
Confidence               99999974

>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=99.88  E-value=1.6e-22  Score=133.93  Aligned_cols=80  Identities=25%  Similarity=0.462  Sum_probs=73.8

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCc
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPT  161 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~  161 (184)
                      .++|||+|||.++++++|+++|++||.|.+|+++.+   ...++++|||||+|.+.++|++|++.|||..+.|+.     
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~---~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~-----   73 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRD---KITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKT-----   73 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEC---TTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE-----
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceee---ccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEE-----
Confidence            357999999999999999999999999999999874   334789999999999999999999999999999997     


Q ss_pred             eEEEeecC
Q 030012          162 LKIQFAHF  169 (184)
Q Consensus       162 l~V~~a~~  169 (184)
                      |+|+||++
T Consensus        74 l~v~~AkP   81 (82)
T d1fxla1          74 IKVSYARP   81 (82)
T ss_dssp             CEEEECCC
T ss_pred             EEEEEeeC
Confidence            99999974

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=3e-22  Score=133.80  Aligned_cols=81  Identities=25%  Similarity=0.425  Sum_probs=73.4

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      .+++|||+|||+++|+++|+++|++||.|.+++++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+.   .
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d---~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~---~   78 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVD---QVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGAT---E   78 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---TTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCS---S
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccc---cccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCC---E
Confidence            4678999999999999999999999999999999984   334789999999999999999999999999999863   4


Q ss_pred             ceEEEee
Q 030012          161 TLKIQFA  167 (184)
Q Consensus       161 ~l~V~~a  167 (184)
                      +|+|+||
T Consensus        79 ~i~V~~A   85 (85)
T d1fxla2          79 PITVKFA   85 (85)
T ss_dssp             CCEEEEC
T ss_pred             EEEEEeC
Confidence            6999997

>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=99.87  E-value=2.5e-22  Score=138.63  Aligned_cols=85  Identities=24%  Similarity=0.469  Sum_probs=76.9

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      +++++|||+|||+++++++|+++|++||.|++++++.+   +.+++++|||||+|.+.++|+.|++.|||..|.|+.   
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~---~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~---   89 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID---KQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKR---   89 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEEC---SSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEE---
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeee---cccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEE---
Confidence            45678999999999999999999999999999999874   334799999999999999999999999999999997   


Q ss_pred             CceEEEeecCCCC
Q 030012          160 PTLKIQFAHFPFH  172 (184)
Q Consensus       160 ~~l~V~~a~~~~~  172 (184)
                        |+|+|++....
T Consensus        90 --i~V~~a~~k~~  100 (102)
T d2cpza1          90 --LKVQLKRSKND  100 (102)
T ss_dssp             --CEEECCCCSCC
T ss_pred             --EEEEEeCCCCC
Confidence              99999976543

>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=99.87  E-value=5.3e-22  Score=144.02  Aligned_cols=88  Identities=20%  Similarity=0.374  Sum_probs=78.5

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++|+++|+++|++||.|.+|+++.+.   .+++++|||||+|.+.++|++|++.|||.+|.|+.  
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~---~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~--  113 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDR---ETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKR--  113 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEET---TTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCE--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhcccccccccccc---ccccccceeeEEECCHHHHHHHHHHhCCCEECCEE--
Confidence            3456799999999999999999999999999999998853   34789999999999999999999999999999998  


Q ss_pred             CCceEEEeecCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLP  174 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~  174 (184)
                         |+|+|++....++
T Consensus       114 ---l~V~~a~~~~~~p  126 (139)
T d1u6fa1         114 ---LKVALAASGHQRP  126 (139)
T ss_dssp             ---EEEEESSCCCCCC
T ss_pred             ---EEEEEcCCCCCCC
Confidence               9999997655443

>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=99.87  E-value=8.9e-23  Score=137.51  Aligned_cols=83  Identities=19%  Similarity=0.360  Sum_probs=75.7

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ...++|||+|||+++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+.   
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d---~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~---   76 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD---YETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRT---   76 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCC---SSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEE---
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccc---cccccccceeEEEECCHHHHHHHHHHcCCCEECCEE---
Confidence            34689999999999999999999999999999999874   334789999999999999999999999999999997   


Q ss_pred             CceEEEeecCC
Q 030012          160 PTLKIQFAHFP  170 (184)
Q Consensus       160 ~~l~V~~a~~~  170 (184)
                        |+|+||++.
T Consensus        77 --l~v~~a~p~   85 (89)
T d2cqba1          77 --IRVNLAKPM   85 (89)
T ss_dssp             --EEEEECCCC
T ss_pred             --EEEEEeCCC
Confidence              999999754

>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=99.87  E-value=4.5e-22  Score=136.48  Aligned_cols=85  Identities=20%  Similarity=0.280  Sum_probs=76.7

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ..+++|||+|||+++++++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.|||+.+.|+.   
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d---~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~---   79 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPID---SLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRM---   79 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCC---TTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCE---
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeeccc---ccccccCcceEEEECCHHHHHHHHHHcCCCEECCEE---
Confidence            44678999999999999999999999999999999874   334789999999999999999999999999999997   


Q ss_pred             CceEEEeecCCCC
Q 030012          160 PTLKIQFAHFPFH  172 (184)
Q Consensus       160 ~~l~V~~a~~~~~  172 (184)
                        |+|.+++....
T Consensus        80 --i~V~~a~~~~~   90 (99)
T d1whwa_          80 --LHVLPSTIKKE   90 (99)
T ss_dssp             --EEEEECCCCST
T ss_pred             --EEEEECCCCCc
Confidence              99999986543

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.87  E-value=4.8e-22  Score=135.25  Aligned_cols=86  Identities=23%  Similarity=0.398  Sum_probs=76.8

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHh-cCCeeCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDAL-HGYKFDDKKP  157 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l-~g~~~~g~~~  157 (184)
                      ...+++|||+|||+++++++|+++|++||.|.+|+|+.+..  .+|+++|||||+|.+.++|++|++.| ||..+.|+. 
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~--~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~-   81 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMT--GTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRR-   81 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCS--SSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCB-
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccc--cCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEE-
Confidence            35668899999999999999999999999999999987532  23789999999999999999999998 899999997 


Q ss_pred             CCCceEEEeecCCC
Q 030012          158 DSPTLKIQFAHFPF  171 (184)
Q Consensus       158 ~~~~l~V~~a~~~~  171 (184)
                          |+|+||+...
T Consensus        82 ----l~V~~A~~~~   91 (94)
T d2cpha1          82 ----LVLEWADSEV   91 (94)
T ss_dssp             ----CEEEECCCCC
T ss_pred             ----EEEEEcCCCC
Confidence                9999997644

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.87  E-value=2.2e-22  Score=134.26  Aligned_cols=81  Identities=22%  Similarity=0.366  Sum_probs=73.2

Q ss_pred             EEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceEE
Q 030012           85 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKI  164 (184)
Q Consensus        85 lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~V  164 (184)
                      |||+|||+++|+++|+++|++||.|.+++++.+......++++|||||+|.+.++|++|++.|||..+.|+.     |+|
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~-----i~V   75 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHK-----LEV   75 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEE-----CEE
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEE-----EEE
Confidence            799999999999999999999999999999886544433468999999999999999999999999999997     999


Q ss_pred             EeecCC
Q 030012          165 QFAHFP  170 (184)
Q Consensus       165 ~~a~~~  170 (184)
                      +|++..
T Consensus        76 ~~a~~~   81 (85)
T d2cpfa1          76 RISERA   81 (85)
T ss_dssp             ECSSCS
T ss_pred             EECCCC
Confidence            998643

>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=99.87  E-value=7.9e-22  Score=131.63  Aligned_cols=82  Identities=18%  Similarity=0.327  Sum_probs=73.1

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ..+++|||+|||+++++++|+++|++||.|.+++++.+.   .+++++|||||+|.+.++|++|++.|||..+.|..   
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~---~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~---   77 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK---LTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGS---   77 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCS---
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeeccc---ccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCC---
Confidence            356789999999999999999999999999999998853   34789999999999999999999999999998731   


Q ss_pred             CceEEEee
Q 030012          160 PTLKIQFA  167 (184)
Q Consensus       160 ~~l~V~~a  167 (184)
                      .+|+|+||
T Consensus        78 ~~l~V~~A   85 (85)
T d1b7fa2          78 QPLSVRLA   85 (85)
T ss_dssp             SCCEEEEC
T ss_pred             eEEEEEEC
Confidence            25999997

>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=99.87  E-value=2.6e-22  Score=134.15  Aligned_cols=81  Identities=25%  Similarity=0.396  Sum_probs=74.6

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      ++|||+|||+++|+++|+++|++||.|.+|+++.+   +.+|+++|||||+|.+.++|+.|++.|||..+.|+.     |
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d---~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~-----l   73 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKD---SATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK-----L   73 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECC---CSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSC-----C
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeecc---ccccccceeEEEEECCHHHHHHHHHHhCCCEECCEE-----E
Confidence            57999999999999999999999999999999884   344789999999999999999999999999999998     9


Q ss_pred             EEEeecCCC
Q 030012          163 KIQFAHFPF  171 (184)
Q Consensus       163 ~V~~a~~~~  171 (184)
                      +|+||+...
T Consensus        74 ~V~~A~~~~   82 (85)
T d2u2fa_          74 LVQRASVGA   82 (85)
T ss_dssp             EEEECCCCC
T ss_pred             EEEECCCCC
Confidence            999997543

>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=99.87  E-value=2.2e-22  Score=132.90  Aligned_cols=77  Identities=25%  Similarity=0.359  Sum_probs=72.4

Q ss_pred             EEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceE
Q 030012           84 LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLK  163 (184)
Q Consensus        84 ~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~  163 (184)
                      .|||+|||+++||++|+++|++||.|.+++|+.+   +.+++++|||||+|.+.++|+.|++.|||..+.|+.     |+
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d---~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~-----i~   73 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRD---MITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKP-----VR   73 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---TTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEE-----CE
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEec---ccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEE-----EE
Confidence            6999999999999999999999999999999984   344789999999999999999999999999999997     99


Q ss_pred             EEeec
Q 030012          164 IQFAH  168 (184)
Q Consensus       164 V~~a~  168 (184)
                      |+||+
T Consensus        74 v~~a~   78 (80)
T d1cvja1          74 IMWSQ   78 (80)
T ss_dssp             EEECC
T ss_pred             EEEeC
Confidence            99985

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=6.1e-22  Score=136.89  Aligned_cols=87  Identities=24%  Similarity=0.293  Sum_probs=75.9

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ...++|||+|||++++|++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.+++ .+.|+.   
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d---~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~---   80 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITD---RQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRK---   80 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCC---SSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEE---
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceecccc---ccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEE---
Confidence            44578999999999999999999999999999999874   33478999999999999999999998876 799997   


Q ss_pred             CceEEEeecCCCCCCC
Q 030012          160 PTLKIQFAHFPFHLPS  175 (184)
Q Consensus       160 ~~l~V~~a~~~~~~~~  175 (184)
                        |+|+|+......++
T Consensus        81 --l~V~~a~~~~~pr~   94 (103)
T d2cqda1          81 --ANVNLAYLGAKPRS   94 (103)
T ss_dssp             --CEEEESTTTCCCCC
T ss_pred             --EEEEEcCCCCCCCC
Confidence              99999976544433

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=4.7e-22  Score=134.03  Aligned_cols=86  Identities=24%  Similarity=0.411  Sum_probs=76.8

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ...++|||+|||+++++++|+++|++||.|..+.++..   ...++++|||||+|.+.++|+.|++.|||+.+.|+.   
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~---~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~---   76 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKD---RETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQ---   76 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCC---SSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCC---
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccc---cccccccceEEEEECCHHHHHHHHHHcCCCEECCEE---
Confidence            34678999999999999999999999999999988774   334789999999999999999999999999999998   


Q ss_pred             CceEEEeecCCCCC
Q 030012          160 PTLKIQFAHFPFHL  173 (184)
Q Consensus       160 ~~l~V~~a~~~~~~  173 (184)
                        |+|+||......
T Consensus        77 --l~V~~a~~~~~~   88 (90)
T d1x5sa1          77 --IRVDQAGKSSDN   88 (90)
T ss_dssp             --CEEEEEECCCCC
T ss_pred             --EEEEEcCCCCCC
Confidence              999999765543

>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=99.86  E-value=1e-21  Score=130.51  Aligned_cols=77  Identities=19%  Similarity=0.378  Sum_probs=70.7

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      .++++|||+|||+++|+++|+++|++||.|.+|+++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+.   
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~---~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~---   80 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYD---QQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR---   80 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEEC---SSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEE---
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCcccccccc---ccccccccceEEEECCHHHHHHHHHHcCCCEECCEE---
Confidence            45689999999999999999999999999999999874   334789999999999999999999999999999987   


Q ss_pred             CceEE
Q 030012          160 PTLKI  164 (184)
Q Consensus       160 ~~l~V  164 (184)
                        |+|
T Consensus        81 --i~V   83 (83)
T d2cqca1          81 --IRV   83 (83)
T ss_dssp             --EEE
T ss_pred             --eEC
Confidence              876

>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=99.86  E-value=8e-22  Score=129.62  Aligned_cols=77  Identities=22%  Similarity=0.315  Sum_probs=71.8

Q ss_pred             EEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceE
Q 030012           84 LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLK  163 (184)
Q Consensus        84 ~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~  163 (184)
                      +|||+|||+++++++|+++|++||.|.++++..+++    ++++|||||+|.+.++|++|++.|||..+.|+.     |+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~----g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~-----l~   72 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS----GRSLGTADVHFERKADALKAMKQYNGVPLDGRP-----MN   72 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSC----CCSCCEEEEEESCHHHHHHHHHHHTTCEETTEE-----CE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeec----cccceeEEEEECCHHHHHHHHHHhCCCEECCEE-----EE
Confidence            699999999999999999999999999999987543    788999999999999999999999999999997     99


Q ss_pred             EEeecC
Q 030012          164 IQFAHF  169 (184)
Q Consensus       164 V~~a~~  169 (184)
                      |+++.+
T Consensus        73 V~~a~S   78 (78)
T d1no8a_          73 IQLVTS   78 (78)
T ss_dssp             EEEECC
T ss_pred             EEEeeC
Confidence            999853

>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=99.85  E-value=1.8e-21  Score=132.48  Aligned_cols=82  Identities=24%  Similarity=0.521  Sum_probs=73.6

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ...+++|||+|||+++|+++|+++|++||.|..+++..+      ..++|||||+|++.++|+.|++.|||+++.|++  
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~------~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~--   82 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR------RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYR--   82 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS------SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEE--
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc------ccccceEEEEECCHHHHHHHHHHhCCCEECCEE--
Confidence            355679999999999999999999999999999987543      356789999999999999999999999999998  


Q ss_pred             CCceEEEeecCCC
Q 030012          159 SPTLKIQFAHFPF  171 (184)
Q Consensus       159 ~~~l~V~~a~~~~  171 (184)
                         |+|+||+..+
T Consensus        83 ---l~V~~a~~~r   92 (95)
T d1x4aa1          83 ---LRVEFPRSGR   92 (95)
T ss_dssp             ---CEEECCCCCC
T ss_pred             ---EEEEeccCCC
Confidence               9999998653

>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=99.85  E-value=2.2e-21  Score=130.77  Aligned_cols=85  Identities=27%  Similarity=0.441  Sum_probs=75.7

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ...+++|||+|||.++|+++|+++|++||.|.+|+++.+..     ..+|||||+|.+.++|+.|++.|||..+.|+.  
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~-----~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~--   77 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT-----SNDPYCFVEFYEHRDAAAALAAMNGRKILGKE--   77 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC-----SSCCEEEEEESSHHHHHHHHHHHTTEEETTEE--
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccC-----ccceeeEEEECCHHHHHHHHHHcCCCEECCEE--
Confidence            34568999999999999999999999999999999987532     24789999999999999999999999999997  


Q ss_pred             CCceEEEeecCCCCC
Q 030012          159 SPTLKIQFAHFPFHL  173 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~  173 (184)
                         |+|+||+.+..+
T Consensus        78 ---i~v~~a~~~~~~   89 (90)
T d2cqia1          78 ---VKVNWATTPSSQ   89 (90)
T ss_dssp             ---EEEEECCCTTCC
T ss_pred             ---EEEEEcCCCCCC
Confidence               999999876654

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=2e-21  Score=136.30  Aligned_cols=80  Identities=23%  Similarity=0.369  Sum_probs=73.5

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ...+++|||+|||.++++++|+++|++||.|++|++..+      ++++|||||+|.+.++|..|++.|||..|.|+.  
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~------~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~--   75 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT------PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRY--   75 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS------TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEE--
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc------CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEE--
Confidence            456789999999999999999999999999999998753      467899999999999999999999999999997  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |+|.|+..
T Consensus        76 ---l~V~~a~~   83 (114)
T d2f9da1          76 ---LVVLYYNA   83 (114)
T ss_dssp             ---CEEEECCH
T ss_pred             ---EEEEEcCC
Confidence               99999864

>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=99.85  E-value=5.6e-22  Score=137.16  Aligned_cols=83  Identities=20%  Similarity=0.352  Sum_probs=75.5

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ..++|||+|||+++++++|+++|++||.|.+|+++.+.   .+++++|||||+|.+.++|++|++.|||..+.|+.    
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~---~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~----   79 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDR---ETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRA----   79 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEET---TTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSC----
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhcccccccccccccc---ceeccCCceEEEECCHHHHHHHHHHcCCCEECCEE----
Confidence            34789999999999999999999999999999998753   33789999999999999999999999999999998    


Q ss_pred             ceEEEeecCCC
Q 030012          161 TLKIQFAHFPF  171 (184)
Q Consensus       161 ~l~V~~a~~~~  171 (184)
                       |+|+|+....
T Consensus        80 -i~V~~a~~~~   89 (104)
T d1p1ta_          80 -LRVDNAASEK   89 (104)
T ss_dssp             -BEEEETTCTT
T ss_pred             -EEEEECCCCC
Confidence             9999987643

>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=99.85  E-value=1.1e-21  Score=129.76  Aligned_cols=79  Identities=14%  Similarity=0.229  Sum_probs=68.3

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      ++|||+|||+++|+++|+++|++||.|..+.++.+   ...++++|||||+|.+.++|++|++.|||..+.|+.     |
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~---~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~-----i   73 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPS---LRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYT-----L   73 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC----------CCEEEEECSSHHHHHHHHHHHTTCEETTEE-----C
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecc---cccccccceeEEEECCHHHHHHHHHHhCCCEECCEE-----E
Confidence            69999999999999999999999999988877653   233789999999999999999999999999999997     9


Q ss_pred             EEEeecC
Q 030012          163 KIQFAHF  169 (184)
Q Consensus       163 ~V~~a~~  169 (184)
                      +|+|+++
T Consensus        74 ~V~~a~P   80 (81)
T d2ghpa1          74 VTKVSNP   80 (81)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999975

>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=99.84  E-value=1e-20  Score=128.22  Aligned_cols=81  Identities=22%  Similarity=0.384  Sum_probs=73.9

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++++++|+++|++||.|.+|+++.+.     +.++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~-----~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~--   80 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-----RGSKGFGFVTFENSADADRAREKLHGTVVEGRK--   80 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT-----TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEE--
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc-----cCCcceeEEEECCHHHHHHHHHHcCCCEECCEE--
Confidence            4556789999999999999999999999999999998753     236899999999999999999999999999998  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |+|+||+.
T Consensus        81 ---l~V~~A~~   88 (93)
T d2cq3a1          81 ---IEVNNATA   88 (93)
T ss_dssp             ---CEEEECCS
T ss_pred             ---EEEEecCc
Confidence               99999975

>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=99.84  E-value=8.3e-21  Score=129.49  Aligned_cols=84  Identities=20%  Similarity=0.385  Sum_probs=74.6

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhc------CCe
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALH------GYK  151 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~------g~~  151 (184)
                      ...++++|||+|||+++|+++|+++|++||.|.+++++.+   +..++++|||||+|.+.++|++|++.||      |..
T Consensus         4 ~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~---~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~   80 (98)
T d1x4ha1           4 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLH---PDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLK   80 (98)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBC---SSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEE
T ss_pred             CCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccc---cccccccceEEEEEcCHHHHHHHHHHcccccccCCcE
Confidence            4566789999999999999999999999999999998774   3346889999999999999999999986      678


Q ss_pred             eCCCCCCCCceEEEeecC
Q 030012          152 FDDKKPDSPTLKIQFAHF  169 (184)
Q Consensus       152 ~~g~~~~~~~l~V~~a~~  169 (184)
                      +.|+.     |+|+|++.
T Consensus        81 ~~gr~-----l~v~~a~~   93 (98)
T d1x4ha1          81 LDGRQ-----LKVDLAVT   93 (98)
T ss_dssp             SSSCE-----EEEECCCC
T ss_pred             ECCEE-----EEEEECCC
Confidence            88887     99999975

>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=99.84  E-value=8.8e-21  Score=127.96  Aligned_cols=83  Identities=17%  Similarity=0.198  Sum_probs=73.3

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++|+++|+++|++||.|.+|+|+.+   +.+|+++|||||+|.+.++|++|++.  ...++|+.  
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d---~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~--   77 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKD---LKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRW--   77 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEEC---SSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEE--
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccC---CCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEE--
Confidence            456789999999999999999999999999999999985   33489999999999999999999984  45889987  


Q ss_pred             CCceEEEeecCCC
Q 030012          159 SPTLKIQFAHFPF  171 (184)
Q Consensus       159 ~~~l~V~~a~~~~  171 (184)
                         |.|.++....
T Consensus        78 ---i~v~~a~~k~   87 (90)
T d2cqga1          78 ---CDCKLPNSKQ   87 (90)
T ss_dssp             ---EEEECCCTTC
T ss_pred             ---eEEEeCCCCC
Confidence               9999997643

>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=99.84  E-value=2e-21  Score=130.81  Aligned_cols=80  Identities=18%  Similarity=0.308  Sum_probs=72.8

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCc
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPT  161 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~  161 (184)
                      ..+|||+|||+++++++|+++|++||.|.+++++.+.     +.++|||||+|.+.++|++|++.|||..+.|+.     
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~-----~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~-----   77 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-----NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRK-----   77 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT-----TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEE-----
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec-----CCCcceeEEEECCHHHHHHHHHHcCCCEECCEE-----
Confidence            4689999999999999999999999999999998753     346899999999999999999999999999997     


Q ss_pred             eEEEeecCCC
Q 030012          162 LKIQFAHFPF  171 (184)
Q Consensus       162 l~V~~a~~~~  171 (184)
                      |+|+|++...
T Consensus        78 i~V~~a~~~~   87 (89)
T d1cvja2          78 VFVGRFKSRK   87 (89)
T ss_dssp             EEEEECCCTT
T ss_pred             EEEEECCCCC
Confidence            9999997543

>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=99.84  E-value=1e-20  Score=130.57  Aligned_cols=87  Identities=20%  Similarity=0.357  Sum_probs=74.2

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ..+.++|||+|||+++|+++|+++|+.|| +++++++.+.  ...++++|||||+|.+.++|++|+ .||+.+|.|+.  
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~--~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~--   85 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREP--SNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKR--   85 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCS--SCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEE--
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeee--ccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEE--
Confidence            34568999999999999999999999998 8888887653  234789999999999999998777 59999999998  


Q ss_pred             CCceEEEeecCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLP  174 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~  174 (184)
                         |+|+||+....+.
T Consensus        86 ---l~V~~a~~~~~~~   98 (104)
T d1wi8a_          86 ---IRVDVADQAQDKD   98 (104)
T ss_dssp             ---CEEEECCCCCCCC
T ss_pred             ---EEEEECCCCCCCC
Confidence               9999998655443

>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=99.84  E-value=1.1e-20  Score=125.54  Aligned_cols=78  Identities=31%  Similarity=0.606  Sum_probs=69.3

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      .+++++|||+|||.++++++|+++|++||.|.+|+++.+        .+|||||+|.+.++|+.|++.|||+.+.+.+  
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~--------~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~--   74 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN--------RHDIAFVEFTTELQSNAAKEALQGFKITPTH--   74 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT--------TCSCEEEEESSHHHHHHHHHHHTTCBSSTTC--
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc--------cceeEEEecCCHHHHHHHHHHhCCcEeCCCc--
Confidence            456789999999999999999999999999999999752        2569999999999999999999999996532  


Q ss_pred             CCceEEEeec
Q 030012          159 SPTLKIQFAH  168 (184)
Q Consensus       159 ~~~l~V~~a~  168 (184)
                        +|+|+||+
T Consensus        75 --~i~v~~ak   82 (83)
T d2b0ga1          75 --AMKITFAK   82 (83)
T ss_dssp             --BCEEEECC
T ss_pred             --EEEEEEec
Confidence              49999997

>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=99.84  E-value=7.8e-21  Score=126.59  Aligned_cols=80  Identities=19%  Similarity=0.259  Sum_probs=72.5

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ...++|||+|||+++|+++|+++|++||.|.+++|+.+   +.+++++|||||+|.+.++|++|++ +++..+.|+.   
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d---~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~---   76 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRD---PNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRV---   76 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---TTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEE---
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeeccc---ccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEE---
Confidence            34579999999999999999999999999999999884   3447999999999999999999997 6999999997   


Q ss_pred             CceEEEeec
Q 030012          160 PTLKIQFAH  168 (184)
Q Consensus       160 ~~l~V~~a~  168 (184)
                        |+|..|.
T Consensus        77 --i~V~~A~   83 (84)
T d1l3ka1          77 --VEPKRAV   83 (84)
T ss_dssp             --CEEEECC
T ss_pred             --EEEEeee
Confidence              9999875

>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=99.84  E-value=7.4e-21  Score=130.50  Aligned_cols=86  Identities=20%  Similarity=0.367  Sum_probs=73.9

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEE--------EEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYRE--------IRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHG  149 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~--------v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g  149 (184)
                      ....+++|||+|||+++|+++|+++|++||.|..        +.+..   ++..++++|||||+|.+.++|++|++.|||
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~---d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g   80 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYL---DKETGKPKGDATVSYEDPPTAKAAVEWFDG   80 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCB---CTTTCSBCSEEEEEBSSHHHHHHHHHHHTT
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEee---ccccccccceeeEEecCHHHHHHHHHHhCC
Confidence            4566789999999999999999999999998853        33333   334478999999999999999999999999


Q ss_pred             CeeCCCCCCCCceEEEeecCCC
Q 030012          150 YKFDDKKPDSPTLKIQFAHFPF  171 (184)
Q Consensus       150 ~~~~g~~~~~~~l~V~~a~~~~  171 (184)
                      +.+.|+.     |+|+||+...
T Consensus        81 ~~~~gr~-----i~V~~a~~~~   97 (101)
T d2cpea1          81 KDFQGSK-----LKVSLARKKP   97 (101)
T ss_dssp             CEETTEE-----CEEECSSCCC
T ss_pred             CEECCEE-----EEEEEcCCCC
Confidence            9999997     9999998643

>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=99.84  E-value=2.3e-21  Score=133.58  Aligned_cols=79  Identities=20%  Similarity=0.381  Sum_probs=72.4

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ..++|||+|||+++++++|+++|+.||.|.+|+|+.+   +.+|+++|||||+|.+.++|++|++ |||..+.|+.    
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d---~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~----   88 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISD---RNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVP----   88 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCS---CCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEE----
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeec---CCCccccceEEEEECCHHHHHHHHH-HCCCEECCEE----
Confidence            3579999999999999999999999999999999874   3347899999999999999999995 9999999997    


Q ss_pred             ceEEEeec
Q 030012          161 TLKIQFAH  168 (184)
Q Consensus       161 ~l~V~~a~  168 (184)
                       |+|+++.
T Consensus        89 -l~V~~a~   95 (101)
T d2cq4a1          89 -IIVQASQ   95 (101)
T ss_dssp             -EEEEEHH
T ss_pred             -EEEEECC
Confidence             9999975

>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=99.84  E-value=2.7e-21  Score=128.30  Aligned_cols=78  Identities=13%  Similarity=0.320  Sum_probs=69.9

Q ss_pred             EEEcCCCCCCcHHHHHHhhcCCCCEEEE-EEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceE
Q 030012           85 LFVDGLPTDCTRREVSHLFRPFVGYREI-RVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLK  163 (184)
Q Consensus        85 lfVgnLp~~~te~~L~~~F~~~G~i~~v-~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~  163 (184)
                      |||+|||+++|+++|+++|++||.|.++ +++.+   +.+++++|||||+|.+.++|++|++.|||..+.|+.     |+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~---~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~-----l~   72 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRD---PDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRP-----IT   72 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCC---TTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEE-----CE
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEee---ccccccCceEEEEECCHHHHHHHHHhCCCcEECCEE-----EE
Confidence            7999999999999999999999999765 66653   334789999999999999999999999999999997     99


Q ss_pred             EEeecCC
Q 030012          164 IQFAHFP  170 (184)
Q Consensus       164 V~~a~~~  170 (184)
                      |+||...
T Consensus        73 v~~a~~k   79 (83)
T d1x5ta1          73 VSYAFKK   79 (83)
T ss_dssp             EEESCCC
T ss_pred             EEEecCC
Confidence            9999753

>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=99.83  E-value=2.3e-21  Score=127.15  Aligned_cols=76  Identities=21%  Similarity=0.302  Sum_probs=70.0

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      ++|||+|||+++|+++|+++|++||.|.+++++.+   +.+++++|||||+|.+.++|++|++ +++..++|+.     |
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d---~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~-----i   71 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRD---PLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKT-----I   71 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECC---CCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCC-----C
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecc---cCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeE-----E
Confidence            57999999999999999999999999999999874   3447899999999999999999997 7999999997     9


Q ss_pred             EEEee
Q 030012          163 KIQFA  167 (184)
Q Consensus       163 ~V~~a  167 (184)
                      +|++|
T Consensus        72 ~V~~A   76 (77)
T d1uawa_          72 DPKVA   76 (77)
T ss_dssp             EEEEC
T ss_pred             EEEEC
Confidence            99886

>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=99.83  E-value=1e-20  Score=126.92  Aligned_cols=78  Identities=15%  Similarity=0.267  Sum_probs=69.6

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeC-CCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFD-DKKPD  158 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~-g~~~~  158 (184)
                      +++++|||+|||.++++++|+++|++||.|.++.+..       ++++|||||+|++.++|.+|+..|||+.+. |+.  
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~-------~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~--   78 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF-------QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHH--   78 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC-------SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCB--
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee-------ecccceeEEEECCHHHHHHHHHhccCCEecCCCE--
Confidence            4578999999999999999999999999999887764       345679999999999999999999999984 676  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |+|+|+++
T Consensus        79 ---l~v~~sk~   86 (88)
T d2adca2          79 ---LRVSFSKS   86 (88)
T ss_dssp             ---CEEEECSS
T ss_pred             ---EEEEeCCC
Confidence               99999975

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=2.7e-20  Score=128.02  Aligned_cols=81  Identities=11%  Similarity=0.259  Sum_probs=71.2

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||.++++++|+++|++||.|..+++..+.+    ++++|||||+|.+.++|++|++.|||..|.|+.  
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~----~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~--   88 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSS----GTSRGVGFARMESTEKCEAVIGHFNGKFIKTPP--   88 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSS----SCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCT--
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccc----cccccceeEEeCCHHHHHHHHHHhCCCEECCcC--
Confidence            34567999999999999999999999999999999887532    688999999999999999999999999999986  


Q ss_pred             CCceEEEeec
Q 030012          159 SPTLKIQFAH  168 (184)
Q Consensus       159 ~~~l~V~~a~  168 (184)
                         +.|.+++
T Consensus        89 ---~~v~~~~   95 (101)
T d1x5oa1          89 ---GVSAPTE   95 (101)
T ss_dssp             ---TSCCCSS
T ss_pred             ---CccCCCC
Confidence               6555543

>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=99.83  E-value=2.3e-20  Score=122.61  Aligned_cols=77  Identities=16%  Similarity=0.287  Sum_probs=70.1

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCc
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPT  161 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~  161 (184)
                      -++|||+|||+++|+++|+++|++||.|..+++..++   .+++++|||||+|.+.++|++|++ ++|.+|+|+.     
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~---~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~-----   72 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR---GSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHN-----   72 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEE-----
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCC---CCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEE-----
Confidence            4789999999999999999999999999999998743   347899999999999999999985 8999999997     


Q ss_pred             eEEEee
Q 030012          162 LKIQFA  167 (184)
Q Consensus       162 l~V~~a  167 (184)
                      |+|+.|
T Consensus        73 i~V~~A   78 (79)
T d1l3ka2          73 CEVRKA   78 (79)
T ss_dssp             CEEEEC
T ss_pred             EEEEEC
Confidence            999876

>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=99.83  E-value=1.8e-20  Score=128.27  Aligned_cols=80  Identities=19%  Similarity=0.259  Sum_probs=70.4

Q ss_pred             CCCCCEEEEcCCC-CCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           79 KGESNLLFVDGLP-TDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        79 ~~~~~~lfVgnLp-~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      ...+++|||+||+ ..+++++|+++|++||.|++|++.           +|||||+|++.++|++|++.|||.++.|+. 
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~-----------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~-   79 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-----------KGFAFVQYVNERNARAAVAGEDGRMIAGQV-   79 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE-----------TEEEEEEESSHHHHHHHHHTTTTCEETTEE-
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe-----------CCeEEEEECCHHHHHHHHHHcCCCEECCEE-
Confidence            4556789999997 578899999999999999999883           479999999999999999999999999997 


Q ss_pred             CCCceEEEeecCCCCCC
Q 030012          158 DSPTLKIQFAHFPFHLP  174 (184)
Q Consensus       158 ~~~~l~V~~a~~~~~~~  174 (184)
                          |+|+|++.++..+
T Consensus        80 ----l~V~~a~~~~~~~   92 (98)
T d1wf2a_          80 ----LDINLAAEPKVNR   92 (98)
T ss_dssp             ----CEEEETTSCCCCS
T ss_pred             ----EEEEECCCCCCCC
Confidence                9999998654433

>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=99.83  E-value=4.3e-21  Score=128.32  Aligned_cols=81  Identities=14%  Similarity=0.274  Sum_probs=70.1

Q ss_pred             CCCEEEEcCCCCCCc-HHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCT-RREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        81 ~~~~lfVgnLp~~~t-e~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      +.++|||+|||++++ |++|+++|++||.|.+|++...  .+.+++++|||||+|.+.++|++|++ |||..+.|+.   
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~--~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~---   76 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAG--QKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNRE---   76 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSC--CC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEE---
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecc--cCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEE---
Confidence            578999999999876 5679999999999999998764  23347899999999999999999996 9999999997   


Q ss_pred             CceEEEeecC
Q 030012          160 PTLKIQFAHF  169 (184)
Q Consensus       160 ~~l~V~~a~~  169 (184)
                        |+|+|++.
T Consensus        77 --l~V~~a~~   84 (86)
T d2ghpa3          77 --ISVSLADK   84 (86)
T ss_dssp             --EEEEECCC
T ss_pred             --EEEEEcCC
Confidence              99999974

>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=99.82  E-value=1e-20  Score=123.41  Aligned_cols=75  Identities=21%  Similarity=0.332  Sum_probs=67.9

Q ss_pred             EEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceE
Q 030012           84 LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLK  163 (184)
Q Consensus        84 ~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~  163 (184)
                      +|||+|||+++||++|+++|++||.|.+++++.+   +.+++++|||||+|.+.++|++|++ +++..+.|+.     |+
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d---~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~-----i~   71 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLD---PITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKV-----ID   71 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCB---TTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBC-----CE
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccC---CCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCE-----EE
Confidence            5899999999999999999999999999999874   3347899999999999999999997 7999999997     98


Q ss_pred             EEee
Q 030012          164 IQFA  167 (184)
Q Consensus       164 V~~a  167 (184)
                      |..|
T Consensus        72 V~rA   75 (75)
T d1hd0a_          72 PKRA   75 (75)
T ss_dssp             ECCC
T ss_pred             eeEC
Confidence            8654

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1.8e-20  Score=125.19  Aligned_cols=78  Identities=22%  Similarity=0.258  Sum_probs=70.0

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ...++|||+|||+++++++|+++|++||.+..+++.         +++|||||+|.+.++|+.|+..|||..+.|+.   
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~---------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~---   73 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK---------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSP---   73 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE---------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEE---
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc---------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEE---
Confidence            345799999999999999999999999998887763         34679999999999999999999999999997   


Q ss_pred             CceEEEeecCCC
Q 030012          160 PTLKIQFAHFPF  171 (184)
Q Consensus       160 ~~l~V~~a~~~~  171 (184)
                        |+|+||+++.
T Consensus        74 --i~V~~akP~~   83 (86)
T d2cpda1          74 --IEVTLAKPVD   83 (86)
T ss_dssp             --EEEECCCCCC
T ss_pred             --EEEEeccCCC
Confidence              9999998543

>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=99.82  E-value=2.6e-20  Score=124.56  Aligned_cols=78  Identities=24%  Similarity=0.379  Sum_probs=71.2

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ..++|||+|||.++++++|+++|++||.|.+|++..         .+|||||+|++.++|++|++.|||..+.|+.    
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~---------~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~----   73 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK---------DKGFGFIRLETRTLAEIAKVELDNMPLRGKQ----   73 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET---------TTTEEEEECSSSHHHHHHHHHHTTCCBTTBC----
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeec---------ccceEEEEECCHHHHHHHHHHhCCCEECCEE----
Confidence            356899999999999999999999999999999864         2469999999999999999999999999998    


Q ss_pred             ceEEEeecCCCC
Q 030012          161 TLKIQFAHFPFH  172 (184)
Q Consensus       161 ~l~V~~a~~~~~  172 (184)
                       |+|+||.....
T Consensus        74 -l~V~~A~~~~~   84 (86)
T d2cpja1          74 -LRVRFACHSAS   84 (86)
T ss_dssp             -CEEEESSCCSC
T ss_pred             -EEEEECCCcCC
Confidence             99999987653

>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=99.82  E-value=1.1e-20  Score=130.65  Aligned_cols=80  Identities=18%  Similarity=0.250  Sum_probs=72.4

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ..++|||+|||+++++++|+++|++||.|.++.|..+   +.++.++|||||+|.+.++|++|++ +++..|.|+.    
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d---~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~----   90 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRD---PASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRV----   90 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECC---TTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEE----
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeeccc---ccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEE----
Confidence            3479999999999999999999999999999999874   3346899999999999999999996 7999999997    


Q ss_pred             ceEEEeecC
Q 030012          161 TLKIQFAHF  169 (184)
Q Consensus       161 ~l~V~~a~~  169 (184)
                       |.|.+|..
T Consensus        91 -i~V~~a~~   98 (103)
T d1x4ba1          91 -VEPKRAVA   98 (103)
T ss_dssp             -EEEECCSS
T ss_pred             -EEEEECcc
Confidence             99999874

>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=99.82  E-value=2e-21  Score=133.66  Aligned_cols=86  Identities=22%  Similarity=0.354  Sum_probs=76.5

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ..++++|||+|||.++++++|+++|++||.|..+.+..+.   .+++++|||||+|.+.++|+.|++.|||..+.|+.  
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~---~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~--   89 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM---MTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKI--   89 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEE---ECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCB--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeeccc---ccccccccceEEeccHHHHHHHHHHhCCCEECCEE--
Confidence            3567899999999999999999999999999988877642   23688999999999999999999999999999997  


Q ss_pred             CCceEEEeecCCCC
Q 030012          159 SPTLKIQFAHFPFH  172 (184)
Q Consensus       159 ~~~l~V~~a~~~~~  172 (184)
                         |+|+||++...
T Consensus        90 ---l~V~~ak~k~~  100 (102)
T d2cpxa1          90 ---LVIEFGKNKKQ  100 (102)
T ss_dssp             ---CEEEECCCCSC
T ss_pred             ---EEEEeCCCccc
Confidence               99999987544

>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=99.82  E-value=1.9e-20  Score=127.73  Aligned_cols=76  Identities=21%  Similarity=0.352  Sum_probs=70.4

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      +.+++|||+|||.++++++|+++|++||.|.+|+++.+         +|||||+|.+.++|++|++.|||..+.|+.   
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~---------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~---   83 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE---------KGYSFVRFSTHESAAHAIVSVNGTTIEGHV---   83 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT---------TTEEEEEESSHHHHHHHHHHHTTCEETTEE---
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec---------ceEEEEEECCHHHHHHHHHHhCCCEECCEE---
Confidence            44679999999999999999999999999999999752         579999999999999999999999999997   


Q ss_pred             CceEEEeecC
Q 030012          160 PTLKIQFAHF  169 (184)
Q Consensus       160 ~~l~V~~a~~  169 (184)
                        |+|.|++.
T Consensus        84 --l~v~~ak~   91 (96)
T d1x4ga1          84 --VKCYWGKE   91 (96)
T ss_dssp             --CEEECCCC
T ss_pred             --EEEEEcCC
Confidence              99999975

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.82  E-value=1.7e-20  Score=127.80  Aligned_cols=83  Identities=13%  Similarity=0.241  Sum_probs=73.0

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++|+++|+++|++||.|..++.        .++++|||||+|.+.++|++|++.|||..+.|+.  
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~--------~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~--   82 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ--------DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRS--   82 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE--------TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEE--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee--------cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEE--
Confidence            455789999999999999999999999998876643        1678999999999999999999999999999997  


Q ss_pred             CCceEEEeecCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLP  174 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~  174 (184)
                         |+|+|+...+..+
T Consensus        83 ---i~V~~a~~k~~~r   95 (96)
T d1fjca_          83 ---VSLYYTGEKGGTR   95 (96)
T ss_dssp             ---EEEEECSSSCCCC
T ss_pred             ---EEEEEeCCCCCCC
Confidence               9999998655443

>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=99.81  E-value=1.6e-20  Score=122.00  Aligned_cols=75  Identities=23%  Similarity=0.400  Sum_probs=68.7

Q ss_pred             EEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceE
Q 030012           84 LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLK  163 (184)
Q Consensus        84 ~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~  163 (184)
                      +|||+|||+++||++|+++|++||.|..+.++.+   +..+.++|||||+|.+.++|++|++ +||..+.|+.     |+
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~---~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~-----i~   71 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFD---KTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKM-----VE   71 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCC---TTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBC-----CE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeee---ccccccCceeEEEECCHHHHHHHHh-cCCCEECCeE-----EE
Confidence            5899999999999999999999999999988774   3346889999999999999999996 9999999998     99


Q ss_pred             EEee
Q 030012          164 IQFA  167 (184)
Q Consensus       164 V~~a  167 (184)
                      |++|
T Consensus        72 V~~A   75 (75)
T d2msta_          72 CKKA   75 (75)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            9986

>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=99.81  E-value=3.8e-20  Score=128.87  Aligned_cols=77  Identities=22%  Similarity=0.326  Sum_probs=69.8

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ..+++|||+|||+++++++|+++|++||.|..|.|.         +++|||||+|.+.++|++|++.|||..|.|+.   
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~---------~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~---   75 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP---------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVP---   75 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC---------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSB---
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee---------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCe---
Confidence            345799999999999999999999999999999873         34679999999999999999999999999997   


Q ss_pred             CceEEEeecCC
Q 030012          160 PTLKIQFAHFP  170 (184)
Q Consensus       160 ~~l~V~~a~~~  170 (184)
                        |+|+|+...
T Consensus        76 --l~v~~a~~~   84 (111)
T d1whxa_          76 --LYLEWAPIG   84 (111)
T ss_dssp             --CEEEEEETT
T ss_pred             --EEEEECCCC
Confidence              999999653

>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=99.81  E-value=6.5e-21  Score=125.81  Aligned_cols=77  Identities=19%  Similarity=0.267  Sum_probs=68.2

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCC-eeCCCCCCCCc
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGY-KFDDKKPDSPT  161 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~-~~~g~~~~~~~  161 (184)
                      ++|||+|||+++|+++|+++|++||.|.++++..         ++|||||+|.+.++|++|++.|||. ++.|+.     
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~---------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~-----   67 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL---------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKI-----   67 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE---------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEE-----
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec---------ccceEEEEECCHHHHHHHHHHhCCCeEECCEE-----
Confidence            4799999999999999999999999988776653         4579999999999999999999995 799997     


Q ss_pred             eEEEeecCCCCC
Q 030012          162 LKIQFAHFPFHL  173 (184)
Q Consensus       162 l~V~~a~~~~~~  173 (184)
                      |+|+|+.+.+.+
T Consensus        68 i~V~~a~~k~~r   79 (80)
T d2cqha1          68 MEVDYSVSKKLR   79 (80)
T ss_dssp             CEEEECCCCCCC
T ss_pred             EEEEEcCCcCcC
Confidence            999999865443

>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=99.81  E-value=7.1e-20  Score=122.10  Aligned_cols=79  Identities=20%  Similarity=0.302  Sum_probs=71.8

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ..++|||+|||.++|+++|+++|+.||.|.+|++..+.+    ++++|||||+|.+.++|++|++ +++.++.|+.    
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~----~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~----   75 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH----KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETD----   75 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTT----CCEEEEEEEEESCHHHHHHHHT-CCCCEETTEE----
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeecc----CCcceEEEEEEcCHHHHHHHHH-HCCCEECCEE----
Confidence            357999999999999999999999999999999987532    7899999999999999999996 7999999997    


Q ss_pred             ceEEEeecC
Q 030012          161 TLKIQFAHF  169 (184)
Q Consensus       161 ~l~V~~a~~  169 (184)
                       |+|.|.+.
T Consensus        76 -l~v~~~~d   83 (85)
T d1zh5a2          76 -LLILFKDD   83 (85)
T ss_dssp             -CEEEEGGG
T ss_pred             -EEEEEcCC
Confidence             99999753

>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=99.81  E-value=5.3e-20  Score=121.03  Aligned_cols=74  Identities=23%  Similarity=0.339  Sum_probs=67.6

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ..+++|||+||+  +|+++|+++|++||.|.++++.+         .+|||||+|.+.++|+.|++.|||..+.|+.   
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~---------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~---   68 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP---------PRNCAFVTYEKMESADQAVAELNGTQVESVQ---   68 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET---------TTTEEEEECSSHHHHHHHHHHHTTCBCSSCB---
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeecc---------CCCEEEEEEcccHHHHHHHHHhCCCEECCEE---
Confidence            567899999995  89999999999999999999853         3469999999999999999999999999998   


Q ss_pred             CceEEEeecC
Q 030012          160 PTLKIQFAHF  169 (184)
Q Consensus       160 ~~l~V~~a~~  169 (184)
                        |+|+|++.
T Consensus        69 --l~V~~a~~   76 (79)
T d2bz2a1          69 --LKVNIARK   76 (79)
T ss_dssp             --CEEEECCS
T ss_pred             --EEEEEecC
Confidence              99999974

>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=99.81  E-value=1.1e-20  Score=123.32  Aligned_cols=75  Identities=20%  Similarity=0.360  Sum_probs=67.7

Q ss_pred             EEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceE
Q 030012           84 LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLK  163 (184)
Q Consensus        84 ~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~  163 (184)
                      +|||+|||+++|+++|+++|++||.|.+|+|+.+   +.+++++|||||+|.+.++|++|++ .++.++.|+.     |+
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d---~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~-----i~   71 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMD---NKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSK-----CE   71 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCC---TTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBC-----CE
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCccccccccc---ccccccccEEEEEECCHHHHHHHHh-hCCCEECCEE-----eE
Confidence            6999999999999999999999999999999874   3347899999999999999999996 5778899987     99


Q ss_pred             EEee
Q 030012          164 IQFA  167 (184)
Q Consensus       164 V~~a  167 (184)
                      |..|
T Consensus        72 vk~A   75 (75)
T d1x0fa1          72 IKVA   75 (75)
T ss_dssp             EECC
T ss_pred             EEEC
Confidence            8865

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=2.8e-20  Score=125.54  Aligned_cols=79  Identities=23%  Similarity=0.428  Sum_probs=70.8

Q ss_pred             CCCEEEEcCCCCCCcHHHHHH----hhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSH----LFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~----~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      ++++|||+|||++++++||++    +|++||.|.+|++...      ++++|||||+|.+.++|++|++.|||..+.|+.
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~------~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~   75 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS------LKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   75 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHH------HHHTTCEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeee------ccCCCceEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            478999999999999999864    6899999999987542      567899999999999999999999999999997


Q ss_pred             CCCCceEEEeecCC
Q 030012          157 PDSPTLKIQFAHFP  170 (184)
Q Consensus       157 ~~~~~l~V~~a~~~  170 (184)
                           |+|.||+..
T Consensus        76 -----l~v~~ak~~   84 (91)
T d1nu4a_          76 -----MRIQYAKTD   84 (91)
T ss_dssp             -----CEEEECSSC
T ss_pred             -----EEEEEeCCC
Confidence                 999999764

>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=99.80  E-value=1.9e-19  Score=122.78  Aligned_cols=80  Identities=18%  Similarity=0.374  Sum_probs=70.6

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      .++++|||+|||+++++++|+++|++||.|..+++.+         .++||||+|.+.++|+.|++.||+..|.++.   
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~---------~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~---   82 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK---------GDSFAYIQYESLDAAQAACAKMRGFPLGGPD---   82 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS---------SSCCEEEEESSHHHHHHHHHHHTTCBCSSSS---
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeec---------cccEEEeccCCHHHHHHHHHHhCCCEeCCCc---
Confidence            4568999999999999999999999999999999864         2469999999999999999999999998752   


Q ss_pred             CceEEEeecCCC
Q 030012          160 PTLKIQFAHFPF  171 (184)
Q Consensus       160 ~~l~V~~a~~~~  171 (184)
                      ..|+|+||+...
T Consensus        83 ~~l~v~~ak~~~   94 (97)
T d1whya_          83 RRLRVDFAKSGP   94 (97)
T ss_dssp             CBCEEEECCCCC
T ss_pred             eEEEEEeCCCCC
Confidence            359999998643

>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=99.80  E-value=2e-21  Score=131.41  Aligned_cols=81  Identities=15%  Similarity=0.251  Sum_probs=72.6

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      .....+|||+|||+++++++|+++|++||.|.+++++.+.+    |+++|||||+|.+.++|++|++ |||..+.|+.  
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~----g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~--   82 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT----GTNRKFGYVDFESAEDLEKALE-LTGLKVFGNE--   82 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEE----ETTTTEEEEEESSHHHHHHHHH-GGGEEETTEE--
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCC----CCccEEeEEeeCCHHHHHHHHh-cCCcEECCEE--
Confidence            34567999999999999999999999999999888865432    7889999999999999999996 9999999998  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |+|+||+.
T Consensus        83 ---i~V~~ak~   90 (91)
T d1fjeb1          83 ---IKLEKPKG   90 (91)
T ss_dssp             ---EEEECCCC
T ss_pred             ---EEEEecCC
Confidence               99999974

>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=99.80  E-value=5e-20  Score=123.62  Aligned_cols=78  Identities=28%  Similarity=0.402  Sum_probs=67.4

Q ss_pred             CCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           81 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        81 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      .+++|||+|||++++++||+++|++|| ++.+.+         ++++|||||+|.+.++|++|++.|||+++.|++    
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~---------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~----   69 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV---------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKD----   69 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE---------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEE----
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee---------eccCCceEEEECCHHHHHHHHHHhCCCEECCEE----
Confidence            357899999999999999999999999 333433         345789999999999999999999999999998    


Q ss_pred             ceEEEeecCCCCC
Q 030012          161 TLKIQFAHFPFHL  173 (184)
Q Consensus       161 ~l~V~~a~~~~~~  173 (184)
                       |+|+|++.....
T Consensus        70 -l~V~~a~~~~~~   81 (88)
T d1wg1a_          70 -LIVQLQPTDALL   81 (88)
T ss_dssp             -EEEEECCCCCCC
T ss_pred             -EEEEEcCCCCCC
Confidence             999999765433

>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=99.80  E-value=6.4e-20  Score=124.89  Aligned_cols=84  Identities=17%  Similarity=0.254  Sum_probs=71.6

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCC-EEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcC--CeeCCCCCC
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVG-YREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHG--YKFDDKKPD  158 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~-i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g--~~~~g~~~~  158 (184)
                      +++|||+|||.++++++|+++|++||. |.+++++.+..  ..++++|||||+|.+.++|..|++.|++  ..+.|+.  
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~--~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~--   76 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAA--DKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQ--   76 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSC--TTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBC--
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeecc--ccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEE--
Confidence            468999999999999999999999995 89999887532  2378999999999999999999999964  5556776  


Q ss_pred             CCceEEEeecCCCC
Q 030012          159 SPTLKIQFAHFPFH  172 (184)
Q Consensus       159 ~~~l~V~~a~~~~~  172 (184)
                         |+|+||++...
T Consensus        77 ---i~V~~A~p~~~   87 (96)
T d2disa1          77 ---IAVDWAEPEID   87 (96)
T ss_dssp             ---CEEEESCSSCS
T ss_pred             ---EEEEEcCCCCC
Confidence               99999976443

>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=99.80  E-value=3.9e-20  Score=124.41  Aligned_cols=81  Identities=20%  Similarity=0.279  Sum_probs=70.7

Q ss_pred             CCCCEEEEcCCCCCCcHHHH---HHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREV---SHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L---~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      ...++|||+|||++++++||   +++|++||.|.+|.++++.........+|||||+|.+.++|++|++.|||..+.|+.
T Consensus         6 iq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~   85 (89)
T d2cpia1           6 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   85 (89)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             EecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEE
Confidence            34578999999999999999   778999999999999886544433456799999999999999999999999999997


Q ss_pred             CCCCceEEE
Q 030012          157 PDSPTLKIQ  165 (184)
Q Consensus       157 ~~~~~l~V~  165 (184)
                           |+|.
T Consensus        86 -----lkvS   89 (89)
T d2cpia1          86 -----LKAS   89 (89)
T ss_dssp             -----EEEE
T ss_pred             -----EEEC
Confidence                 8874

>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=99.80  E-value=1.8e-19  Score=123.30  Aligned_cols=78  Identities=15%  Similarity=0.165  Sum_probs=70.8

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKP  157 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~  157 (184)
                      .....++|||+|||++++++||+++|++||.|+++++..          +|||||+|.+.++|++||+.|||.++.|+. 
T Consensus        11 ~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~----------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~-   79 (98)
T d1wg4a_          11 TRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK----------DGMGMVEYLRKEDMEYALRKLDDTKFRSHE-   79 (98)
T ss_dssp             CCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET----------TTEEEEEESSHHHHHHHHHHHSSEEEECTT-
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc----------cceEEEEECCHHHHHHHHHHhCCCEeCCeE-
Confidence            345677999999999999999999999999999998853          369999999999999999999999999998 


Q ss_pred             CCCceEEEeecCC
Q 030012          158 DSPTLKIQFAHFP  170 (184)
Q Consensus       158 ~~~~l~V~~a~~~  170 (184)
                          |+|.|++..
T Consensus        80 ----i~v~~~~~~   88 (98)
T d1wg4a_          80 ----GETSYIRVY   88 (98)
T ss_dssp             ----SCEEEEEEE
T ss_pred             ----EEEEEEecC
Confidence                999998753

>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=99.80  E-value=1.2e-19  Score=126.00  Aligned_cols=77  Identities=21%  Similarity=0.350  Sum_probs=69.5

Q ss_pred             CCEEEEcCCCC-CCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           82 SNLLFVDGLPT-DCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        82 ~~~lfVgnLp~-~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      +++|||+||++ .+|+++|+++|++||.|.+|+++.+        .+|||||+|++.++|++|++.|||..+.|+.    
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~--------~kg~afV~f~~~~~A~~ai~~lng~~l~g~~----   69 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN--------KKENALVQMADGNQAQLAMSHLNGHKLHGKP----   69 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCT--------TSCCEEEEESCHHHHHHHHHHHTTCBCSSSB----
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEec--------ccceEEEEECCHHHHHHHHHHhCCCEECCEE----
Confidence            57999999965 5999999999999999999999763        2579999999999999999999999999997    


Q ss_pred             ceEEEeecCCC
Q 030012          161 TLKIQFAHFPF  171 (184)
Q Consensus       161 ~l~V~~a~~~~  171 (184)
                       |+|+|++...
T Consensus        70 -l~v~~s~~~~   79 (109)
T d2adca1          70 -IRITLSKHQN   79 (109)
T ss_dssp             -CEEECCSCCC
T ss_pred             -EEEEECCCCC
Confidence             9999997543

>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=99.80  E-value=1.8e-19  Score=123.99  Aligned_cols=86  Identities=16%  Similarity=0.178  Sum_probs=74.0

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+++||+||+++|..|+ ++.++++.+..    ++++|||||+|.+.++|++|++ +|+..|.||.  
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~----g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~--   83 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD----GRVTGEADVEFATHEDAVAAMA-KDKANMQHRY--   83 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSS----SCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSC--
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecC----CcceEEEEEEECCHHHHHHHHH-cCCCEECCEE--
Confidence            45568999999999999999999999997 56777776432    6889999999999999999986 8999999998  


Q ss_pred             CCceEEEeecCCCCCCC
Q 030012          159 SPTLKIQFAHFPFHLPS  175 (184)
Q Consensus       159 ~~~l~V~~a~~~~~~~~  175 (184)
                         |+|.|+.......+
T Consensus        84 ---I~V~~s~~~~~~~~   97 (102)
T d1weza_          84 ---VELFLNSTAGTSGS   97 (102)
T ss_dssp             ---CEEEEECCCCCCCC
T ss_pred             ---EEEEEcCCCCCCCC
Confidence               99999987654443

>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=99.79  E-value=3.5e-20  Score=124.09  Aligned_cols=71  Identities=20%  Similarity=0.192  Sum_probs=65.6

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      ++|||+|||+++++++|+++|++||.|.++++..          .|||||+|.+.++|++||+.|||.++.|+.     |
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~----------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~-----i   65 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR----------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHE-----G   65 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT----------TSEEEEEESSHHHHHHHHHHHTTCBCCCTT-----S
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc----------cceeeEEeCCHHHHHHHHHHhCCCEECCcE-----e
Confidence            5799999999999999999999999999999853          259999999999999999999999999998     8


Q ss_pred             EEEeec
Q 030012          163 KIQFAH  168 (184)
Q Consensus       163 ~V~~a~  168 (184)
                      +|.|++
T Consensus        66 ~v~~~~   71 (87)
T d3begb1          66 ETAYIR   71 (87)
T ss_dssp             CCCBCE
T ss_pred             EEeEEe
Confidence            888875

>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=99.79  E-value=4.2e-19  Score=123.29  Aligned_cols=81  Identities=21%  Similarity=0.278  Sum_probs=69.9

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      .+..+|||+|||+++|+++|+++|++||.|.+|++..+       +++|||||+|.+.++|+.|++.|||..+.++.   
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~-------~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~---   74 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-------NNQFQALLQYADPVSAQHAKLSLDGQNIYNAC---   74 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEE-------TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTC---
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEee-------CCCCeEEEEECCHHHHHHHHHHHCCCEeccCC---
Confidence            34568999999999999999999999999999999863       35789999999999999999999999995431   


Q ss_pred             CceEEEeecCC
Q 030012          160 PTLKIQFAHFP  170 (184)
Q Consensus       160 ~~l~V~~a~~~  170 (184)
                      ..|+|.|++..
T Consensus        75 ~~l~v~~s~~~   85 (108)
T d2adba1          75 CTLRIDFSKLT   85 (108)
T ss_dssp             CCCEEEECSSC
T ss_pred             cEEEEEecCCc
Confidence            23999998753

>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=99.79  E-value=7.5e-20  Score=118.07  Aligned_cols=69  Identities=25%  Similarity=0.451  Sum_probs=64.1

Q ss_pred             EEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           85 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        85 lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      |||+|||+++|+++|+++|++||.|..+++..+.   .+++++|||||+|.+.++|++|++.|||..+.|+.
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~---~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~   69 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDK---TTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQM   69 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCS---SSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEES
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhcccccccccccc---ccccccceeEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            7999999999999999999999999999988743   34789999999999999999999999999999985

>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=99.78  E-value=3.5e-19  Score=115.99  Aligned_cols=71  Identities=24%  Similarity=0.426  Sum_probs=64.0

Q ss_pred             EEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceEE
Q 030012           85 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKI  164 (184)
Q Consensus        85 lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~V  164 (184)
                      |||+|||++++++||+++|++|| +..+++         ++++|||||+|.+.++|++|++.|||+++.|+.     |+|
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~---------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~-----l~V   65 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV---------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERE-----LSV   65 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE---------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCE-----EEE
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee---------cccceeEEEEECCHHHHHHHHHHhCCccCCCCE-----EEE
Confidence            79999999999999999999998 555554         345689999999999999999999999999997     999


Q ss_pred             EeecCC
Q 030012          165 QFAHFP  170 (184)
Q Consensus       165 ~~a~~~  170 (184)
                      +|++..
T Consensus        66 ~~a~~d   71 (75)
T d1wi6a1          66 QLQPTD   71 (75)
T ss_dssp             EECCST
T ss_pred             EEeCCC
Confidence            999754

>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=99.78  E-value=7.9e-20  Score=122.59  Aligned_cols=78  Identities=18%  Similarity=0.232  Sum_probs=68.6

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDS  159 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~  159 (184)
                      ..+++|||+|||+++||++|+++|++||.|.+|++..        .++|||||+|.+.++|++|+.  ++.++.|+.   
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~--------~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~---   69 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK--------PFRAFAFVTFADDQIAQSLCG--EDLIIKGIS---   69 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS--------SCCSCCEEECSCHHHHHHTTT--CEEEETTEE---
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee--------ccCceEEEEECCHHHHHHHHh--CCCEECCEE---
Confidence            3578999999999999999999999999999997643        356799999999999999985  889999997   


Q ss_pred             CceEEEeecCCCC
Q 030012          160 PTLKIQFAHFPFH  172 (184)
Q Consensus       160 ~~l~V~~a~~~~~  172 (184)
                        |+|+|+++...
T Consensus        70 --l~v~~a~~k~~   80 (88)
T d1wf0a_          70 --VHISNAEPKHN   80 (88)
T ss_dssp             --EEEECCCCCCC
T ss_pred             --eEEEeCCCCCC
Confidence              99999976443

>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=99.78  E-value=3.5e-19  Score=118.69  Aligned_cols=79  Identities=15%  Similarity=0.208  Sum_probs=69.3

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEE-EEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYRE-IRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~-v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      +...+|||+|||++++++||+++|+.||.+.. +.+..++    .++++|||||+|.+.++|++|++.||+..+.|+.  
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~----~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~--   80 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE----KGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRK--   80 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECS----SSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEE--
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCC----CCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEE--
Confidence            34568999999999999999999999999876 4555433    2789999999999999999999999999999997  


Q ss_pred             CCceEEEee
Q 030012          159 SPTLKIQFA  167 (184)
Q Consensus       159 ~~~l~V~~a  167 (184)
                         |+|.++
T Consensus        81 ---i~v~l~   86 (86)
T d2cqpa1          81 ---VKLVLG   86 (86)
T ss_dssp             ---CEEEES
T ss_pred             ---EEEEEC
Confidence               999875

>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=99.77  E-value=2.1e-18  Score=118.89  Aligned_cols=84  Identities=17%  Similarity=0.268  Sum_probs=72.1

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      .....+|||+|||+++|++||+++|+.+|.+..+.++...   ..++++|||||+|.+.++|++|++ +|+..|.++.  
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~---~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~--   85 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD---FQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRY--   85 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC---SSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSC--
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeC---CCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceE--
Confidence            4556789999999999999999999999998876555432   236899999999999999999996 9999999998  


Q ss_pred             CCceEEEeecCCC
Q 030012          159 SPTLKIQFAHFPF  171 (184)
Q Consensus       159 ~~~l~V~~a~~~~  171 (184)
                         |+|.+++...
T Consensus        86 ---i~V~~~~~~~   95 (104)
T d1wg5a_          86 ---IEIFKSSRAE   95 (104)
T ss_dssp             ---CEEEEECTTT
T ss_pred             ---EEEEECCHHH
Confidence               9999997654

>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=99.77  E-value=4e-18  Score=117.51  Aligned_cols=80  Identities=13%  Similarity=0.130  Sum_probs=70.2

Q ss_pred             CCCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHh--cCCeeCCC
Q 030012           78 KKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDAL--HGYKFDDK  155 (184)
Q Consensus        78 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l--~g~~~~g~  155 (184)
                      ...++++|||+|||.++||+||+++|++||.|+++++.+         .+++|||+|++.++|+.|++.|  ++..+.|+
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~---------~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~   81 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP---------FKRQALVEFENIDSAKECVTFAADVPVYIAGQ   81 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET---------TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe---------cceeEEEEeCCHHHHHHHHHHHcCCCcEEeeE
Confidence            346688999999999999999999999999999999864         3569999999999999999988  56778888


Q ss_pred             CCCCCceEEEeecCCC
Q 030012          156 KPDSPTLKIQFAHFPF  171 (184)
Q Consensus       156 ~~~~~~l~V~~a~~~~  171 (184)
                      .     |+|+|++...
T Consensus        82 ~-----l~v~~s~~~~   92 (104)
T d1wexa_          82 Q-----AFFNYSTSKR   92 (104)
T ss_dssp             B-----CEEEECSSSS
T ss_pred             E-----EEEEEcCCCc
Confidence            7     9999997643

>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=99.77  E-value=1.9e-18  Score=115.64  Aligned_cols=79  Identities=22%  Similarity=0.281  Sum_probs=70.1

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHh--cCCeeCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDAL--HGYKFDDKK  156 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l--~g~~~~g~~  156 (184)
                      ..++++|||+|||.++++++|+++|++||.|.++++..         +++||||+|.+.++|++|++.+  ++..+.|+.
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~---------~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~   75 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK---------GKNQAFLELATEEAAITMVNYYSAVTPHLRNQP   75 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEET---------TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccc---------cceEEEEEeCCHHHHHHHHHHHccCCCccCCCE
Confidence            56789999999999999999999999999999998864         2459999999999999999866  578999987


Q ss_pred             CCCCceEEEeecCCC
Q 030012          157 PDSPTLKIQFAHFPF  171 (184)
Q Consensus       157 ~~~~~l~V~~a~~~~  171 (184)
                           |+|+|++...
T Consensus        76 -----l~v~~sk~~~   85 (88)
T d2cq1a1          76 -----IYIQYSNHKE   85 (88)
T ss_dssp             -----CEEEECSCSS
T ss_pred             -----EEEEECCCCC
Confidence                 9999997543

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=7.7e-18  Score=115.17  Aligned_cols=79  Identities=14%  Similarity=0.246  Sum_probs=69.6

Q ss_pred             CCCCCEEEEcCCCCC-CcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHH--HhcCCeeCCC
Q 030012           79 KGESNLLFVDGLPTD-CTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMD--ALHGYKFDDK  155 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~-~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~--~l~g~~~~g~  155 (184)
                      ...+++|||+|||.+ +|+++|.++|++||.|.++++..         ++|||||+|.+.++|.+|++  .+++..+.|+
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~---------~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr   85 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR---------MKSQAFIEMETREDAMAMVDHCLKKALWFQGR   85 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET---------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSS
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEee---------cCCcEEEEecchHHHHHHHHHHhcCCceECCE
Confidence            456789999999985 89999999999999999999864         24699999999999999998  5788999999


Q ss_pred             CCCCCceEEEeecCCC
Q 030012          156 KPDSPTLKIQFAHFPF  171 (184)
Q Consensus       156 ~~~~~~l~V~~a~~~~  171 (184)
                      .     |+|+|++...
T Consensus        86 ~-----l~V~~s~~~~   96 (99)
T d1x4fa1          86 C-----VKVDLSEKYK   96 (99)
T ss_dssp             C-----CEEEEECSCS
T ss_pred             E-----EEEEEcCCcc
Confidence            8     9999996543

>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=99.74  E-value=3e-18  Score=111.49  Aligned_cols=74  Identities=14%  Similarity=0.187  Sum_probs=66.0

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      .+|||+|||+++++++|+++|+.||.|.++++..+..     ..++||||+|.+.++|++|+. +|+..|+|+.     |
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~-----~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~-----i   69 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK-----KNFRFARIEFARYDGALAAIT-KTHKVVGQNE-----I   69 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT-----SSSEEEEEEESSHHHHHHHHT-TTTCEETTEE-----C
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc-----ccceEEEEEEcchHHhHHHHH-hcCcEECCEE-----E
Confidence            4899999999999999999999999999999987532     335799999999999999985 8999999987     9


Q ss_pred             EEEee
Q 030012          163 KIQFA  167 (184)
Q Consensus       163 ~V~~a  167 (184)
                      .|+.+
T Consensus        70 ~V~~~   74 (75)
T d2ghpa2          70 IVSHL   74 (75)
T ss_dssp             EEEEC
T ss_pred             EEEEC
Confidence            88764

>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=99.72  E-value=1.2e-17  Score=112.10  Aligned_cols=80  Identities=14%  Similarity=0.176  Sum_probs=70.5

Q ss_pred             CCCCCEEEEcCCCCC-CcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHh--cCCeeCCC
Q 030012           79 KGESNLLFVDGLPTD-CTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDAL--HGYKFDDK  155 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~-~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l--~g~~~~g~  155 (184)
                      .+.+++|||+|||.. +|++||.++|++||.|.++++..+         +++|||+|++.++|+.|++.|  ++..+.|+
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~---------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr   75 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK---------INEAFIEMATTEDAQAAVDYYTTTPALVFGK   75 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS---------SSCEEEEESSHHHHHHHHHHHHHSCCEETTE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc---------ceEEEEEEcchhhHHHHHHHHhhCCCccCCc
Confidence            567899999999986 889999999999999999999652         359999999999999999966  68899999


Q ss_pred             CCCCCceEEEeecCCCC
Q 030012          156 KPDSPTLKIQFAHFPFH  172 (184)
Q Consensus       156 ~~~~~~l~V~~a~~~~~  172 (184)
                      .     |+|+|++....
T Consensus        76 ~-----l~V~~s~~~~~   87 (89)
T d1x4da1          76 P-----VRVHLSQKYKR   87 (89)
T ss_dssp             E-----CEEEEECCCTT
T ss_pred             e-----EEEEECCCccc
Confidence            7     99999986543

>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=99.71  E-value=4.2e-18  Score=117.08  Aligned_cols=79  Identities=14%  Similarity=0.240  Sum_probs=68.5

Q ss_pred             CCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEE-EEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           80 GESNLLFVDGLPTDCTRREVSHLFRPFVGYREI-RVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v-~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....+|||+|||+++|+++|+++|..||.+..+ .+..+.    .|+++|||||+|.+.++|++|++ ||+..|.|+.  
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~----~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~--   78 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN----NGQGLGQALVQFKNEDDARKSER-LHRKKLNGRE--   78 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT----TSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEE--
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCC----CCCcCccEEEEECCHHHHHHHHh-cCCCeECCcE--
Confidence            345689999999999999999999999998764 444332    37899999999999999999996 9999999998  


Q ss_pred             CCceEEEeec
Q 030012          159 SPTLKIQFAH  168 (184)
Q Consensus       159 ~~~l~V~~a~  168 (184)
                         |.|.++.
T Consensus        79 ---i~V~~~~   85 (103)
T d2cpya1          79 ---AFVHVVT   85 (103)
T ss_dssp             ---EEEEEEC
T ss_pred             ---EEEEECC
Confidence               9999874

>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=1.4e-17  Score=116.31  Aligned_cols=81  Identities=16%  Similarity=0.235  Sum_probs=69.2

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      .....+|||+|||+++|++||+++|+.||.+..+.++..   ...|+++|||||+|.+.++|++|++ |||..|.|+.  
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~---~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~--   88 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAY---GPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRF--   88 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEE---CTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSC--
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeec---CcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEE--
Confidence            456779999999999999999999999999876544432   1237899999999999999999996 9999999998  


Q ss_pred             CCceEEEeec
Q 030012          159 SPTLKIQFAH  168 (184)
Q Consensus       159 ~~~l~V~~a~  168 (184)
                         |.|..+.
T Consensus        89 ---i~V~~~~   95 (112)
T d1wela1          89 ---IQVHPIT   95 (112)
T ss_dssp             ---BEEEEEC
T ss_pred             ---EEEEEcC
Confidence               9998763

>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=99.68  E-value=1.2e-17  Score=115.16  Aligned_cols=78  Identities=23%  Similarity=0.278  Sum_probs=68.0

Q ss_pred             CCCCEEEEcCCCCCC-c----HHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCC
Q 030012           80 GESNLLFVDGLPTDC-T----RREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDD  154 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~-t----e~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g  154 (184)
                      ..+++|||+||+.++ +    +++|+++|++||.|+++++.+         +++||||+|.+.++|++|++.|||+.+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k---------~~~~afV~f~~~~~A~~Ai~~lng~~~~g   73 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK---------SFKRVRINFSNPLSAADARLRLHKTEFLG   73 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET---------TTTEEEEECSSTTHHHHHHHTSTTSEETT
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec---------CCCEEEEEECCHHHHHHHHHHhcccccCC
Confidence            356799999999875 3    356999999999999999863         35699999999999999999999999999


Q ss_pred             CCCCCCceEEEeecCCC
Q 030012          155 KKPDSPTLKIQFAHFPF  171 (184)
Q Consensus       155 ~~~~~~~l~V~~a~~~~  171 (184)
                      +.     |+|.|++...
T Consensus        74 ~~-----l~v~~a~~~~   85 (104)
T d1weya_          74 KE-----MKLYFAQTLH   85 (104)
T ss_dssp             EE-----CEEECCCCSS
T ss_pred             CE-----eEEeecccCC
Confidence            97     9999997544

>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=99.68  E-value=1.7e-19  Score=121.24  Aligned_cols=82  Identities=20%  Similarity=0.270  Sum_probs=67.2

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecC--CCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCC
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKE--PRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~--~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      ++|||+|||+++||++|+++|++||.+..+.+....  .....++++|||||+|.+.++|++|++ |||+.+.|+.    
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~----   76 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQS----   76 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSC----
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEE----
Confidence            689999999999999999999999988766553211  011225788999999999999999985 9999999998    


Q ss_pred             ceEEEeecCC
Q 030012          161 TLKIQFAHFP  170 (184)
Q Consensus       161 ~l~V~~a~~~  170 (184)
                       |+|+.++..
T Consensus        77 -l~V~r~k~~   85 (90)
T d1u2fa_          77 -LKIRRPHDY   85 (90)
T ss_dssp             -CCCBCTTCC
T ss_pred             -EEECCCCCC
Confidence             999876543

>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=99.65  E-value=3.2e-16  Score=117.09  Aligned_cols=82  Identities=16%  Similarity=0.252  Sum_probs=73.9

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCC
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPD  158 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~  158 (184)
                      ....++|||+|||+.+|+++|+++|+.||.|..+.++.+   +.+++++|||||+|.+.++|++|++ +++..+.|++  
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~---~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~--  167 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD---RGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHN--  167 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEEC---TTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEE--
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecc---cccCccceeEEEEECCHHHHHHHHH-hCCCeECCEE--
Confidence            456789999999999999999999999999999999874   3347899999999999999999997 7999999987  


Q ss_pred             CCceEEEeecC
Q 030012          159 SPTLKIQFAHF  169 (184)
Q Consensus       159 ~~~l~V~~a~~  169 (184)
                         |+|.||.+
T Consensus       168 ---i~V~~A~~  175 (183)
T d1u1qa_         168 ---CEVRKALS  175 (183)
T ss_dssp             ---EEEEECCC
T ss_pred             ---EEEEecCC
Confidence               99999854

>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=99.64  E-value=1.9e-16  Score=108.58  Aligned_cols=80  Identities=16%  Similarity=0.194  Sum_probs=64.2

Q ss_pred             CCCCCEEEE--cCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           79 KGESNLLFV--DGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        79 ~~~~~~lfV--gnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      ..+.++|||  ||||.++|+++|+++|++||.|.++++..         .++||||+|.+.++|++|++.|||+++....
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~---------~k~~aFV~f~~~e~A~~A~~~lng~~i~~~~   85 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP---------NKPYSFARYRTTEESKRAYVTLNGKEVVDDL   85 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT---------TCSCEEEEESSHHHHHHHHHHTTTCEEECTT
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeecc---------CccEEEEEECCHHHHHHHHHHhCCCCCCCCC
Confidence            456788999  45999999999999999999999998754         2469999999999999999999999886543


Q ss_pred             CCCCceEEEee
Q 030012          157 PDSPTLKIQFA  167 (184)
Q Consensus       157 ~~~~~l~V~~a  167 (184)
                      +.+-++.+.|.
T Consensus        86 ~~~i~~~~~~~   96 (101)
T d2cq2a1          86 GQKITLYLNFV   96 (101)
T ss_dssp             SCEEECEEEEE
T ss_pred             CcEEEEEEEee
Confidence            22223444554

>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=99.62  E-value=2.5e-17  Score=113.56  Aligned_cols=76  Identities=13%  Similarity=0.171  Sum_probs=69.6

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      ..++|.++..+++|++|+++|++||.|.+|+|+++.    .++++|||||+|.+.++|++|++.|||..+.|+.     |
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~----~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~-----i   98 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL----GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQP-----I   98 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS----SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEE-----C
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC----CCCEeeEEEEEEechhHHHHHHHHHCCCEECCEE-----E
Confidence            458888999999999999999999999999998643    2789999999999999999999999999999997     9


Q ss_pred             EEEee
Q 030012          163 KIQFA  167 (184)
Q Consensus       163 ~V~~a  167 (184)
                      +|+|.
T Consensus        99 ~v~~s  103 (104)
T d1jmta_          99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEC
Confidence            99985

>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=99.59  E-value=2.5e-15  Score=104.80  Aligned_cols=73  Identities=14%  Similarity=0.150  Sum_probs=63.3

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCH-HHHHHHHHHhcCCeeCCCCCCCC
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDP-KCARTAMDALHGYKFDDKKPDSP  160 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~-~~A~~Ai~~l~g~~~~g~~~~~~  160 (184)
                      .-.+||||||+.+|+++|+++|++||.|.+|+++.         .+|||||.|.+. ++|..|+..|++..+.++.    
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~---------~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~----   77 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR---------GAKEGIILFKEKAKEALGKAKDANNGNLQLRN----   77 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCT---------TCSEEEEEESSCHHHHHHHHHHTTTSCBCTTS----
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEec---------CCceEEEEecCcHHHHHHHHHHhcCCceecCc----
Confidence            34669999999999999999999999999999964         257999999995 7899999999999998886    


Q ss_pred             ceEEEeec
Q 030012          161 TLKIQFAH  168 (184)
Q Consensus       161 ~l~V~~a~  168 (184)
                       +.|.|+.
T Consensus        78 -~~v~~~~   84 (113)
T d1owxa_          78 -KEVTWEV   84 (113)
T ss_dssp             -SSEEEEE
T ss_pred             -eEEEEee
Confidence             6666653

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=1.4e-14  Score=98.63  Aligned_cols=80  Identities=18%  Similarity=0.285  Sum_probs=68.0

Q ss_pred             CCCCCCEEEEcCC--CCCC---------cHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHH
Q 030012           78 KKGESNLLFVDGL--PTDC---------TRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDA  146 (184)
Q Consensus        78 ~~~~~~~lfVgnL--p~~~---------te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~  146 (184)
                      ....+++|+|.||  |.++         .++||++.|++||.|..+++..       .+.+||+||+|.+.++|++|++.
T Consensus         4 ~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~-------~~~~G~~fV~f~~~e~A~~A~~~   76 (99)
T d2dita1           4 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFD-------RHPDGVASVSFRDPEEADYCIQT   76 (99)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEET-------TCTTCEEEEECSCHHHHHHHHHH
T ss_pred             CCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccC-------CCCccEEEEEECCHHHHHHHHHH
Confidence            3567899999999  5432         2368999999999999998865       34568999999999999999999


Q ss_pred             hcCCeeCCCCCCCCceEEEeecC
Q 030012          147 LHGYKFDDKKPDSPTLKIQFAHF  169 (184)
Q Consensus       147 l~g~~~~g~~~~~~~l~V~~a~~  169 (184)
                      |||..+.|+.     |+|+|+.+
T Consensus        77 lng~~~~gr~-----i~v~~~~g   94 (99)
T d2dita1          77 LDGRWFGGRQ-----ITAQAWDG   94 (99)
T ss_dssp             STTCEETTEE-----CEEEECCS
T ss_pred             hCCcEECCEE-----EEEEEeCC
Confidence            9999999997     99999853

>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=99.48  E-value=6.4e-14  Score=104.34  Aligned_cols=78  Identities=21%  Similarity=0.277  Sum_probs=65.6

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCc
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPT  161 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~  161 (184)
                      .++|||+|||+++|+++|+++|++||.|.+++++.+   ...++++|||||+|.+.++|++|+.. ++..+..+.     
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~---~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~-----   76 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRD---PNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRV-----   76 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---TTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEE-----
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeec---ccCCCccCceecccCCHHHHHHHHHh-cCCcccccc-----
Confidence            479999999999999999999999999999999874   33478999999999999999999974 555566654     


Q ss_pred             eEEEeec
Q 030012          162 LKIQFAH  168 (184)
Q Consensus       162 l~V~~a~  168 (184)
                      +.+.+..
T Consensus        77 ~~~~~~~   83 (183)
T d1u1qa_          77 VEPKRAV   83 (183)
T ss_dssp             CEEEECC
T ss_pred             hhhhhhh
Confidence            6665543

>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=99.46  E-value=8.1e-14  Score=91.44  Aligned_cols=64  Identities=14%  Similarity=0.165  Sum_probs=55.6

Q ss_pred             CCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCC
Q 030012           82 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKK  156 (184)
Q Consensus        82 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~  156 (184)
                      .+.|||+++|++++++.| +.|++||.|.++++.         +++|||||+|.+.++|++|++ +||..+.|+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~---------~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~   67 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS---------NTGNWMHIRYQSKLQARKALS-KDGRIFGESI   67 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC---------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTE
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEec---------CCCCEEEEEEcccHHHHHHHh-cCCCeECCcE
Confidence            467999999999987656 579999999999873         346799999999999999996 9999999983

>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=99.43  E-value=1.8e-13  Score=93.77  Aligned_cols=83  Identities=17%  Similarity=0.225  Sum_probs=68.2

Q ss_pred             CCCCEEEEcCC--CCCC--------cHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcC
Q 030012           80 GESNLLFVDGL--PTDC--------TRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHG  149 (184)
Q Consensus        80 ~~~~~lfVgnL--p~~~--------te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g  149 (184)
                      .+++.|.|.||  +.++        ..+||++.|++||.|.+|.|.++..... ....|++||+|.+.++|.+|++.|||
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~-~~~~g~vfV~f~~~e~A~~A~~~l~G   80 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVE-VPGCGKIFVEFTSVFDCQKAMQGLTG   80 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSS-CTTCCEEEEEESCHHHHHHHHHHHSS
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCc-cCCceEEEEEECCHHHHHHHHHHHCC
Confidence            35788999999  4443        3357899999999999999876433221 34568999999999999999999999


Q ss_pred             CeeCCCCCCCCceEEEeec
Q 030012          150 YKFDDKKPDSPTLKIQFAH  168 (184)
Q Consensus       150 ~~~~g~~~~~~~l~V~~a~  168 (184)
                      ..+.||.     |+|.|..
T Consensus        81 r~f~gR~-----v~v~f~~   94 (104)
T d1o0pa_          81 RKFANRV-----VVTKYCD   94 (104)
T ss_dssp             CCSSSSC-----CEEEEEC
T ss_pred             CEECCeE-----EEEEEcC
Confidence            9999998     9999985

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.88  E-value=8.7e-05  Score=48.29  Aligned_cols=86  Identities=16%  Similarity=0.294  Sum_probs=68.3

Q ss_pred             CEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCce
Q 030012           83 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTL  162 (184)
Q Consensus        83 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l  162 (184)
                      .+|-|..||+..||+++.+.+...+.+........+.. .....-.-|+|.|.+.++...-.+.++|+.+.+.++...+-
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s-~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a   80 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTS-LYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPA   80 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCS-STTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcC-CCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeee
Confidence            47889999999999999999999998877666553211 11223457999999999999999999999999988666666


Q ss_pred             EEEeecC
Q 030012          163 KIQFAHF  169 (184)
Q Consensus       163 ~V~~a~~  169 (184)
                      .|+||-.
T Consensus        81 ~VE~AP~   87 (91)
T d1uw4a_          81 IVEFAPF   87 (91)
T ss_dssp             EEEECSS
T ss_pred             EEEEcCc
Confidence            7888743

>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=97.28  E-value=0.00015  Score=46.76  Aligned_cols=71  Identities=17%  Similarity=0.226  Sum_probs=54.4

Q ss_pred             CCCCEEEEcCCCCCC------cH---HHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCC
Q 030012           80 GESNLLFVDGLPTDC------TR---REVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGY  150 (184)
Q Consensus        80 ~~~~~lfVgnLp~~~------te---~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~  150 (184)
                      ++..||.|.=..+..      .|   ++|.+.|..||+|.-+|++.+           --.|+|.+-++|.+|++ ++|.
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d-----------~mwVTF~dG~SAL~al~-l~g~   80 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG-----------QMLVTFADSHSALSVLD-VDGM   80 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT-----------EEEEECSCSHHHHHHHH-GGGS
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC-----------eEEEEECCcHHHHHHhc-cCCe
Confidence            344577675443332      22   367788899999999999863           57999999999999995 9999


Q ss_pred             eeCCCCCCCCceEEEee
Q 030012          151 KFDDKKPDSPTLKIQFA  167 (184)
Q Consensus       151 ~~~g~~~~~~~l~V~~a  167 (184)
                      ++.|+.     |+|...
T Consensus        81 ~v~G~~-----l~It~~   92 (95)
T d1ufwa_          81 KVKGRA-----VKISGP   92 (95)
T ss_dssp             EETTEE-----EEEECC
T ss_pred             EEcceE-----EEEecC
Confidence            999997     887643

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.22  E-value=0.00056  Score=41.96  Aligned_cols=60  Identities=18%  Similarity=0.292  Sum_probs=50.2

Q ss_pred             HHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCCCCCCCceEEEeec
Q 030012           98 EVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAH  168 (184)
Q Consensus        98 ~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~~~g~~~~~~~l~V~~a~  168 (184)
                      .|...|.+++.|.++.+.....    +.  -.|-|...+..+|..|+..|+-++|+.++     |.|.|+.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~d----g~--~~A~V~v~~~q~A~~~v~~LhR~KiG~KR-----I~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHTD----YQ--LKAVVQMENLQDAIGAVNSLHRYKIGSKK-----ILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCCS----TT--CCEEEEESSHHHHHHHHHHHTTEEETTEE-----EEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEeccC----Cc--EEEEEEcCCHHHHHHHHHHHHHHhcCCeE-----EEEEEec
Confidence            3557788999999999865322    22  37899999999999999999999999998     9999975

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.37  E-value=0.034  Score=35.95  Aligned_cols=59  Identities=17%  Similarity=0.347  Sum_probs=47.0

Q ss_pred             CCCCCEEEEcCCCCCCcHHHHHHhhcCCCCEEEEEEeecCCCCCCCCcceEEEEEECCHHHHHHHHHHhc
Q 030012           79 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALH  148 (184)
Q Consensus        79 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~v~l~~~~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~  148 (184)
                      .+....||.-..|.++...||.++|+.||.|. |-++.+ +         -|||...+.+.|+.++..+.
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIdd-T---------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDD-T---------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEET-T---------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecC-c---------eEEEEecCHHHHHHHHHHhc
Confidence            34455788889999999999999999999864 344432 2         79999999999999987654