Psyllid ID: psy1680

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------
Protein Sequence
YGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL
Secondary Structure (PSIPRED)
ccccccccccccccEEEEccccccccHHHHHHHcccccEEEEEEcccccccccccEEEEEEccHHHHHHHHHHccccccccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccEEEEEEccHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccEEEEEEcccccccHHHHHHHHHcccEEEEEEEEcccccccccEEEEEEccHHHHHHHHHccccEEEcccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEEEEEEEccccccccccEEEEEEccHHHHHHHHHcccEEEEccc
Coil and Loop (DISEMBL)
ygrnqktlpteppytafvgnlpngitqgdverffpeqkLVSVRLVKdketdrfkgfcyveFVDVENLRQALLkdgritvdglqvrldiadgkrndnkggfnnkqnrgggsggmggnkynqhqggsfnrdnmrnnsrgggassgggfndfsrggegpggfrnnngpnrsnsmndhglmVTEVTTLVSVRLVKdketdrfkgfcyveFVDVENLRQALLkdgritvdgl
Flexible Loop (DISEMBL)
ygrnqktlpteppytafVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALlkdgritvdglqvrldiadgkrndnkggfnnkqnrgggsggmGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVkdketdrfkgfcyvefvdvenlrqallkdgritvdgl
Low Complexity Region (SEG)
YGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRgggsggmggNKYNQHQGGSFNRDNMRNNsrgggassgggFNDfsrggegpggfrnnngpnrsnsmnDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL
Disordered region (IsUnstruct)
*************YTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA*************************************************************************************GLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRI*****
Disordered Region (DISOPRED)
******T****PPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRL******************************************DNMRNNSRGGGASSGGGFNDFSRG******************************************TDRFKGFCYVEFVDVENLRQALLKDGRITVDG*
Disordered Region (DISEMBL)
YGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL
Disordered Region (DISPRO)
****QKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIAD**********************************************************************************DHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
YGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL
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	227	2.2.26 [Sep-21-2011]
Q5XI72	248	Eukaryotic translation in	yes	N/A	0.696	0.637	0.435	3e-25
Q9WUK2	248	Eukaryotic translation in	yes	N/A	0.696	0.637	0.435	4e-25
Q15056	248	Eukaryotic translation in	yes	N/A	0.696	0.637	0.429	3e-24
Q5RBR8	228	Eukaryotic translation in	yes	N/A	0.409	0.407	0.553	9e-24
Q1JPH6	228	Eukaryotic translation in	yes	N/A	0.409	0.407	0.553	1e-23
O14369	388	Probable RNA-binding prot	yes	N/A	0.405	0.237	0.414	1e-10
Q04836	329	31 kDa ribonucleoprotein,	yes	N/A	0.361	0.249	0.349	2e-07
Q9FVQ1	557	Nucleolin 1 OS=Arabidopsi	no	N/A	0.612	0.249	0.324	2e-07
Q8BGD9	611	Eukaryotic translation in	no	N/A	0.361	0.134	0.369	2e-07
P23588	611	Eukaryotic translation in	no	N/A	0.361	0.134	0.357	5e-07

>sp|Q5XI72|IF4H_RAT Eukaryotic translation initiation factor 4H OS=Rattus norvegicus GN=Eif4h PE=1 SV=1

 Score =  115 bits (287), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 71/163 (43%), Positives = 100/163 (61%), Gaps = 5/163 (3%)

Query: 3   RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 62
           R+QK LPTEPPYTA+VGNLP    QGD++  F +  + SVRLV+DK+TD+FKGFCYVEF 
Sbjct: 31  RSQKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFD 90

Query: 63  DVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQ 122
           +V++L++AL  DG +  D   +R+DIA+G++ D  G     +  G    GMGG++  + +
Sbjct: 91  EVDSLKEALTYDGALLGD-RSLRVDIAEGRKQDKGG--FGFRKGGPDDRGMGGSR--EPR 145

Query: 123 GGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGP 165
           GG  +RD+  +  R       GG     R    P G R  +GP
Sbjct: 146 GGWDSRDDFSSGYRDDFLGGRGGSRPGDRRAGPPMGSRFRDGP 188

Stimulates the RNA helicase activity of EIF4A in the translation initiation complex. Binds weakly mRNA.
Rattus norvegicus (taxid: 10116)

>sp|Q9WUK2|IF4H_MOUSE Eukaryotic translation initiation factor 4H OS=Mus musculus GN=Eif4h PE=1 SV=3

 Score =  115 bits (287), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 71/163 (43%), Positives = 100/163 (61%), Gaps = 5/163 (3%)

Query: 3   RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 62
           R+QK LPTEPPYTA+VGNLP    QGD++  F +  + SVRLV+DK+TD+FKGFCYVEF 
Sbjct: 31  RSQKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFD 90

Query: 63  DVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQ 122
           +V++L++AL  DG +  D   +R+DIA+G++ D  G     +  G    GMGG++  + +
Sbjct: 91  EVDSLKEALTYDGALLGD-RSLRVDIAEGRKQDKGG--FGFRKGGPDDRGMGGSR--ESR 145

Query: 123 GGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGP 165
           GG  +RD+  +  R       GG     R    P G R  +GP
Sbjct: 146 GGWDSRDDFNSGYRDDFLGGRGGSRPGDRRAGPPMGSRFRDGP 188

Stimulates the RNA helicase activity of EIF4A in the translation initiation complex. Binds weakly mRNA.

Mus musculus (taxid: 10090)

>sp|Q15056|IF4H_HUMAN Eukaryotic translation initiation factor 4H OS=Homo sapiens GN=EIF4H PE=1 SV=5

 Score =  112 bits (279), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 70/163 (42%), Positives = 99/163 (60%), Gaps = 5/163 (3%)

Query: 3   RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 62
           R+QK LPTEPPYTA+VGNLP    QGD++  F +  + SVRLV+DK+TD+FKGFCYVEF 
Sbjct: 31  RSQKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFD 90

Query: 63  DVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQ 122
           +V++L++AL  DG +  D   +R+DIA+G++ D  G     +  G    GMG ++  + +
Sbjct: 91  EVDSLKEALTYDGALLGD-RSLRVDIAEGRKQDKGG--FGFRKGGPDDRGMGSSR--ESR 145

Query: 123 GGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGP 165
           GG  +RD+  +  R       GG     R    P G R  +GP
Sbjct: 146 GGWDSRDDFNSGFRDDFLGGRGGSRPGDRRTGPPMGSRFRDGP 188

Stimulates the RNA helicase activity of EIF4A in the translation initiation complex. Binds weakly mRNA.

Homo sapiens (taxid: 9606)

>sp|Q5RBR8|IF4H_PONAB Eukaryotic translation initiation factor 4H OS=Pongo abelii GN=EIF4H PE=2 SV=1

 Score =  110 bits (274), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 52/94 (55%), Positives = 72/94 (76%), Gaps = 1/94 (1%)

Query: 2   GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEF 61
            R+QK LPTEPPYTA+VGNLP    QGD++  F +  + SVRLV+DK+TD+FKGFCYVEF
Sbjct: 30  SRSQKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEF 89

Query: 62  VDVENLRQALLKDGRITVDGLQVRLDIADGKRND 95
            +V++L++AL  DG +  D   +R+DIA+G++ D
Sbjct: 90  DEVDSLKEALTYDGALLGD-RSLRVDIAEGRKQD 122

Stimulates the RNA helicase activity of EIF4A in the translation initiation complex. Binds weakly mRNA.

Pongo abelii (taxid: 9601)

>sp|Q1JPH6|IF4H_BOVIN Eukaryotic translation initiation factor 4H OS=Bos taurus GN=EIF4H PE=2 SV=1

 Score =  109 bits (273), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 52/94 (55%), Positives = 72/94 (76%), Gaps = 1/94 (1%)

Query: 2   GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEF 61
            R+QK LPTEPPYTA+VGNLP    QGD++  F +  + SVRLV+DK+TD+FKGFCYVEF
Sbjct: 30  SRSQKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEF 89

Query: 62  VDVENLRQALLKDGRITVDGLQVRLDIADGKRND 95
            +V++L++AL  DG +  D   +R+DIA+G++ D
Sbjct: 90  DEVDSLKEALTYDGALLGD-RSLRVDIAEGRKQD 122

Stimulates the RNA helicase activity of EIF4A in the translation initiation complex. Binds weakly mRNA.

Bos taurus (taxid: 9913)

>sp|O14369|SCE3_SCHPO Probable RNA-binding protein sce3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=sce3 PE=1 SV=1

 Score = 67.0 bits (162), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 39/94 (41%), Positives = 57/94 (60%), Gaps = 2/94 (2%)

Query: 1   YGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVE 60
           Y R+   +P+EPP+TA VGNL   +T+ D+  FF E  + S+RLV D  T+R +GF YVE
Sbjct: 81  YQRDAIPIPSEPPFTAHVGNLSFDLTENDLGDFFGEG-VTSIRLVIDPLTERSRGFGYVE 139

Query: 61  FVDVENLRQALLKDGRITVDGLQVRLDIADGKRN 94
           F   + L  AL   G   + G  VR+ +A+ +R+
Sbjct: 140 FETADTLSAALALSGEDLM-GRPVRITVAEPRRS 172

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

>sp|Q04836|ROC3_ARATH 31 kDa ribonucleoprotein, chloroplastic OS=Arabidopsis thaliana GN=RBP31 PE=1 SV=1

 Score = 56.6 bits (135), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 50/83 (60%), Gaps = 1/83 (1%)

Query: 11  EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 69
           EP +  +VGNLP  +  G +E+ F E  K+V  R+V D+ET R +GF +V   DV+ L +
Sbjct: 241 EPAFRVYVGNLPWDVDNGRLEQLFSEHGKVVEARVVYDRETGRSRGFGFVTMSDVDELNE 300

Query: 70  ALLKDGRITVDGLQVRLDIADGK 92
           A+       ++G  +R+++A+ +
Sbjct: 301 AISALDGQNLEGRAIRVNVAEER 323

Probably involved in the 3'-end processing of chloroplast mRNA's.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FVQ1|NUCL1_ARATH Nucleolin 1 OS=Arabidopsis thaliana GN=NUCL1 PE=1 SV=1

 Score = 56.2 bits (134), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 48/148 (32%), Positives = 71/148 (47%), Gaps = 9/148 (6%)

Query: 4   NQKTLPTEPPY----TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCY 58
            Q   P+ P      T F  NL   I + DVE FF E  ++V VR   +++   F+GF +
Sbjct: 283 KQPKTPSTPAAGGSKTLFAANLSFNIERADVENFFKEAGEVVDVRFSTNRDDGSFRGFGH 342

Query: 59  VEFVDVENLRQALLKDGRITVDGLQVRLDIAD--GKRNDNKGGFNNKQN-RGGGSGGMGG 115
           VEF   E  ++AL   GR  + G ++RLDIA   G+R +         N R GG GG   
Sbjct: 343 VEFASSEEAQKALEFHGRPLL-GREIRLDIAQERGERGERPAFTPQSGNFRSGGDGGDEK 401

Query: 116 NKYNQHQGGSFNRDNMRNNSRGGGASSG 143
             + +    S + D+++N  R   +S G
Sbjct: 402 KIFVKGFDASLSEDDIKNTLREHFSSCG 429

Involved in pre-rRNA processing and ribosome assembly. Is associated with intranucleolar chromatin and pre-ribosomal particles and plays a role in controlling activation and repression of a specific subset of rRNA genes located in distinctive nucleolar organizer regions. Binds specifically rDNA chromatin and may be required to maintain rDNA chromatin structure, but is probably not required for the overall histone methylation status of 45S rRNA genes.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8BGD9|IF4B_MOUSE Eukaryotic translation initiation factor 4B OS=Mus musculus GN=Eif4b PE=1 SV=1

 Score = 55.8 bits (133), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 31/84 (36%), Positives = 49/84 (58%), Gaps = 2/84 (2%)

Query: 8   LPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKE-TDRFKGFCYVEFVDVEN 66
           LP  PPYTAF+GNLP  +T+  ++ FF    + +VRL ++    DR KGF Y EF +  +
Sbjct: 90  LPKSPPYTAFLGNLPYDVTEDSIKDFFRGLNISAVRLPREPSNPDRLKGFGYAEF-EDLD 148

Query: 67  LRQALLKDGRITVDGLQVRLDIAD 90
              + L     ++   ++R+D+AD
Sbjct: 149 SLLSALSLNEESLGNRRIRVDVAD 172

Required for the binding of mRNA to ribosomes. Functions in close association with EIF4-F and EIF4-A. Binds near the 5'-terminal cap of mRNA in presence of EIF-4F and ATP. Promotes the ATPase activity and the ATP-dependent RNA unwinding activity of both EIF4-A and EIF4-F.

Mus musculus (taxid: 10090)

>sp|P23588|IF4B_HUMAN Eukaryotic translation initiation factor 4B OS=Homo sapiens GN=EIF4B PE=1 SV=2

 Score = 54.7 bits (130), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 30/84 (35%), Positives = 49/84 (58%), Gaps = 2/84 (2%)

Query: 8   LPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKE-TDRFKGFCYVEFVDVEN 66
           LP  PPYTAF+GNLP  +T+  ++ FF    + +VRL ++    +R KGF Y EF +  +
Sbjct: 90  LPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEF-EDLD 148

Query: 67  LRQALLKDGRITVDGLQVRLDIAD 90
              + L     ++   ++R+D+AD
Sbjct: 149 SLLSALSLNEESLGNRRIRVDVAD 172

Required for the binding of mRNA to ribosomes. Functions in close association with EIF4-F and EIF4-A. Binds near the 5'-terminal cap of mRNA in presence of EIF-4F and ATP. Promotes the ATPase activity and the ATP-dependent RNA unwinding activity of both EIF4-A and EIF4-F.

Homo sapiens (taxid: 9606)

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	227
380027391	270	PREDICTED: eukaryotic translation initia	0.440	0.370	0.613	1e-28
48103761	274	PREDICTED: eukaryotic translation initia	0.440	0.364	0.613	2e-28
340722741	280	PREDICTED: eukaryotic translation initia	0.418	0.339	0.610	5e-27
350424096	278	PREDICTED: eukaryotic translation initia	0.414	0.338	0.606	2e-26
332022959	285	Eukaryotic translation initiation factor	0.405	0.322	0.586	7e-26
345484780	277	PREDICTED: eukaryotic translation initia	0.405	0.332	0.586	9e-26
383858995	286	PREDICTED: eukaryotic translation initia	0.396	0.314	0.6	1e-25
346468341	273	hypothetical protein [Amblyomma maculatu	0.444	0.369	0.529	5e-25
307203767	249	Eukaryotic translation initiation factor	0.409	0.373	0.580	8e-25
198468371	368	GA18178, isoform A [Drosophila pseudoobs	0.409	0.252	0.610	2e-24

>gi|380027391|ref|XP_003697409.1| PREDICTED: eukaryotic translation initiation factor 4H-like [Apis florea]

 Score =  132 bits (331), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 62/101 (61%), Positives = 78/101 (77%), Gaps = 1/101 (0%)

Query: 1   YGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVE 60
           Y   +K LPTEPPYTAFVGNLPNGI QGDV++ F +  +  +RLVKDKETDRFKGFCYVE
Sbjct: 17  YRSGRKPLPTEPPYTAFVGNLPNGIVQGDVDKIFKKLNVKGIRLVKDKETDRFKGFCYVE 76

Query: 61  FVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFN 101
           F D+ +L  AL  DG + VD   +++D+A+GKRND +GGF+
Sbjct: 77  FEDLADLEAALEMDGAVEVDKSVIKIDVAEGKRND-RGGFD 116

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|48103761|ref|XP_392894.1| PREDICTED: eukaryotic translation initiation factor 4H-like [Apis mellifera]

 Score =  132 bits (331), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 62/101 (61%), Positives = 78/101 (77%), Gaps = 1/101 (0%)

Query: 1   YGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVE 60
           Y   +K LPTEPPYTAFVGNLPNGI QGDV++ F +  +  +RLVKDKETDRFKGFCYVE
Sbjct: 17  YRSGRKPLPTEPPYTAFVGNLPNGIVQGDVDKIFKKLNVKGIRLVKDKETDRFKGFCYVE 76

Query: 61  FVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFN 101
           F D+ +L  AL  DG + VD   +++D+A+GKRND +GGF+
Sbjct: 77  FEDLADLEAALEMDGAVEVDKSVIKIDVAEGKRND-RGGFD 116

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340722741|ref|XP_003399761.1| PREDICTED: eukaryotic translation initiation factor 4H-like [Bombus terrestris]

 Score =  126 bits (317), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 58/95 (61%), Positives = 73/95 (76%)

Query: 1   YGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVE 60
           Y   +K LPTEPPYTAFVGNLPNGI QGDV++ F +  +  +RLVKDKETDRFKGFCYVE
Sbjct: 17  YRSGRKPLPTEPPYTAFVGNLPNGIVQGDVDKIFKKLNVKGIRLVKDKETDRFKGFCYVE 76

Query: 61  FVDVENLRQALLKDGRITVDGLQVRLDIADGKRND 95
           F ++ +L  AL  DG + VD   +++D+A+GKRND
Sbjct: 77  FEELADLEAALEMDGAVEVDKSVIKIDVAEGKRND 111

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350424096|ref|XP_003493687.1| PREDICTED: eukaryotic translation initiation factor 4H-like [Bombus impatiens]

 Score =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 57/94 (60%), Positives = 72/94 (76%)

Query: 1   YGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVE 60
           Y   +K LPTEPPYTAFVGNLPNGI QGDV++ F +  +  +RLVKDKETDRFKGFCYVE
Sbjct: 17  YRSGRKPLPTEPPYTAFVGNLPNGIVQGDVDKIFKKLNVKGIRLVKDKETDRFKGFCYVE 76

Query: 61  FVDVENLRQALLKDGRITVDGLQVRLDIADGKRN 94
           F ++ +L  AL  DG + VD   +++D+A+GKRN
Sbjct: 77  FEELADLEAALEMDGAVEVDKSVIKIDVAEGKRN 110

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332022959|gb|EGI63225.1| Eukaryotic translation initiation factor 4H [Acromyrmex echinatior]

 Score =  123 bits (308), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 54/92 (58%), Positives = 73/92 (79%)

Query: 3   RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 62
           R++K LPTEPPYTA+VGNLPNGI QGDV++ F +  +  +RLVKD++TD+FKGFCYVEF 
Sbjct: 34  RSRKPLPTEPPYTAYVGNLPNGIVQGDVDKIFEKLNVKVIRLVKDRDTDKFKGFCYVEFE 93

Query: 63  DVENLRQALLKDGRITVDGLQVRLDIADGKRN 94
           D+ +L  AL  DG + VD   +++D+A+GKRN
Sbjct: 94  DLADLEAALEMDGAVEVDKCLIKIDVAEGKRN 125

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345484780|ref|XP_001599359.2| PREDICTED: eukaryotic translation initiation factor 4H-like [Nasonia vitripennis]

 Score =  122 bits (307), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 54/92 (58%), Positives = 74/92 (80%)

Query: 3   RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 62
           R+ K LPTEPPYTA+VGNLPNGI QGDV++ F    + ++RLVKD+ETDRFKGFCYVEF 
Sbjct: 17  RSSKPLPTEPPYTAYVGNLPNGIVQGDVDKIFQNMNVKNIRLVKDRETDRFKGFCYVEFE 76

Query: 63  DVENLRQALLKDGRITVDGLQVRLDIADGKRN 94
           D+ +L+ A+  +G + V+G  +++D+A+GKRN
Sbjct: 77  DLSDLKNAIKLNGCVEVEGSLLKIDVAEGKRN 108

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383858995|ref|XP_003704984.1| PREDICTED: eukaryotic translation initiation factor 4H-like [Megachile rotundata]

 Score =  122 bits (307), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 54/90 (60%), Positives = 71/90 (78%)

Query: 5   QKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDV 64
           +K LPTEPPYTA+VGNLPNG+ QGDV++ F +  +  +RLVKDKETD+FKGFCYVEF D+
Sbjct: 21  RKPLPTEPPYTAYVGNLPNGVVQGDVDKIFEKLNVKGIRLVKDKETDKFKGFCYVEFEDL 80

Query: 65  ENLRQALLKDGRITVDGLQVRLDIADGKRN 94
            +L  AL  DG + VD   +++D+A+GKRN
Sbjct: 81  ADLEMALDMDGAVEVDKSLIKIDVAEGKRN 110

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|346468341|gb|AEO34015.1| hypothetical protein [Amblyomma maculatum]

 Score =  120 bits (300), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 54/102 (52%), Positives = 78/102 (76%), Gaps = 1/102 (0%)

Query: 1   YGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVE 60
           YG+  + +PTEPP+TAFVGNLP+G+ Q D++  F   K+ S RLV+DKETD+FKG+CYVE
Sbjct: 20  YGKPSRPMPTEPPFTAFVGNLPDGVVQSDIDEIFHGIKIKSTRLVRDKETDKFKGYCYVE 79

Query: 61  FVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNN 102
           F D+++L++AL  D    + G  +R+DIA+G+R+D  GGF+N
Sbjct: 80  FFDLDSLKEALEFDS-ADLQGRSLRVDIAEGRRSDRGGGFSN 120

Source: Amblyomma maculatum

Species: Amblyomma maculatum

Genus: Amblyomma

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307203767|gb|EFN82710.1| Eukaryotic translation initiation factor 4H [Harpegnathos saltator]

 Score =  119 bits (299), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 54/93 (58%), Positives = 72/93 (77%)

Query: 3  RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 62
          R++K LPT PPYTA+VGNLPNGI QGDV++ F +  +  +RLVKDK+TD+FKGFCYVEF 
Sbjct: 3  RSRKPLPTGPPYTAYVGNLPNGIVQGDVDKIFEKLNVKVIRLVKDKDTDKFKGFCYVEFE 62

Query: 63 DVENLRQALLKDGRITVDGLQVRLDIADGKRND 95
          D+ +L  AL  DG + VD   +++D+A+ KRND
Sbjct: 63 DLADLEAALEMDGAVEVDKSLIKIDVAEIKRND 95

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198468371|ref|XP_001354678.2| GA18178, isoform A [Drosophila pseudoobscura pseudoobscura] gi|198146383|gb|EAL31733.2| GA18178, isoform A [Drosophila pseudoobscura pseudoobscura]

 Score =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 58/95 (61%), Positives = 72/95 (75%), Gaps = 2/95 (2%)

Query: 3   RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 62
           R  K LPTEPP+ AFVGNLP G+ QGDV + F + ++ +VRLVKD+ETD FKGFCYVEF 
Sbjct: 18  RQMKVLPTEPPFLAFVGNLPQGLVQGDVMKIFQDFEVKNVRLVKDRETDMFKGFCYVEFE 77

Query: 63  DVENLRQALLKDGRITVDGLQ--VRLDIADGKRND 95
            +ENL +AL  DGRI +D L   +R+DIAD K+ND
Sbjct: 78  TLENLERALEFDGRIKLDDLSAPLRIDIADRKKND 112

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	227
FB|FBgn0262734	358	Rbp2 "RNA-binding protein 2" [	0.427	0.270	0.585	2.5e-26
UNIPROTKB|E1BZH4	254	LOC100859865 "Uncharacterized	0.422	0.377	0.581	3.2e-26
UNIPROTKB|F1NYA2	146	LOC100859865 "Uncharacterized	0.422	0.657	0.581	3.2e-26
UNIPROTKB|A7MBG9	222	WBSCR1 "WBSCR1 protein" [Bos t	0.422	0.432	0.571	3.2e-26
UNIPROTKB|Q1JPH6	228	EIF4H "Eukaryotic translation	0.422	0.421	0.571	3.2e-26
UNIPROTKB|E2RQG8	251	EIF4H "Uncharacterized protein	0.422	0.382	0.571	3.2e-26
UNIPROTKB|Q15056	248	EIF4H "Eukaryotic translation	0.422	0.387	0.571	3.2e-26
UNIPROTKB|I3L594	228	EIF4H "Uncharacterized protein	0.422	0.421	0.571	3.2e-26
UNIPROTKB|I3LRD5	248	EIF4H "Uncharacterized protein	0.422	0.387	0.571	3.2e-26
MGI|MGI:1341822	248	Eif4h "eukaryotic translation	0.422	0.387	0.571	3.2e-26

FB|FBgn0262734 Rbp2 "RNA-binding protein 2" [Drosophila melanogaster (taxid:7227)]

 Score = 297 (109.6 bits), Expect = 2.5e-26, P = 2.5e-26
 Identities = 58/99 (58%), Positives = 74/99 (74%)

Query:     3 RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 62
             R  K LPTEPP+ AFVGNLP G+ QGDV + F + ++  VRLVKD+ETD+FKGFCYVEF 
Sbjct:    18 RASKQLPTEPPFIAFVGNLPQGLVQGDVIKIFQDFEVKYVRLVKDRETDQFKGFCYVEFE 77

Query:    63 DVENLRQALLKDGRITVDGLQ--VRLDIADGKRNDNKGG 99
              ++NL +AL  DGRI +D L   +R+DIAD ++ND  GG
Sbjct:    78 TLDNLERALECDGRIKLDDLSAPLRIDIADRRKNDRPGG 116

GO:0003729 "mRNA binding" evidence=ISS;NAS

GO:0006413 "translational initiation" evidence=ISS

GO:0005829 "cytosol" evidence=ISS

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005875 "microtubule associated complex" evidence=IDA

UNIPROTKB|E1BZH4 LOC100859865 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 296 (109.3 bits), Expect = 3.2e-26, P = 3.2e-26
 Identities = 57/98 (58%), Positives = 75/98 (76%)

Query:     3 RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 62
             R QK LPTEPP+TA+VGNLP    QGD++  F +  + SVRLV+DKETD+FKGFCYVEF 
Sbjct:    29 RKQKELPTEPPFTAYVGNLPFNTVQGDIDAIFKDLSVRSVRLVRDKETDKFKGFCYVEFD 88

Query:    63 DVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGF 100
             +VE+L++AL  DG +  D   +R+DIA+G++ D KGGF
Sbjct:    89 EVESLKEALTYDGALLGDR-SLRVDIAEGRKQD-KGGF 124

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0019953 "sexual reproduction" evidence=IEA

GO:0048589 "developmental growth" evidence=IEA

UNIPROTKB|F1NYA2 LOC100859865 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 296 (109.3 bits), Expect = 3.2e-26, P = 3.2e-26
 Identities = 57/98 (58%), Positives = 75/98 (76%)

Query:     3 RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 62
             R QK LPTEPP+TA+VGNLP    QGD++  F +  + SVRLV+DKETD+FKGFCYVEF 
Sbjct:    29 RKQKELPTEPPFTAYVGNLPFNTVQGDIDAIFKDLSVRSVRLVRDKETDKFKGFCYVEFD 88

Query:    63 DVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGF 100
             +VE+L++AL  DG +  D   +R+DIA+G++ D KGGF
Sbjct:    89 EVESLKEALTYDGALLGDR-SLRVDIAEGRKQD-KGGF 124

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|A7MBG9 WBSCR1 "WBSCR1 protein" [Bos taurus (taxid:9913)]

 Score = 296 (109.3 bits), Expect = 3.2e-26, P = 3.2e-26
 Identities = 56/98 (57%), Positives = 76/98 (77%)

Query:     3 RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 62
             R+QK LPTEPPYTA+VGNLP    QGD++  F +  + SVRLV+DK+TD+FKGFCYVEF 
Sbjct:    31 RSQKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFD 90

Query:    63 DVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGF 100
             +V++L++AL  DG +  D   +R+DIA+G++ D KGGF
Sbjct:    91 EVDSLKEALTYDGALLGDR-SLRVDIAEGRKQD-KGGF 126

GO:0048589 "developmental growth" evidence=IEA

GO:0019953 "sexual reproduction" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q1JPH6 EIF4H "Eukaryotic translation initiation factor 4H" [Bos taurus (taxid:9913)]

 Score = 296 (109.3 bits), Expect = 3.2e-26, P = 3.2e-26
 Identities = 56/98 (57%), Positives = 76/98 (77%)

Query:     3 RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 62
             R+QK LPTEPPYTA+VGNLP    QGD++  F +  + SVRLV+DK+TD+FKGFCYVEF 
Sbjct:    31 RSQKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFD 90

Query:    63 DVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGF 100
             +V++L++AL  DG +  D   +R+DIA+G++ D KGGF
Sbjct:    91 EVDSLKEALTYDGALLGDR-SLRVDIAEGRKQD-KGGF 126

GO:0048471 "perinuclear region of cytoplasm" evidence=IEA

GO:0048589 "developmental growth" evidence=IEA

GO:0019953 "sexual reproduction" evidence=IEA

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

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2RQG8 EIF4H "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 296 (109.3 bits), Expect = 3.2e-26, P = 3.2e-26
 Identities = 56/98 (57%), Positives = 76/98 (77%)

Query:     3 RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 62
             R+QK LPTEPPYTA+VGNLP    QGD++  F +  + SVRLV+DK+TD+FKGFCYVEF 
Sbjct:    34 RSQKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFD 93

Query:    63 DVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGF 100
             +V++L++AL  DG +  D   +R+DIA+G++ D KGGF
Sbjct:    94 EVDSLKEALTYDGALLGDR-SLRVDIAEGRKQD-KGGF 129

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q15056 EIF4H "Eukaryotic translation initiation factor 4H" [Homo sapiens (taxid:9606)]

 Score = 296 (109.3 bits), Expect = 3.2e-26, P = 3.2e-26
 Identities = 56/98 (57%), Positives = 76/98 (77%)

Query:     3 RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 62
             R+QK LPTEPPYTA+VGNLP    QGD++  F +  + SVRLV+DK+TD+FKGFCYVEF 
Sbjct:    31 RSQKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFD 90

Query:    63 DVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGF 100
             +V++L++AL  DG +  D   +R+DIA+G++ D KGGF
Sbjct:    91 EVDSLKEALTYDGALLGDR-SLRVDIAEGRKQD-KGGF 126

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0019048 "virus-host interaction" evidence=IEA

GO:0019953 "sexual reproduction" evidence=IEA

GO:0048589 "developmental growth" evidence=IEA

GO:0048471 "perinuclear region of cytoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=TAS

GO:0006446 "regulation of translational initiation" evidence=TAS

GO:0008135 "translation factor activity, nucleic acid binding" evidence=TAS

GO:0016281 "eukaryotic translation initiation factor 4F complex" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006412 "translation" evidence=TAS

GO:0006413 "translational initiation" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0044267 "cellular protein metabolic process" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|I3L594 EIF4H "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 296 (109.3 bits), Expect = 3.2e-26, P = 3.2e-26
 Identities = 56/98 (57%), Positives = 76/98 (77%)

Query:     3 RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 62
             R+QK LPTEPPYTA+VGNLP    QGD++  F +  + SVRLV+DK+TD+FKGFCYVEF 
Sbjct:    31 RSQKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFD 90

Query:    63 DVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGF 100
             +V++L++AL  DG +  D   +R+DIA+G++ D KGGF
Sbjct:    91 EVDSLKEALTYDGALLGDR-SLRVDIAEGRKQD-KGGF 126

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|I3LRD5 EIF4H "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 296 (109.3 bits), Expect = 3.2e-26, P = 3.2e-26
 Identities = 56/98 (57%), Positives = 76/98 (77%)

Query:     3 RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 62
             R+QK LPTEPPYTA+VGNLP    QGD++  F +  + SVRLV+DK+TD+FKGFCYVEF 
Sbjct:    31 RSQKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFD 90

Query:    63 DVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGF 100
             +V++L++AL  DG +  D   +R+DIA+G++ D KGGF
Sbjct:    91 EVDSLKEALTYDGALLGDR-SLRVDIAEGRKQD-KGGF 126

GO:0048589 "developmental growth" evidence=IEA

GO:0019953 "sexual reproduction" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:1341822 Eif4h "eukaryotic translation initiation factor 4H" [Mus musculus (taxid:10090)]

 Score = 296 (109.3 bits), Expect = 3.2e-26, P = 3.2e-26
 Identities = 56/98 (57%), Positives = 76/98 (77%)

Query:     3 RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 62
             R+QK LPTEPPYTA+VGNLP    QGD++  F +  + SVRLV+DK+TD+FKGFCYVEF 
Sbjct:    31 RSQKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFD 90

Query:    63 DVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGF 100
             +V++L++AL  DG +  D   +R+DIA+G++ D KGGF
Sbjct:    91 EVDSLKEALTYDGALLGDR-SLRVDIAEGRKQD-KGGF 126

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0006413 "translational initiation" evidence=IEA

GO:0019953 "sexual reproduction" evidence=IMP

GO:0048589 "developmental growth" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9WUK2	IF4H_MOUSE	No assigned EC number	0.4355	0.6960	0.6370	yes	N/A
Q5XI72	IF4H_RAT	No assigned EC number	0.4355	0.6960	0.6370	yes	N/A
Q5RBR8	IF4H_PONAB	No assigned EC number	0.5531	0.4096	0.4078	yes	N/A
Q1JPH6	IF4H_BOVIN	No assigned EC number	0.5531	0.4096	0.4078	yes	N/A
Q15056	IF4H_HUMAN	No assigned EC number	0.4294	0.6960	0.6370	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	227
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	1e-31
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	3e-15
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	2e-14
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	1e-13
smart00360	73	smart00360, RRM, RNA recognition motif	2e-13
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-12
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-11
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	4e-11
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	5e-11
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	8e-11
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	1e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-10
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	4e-10
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-09
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-09
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-08
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	8e-08
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-07
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	3e-07
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	3e-07
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	5e-07
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	6e-07
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	7e-07
smart00360	73	smart00360, RRM, RNA recognition motif	1e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-06
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-06
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-06
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-06
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-06
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	4e-06
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	4e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	5e-06
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	6e-06
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	8e-06
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-05
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-05
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-05
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-05
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	4e-05
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	4e-05
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	4e-05
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	4e-05
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	6e-05
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	6e-05
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	6e-05
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	9e-05
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	1e-04
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-04
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-04
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-04
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	2e-04
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	2e-04
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-04
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	3e-04
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	3e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	3e-04
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	4e-04
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	4e-04
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	5e-04
cd12536	85	cd12536, RRM1_RBM39, RNA recognition motif 1 in ve	5e-04
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	5e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	6e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	7e-04
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	8e-04
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	8e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	9e-04
cd12514	73	cd12514, RRM4_RBM12_like, RNA recognition motif 4	9e-04
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	0.001
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	0.001
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	0.001
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	0.001
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	0.001
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	0.002
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	0.002
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	0.002
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	0.002
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	0.002
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	0.002
cd12537	85	cd12537, RRM1_RBM23, RNA recognition motif 1 in ve	0.002
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	0.002
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	0.003
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	0.004
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	0.004

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

 Score =  110 bits (277), Expect = 1e-31
 Identities = 45/77 (58%), Positives = 58/77 (75%), Gaps = 1/77 (1%)

Query: 13 PYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 72
          P+TAFVGNLP    QGD++  F +  + SVRLV+DKETD+FKGFCYVEF DVE+L++AL 
Sbjct: 1  PFTAFVGNLPFNTVQGDLDAIFKDLSVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE 60

Query: 73 KDGRITVDGLQVRLDIA 89
           DG +  D   +R+DIA
Sbjct: 61 YDGAL-FDDRSLRVDIA 76

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|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 67.8 bits (166), Expect = 3e-15
 Identities = 33/79 (41%), Positives = 50/79 (63%), Gaps = 4/79 (5%)

Query: 13 PYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDK-ETDRFKGFCYVEFVDVENLRQAL 71
          PYTA++GNLP  +T+ D++ FF    + SVRL ++  +  R +GF Y EF D ++L QAL
Sbjct: 1  PYTAYLGNLPYDVTEEDIKEFFRGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQAL 60

Query: 72 -LKDGRITVDGLQVRLDIA 89
           L D  +     ++R+DIA
Sbjct: 61 SLNDESLK--NRRIRVDIA 77

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

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

 Score = 65.4 bits (160), Expect = 2e-14
 Identities = 27/40 (67%), Positives = 35/40 (87%)

Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRI 222
           ++ SVRLV+DKETD+FKGFCYVEF DVE+L++AL  DG +
Sbjct: 26  SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALEYDGAL 65

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

 Score = 63.6 bits (155), Expect = 1e-13
 Identities = 31/61 (50%), Positives = 39/61 (63%)

Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 74
          T ++GNL   IT+ DV  FF   ++ SVRL  DKET  FKGF +V+F D E+L  AL  D
Sbjct: 1  TVYIGNLAWDITEDDVREFFKGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALKLD 60

Query: 75 G 75
          G
Sbjct: 61 G 61

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

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

 Score = 62.6 bits (153), Expect = 2e-13
 Identities = 30/73 (41%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 15 TAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
          T FVGNLP   T+ ++   F    K+ SVRLV+DKET + KGF +VEF   E+  +AL  
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 74 DGRITVDGLQVRL 86
               +DG  +++
Sbjct: 61 LNGKELDGRPLKV 73

Length = 73

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

 Score = 60.8 bits (148), Expect = 1e-12
 Identities = 29/72 (40%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          FVGNL     +  +   F E  ++ SVRL  D ++ R KGF YVEF   E  + AL   G
Sbjct: 2  FVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDALG 61

Query: 76 RITVDGLQVRLD 87
             + G  VRLD
Sbjct: 62 GTDLLGRPVRLD 73

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

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

 Score = 57.3 bits (139), Expect = 2e-11
 Identities = 32/76 (42%), Positives = 46/76 (60%), Gaps = 3/76 (3%)

Query: 15 TAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
          T FVGNL     Q D+E FF E  ++V VR+ +D +  R KGF +VEF   E  ++AL K
Sbjct: 1  TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALEK 59

Query: 74 DGRITVDGLQVRLDIA 89
           G   + G ++R+D+A
Sbjct: 60 SGE-ELLGREIRVDLA 74

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

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

 Score = 56.8 bits (138), Expect = 4e-11
 Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
          T FV  L   + + D+  FF +  K+  VR+++D+ + R KG  YVEF D E++  AL  
Sbjct: 1  TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGL 60

Query: 74 DGRI 77
           G+ 
Sbjct: 61 TGQR 64

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

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

 Score = 56.5 bits (137), Expect = 5e-11
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 15 TAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
            +VGNLP  +T+ D++  F    ++ S R++ D+ET R +GF +VE    E    A+ K
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 74 DGRITVDGLQVRLDIA 89
                 G  + ++ A
Sbjct: 61 LNGTDFGGRTLTVNEA 76

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

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

 Score = 55.8 bits (135), Expect = 8e-11
 Identities = 28/74 (37%), Positives = 38/74 (51%), Gaps = 7/74 (9%)

Query: 14 YTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL- 71
          +  FVGNLP   T  D+   F       SVRL+ DK+T + KG  +VEF   E + +AL 
Sbjct: 1  FILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK 60

Query: 72 -----LKDGRITVD 80
               LK  +I V+
Sbjct: 61 LHHTLLKGRKINVE 74

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

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

 Score = 55.7 bits (135), Expect = 1e-10
 Identities = 23/68 (33%), Positives = 40/68 (58%), Gaps = 3/68 (4%)

Query: 15 TAFVGNLPNGITQGDVERFFPEQKLV-SVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
          T FV NL   + + ++ + F +   +  VRLVK+ +  + KG+ YVEF + E++++AL  
Sbjct: 1  TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKG-KSKGYAYVEFENEESVQEALKL 59

Query: 74 DGRITVDG 81
          D R  + G
Sbjct: 60 D-RELIKG 66

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

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

 Score = 54.1 bits (131), Expect = 3e-10
 Identities = 29/70 (41%), Positives = 42/70 (60%), Gaps = 3/70 (4%)

Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          +V NLP  +T+ D+  FF P  K+  VRLV++K  DR +GF +VEF   E+   AL K  
Sbjct: 2  YVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKLN 59

Query: 76 RITVDGLQVR 85
           + +DG  +R
Sbjct: 60 GLVLDGRTLR 69

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

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

 Score = 54.1 bits (131), Expect = 4e-10
 Identities = 26/73 (35%), Positives = 45/73 (61%), Gaps = 2/73 (2%)

Query: 15 TAFVGNLPNGITQGDVERFFPEQKLV-SVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
          + FVGNLP  I + ++ + F +   V +VR+V+D++T   KGF YV F   +++  AL  
Sbjct: 1  SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL 60

Query: 74 DGRITVDGLQVRL 86
          +G I + G ++R+
Sbjct: 61 NG-IKLKGRKIRV 72

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

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

 Score = 52.2 bits (126), Expect = 1e-09
 Identities = 28/70 (40%), Positives = 42/70 (60%), Gaps = 2/70 (2%)

Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          FVGNLP   T+ D++  F +   + S+R+V+D ET R KGF +VEF D E+  +AL    
Sbjct: 2  FVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 76 RITVDGLQVR 85
             + G ++R
Sbjct: 61 GKELGGRELR 70

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

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

 Score = 51.9 bits (125), Expect = 2e-09
 Identities = 26/72 (36%), Positives = 42/72 (58%), Gaps = 2/72 (2%)

Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          FVGNLP   T+ D+   F +  ++ SVR+V+DK   + KGF +VEF   E+  +AL    
Sbjct: 2  FVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEALN 60

Query: 76 RITVDGLQVRLD 87
             +DG ++++ 
Sbjct: 61 GKELDGRKLKVS 72

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

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

 Score = 55.7 bits (133), Expect = 3e-09
 Identities = 35/170 (20%), Positives = 63/170 (37%), Gaps = 4/170 (2%)

Query: 9   PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENL 67
             E   T FVGNLP  +T+ D+   F +   +  VRLV+D+ET + +GF +VEF   E+ 
Sbjct: 111 SKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESA 170

Query: 68  RQALLKDGRITVDGLQVRLDIA---DGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGG 124
            +A+ +     ++G  +R+  A      R++     +    +    G     + + +   
Sbjct: 171 EKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYV 230

Query: 125 SFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSMNDH 174
                            S G     S      G    +     + +  D 
Sbjct: 231 GNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDA 280

Length = 306

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

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 8/72 (11%)

Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVD-------VENLR 68
          ++G LP  +T+GD+   F +  ++V + LV+DK+T + KGF ++ + D       V+NL 
Sbjct: 13 YIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLN 72

Query: 69 QALLKDGRITVD 80
             L    I VD
Sbjct: 73 GIKLLGRTIRVD 84

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

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

 Score = 47.9 bits (115), Expect = 8e-08
 Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 6/76 (7%)

Query: 20 NLPNGITQGDVERFF---PEQKLVSVRLVKDKETDRFKGFCYVEFVDVEN---LRQALLK 73
           L    T+ D+ +         +  VRL++DK T   +GF +VEF  +E+      AL  
Sbjct: 9  GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNN 68

Query: 74 DGRITVDGLQVRLDIA 89
               +DG  VR+  A
Sbjct: 69 LDPFVIDGRVVRVSYA 84

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

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

 Score = 46.9 bits (112), Expect = 2e-07
 Identities = 16/60 (26%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 15 TAFVGNLPNGITQGDVER-FFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
          T ++G+L   + +  +   F    ++ SV+++++K+T +  G+ +VEF   E   QAL  
Sbjct: 1  TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

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

 Score = 46.5 bits (111), Expect = 3e-07
 Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 1/79 (1%)

Query: 15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
          T FV NLP   T   +E FF E   +    +VKDK + + +GF YV F   E+ ++AL +
Sbjct: 1  TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 74 DGRITVDGLQVRLDIADGK 92
            +    G ++ ++ A  K
Sbjct: 61 KKKTKFGGRKIHVEFAKKK 79

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

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

 Score = 46.2 bits (110), Expect = 3e-07
 Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 15 TAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
          T FVGNL   +    ++  F +   +V  R++ D+ET R +GF YV+F   E+ ++A+  
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 74 DGRITVDGLQVRLDIA 89
               +DG  + +D +
Sbjct: 61 MDGKELDGRPINVDFS 76

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

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 45.7 bits (109), Expect = 5e-07
 Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          FVGN+P   T+  +   F E   +VS RLV D++T + KG+ + EF D+E    A+    
Sbjct: 2  FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 76 RITVDGLQVRLDIA 89
              +G  +R+D A
Sbjct: 62 GYEFNGRALRVDFA 75

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

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

 Score = 45.1 bits (107), Expect = 6e-07
 Identities = 21/35 (60%), Positives = 24/35 (68%)

Query: 186 SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 220
           SVRL  DKET  FKGF +V+F D E+L  AL  DG
Sbjct: 27  SVRLATDKETGEFKGFGHVDFADEESLDAALKLDG 61

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

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

 Score = 45.3 bits (108), Expect = 7e-07
 Identities = 17/44 (38%), Positives = 28/44 (63%), Gaps = 2/44 (4%)

Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
            +  VRLVK+ +  + KG+ YVEF + E++++AL  D R  + G
Sbjct: 25  EITDVRLVKNYKG-KSKGYAYVEFENEESVQEALKLD-RELIKG 66

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

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

 Score = 44.5 bits (106), Expect = 1e-06
 Identities = 20/44 (45%), Positives = 27/44 (61%)

Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
            + SVRLV+DKET + KGF +VEF   E+  +AL       +DG
Sbjct: 25  KVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDG 68

Length = 73

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

 Score = 48.0 bits (114), Expect = 1e-06
 Identities = 24/62 (38%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 15  TAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
           T FV  L     + D+  FF +  K+  V+ +KD+ + R KG  YVEF DVE++ +AL  
Sbjct: 91  TVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALAL 150

Query: 74  DG 75
            G
Sbjct: 151 TG 152

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

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

 Score = 44.4 bits (105), Expect = 2e-06
 Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
          T FV NL   +TQ D+  FF +   +    +V D ET   +G+ +V F  +E+ ++AL K
Sbjct: 1  TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 74 DGRITVDGLQVRLDIA 89
               + G  +RLDIA
Sbjct: 61 LKNKKLHGRILRLDIA 76

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

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

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 22/56 (39%), Positives = 36/56 (64%), Gaps = 1/56 (1%)

Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
          +VGNL   IT+ D+   F P  ++  V+L +D ET R KG+ +++F D E+ ++AL
Sbjct: 2  YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKAL 57

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

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 4/74 (5%)

Query: 15 TAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
            FVGNLP  +   +++ +F +  K+ S  +  DKET   KG+ +V F   + L  AL K
Sbjct: 1  KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 74 DGRITVDG--LQVR 85
            +  ++G  LQV+
Sbjct: 61 Q-KHILEGNKLQVQ 73

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

>gnl|CDD|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 = 43.4 bits (103), Expect = 3e-06
 Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 16 AFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 74
           FV NLP   T+ ++   F    ++  V L  DKET R KGF +V F+  E+  +A  + 
Sbjct: 2  LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 75 GRITVDG 81
                G
Sbjct: 62 DGSIFQG 68

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

 Score = 43.0 bits (102), Expect = 4e-06
 Identities = 15/37 (40%), Positives = 23/37 (62%)

Query: 186 SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRI 222
            VR+++D+ + R KG  YVEF D E++  AL   G+ 
Sbjct: 28  DVRIIRDRNSRRSKGVAYVEFYDEESVPLALGLTGQR 64

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

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

 Score = 43.3 bits (103), Expect = 4e-06
 Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 3/47 (6%)

Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVEN---LRQALLKDGRITVDG 226
            +  VRL++DK T   +GF +VEF  +E+      AL       +DG
Sbjct: 30  PIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNNLDPFVIDG 76

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

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

 Score = 42.7 bits (101), Expect = 5e-06
 Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 15 TAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 70
          T +V NLP  +T  D+ + F    K+V V +VKDKET + KG  ++ F+D E+  + 
Sbjct: 3  TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKC 59

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

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

 Score = 42.7 bits (101), Expect = 6e-06
 Identities = 20/60 (33%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 17 FVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          FVGN+  G T  +++  F     ++ + ++ DK T + KGF Y+EF+D  ++  ALL + 
Sbjct: 3  FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNE 62

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

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

 Score = 42.4 bits (100), Expect = 8e-06
 Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-D 74
          FV NLP    + D+E+ F    +L  V +  DK++ + KGF YV F+D E+  +A  + D
Sbjct: 6  FVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKELD 65

Query: 75 GRI 77
          G++
Sbjct: 66 GKV 68

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

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 13/40 (32%), Positives = 23/40 (57%)

Query: 179 TEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 218
            E   + SV+++++K+T +  G+ +VEF   E   QAL  
Sbjct: 21  AECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

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

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 25/82 (30%), Positives = 44/82 (53%), Gaps = 8/82 (9%)

Query: 15 TAFVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVEN----LR 68
          T F+ NLP   T+ +++  F  Q  ++   R+VKDK T   KG  +V+F   E+    L 
Sbjct: 2  TVFIRNLPFDATEEELKELF-SQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 69 QAL-LKDGRITVDGLQVRLDIA 89
           A   +D  +++DG ++ + +A
Sbjct: 61 AADNAEDSGLSLDGRRLIVTLA 82

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

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

 Score = 41.3 bits (97), Expect = 2e-05
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          FVGN+P   T+  ++  F E   +VS RLV D+ET + KG+ + E+ D E    A+    
Sbjct: 2  FVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLN 61

Query: 76 RITVDGLQVRLDIA 89
             ++G Q+R+D A
Sbjct: 62 GYELNGRQLRVDNA 75

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

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

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 11 EPPYTAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 69
          +P  T FVG L    T+  +   F     +  +RLV+D  T   KG+ +VE+    +  +
Sbjct: 1  DPYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALR 60

Query: 70 ALLKDGRITVDGLQVRLD 87
          A     ++ +DG ++ +D
Sbjct: 61 AYRDAHKLVIDGSEIFVD 78

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

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

 Score = 43.7 bits (103), Expect = 3e-05
 Identities = 36/168 (21%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 3   RNQKTLPTEPP--YTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYV 59
           +     P + P     +VGNL   IT+ ++ + F P   +  V+L +D ET R KGF ++
Sbjct: 174 KAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFI 233

Query: 60  EFVDVENLRQALLKDGRITVDGLQVRLDIADG--KRNDNKGGFNNKQNRGGGSGGMGGNK 117
           +F D E  ++AL       + G  +++  A       D    F +   +      +   +
Sbjct: 234 QFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEE 293

Query: 118 YNQHQGGSFNRDNMRNNSRGGGASSGGG-----FNDFSRGGEGPGGFR 160
             Q           R++  GG    G G          R G       
Sbjct: 294 REQ-----LMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIP 336

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

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

 Score = 40.6 bits (96), Expect = 3e-05
 Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
          +VG+L   +T+  +   F P   ++S+R+ +D  T R  G+ YV F +  +  +AL
Sbjct: 3  YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERAL 58

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

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

 Score = 40.3 bits (95), Expect = 4e-05
 Identities = 12/34 (35%), Positives = 19/34 (55%)

Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
            + S R++ D+ET R +GF +VE    E    A+
Sbjct: 25  EVTSARVITDRETGRSRGFGFVEMETAEEANAAI 58

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

 Score = 40.5 bits (95), Expect = 4e-05
 Identities = 23/74 (31%), Positives = 43/74 (58%), Gaps = 7/74 (9%)

Query: 13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
           +  FV  LP  +T+ ++E+ F +   + SVRLV ++ + + KG  YVE+ +  +  QA+
Sbjct: 2  KHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAV 60

Query: 72 LKDGRITVDGLQVR 85
          LK     +DG +++
Sbjct: 61 LK-----MDGTEIK 69

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

 Score = 40.6 bits (95), Expect = 4e-05
 Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 17 FVGNLP-NGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          FVGNL    + +G    F     +  VR+V+D +T+  KGF YV+F D   + +ALL + 
Sbjct: 3  FVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLNE 62

Query: 76 R 76
          +
Sbjct: 63 K 63

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

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 40.6 bits (95), Expect = 4e-05
 Identities = 25/74 (33%), Positives = 44/74 (59%), Gaps = 1/74 (1%)

Query: 17 FVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          F+G L     +  +E+ F +   +S V +VKD+ET R +GF +V F + ++ + A++   
Sbjct: 4  FIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMN 63

Query: 76 RITVDGLQVRLDIA 89
            +VDG Q+R+D A
Sbjct: 64 GKSVDGRQIRVDQA 77

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

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

 Score = 39.6 bits (93), Expect = 6e-05
 Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 6/47 (12%)

Query: 185 VSVRLVKDKETDRFKGFCYVEFVDVENLRQAL------LKDGRITVD 225
            SVRL+ DK+T + KG  +VEF   E + +AL      LK  +I V+
Sbjct: 28  PSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLHHTLLKGRKINVE 74

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

>gnl|CDD|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 = 39.9 bits (94), Expect = 6e-05
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          FV  L    T+ ++E  F    ++  V L+KD ET   +GF +V F  VE+   A+    
Sbjct: 5  FVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDLN 64

Query: 76 RITVDGLQVRLDIA 89
             ++G  ++++ A
Sbjct: 65 GKELEGRVIKVEKA 78

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

 Score = 40.0 bits (94), Expect = 6e-05
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 1/80 (1%)

Query: 15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
          + +V N+ +     D+ R F +   +V V +  D  T R +GF YV+F DV +   AL  
Sbjct: 2  SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 74 DGRITVDGLQVRLDIADGKR 93
            R    G ++ +  A G R
Sbjct: 62 LDRTRFLGREIEIQFAQGDR 81

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

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

 Score = 39.5 bits (93), Expect = 9e-05
 Identities = 16/51 (31%), Positives = 32/51 (62%), Gaps = 3/51 (5%)

Query: 17 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVE 65
          ++G+LP+G  + ++ ++F  Q   +  +RL + K+T + KG+ +VEF   E
Sbjct: 3  YIGHLPHGFYEPELRKYF-SQFGTVTRLRLSRSKKTGKSKGYAFVEFESPE 52

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

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

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 3/80 (3%)

Query: 15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL-L 72
          T FV  L    T+  + R F E   +  +RLV+DK+T + +G+ ++EF    +++ A   
Sbjct: 3  TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKY 62

Query: 73 KDGRITVDGLQVRLDIADGK 92
           DG   +DG +V +D+  G+
Sbjct: 63 ADG-KKIDGRRVLVDVERGR 81

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

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

 Score = 38.8 bits (91), Expect = 1e-04
 Identities = 20/58 (34%), Positives = 35/58 (60%), Gaps = 1/58 (1%)

Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
          FVG L   +T+ D+  +F +   + SV +V DKET + +GF +V F D + + + +L+
Sbjct: 3  FVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

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

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

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 16/32 (50%), Positives = 19/32 (59%)

Query: 185 VSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
            SVRL  D ++ R KGF YVEF   E  + AL
Sbjct: 26  SSVRLPTDPDSGRPKGFGYVEFSSQEAAQAAL 57

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

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

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 18/44 (40%), Positives = 26/44 (59%), Gaps = 2/44 (4%)

Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
            +  VRLV++K  DR +GF +VEF   E+   AL K   + +DG
Sbjct: 24  KVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKLNGLVLDG 65

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

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

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 18/56 (32%), Positives = 33/56 (58%), Gaps = 1/56 (1%)

Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
          FVG++P  IT+ +V   F E   ++ V ++KDK T   +G C+V++   +   +A+
Sbjct: 3  FVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAI 58

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

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 17 FVGNLPNGITQGDV-ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVE 65
          F+G LPN +++  V E      KL +  LVKD  T   KG+ + E++D  
Sbjct: 4  FIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPS 53

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

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 19/59 (32%), Positives = 37/59 (62%), Gaps = 3/59 (5%)

Query: 31 ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA 89
           R+ P +K   V++V D++T R +GF +V F  VE+ ++A  +   + +DG ++R+D +
Sbjct: 21 SRYGPIEK---VQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRIRVDYS 76

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

>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 37.7 bits (88), Expect = 3e-04
 Identities = 21/49 (42%), Positives = 29/49 (59%), Gaps = 7/49 (14%)

Query: 184 LVSVRLVKDK-ETDRFKGFCYVEFVDVENLRQAL------LKDGRITVD 225
           + SVRL ++  +  R +GF Y EF D ++L QAL      LK+ RI VD
Sbjct: 27  VSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSLNDESLKNRRIRVD 75

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

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

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 2/74 (2%)

Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          FVG L    T+  +  +F +   +V + L  DK+T++ +GFC++ F D E   + +L+  
Sbjct: 3  FVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITF-DSEEPVKKILETQ 61

Query: 76 RITVDGLQVRLDIA 89
             + G +V +  A
Sbjct: 62 FHVIGGKKVEVKKA 75

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

>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 37.7 bits (88), Expect = 3e-04
 Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 3/62 (4%)

Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
          T  VG +   +++ D++ FF     V+ VRL  D++      F +VEF D E+   AL  
Sbjct: 2  TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHS--ARFAFVEFADAESALSALNL 59

Query: 74 DG 75
           G
Sbjct: 60 SG 61

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 37.2 bits (87), Expect = 4e-04
 Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 3/62 (4%)

Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 74
          T  V NLP   T+  + +FF +     +R VK  E++       +EF   +    AL KD
Sbjct: 2  TVKVKNLPKDTTENKIRQFFKDCG--EIREVKIVESEGGL-VAVIEFETEDEALAALTKD 58

Query: 75 GR 76
           +
Sbjct: 59 HK 60

This subfamily corresponds to the RRM1 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 71

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

 Score = 37.8 bits (87), Expect = 4e-04
 Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 14 YTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 72
          +  FVG+L   IT  D++  F P  K+   R+VKD  T + KG+ +V F +  +   A++
Sbjct: 2  FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 61

Query: 73 KDGRITVDGLQVRLDIA 89
            G   + G Q+R + A
Sbjct: 62 HMGGQWLGGRQIRTNWA 78

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

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

 Score = 37.2 bits (87), Expect = 5e-04
 Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 1/56 (1%)

Query: 17 FVGNLPNGITQGDV-ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
          +VG L   + +  +   F P   +  +++  D ET + +GF +VEF + E+   A+
Sbjct: 2  YVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAI 57

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

>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)

 Score = 37.7 bits (87), Expect = 5e-04
 Identities = 21/50 (42%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 15 TAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVD 63
          T F   L   I   D+E FF    K+  VR++ D+ + R KG  YVEFVD
Sbjct: 3  TVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVD 52

This subgroup corresponds to the RRM1 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor 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. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

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

 Score = 37.1 bits (87), Expect = 5e-04
 Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 18 VGNLPNGITQGDVER-FFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-DG 75
          V NL     + D+   F P   +  V L KDKET + +GF +V F   E+  +A+ K +G
Sbjct: 4  VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

Query: 76 R 76
           
Sbjct: 64 F 64

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

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 4/67 (5%)

Query: 17 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 74
          FVG LP   T   + ++F  Q  ++    ++ D++T + +G+ +V F D E+  +A  KD
Sbjct: 4  FVGGLPYHTTDDSLRKYF-SQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERA-CKD 61

Query: 75 GRITVDG 81
              +DG
Sbjct: 62 PNPIIDG 68

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

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

 Score = 37.1 bits (86), Expect = 7e-04
 Identities = 12/52 (23%), Positives = 34/52 (65%), Gaps = 1/52 (1%)

Query: 15 TAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVE 65
            ++G+LP+G  + +++++F +   + +VR+ + K+T   K + +++F++ E
Sbjct: 1  VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPE 52

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

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

 Score = 36.8 bits (86), Expect = 8e-04
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 186 SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 220
           +VR+V+D++T   KGF YV F   +++  AL  +G
Sbjct: 28  AVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNG 62

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

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

 Score = 36.8 bits (86), Expect = 8e-04
 Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 14 YTAFVGNLPNGITQGDVERFFPEQK-LVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
          +  FVG+L N +T   + R F +       ++V+DK T + KG+ +V F D  +  +A+
Sbjct: 7  FRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAM 65

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

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

 Score = 36.5 bits (85), Expect = 9e-04
 Identities = 14/38 (36%), Positives = 24/38 (63%)

Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 220
           T+  + ++ DK T + KGF Y+EF+D  ++  ALL + 
Sbjct: 25  TINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNE 62

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

>gnl|CDD|240958 cd12514, RRM4_RBM12_like, RNA recognition motif 4 in RNA-binding protein RBM12, RBM12B and similar proteins

 Score = 36.5 bits (85), Expect = 9e-04
 Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 3/54 (5%)

Query: 20 NLPNGITQGDVERFFPEQKLV--SVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
          N+P  +T+G+V  FF    +    + ++ DK T +  G  YVEFV  E+  +A 
Sbjct: 6  NIPFDVTKGEVLAFFAGIAIAEQGIHILYDK-TGKTLGEAYVEFVSEEDAMRAE 58

This subfamily corresponds to the RRM4 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear. . Length = 73

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

 Score = 36.2 bits (84), Expect = 0.001
 Identities = 16/44 (36%), Positives = 27/44 (61%)

Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
           T+V  R++ D+ET R +GF YV+F   E+ ++A+       +DG
Sbjct: 25  TVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDG 68

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

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 16/37 (43%), Positives = 24/37 (64%)

Query: 180 EVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 216
           EV  +VS RLV D++T + KG+ + EF D+E    A+
Sbjct: 21  EVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAI 57

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

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

 Score = 36.6 bits (84), Expect = 0.001
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 14 YTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 72
          +  FVG+L   IT  D++  F P  ++   R+VKD  T + KG+ +V F +  +   A+ 
Sbjct: 2  FHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 61

Query: 73 KDGRITVDGLQVRLDIA 89
          + G   + G Q+R + A
Sbjct: 62 QMGGQWLGGRQIRTNWA 78

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

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

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 4/61 (6%)

Query: 14 YTAFVGNLPNGITQGDVERFFPEQKLVSVRLVK---DKETDRFKGFCYVEFVDVENLRQA 70
          ++ FVG+L   +T   ++  F   +  SVR  K   D  T R KG+ +V F D +   +A
Sbjct: 2  HSIFVGDLAPDVTDYMLQETF-RARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRA 60

Query: 71 L 71
          L
Sbjct: 61 L 61

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

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

 Score = 36.1 bits (84), Expect = 0.001
 Identities = 18/48 (37%), Positives = 29/48 (60%), Gaps = 7/48 (14%)

Query: 15 TAFVGNLPNGITQGDVERFFPEQKLV-SVRLVKDKETDRFKGFCYVEF 61
          T +VGNLP+G+T+ +++R F     +  VR+ KD      KG+ +V F
Sbjct: 2  TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRF 43

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

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 7/48 (14%)

Query: 185 VSVRLVKDKETDRFKGFCYVEFVD-------VENLRQALLKDGRITVD 225
           V + LV+DK+T + KGF ++ + D       V+NL    L    I VD
Sbjct: 37  VDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGRTIRVD 84

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

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

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 15 TAFVGNLPNGITQGDVER-FFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
          T +VGNLP  I + +VE  F+    +V + L   K   R  G+ ++EF D  +   A+  
Sbjct: 1  TVYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAEDAIRG 57

Query: 74 DGRITVDGLQVRLDI 88
                DG ++R+++
Sbjct: 58 RDGYDFDGQRLRVEL 72

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

>gnl|CDD|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 = 35.6 bits (83), Expect = 0.002
 Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 3/59 (5%)

Query: 20 NLPNGITQGDVERFF--PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 76
           LP   T+ D+  FF   +     + +V D +  R  G  YVEF   E+ R+AL K   
Sbjct: 6  GLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDG-RPTGEAYVEFASPEDARRALRKHNN 63

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|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 19/82 (23%)

Query: 17 FVGNLPNGITQGDVERFF------------PEQKLVSVRLVKDKETDRFKGFCYVEFVDV 64
          +VGNLP GIT+ ++  FF            P   ++SV++  +K       F +VEF  V
Sbjct: 5  YVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKN------FAFVEFRTV 58

Query: 65 ENLRQALLKDGRITVDGLQVRL 86
          E    AL  DG I   G  +++
Sbjct: 59 EEATAALALDG-IIFKGQPLKI 79

The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 82

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 26/78 (33%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          FV N+ +     D+ R F     +V V +  D  T R +GF Y++F DV +   AL    
Sbjct: 4  FVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNLN 63

Query: 76 RITVDGLQVRLDIADGKR 93
          R  V G Q+ +  A G R
Sbjct: 64 RKWVCGRQIEIQFAQGDR 81

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 35.6 bits (83), Expect = 0.002
 Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 10/78 (12%)

Query: 15 TAFVGNLPNGITQGDVERFFPEQ--KLVSVRL--VKDKETDRFKGFCYVEFVDVENLRQA 70
          T +V N P    Q D+   F EQ  +++S+R   ++  +T RF   CYV+F   E+   A
Sbjct: 2  TLWVTNFPPSFDQSDIRDLF-EQYGEILSIRFPSLRFNKTRRF---CYVQFTSPESAAAA 57

Query: 71 LLKDGRITVDG--LQVRL 86
          +        +G  L V++
Sbjct: 58 VALLNGKLGEGYKLVVKI 75

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 15 TAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
          T F   L   I   D+E FF    K+  VR++ D+ + R KG  YVEF +++++  A+
Sbjct: 3  TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 60

This subgroup corresponds to the RRM1 of RBM23, also termed RNA-binding region-containing protein 4, or splicing factor SF2, which may function as a pre-mRNA splicing factor. It shows high sequence homology to RNA-binding protein 39 (RBM39 or HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In contrast to RBM39, RBM23 contains only two RRMs. . Length = 85

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

 Score = 35.7 bits (82), Expect = 0.002
 Identities = 26/78 (33%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          FV N+ +     D+ R F     +V V +  D  T R +GF YV+F DV +   AL    
Sbjct: 4  FVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNLD 63

Query: 76 RITVDGLQVRLDIADGKR 93
          R  + G Q+ +  A G R
Sbjct: 64 RKWICGRQIEIQFAQGDR 81

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

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

 Score = 35.2 bits (81), Expect = 0.003
 Identities = 15/36 (41%), Positives = 24/36 (66%)

Query: 186 SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 221
            VR+V+D +T+  KGF YV+F D   + +ALL + +
Sbjct: 28  YVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLNEK 63

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

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

 Score = 35.0 bits (81), Expect = 0.004
 Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 1/44 (2%)

Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG 226
            + SVR+V+DK   + KGF +VEF   E+  +AL       +DG
Sbjct: 24  EIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEALNGKELDG 66

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

 Score = 34.7 bits (80), Expect = 0.004
 Identities = 23/69 (33%), Positives = 41/69 (59%), Gaps = 2/69 (2%)

Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          FVG LP  +T+ + + +F +  K+V  +L++D +T R +GF +V F D E+  + +   G
Sbjct: 3  FVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTF-DSESAVERVFSAG 61

Query: 76 RITVDGLQV 84
           + + G QV
Sbjct: 62 MLELGGKQV 70

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	227
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.97
KOG0148|consensus	321		99.97
KOG0144|consensus	510		99.97
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.97
KOG0145|consensus	360		99.96
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.96
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.95
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.95
KOG0131|consensus	203		99.95
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.95
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.95
KOG0127|consensus	678		99.95
KOG0117|consensus	506		99.94
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.94
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.94
KOG0127|consensus	678		99.93
KOG0109|consensus	346		99.92
KOG0117|consensus	506		99.91
KOG0147|consensus	549		99.9
KOG0124|consensus	544		99.9
KOG0123|consensus	369		99.88
KOG0110|consensus	725		99.87
KOG0105|consensus	241		99.87
KOG4205|consensus	311		99.86
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.86
KOG0146|consensus	371		99.84
KOG0144|consensus	510		99.84
KOG0123|consensus	369		99.82
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.81
KOG4206|consensus	221		99.79
KOG0148|consensus	321		99.79
KOG1457|consensus	284		99.76
KOG0147|consensus	549		99.75
KOG4211|consensus	510		99.75
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.74
KOG4212|consensus	608		99.72
KOG1548|consensus	382		99.68
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.68
KOG0106|consensus	216		99.68
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.65
KOG0110|consensus	725		99.65
KOG0149|consensus	247		99.64
KOG0121|consensus	153		99.63
KOG0120|consensus	500		99.63
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.63
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.61
KOG0122|consensus	270		99.61
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.61
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.6
KOG0122|consensus	270		99.58
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.58
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.57
KOG0149|consensus	247		99.57
KOG0126|consensus	219		99.54
KOG0124|consensus	544		99.54
PLN03120	260	nucleic acid binding protein; Provisional	99.53
KOG0113|consensus	335		99.52
KOG0113|consensus	335		99.51
KOG0121|consensus	153		99.51
KOG4207|consensus	256		99.51
KOG0125|consensus	376		99.5
KOG0107|consensus	195		99.5
KOG4207|consensus	256		99.5
KOG1190|consensus	492		99.49
PLN03120	260	nucleic acid binding protein; Provisional	99.49
KOG4212|consensus	608		99.48
PLN03121	243	nucleic acid binding protein; Provisional	99.46
KOG4211|consensus	510		99.45
KOG0114|consensus	124		99.44
smart00361	70	RRM_1 RNA recognition motif.	99.44
KOG0114|consensus	124		99.43
PLN03213	759	repressor of silencing 3; Provisional	99.43
KOG0126|consensus	219		99.43
smart00362	72	RRM_2 RNA recognition motif.	99.42
PLN03121	243	nucleic acid binding protein; Provisional	99.41
KOG0107|consensus	195		99.41
KOG0125|consensus	376		99.41
smart00362	72	RRM_2 RNA recognition motif.	99.41
smart00360	71	RRM RNA recognition motif.	99.4
KOG0108|consensus	435		99.4
KOG0129|consensus	520		99.37
smart00360	71	RRM RNA recognition motif.	99.37
PLN03213	759	repressor of silencing 3; Provisional	99.36
KOG0130|consensus	170		99.36
KOG0111|consensus	298		99.36
KOG0130|consensus	170		99.33
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.32
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.32
KOG0120|consensus	500		99.31
KOG1365|consensus	508		99.3
KOG1456|consensus	494		99.29
KOG0108|consensus	435		99.29
KOG0131|consensus	203		99.29
KOG0145|consensus	360		99.28
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.27
KOG0111|consensus	298		99.27
KOG1190|consensus	492		99.23
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.22
KOG4208|consensus	214		99.2
KOG0109|consensus	346		99.17
smart00361	70	RRM_1 RNA recognition motif.	99.16
KOG0415|consensus	479		99.15
KOG1456|consensus	494		99.14
KOG0415|consensus	479		99.11
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.1
KOG0146|consensus	371		99.08
KOG0226|consensus	290		99.05
KOG0105|consensus	241		99.04
KOG4210|consensus	285		99.03
KOG4454|consensus	267		99.02
KOG4205|consensus	311		99.02
KOG0153|consensus	377		98.93
KOG0116|consensus	419		98.92
KOG4208|consensus	214		98.92
KOG4307|consensus	944		98.81
KOG0128|consensus	881		98.8
KOG4307|consensus	944		98.78
KOG1365|consensus	508		98.78
KOG4206|consensus	221		98.77
KOG0132|consensus	894		98.76
KOG0533|consensus	243		98.75
KOG4209|consensus	231		98.67
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.67
KOG4661|consensus	940		98.67
KOG0533|consensus	243		98.66
KOG2193|consensus	584		98.65
KOG0226|consensus	290		98.64
KOG0132|consensus	894		98.55
KOG4660|consensus	549		98.55
KOG4209|consensus	231		98.5
KOG0112|consensus	975		98.48
KOG0153|consensus	377		98.47
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.4
KOG0116|consensus	419		98.31
KOG4661|consensus	940		98.3
KOG1457|consensus	284		98.29
KOG0151|consensus	877		98.25
KOG4454|consensus	267		98.21
KOG0151|consensus	877		98.17
KOG4660|consensus	549		98.09
KOG4676|consensus	479		98.05
KOG4210|consensus	285		97.91
KOG1548|consensus	382		97.9
KOG1855|consensus	484		97.86
KOG0106|consensus	216		97.84
KOG2314|consensus	698		97.83
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.81
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.65
KOG0128|consensus	881		97.63
KOG1995|consensus	351		97.62
KOG4849|consensus	498		97.61
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.59
KOG1996|consensus	378		97.54
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.51
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.46
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.41
KOG1995|consensus	351		97.35
KOG0115|consensus	275		97.33
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.29
KOG3152|consensus	278		97.29
KOG4849|consensus	498		97.13
KOG0129|consensus	520		97.07
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.01
KOG2202|consensus	260		96.86
KOG2416|consensus	718		96.82
KOG2314|consensus	698		96.82
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.55
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.51
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.48
KOG2416|consensus	718		96.41
KOG3152|consensus	278		96.28
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.2
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.1
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.96
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.85
KOG1855|consensus	484		95.85
KOG2068|consensus	327		95.84
KOG4676|consensus	479		95.78
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.71
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.64
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.57
KOG0112|consensus	975		95.35
KOG2202|consensus	260		95.08
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.83
KOG1996|consensus	378		94.22
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	93.89
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.8
KOG0804|consensus	493		93.59
KOG2193|consensus	584		93.34
KOG4574|consensus	1007		93.15
KOG0115|consensus	275		93.08
KOG2068|consensus	327		92.98
KOG0804|consensus	493		92.81
KOG2253|consensus	668		90.56
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	89.66
KOG2135|consensus	526		89.39
KOG4285|consensus	350		88.55
KOG2591|consensus	684		85.92
KOG4483|consensus	528		83.8
KOG2591|consensus	684		83.38
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	82.29
KOG2253|consensus	668		81.29
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	80.56
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	80.41

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=5.1e-35  Score=242.38  Aligned_cols=159  Identities=18%  Similarity=0.281  Sum_probs=144.4

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      ......++|||+|||+++|+++|+++|+.| +|..|+|++|+.+++++|||||+|.+.++|.+||+ |++ ..+.+++|+
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG-~~l~gr~i~  180 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNG-ITVRNKRLK  180 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCC-CccCCceee
Confidence            455678999999999999999999999999 99999999999999999999999999999999998 999 999999999


Q ss_pred             EEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCC
Q psy1680          86 LDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGP  165 (227)
Q Consensus        86 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~  165 (227)
                      |.++.+....                                                         ....+|||+|||.
T Consensus       181 V~~a~p~~~~---------------------------------------------------------~~~~~lfV~nLp~  203 (346)
T TIGR01659       181 VSYARPGGES---------------------------------------------------------IKDTNLYVTNLPR  203 (346)
T ss_pred             eecccccccc---------------------------------------------------------cccceeEEeCCCC
Confidence            9987642210                                                         1234699999976


Q ss_pred             CCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         166 NRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       166 ~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      .+  ++++|+++|++||.|+.|+|++|+.+++++|||||+|.+.++|++||+.||+..|+|
T Consensus       204 ~v--tee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g  262 (346)
T TIGR01659       204 TI--TDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEG  262 (346)
T ss_pred             cc--cHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            55  789999999999999999999999999999999999999999999999999998876

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=1.3e-33  Score=237.15  Aligned_cols=213  Identities=21%  Similarity=0.329  Sum_probs=147.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      +..+|||+|||..+++++|+++|++| +|.+|+|++++.+++++|||||+|.+.++|.+||+ +++ ..|.|+.|.|.++
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g-~~l~g~~i~v~~a   80 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNG-LRLQNKTIKVSYA   80 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhccc-EEECCeeEEEEee
Confidence            47899999999999999999999999 99999999999999999999999999999999999 999 9999999999998


Q ss_pred             CCCCCCCCC----------------------CCC--------------CCCCC------------------CCC-CCCCC
Q psy1680          90 DGKRNDNKG----------------------GFN--------------NKQNR------------------GGG-SGGMG  114 (227)
Q Consensus        90 ~~~~~~~~~----------------------~~~--------------~~~~~------------------~~~-~~~~~  114 (227)
                      .+.......                      .++              ...+.                  .+. ..+..
T Consensus        81 ~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~  160 (352)
T TIGR01661        81 RPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCT  160 (352)
T ss_pred             cccccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCc
Confidence            765431100                      000              00000                  000 00000


Q ss_pred             CC---CCCCCCC----CCCCC-----CCCCCCC----------------------CC-----------------------
Q psy1680         115 GN---KYNQHQG----GSFNR-----DNMRNNS----------------------RG-----------------------  137 (227)
Q Consensus       115 ~~---~~~~~~~----~~~~~-----~~~~~~~----------------------~~-----------------------  137 (227)
                      ..   .+.....    .....     ..+....                      +.                       
T Consensus       161 ~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  240 (352)
T TIGR01661       161 EPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHA  240 (352)
T ss_pred             eeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccc
Confidence            00   0000000    00000     0000000                      00                       


Q ss_pred             -CCCCC------C----CCCCCCCCCCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEE
Q psy1680         138 -GGASS------G----GGFNDFSRGGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEF  206 (227)
Q Consensus       138 -~~~~~------~----~~~~~~~~~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F  206 (227)
                       ...+.      .    .+.........+.+|||+|||+.+  ++++|+++|++||.|.+|+|++|+.|+.++|||||+|
T Consensus       241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~--~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F  318 (352)
T TIGR01661       241 AQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDT--DETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSM  318 (352)
T ss_pred             cccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCC--CHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEE
Confidence             00000      0    000000011223469999997654  7899999999999999999999999999999999999


Q ss_pred             cCHHHHHHHHHHcCCccccCC
Q psy1680         207 VDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       207 ~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+.++|.+|++.|||..|+||
T Consensus       319 ~~~~~A~~Ai~~lnG~~~~gr  339 (352)
T TIGR01661       319 TNYDEAAMAILSLNGYTLGNR  339 (352)
T ss_pred             CCHHHHHHHHHHhCCCEECCe
Confidence            999999999999999999997

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

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

Probab=100.00  E-value=2e-32  Score=238.27  Aligned_cols=169  Identities=16%  Similarity=0.253  Sum_probs=143.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ....++|||+|||+++++++|+++|++| .|.+|.|++|+.+++++|||||+|.+.++|++||+ +|| ..|+|+.|+|.
T Consensus       104 ~~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG-~~i~GR~IkV~  182 (612)
T TIGR01645       104 LAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNG-QMLGGRNIKVG  182 (612)
T ss_pred             hcCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCC-eEEecceeeec
Confidence            3456899999999999999999999999 99999999999999999999999999999999998 999 99999999998


Q ss_pred             ecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCC
Q psy1680          88 IADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNR  167 (227)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~  167 (227)
                      +.........                 .  ....                           ........+|||+|||+.+
T Consensus       183 rp~~~p~a~~-----------------~--~~~~---------------------------~~~~~~~~rLfVgnLp~~v  216 (612)
T TIGR01645       183 RPSNMPQAQP-----------------I--IDMV---------------------------QEEAKKFNRIYVASVHPDL  216 (612)
T ss_pred             cccccccccc-----------------c--cccc---------------------------cccccccceEEeecCCCCC
Confidence            5432111000                 0  0000                           0001234589999997665


Q ss_pred             CCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         168 SNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       168 ~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                        ++++|+++|+.||.|++|+|.+|+.++.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus       217 --teedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr  274 (612)
T TIGR01645       217 --SETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQ  274 (612)
T ss_pred             --CHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCe
Confidence              7899999999999999999999999999999999999999999999999999999986

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.

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

Probab=99.97  E-value=8.9e-31  Score=227.19  Aligned_cols=170  Identities=26%  Similarity=0.332  Sum_probs=145.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEe
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDI   88 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~   88 (227)
                      +...++|||+|||..+++++|+++|++| .|..|.|++++.+++++|||||+|.+.++|.+||.+++ ..+.|++|.|..
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g-~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTG-QMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCC-CEECCeeeEEee
Confidence            4557899999999999999999999999 99999999999999999999999999999999999999 999999999988


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCC
Q psy1680          89 ADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRS  168 (227)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~  168 (227)
                      +............                   ..                          ....+...+|||+|||..+ 
T Consensus       165 ~~~~~~~~~~~~~-------------------~~--------------------------~~~~p~~~~l~v~nl~~~~-  198 (457)
T TIGR01622       165 SQAEKNRAAKAAT-------------------HQ--------------------------PGDIPNFLKLYVGNLHFNI-  198 (457)
T ss_pred             cchhhhhhhhccc-------------------cc--------------------------CCCCCCCCEEEEcCCCCCC-
Confidence            6543322110000                   00                          0001235689999997655 


Q ss_pred             CChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         169 NSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       169 ~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                       ++++|+++|++||.|..|.|++++.+|.++|||||+|.+.++|.+|++.|||..|.|+
T Consensus       199 -te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~  256 (457)
T TIGR01622       199 -TEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGR  256 (457)
T ss_pred             -CHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCE
Confidence             7899999999999999999999999999999999999999999999999999999885

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.

>KOG0148|consensus

Probab=99.97  E-value=4.5e-30  Score=197.55  Aligned_cols=165  Identities=19%  Similarity=0.364  Sum_probs=140.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      ...-|||+-|...++-++|++.|.+| +|.+++|++|..|+++|||+||.|...++|++||. +|| .+|++|.|+-.|+
T Consensus        61 ~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnG-qWlG~R~IRTNWA  139 (321)
T KOG0148|consen   61 QHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNG-QWLGRRTIRTNWA  139 (321)
T ss_pred             cceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCC-eeeccceeecccc
Confidence            35789999999999999999999999 99999999999999999999999999999999999 999 9999999999999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCC
Q psy1680          90 DGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSN  169 (227)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~  169 (227)
                      ..|.....+.               .-.|+..    ++                      ...+...++|++|++.  -.
T Consensus       140 TRKp~e~n~~---------------~ltfdeV----~N----------------------Qssp~NtsVY~G~I~~--~l  176 (321)
T KOG0148|consen  140 TRKPSEMNGK---------------PLTFDEV----YN----------------------QSSPDNTSVYVGNIAS--GL  176 (321)
T ss_pred             ccCccccCCC---------------CccHHHH----hc----------------------cCCCCCceEEeCCcCc--cc
Confidence            8665221100               0000000    00                      0114567899999975  34


Q ss_pred             ChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         170 SMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       170 ~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      ++++|++.|++||.|.+|++.+|      +||+||.|++.|.|..||..+||.+|+|
T Consensus       177 te~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G  227 (321)
T KOG0148|consen  177 TEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGG  227 (321)
T ss_pred             cHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCc
Confidence            78999999999999999999999      5999999999999999999999999987

>KOG0144|consensus

Probab=99.97  E-value=2.9e-30  Score=209.85  Aligned_cols=157  Identities=21%  Similarity=0.342  Sum_probs=138.4

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC--eE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG--LQ   83 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g--~~   83 (227)
                      .++.+.-++||+-||..|+|+||+++|++| .|.+|.|++|+.|+.++|+|||.|.+.++|.+|+. |++.+.|-|  ++
T Consensus        29 ~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~p  108 (510)
T KOG0144|consen   29 NPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHP  108 (510)
T ss_pred             CCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcc
Confidence            345667899999999999999999999999 99999999999999999999999999999999998 777466766  57


Q ss_pred             eEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccC
Q psy1680          84 VRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNN  163 (227)
Q Consensus        84 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl  163 (227)
                      |.|+++....++.                                                        ...++|||+.|
T Consensus       109 vqvk~Ad~E~er~--------------------------------------------------------~~e~KLFvg~l  132 (510)
T KOG0144|consen  109 VQVKYADGERERI--------------------------------------------------------VEERKLFVGML  132 (510)
T ss_pred             eeecccchhhhcc--------------------------------------------------------ccchhhhhhhc
Confidence            8888887654422                                                        13457999999


Q ss_pred             CCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcc
Q psy1680         164 GPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRIT  223 (227)
Q Consensus       164 ~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~  223 (227)
                      +..  .+|.+++++|++||.|++|+|++|.+ +.+||+|||+|.+.|.|..|+++|||..
T Consensus       133 sK~--~te~evr~iFs~fG~Ied~~ilrd~~-~~sRGcaFV~fstke~A~~Aika~ng~~  189 (510)
T KOG0144|consen  133 SKQ--CTENEVREIFSRFGHIEDCYILRDPD-GLSRGCAFVKFSTKEMAVAAIKALNGTQ  189 (510)
T ss_pred             ccc--ccHHHHHHHHHhhCccchhhheeccc-ccccceeEEEEehHHHHHHHHHhhccce
Confidence            544  48999999999999999999999976 9999999999999999999999999863

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

Probab=99.97  E-value=2.2e-29  Score=223.42  Aligned_cols=154  Identities=19%  Similarity=0.295  Sum_probs=137.5

Q ss_pred             eEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecCCC
Q psy1680          15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIADGK   92 (227)
Q Consensus        15 ~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~~~   92 (227)
                      +|||+|||.++||++|+++|++| .|..|+|++|..|++++|||||+|.+.++|++||+ +++ ..+.|+.|+|.++...
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~-~~i~gk~i~i~~s~~~   80 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNF-KRLGGKPIRIMWSQRD   80 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCC-CEECCeeEEeeccccc
Confidence            79999999999999999999999 99999999999999999999999999999999998 999 9999999999987532


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCCChh
Q psy1680          93 RNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSMN  172 (227)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~  172 (227)
                      ...+.                                                       ....+|||+|||.+.  +++
T Consensus        81 ~~~~~-------------------------------------------------------~~~~~vfV~nLp~~~--~~~  103 (562)
T TIGR01628        81 PSLRR-------------------------------------------------------SGVGNIFVKNLDKSV--DNK  103 (562)
T ss_pred             ccccc-------------------------------------------------------cCCCceEEcCCCccC--CHH
Confidence            21110                                                       113369999996655  789


Q ss_pred             hHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         173 DHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       173 ~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +|+++|+.||.|.+|+|+++. +|+++|||||+|.+.++|.+|++.+||..++|+
T Consensus       104 ~L~~~F~~~G~i~~~~i~~~~-~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~  157 (562)
T TIGR01628       104 ALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDK  157 (562)
T ss_pred             HHHHHHHhcCCcceeEeeecC-CCCcccEEEEEECCHHHHHHHHHHhcccEecCc
Confidence            999999999999999999994 689999999999999999999999999998875

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

>KOG0145|consensus

Probab=99.96  E-value=3.9e-28  Score=186.10  Aligned_cols=215  Identities=20%  Similarity=0.261  Sum_probs=150.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      .+..+.|.|.=||.++|+++|+.+|... +|+.|++++|+.+|.+.||+||-|-++++|++|+. +|| ..+..+.|+|.
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNG-LrLQ~KTIKVS  116 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNG-LRLQNKTIKVS  116 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcc-eeeccceEEEE
Confidence            3445788899999999999999999999 99999999999999999999999999999999999 999 99999999999


Q ss_pred             ecCCCCCCCCCC------------------------------------CCCCCC------------------CCCCCCCC
Q psy1680          88 IADGKRNDNKGG------------------------------------FNNKQN------------------RGGGSGGM  113 (227)
Q Consensus        88 ~~~~~~~~~~~~------------------------------------~~~~~~------------------~~~~~~~~  113 (227)
                      +++|-...-.+.                                    -+-.++                  ..|..+..
T Consensus       117 yARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g  196 (360)
T KOG0145|consen  117 YARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSG  196 (360)
T ss_pred             eccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCC
Confidence            999755321100                                    000000                  00100000


Q ss_pred             CCC----CCCCCCCC------------CCCCCCC-C-----CCC-------------C-----CCCCCCCCCCCCCCCCC
Q psy1680         114 GGN----KYNQHQGG------------SFNRDNM-R-----NNS-------------R-----GGGASSGGGFNDFSRGG  153 (227)
Q Consensus       114 ~~~----~~~~~~~~------------~~~~~~~-~-----~~~-------------~-----~~~~~~~~~~~~~~~~~  153 (227)
                      -..    +|...++.            +..+.-. +     ...             +     .+.-+.-.+.+.+....
T Consensus       197 ~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~  276 (360)
T KOG0145|consen  197 CTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPG  276 (360)
T ss_pred             CCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCC
Confidence            000    01000000            0000000 0     000             0     00000001112222223


Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+-.|||.||+++.+  |.-||++|++||.|.+|+|++|..|+++||||||...+.++|..|+..|||+.+++|
T Consensus       277 ~g~ciFvYNLspd~d--e~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~r  348 (360)
T KOG0145|consen  277 GGWCIFVYNLSPDAD--ESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDR  348 (360)
T ss_pred             CeeEEEEEecCCCch--HhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccce
Confidence            346799999987774  567999999999999999999999999999999999999999999999999999886

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

Probab=99.96  E-value=1e-27  Score=210.68  Aligned_cols=182  Identities=19%  Similarity=0.193  Sum_probs=132.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-------------CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCC
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-------------KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG   75 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-------------~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~   75 (227)
                      .....++|||+|||+.+|+++|+++|..+             .|..+.+      ++.+|||||+|.+.++|..||.|+|
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~l~g  244 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMALDS  244 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhcCCC
Confidence            34567899999999999999999999864             2233333      4458999999999999999999999


Q ss_pred             CceeCCeEeEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy1680          76 RITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEG  155 (227)
Q Consensus        76 ~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (227)
                       ..|.|..|.|...............          .....     ..     .....     ...   .........+.
T Consensus       245 -~~~~g~~l~v~r~~~~~~~~~~~~~----------~~~~~-----~~-----~~~~~-----~~~---~~~~~~~~~~~  295 (509)
T TIGR01642       245 -IIYSNVFLKIRRPHDYIPVPQITPE----------VSQKN-----PD-----DNAKN-----VEK---LVNSTTVLDSK  295 (509)
T ss_pred             -eEeeCceeEecCccccCCccccCCC----------CCCCC-----Cc-----ccccc-----ccc---ccccccCCCCC
Confidence             9999999999765433211100000          00000     00     00000     000   00000111345


Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+|||+|||..+  ++++|+++|+.||.|..+.|++++.+|.++|||||+|.+.++|..|++.|||..|+|+
T Consensus       296 ~~l~v~nlp~~~--~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~  365 (509)
T TIGR01642       296 DRIYIGNLPLYL--GEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDN  365 (509)
T ss_pred             CEEEEeCCCCCC--CHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            789999997655  7899999999999999999999999999999999999999999999999999999875

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

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

Probab=99.95  E-value=3.2e-27  Score=207.49  Aligned_cols=187  Identities=16%  Similarity=0.166  Sum_probs=141.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      ...++|||+|||..+++++|+++|+.| .|..+.|++++.+|.++|||||+|.+.++|..||. |+| ..|.|+.|.|.+
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g-~~~~~~~l~v~~  371 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNG-KDTGDNKLHVQR  371 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCC-CEECCeEEEEEE
Confidence            345899999999999999999999999 99999999999999999999999999999999998 999 999999999999


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCC
Q psy1680          89 ADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRS  168 (227)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~  168 (227)
                      +.............         +...  ....         ...       ...  ......+.+..+|+|.|+....+
T Consensus       372 a~~~~~~~~~~~~~---------~~~~--~~~~---------~~~-------~~~--~~~~~~~~~s~v~~l~N~~~~~~  422 (509)
T TIGR01642       372 ACVGANQATIDTSN---------GMAP--VTLL---------AKA-------LSQ--SILQIGGKPTKVVQLTNLVTGDD  422 (509)
T ss_pred             CccCCCCCCccccc---------cccc--cccc---------ccc-------chh--hhccccCCCceEEEeccCCchhH
Confidence            86543221100000         0000  0000         000       000  00011224677899999963221


Q ss_pred             --------CChhhHHhhhccccceEEEEEeecC---CCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         169 --------NSMNDHGLMVTEVTTLVSVRLVKDK---ETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       169 --------~~~~~l~~~f~~~g~i~~v~i~~d~---~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                              .+.++|+++|++||.|+.|.|+++.   .++...|+|||+|.++++|.+|+++|||..|+||
T Consensus       423 l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr  492 (509)
T TIGR01642       423 LMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDR  492 (509)
T ss_pred             hcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCe
Confidence                    1346899999999999999998753   3455679999999999999999999999999996

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

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

Probab=99.95  E-value=3.5e-27  Score=209.44  Aligned_cols=174  Identities=18%  Similarity=0.291  Sum_probs=141.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeC----CeE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVD----GLQ   83 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~----g~~   83 (227)
                      ....++|||+|||.++|+++|+++|+.| .|..+.++.+. +++++|||||.|.+.++|.+|++ +++ ..+.    |+.
T Consensus       175 ~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~-~g~~~G~afV~F~~~e~A~~Av~~l~g-~~i~~~~~g~~  252 (562)
T TIGR01628       175 LKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNG-KKIGLAKEGKK  252 (562)
T ss_pred             ccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCC-cEeccccccee
Confidence            3445789999999999999999999999 99999999884 68899999999999999999999 999 9999    999


Q ss_pred             eEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccC
Q psy1680          84 VRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNN  163 (227)
Q Consensus        84 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl  163 (227)
                      +.|.++..+......-..               .+.....                        .........+|||+||
T Consensus       253 l~v~~a~~k~er~~~~~~---------------~~~~~~~------------------------~~~~~~~~~~l~V~nl  293 (562)
T TIGR01628       253 LYVGRAQKRAEREAELRR---------------KFEELQQ------------------------ERKMKAQGVNLYVKNL  293 (562)
T ss_pred             eEeecccChhhhHHHHHh---------------hHHhhhh------------------------hhhcccCCCEEEEeCC
Confidence            999888765442110000               0000000                        0000123457999999


Q ss_pred             CCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         164 GPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       164 ~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++.+  ++++|+++|++||.|++|+|++| .+|.++|||||+|.+.++|.+|+..|||..|+||
T Consensus       294 ~~~~--~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk  354 (562)
T TIGR01628       294 DDTV--TDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGK  354 (562)
T ss_pred             CCcc--CHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCc
Confidence            6655  78999999999999999999999 6799999999999999999999999999999986

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

>KOG0131|consensus

Probab=99.95  E-value=8.3e-28  Score=175.16  Aligned_cols=160  Identities=19%  Similarity=0.300  Sum_probs=142.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      +.....+|||+||+..++++-|.++|-+. +|..+.|++|+.+...+||||++|.++++|+-|++ +|. .+|.|++|+|
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~-VkLYgrpIrv   83 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNM-VKLYGRPIRV   83 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHH-HHhcCceeEE
Confidence            44567899999999999999999999999 99999999999999999999999999999999999 998 9999999999


Q ss_pred             EecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCC
Q psy1680          87 DIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPN  166 (227)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~  166 (227)
                      ..+.......                                                        ..+..|||+||.+.
T Consensus        84 ~kas~~~~nl--------------------------------------------------------~vganlfvgNLd~~  107 (203)
T KOG0131|consen   84 NKASAHQKNL--------------------------------------------------------DVGANLFVGNLDPE  107 (203)
T ss_pred             Eecccccccc--------------------------------------------------------cccccccccccCcc
Confidence            9987322211                                                        12347999999765


Q ss_pred             CCCChhhHHhhhccccceEEE-EEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         167 RSNSMNDHGLMVTEVTTLVSV-RLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       167 ~~~~~~~l~~~f~~~g~i~~v-~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .  .+..|++.|+.||.|.+. .|++|++||+++|||||.|++.|.+.+|++++||..+..|
T Consensus       108 v--De~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr  167 (203)
T KOG0131|consen  108 V--DEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNR  167 (203)
T ss_pred             h--hHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCC
Confidence            4  688899999999988765 8999999999999999999999999999999999988754

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

Probab=99.95  E-value=4.7e-26  Score=198.16  Aligned_cols=187  Identities=16%  Similarity=0.134  Sum_probs=136.2

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          11 EPPYTAFVGNLPN-GITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        11 ~~~~~l~V~nLp~-~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      .++++|||+|||+ .+|+++|+++|+.| .|..|+|++++     +|+|||+|.+.++|..||. ||+ ..|.|+.|+|.
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng-~~l~g~~l~v~  346 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNG-VKLFGKPLRVC  346 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCC-CEECCceEEEE
Confidence            4678999999998 69999999999999 99999998763     6899999999999999999 999 99999999999


Q ss_pred             ecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCC
Q psy1680          88 IADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNR  167 (227)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~  167 (227)
                      ++.............    ..+     ...+.........+        ....   .........+++.+|||+|||..+
T Consensus       347 ~s~~~~~~~~~~~~~----~~~-----~~~~~d~~~~~~~r--------~~~~---~~~~~~~~~~ps~~L~v~NLp~~~  406 (481)
T TIGR01649       347 PSKQQNVQPPREGQL----DDG-----LTSYKDYSSSRNHR--------FKKP---GSANKNNIQPPSATLHLSNIPLSV  406 (481)
T ss_pred             EcccccccCCCCCcC----cCC-----CcccccccCCcccc--------CCCc---ccccccccCCCCcEEEEecCCCCC
Confidence            986544321100000    000     00000000000000        0000   000001123577899999997655


Q ss_pred             CCChhhHHhhhccccc--eEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         168 SNSMNDHGLMVTEVTT--LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       168 ~~~~~~l~~~f~~~g~--i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                        ++++|+++|+.||.  |+.|++....  +..+|+|||+|.+.++|.+||..|||..|+|+
T Consensus       407 --tee~L~~lF~~~G~~~i~~ik~~~~~--~~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~  464 (481)
T TIGR01649       407 --SEEDLKELFAENGVHKVKKFKFFPKD--NERSKMGLLEWESVEDAVEALIALNHHQLNEP  464 (481)
T ss_pred             --CHHHHHHHHHhcCCccceEEEEecCC--CCcceeEEEEcCCHHHHHHHHHHhcCCccCCC
Confidence              78999999999997  8888887653  23579999999999999999999999999875

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).

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

Probab=99.95  E-value=1.8e-26  Score=200.81  Aligned_cols=199  Identities=15%  Similarity=0.215  Sum_probs=132.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeC-CeEeEEE
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVD-GLQVRLD   87 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~-g~~l~v~   87 (227)
                      ...++|||+|||.+++|++|+++|++| .|.+++|++| .+++++|||||+|.+.++|++||+ +|+ ..+. ++.|.|.
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng-~~i~~Gr~l~V~  133 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNN-YEIRPGRLLGVC  133 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCC-CeecCCcccccc
Confidence            446999999999999999999999999 9999999999 889999999999999999999999 999 8774 6777766


Q ss_pred             ecCCCCC----------CCC---CCCCC------------CCCCCCCCCCCCCCCCCCCCCC-------------CCCCC
Q psy1680          88 IADGKRN----------DNK---GGFNN------------KQNRGGGSGGMGGNKYNQHQGG-------------SFNRD  129 (227)
Q Consensus        88 ~~~~~~~----------~~~---~~~~~------------~~~~~~~~~~~~~~~~~~~~~~-------------~~~~~  129 (227)
                      .+.....          ...   ..+..            .........++.--.|.+....             .+.+.
T Consensus       134 ~S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~  213 (578)
T TIGR01648       134 ISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHV  213 (578)
T ss_pred             ccccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCce
Confidence            5532111          000   00000            0000000001000011111110             00000


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCCChhhHHhhhccc--cceEEEEEeecCCCCcccceEEEEEc
Q psy1680         130 NMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSMNDHGLMVTEV--TTLVSVRLVKDKETDRFKGFCYVEFV  207 (227)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~--g~i~~v~i~~d~~t~~~~g~afV~F~  207 (227)
                      -.-     .+..... ..+.......++|||+||+..+  ++++|+++|+.|  |.|+.|.+++        +||||+|.
T Consensus       214 I~V-----dwA~p~~-~~d~~~~~~~k~LfVgNL~~~~--tee~L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~  277 (578)
T TIGR01648       214 IAV-----DWAEPEE-EVDEDVMAKVKILYVRNLMTTT--TEEIIEKSFSEFKPGKVERVKKIR--------DYAFVHFE  277 (578)
T ss_pred             EEE-----Eeecccc-cccccccccccEEEEeCCCCCC--CHHHHHHHHHhcCCCceEEEEeec--------CeEEEEeC
Confidence            000     0000000 0000011234689999996554  799999999999  9999998754        59999999


Q ss_pred             CHHHHHHHHHHcCCccccCC
Q psy1680         208 DVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       208 ~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +.++|.+|++.|||.+|+||
T Consensus       278 s~e~A~kAi~~lnG~~i~Gr  297 (578)
T TIGR01648       278 DREDAVKAMDELNGKELEGS  297 (578)
T ss_pred             CHHHHHHHHHHhCCCEECCE
Confidence            99999999999999999986

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.

>KOG0127|consensus

Probab=99.95  E-value=2.1e-26  Score=192.20  Aligned_cols=212  Identities=21%  Similarity=0.315  Sum_probs=144.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      +..+|+|+|||+.+.+.+|+.+|+.| .|.+|.|++.+.+ +.+|||||+|....+|..||+ +|+ ..|+|++|.|.|+
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dg-klcGFaFV~fk~~~dA~~Al~~~N~-~~i~gR~VAVDWA  193 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDG-KLCGFAFVQFKEKKDAEKALEFFNG-NKIDGRPVAVDWA  193 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCC-CccceEEEEEeeHHHHHHHHHhccC-ceecCceeEEeee
Confidence            36899999999999999999999999 9999999987664 445999999999999999999 999 9999999999999


Q ss_pred             CCCCCCCCCCCCCCCC-----------C-CCCCCC--------CCCCCCC--CCCCCCCC---CCCCCCCCCCCCCCCCC
Q psy1680          90 DGKRNDNKGGFNNKQN-----------R-GGGSGG--------MGGNKYN--QHQGGSFN---RDNMRNNSRGGGASSGG  144 (227)
Q Consensus        90 ~~~~~~~~~~~~~~~~-----------~-~~~~~~--------~~~~~~~--~~~~~~~~---~~~~~~~~~~~~~~~~~  144 (227)
                      -++............+           . ....+.        .....-.  ...+....   ........-.+..+++.
T Consensus       194 V~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~  273 (678)
T KOG0127|consen  194 VDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGK  273 (678)
T ss_pred             cccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhcccccccccccccccccccc
Confidence            8776432211000000           0 000000        0000000  00000000   00000011111111111


Q ss_pred             CCC-------C-CCCCCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHH
Q psy1680         145 GFN-------D-FSRGGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL  216 (227)
Q Consensus       145 ~~~-------~-~~~~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al  216 (227)
                      ...       . ........+|||+|||+++  ++++|...|+.||.|.++.|+.++.|+.++|.|||.|.+..+|.+||
T Consensus       274 ~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~--tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci  351 (678)
T KOG0127|consen  274 KESDKKAQNKTTRENITEGKTVFVRNLPFDT--TEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCI  351 (678)
T ss_pred             CcccchhccccccccccccceEEEecCCccc--cHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHH
Confidence            110       0 1111345799999997666  89999999999999999999999999999999999999999999999


Q ss_pred             HHc------CCccccCC
Q psy1680         217 LKD------GRITVDGL  227 (227)
Q Consensus       217 ~~l------~g~~i~gr  227 (227)
                      +.-      .+..|+||
T Consensus       352 ~~Aspa~e~g~~ll~GR  368 (678)
T KOG0127|consen  352 EAASPASEDGSVLLDGR  368 (678)
T ss_pred             HhcCccCCCceEEEecc
Confidence            977      23667765

>KOG0117|consensus

Probab=99.94  E-value=8.7e-27  Score=190.39  Aligned_cols=156  Identities=17%  Similarity=0.275  Sum_probs=134.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC--CeEEEEEeecC-CCCCeecEEEEEeCCHHHHHHHHH--hCCCceeCCeEe
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDK-ETDRFKGFCYVEFVDVENLRQALL--KDGRITVDGLQV   84 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~--~i~~v~i~~~~-~~~~~~g~afv~f~~~~~a~~al~--~~~~~~~~g~~l   84 (227)
                      +...++|||+|||.++++++|.+.+++.  .|.+|.+..++ +..+++|||||+|.++..|..|-.  +++.+.++|+.+
T Consensus       161 Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~  240 (506)
T KOG0117|consen  161 SVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAI  240 (506)
T ss_pred             eeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcc
Confidence            4567999999999999999999999998  78888887764 456889999999999999999997  677689999999


Q ss_pred             EEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCC
Q psy1680          85 RLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNG  164 (227)
Q Consensus        85 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~  164 (227)
                      .|.|+.+.......                                                    .....+.|||+||+
T Consensus       241 tVdWAep~~e~ded----------------------------------------------------~ms~VKvLYVRNL~  268 (506)
T KOG0117|consen  241 TVDWAEPEEEPDED----------------------------------------------------TMSKVKVLYVRNLM  268 (506)
T ss_pred             eeeccCcccCCChh----------------------------------------------------hhhheeeeeeeccc
Confidence            99999987753220                                                    00235689999995


Q ss_pred             CCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         165 PNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       165 ~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                        .++|++.|+++|+.||.|+.|+.++|        ||||+|.+.++|.+||+.+||++|+|.
T Consensus       269 --~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~  321 (506)
T KOG0117|consen  269 --ESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGS  321 (506)
T ss_pred             --hhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCc
Confidence              45589999999999999999998877        899999999999999999999999984

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

Probab=99.94  E-value=6.7e-26  Score=197.21  Aligned_cols=157  Identities=14%  Similarity=0.132  Sum_probs=128.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-h--CCCceeCCeEeEEE
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-K--DGRITVDGLQVRLD   87 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~--~~~~~~~g~~l~v~   87 (227)
                      +++.|||+|||+.+++++|+++|++| .|..|.++++      ++||||+|.+.++|++||. +  ++ ..+.|++|.|.
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~-~~l~g~~l~v~   73 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVP-IYIRGQPAFFN   73 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCC-ceEcCeEEEEE
Confidence            57899999999999999999999999 9999999864      6899999999999999998 3  77 89999999999


Q ss_pred             ecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCC
Q psy1680          88 IADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNR  167 (227)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~  167 (227)
                      ++..+....... .            .   ..                             ........+|||.||+.+.
T Consensus        74 ~s~~~~~~~~~~-~------------~---~~-----------------------------~~~~~~~~~v~v~nl~~~v  108 (481)
T TIGR01649        74 YSTSQEIKRDGN-S------------D---FD-----------------------------SAGPNKVLRVIVENPMYPI  108 (481)
T ss_pred             ecCCcccccCCC-C------------c---cc-----------------------------CCCCCceEEEEEcCCCCCC
Confidence            997654222100 0            0   00                             0000112468999996555


Q ss_pred             CCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         168 SNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       168 ~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                        ++++|+++|++||.|.+|.|+++..    +|+|||+|.+.++|.+|++.|||..|.|
T Consensus       109 --t~~~L~~~F~~~G~V~~v~i~~~~~----~~~afVef~~~~~A~~A~~~Lng~~i~~  161 (481)
T TIGR01649       109 --TLDVLYQIFNPYGKVLRIVTFTKNN----VFQALVEFESVNSAQHAKAALNGADIYN  161 (481)
T ss_pred             --CHHHHHHHHhccCCEEEEEEEecCC----ceEEEEEECCHHHHHHHHHHhcCCcccC
Confidence              7899999999999999999988743    4789999999999999999999999965

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).

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

Probab=99.94  E-value=1.3e-24  Score=188.65  Aligned_cols=211  Identities=20%  Similarity=0.259  Sum_probs=138.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      ..++|||+|||..+++++|+++|+.| .|..|.|+.++.+++++|||||+|.+.++|.+||. |+| ..|.|+.|.|.++
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g-~~i~g~~i~v~~a  263 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNG-FELAGRPIKVGYA  263 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCC-cEECCEEEEEEEc
Confidence            36899999999999999999999999 99999999999999999999999999999999999 999 9999999999997


Q ss_pred             CCCCCCCCC--CCCCC-CC-CCCCC----------------CCCCCCCCCCCCC-----CCCCCCCC-CCCCC--CC-CC
Q psy1680          90 DGKRNDNKG--GFNNK-QN-RGGGS----------------GGMGGNKYNQHQG-----GSFNRDNM-RNNSR--GG-GA  140 (227)
Q Consensus        90 ~~~~~~~~~--~~~~~-~~-~~~~~----------------~~~~~~~~~~~~~-----~~~~~~~~-~~~~~--~~-~~  140 (227)
                      .........  ..... .. ..+..                +......+.....     ....+... .....  .. ..
T Consensus       264 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  343 (457)
T TIGR01622       264 QDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGA  343 (457)
T ss_pred             cCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccc
Confidence            633211100  00000 00 00000                0000000000000     00000000 00000  00 00


Q ss_pred             CC---CCC-CCCCCCCCCCCcceeccCCCCCCC--------ChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcC
Q psy1680         141 SS---GGG-FNDFSRGGEGPGGFRNNNGPNRSN--------SMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVD  208 (227)
Q Consensus       141 ~~---~~~-~~~~~~~~~~~~l~v~nl~~~~~~--------~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~  208 (227)
                      ..   ... ........+..+|+|.||-.+...        ..+||+++|++||.|+.|.|...    .+.|++||+|.+
T Consensus       344 ~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~----~~~G~~fV~F~~  419 (457)
T TIGR01622       344 LAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTK----NSAGKIYLKFSS  419 (457)
T ss_pred             cccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCC----CCceeEEEEECC
Confidence            00   000 000112245678999999543321        24789999999999999998643    457999999999


Q ss_pred             HHHHHHHHHHcCCccccCC
Q psy1680         209 VENLRQALLKDGRITVDGL  227 (227)
Q Consensus       209 ~~~a~~Al~~l~g~~i~gr  227 (227)
                      .++|.+|++.|||+.++||
T Consensus       420 ~e~A~~A~~~lnGr~f~gr  438 (457)
T TIGR01622       420 VDAALAAFQALNGRYFGGK  438 (457)
T ss_pred             HHHHHHHHHHhcCcccCCe
Confidence            9999999999999999997

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>KOG0127|consensus

Probab=99.93  E-value=2.3e-25  Score=186.06  Aligned_cols=181  Identities=18%  Similarity=0.214  Sum_probs=144.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      ...+|||++||+.++.++|.++|+.+ +|.++.++.++.++.++||+||.|+-.++++.|++ ..+ ..|.|+.|.|..+
T Consensus         4 ~g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~-~kf~Gr~l~v~~A   82 (678)
T KOG0127|consen    4 SGATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQ-SKFEGRILNVDPA   82 (678)
T ss_pred             CCceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhc-Ccccceecccccc
Confidence            34899999999999999999999999 99999999999999999999999999999999999 899 9999999999999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCC
Q psy1680          90 DGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSN  169 (227)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~  169 (227)
                      ..+.....-.-+.    ..   ....     ...    +..+               ....-..+...|.|+|||+.+  
T Consensus        83 ~~R~r~e~~~~~e----~~---~veK-----~~~----q~~~---------------~k~~v~~~k~rLIIRNLPf~~--  129 (678)
T KOG0127|consen   83 KKRARSEEVEKGE----NK---AVEK-----PIE----QKRP---------------TKAKVDLPKWRLIIRNLPFKC--  129 (678)
T ss_pred             cccccchhccccc----ch---hhhc-----ccc----cCCc---------------chhhccCccceEEeecCCccc--
Confidence            8766533100000    00   0000     000    0000               000001234579999998777  


Q ss_pred             ChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         170 SMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       170 ~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|..+|+.||.|..|.|++.++++.+ |||||.|....+|..||+.+||.+|+||
T Consensus       130 k~~dLk~vFs~~G~V~Ei~IP~k~dgklc-GFaFV~fk~~~dA~~Al~~~N~~~i~gR  186 (678)
T KOG0127|consen  130 KKPDLKNVFSNFGKVVEIVIPRKKDGKLC-GFAFVQFKEKKDAEKALEFFNGNKIDGR  186 (678)
T ss_pred             CcHHHHHHHhhcceEEEEEcccCCCCCcc-ceEEEEEeeHHHHHHHHHhccCceecCc
Confidence            45799999999999999999999885555 9999999999999999999999999998

>KOG0109|consensus

Probab=99.92  E-value=9.2e-25  Score=169.92  Aligned_cols=136  Identities=20%  Similarity=0.371  Sum_probs=125.3

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecCC
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~~   91 (227)
                      .+|||+|||..+++.+|+.+|++| +|.+|.|+        |.||||...+...++.||. |++ .+|+|..|.|+-++.
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv--------KNYgFVHiEdktaaedairNLhg-YtLhg~nInVeaSks   73 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIV--------KNYGFVHIEDKTAAEDAIRNLHG-YTLHGVNINVEASKS   73 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeee--------cccceEEeecccccHHHHhhccc-ceecceEEEEEeccc
Confidence            479999999999999999999999 99999999        4599999999999999999 999 999999999999887


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCCCh
Q psy1680          92 KRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSM  171 (227)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~  171 (227)
                      |..                                                           .+.+|+|+|+.+..  +-
T Consensus        74 Ksk-----------------------------------------------------------~stkl~vgNis~tc--tn   92 (346)
T KOG0109|consen   74 KSK-----------------------------------------------------------ASTKLHVGNISPTC--TN   92 (346)
T ss_pred             cCC-----------------------------------------------------------CccccccCCCCccc--cC
Confidence            632                                                           45689999997666  66


Q ss_pred             hhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         172 NDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       172 ~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++|+..|++||.|.+|.|++|        |+||+|+-.++|..|+..|+|.+++|.
T Consensus        93 ~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk  140 (346)
T KOG0109|consen   93 QELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGK  140 (346)
T ss_pred             HHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccc
Confidence            889999999999999999887        899999999999999999999999984

>KOG0117|consensus

Probab=99.91  E-value=1.7e-23  Score=171.21  Aligned_cols=146  Identities=18%  Similarity=0.271  Sum_probs=127.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCcee-CCeEeEEE
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITV-DGLQVRLD   87 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~-~g~~l~v~   87 (227)
                      ...+.|||+.||.++.|++|.-+|++. +|-+++||.|+.+|.++|||||.|.+.+.|+.||+ ||+ .+| .|+.|.|.
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn-~Eir~GK~igvc  159 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNN-YEIRPGKLLGVC  159 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhC-ccccCCCEeEEE
Confidence            456999999999999999999999999 99999999999999999999999999999999999 999 877 58889988


Q ss_pred             ecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCC
Q psy1680          88 IADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNR  167 (227)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~  167 (227)
                      .+..                                                               .+.|||+|+|.  
T Consensus       160 ~Sva---------------------------------------------------------------n~RLFiG~IPK--  174 (506)
T KOG0117|consen  160 VSVA---------------------------------------------------------------NCRLFIGNIPK--  174 (506)
T ss_pred             Eeee---------------------------------------------------------------cceeEeccCCc--
Confidence            8653                                                               34699999965  


Q ss_pred             CCChhhHHhhhcccc-ceEEEEEeecCC-CCcccceEEEEEcCHHHHHHHHHHcCCc
Q psy1680         168 SNSMNDHGLMVTEVT-TLVSVRLVKDKE-TDRFKGFCYVEFVDVENLRQALLKDGRI  222 (227)
Q Consensus       168 ~~~~~~l~~~f~~~g-~i~~v~i~~d~~-t~~~~g~afV~F~~~~~a~~Al~~l~g~  222 (227)
                      ++++++|.+.+++.+ .|++|.|...++ ..++||||||+|.+...|..|..+|-.-
T Consensus       175 ~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g  231 (506)
T KOG0117|consen  175 TKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPG  231 (506)
T ss_pred             cccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCC
Confidence            448999999999987 677777776554 3478999999999999999998877543

>KOG0147|consensus

Probab=99.90  E-value=8.2e-25  Score=183.16  Aligned_cols=172  Identities=26%  Similarity=0.346  Sum_probs=144.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEe
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDI   88 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~   88 (227)
                      +...++||+--|+..++..+|.+||+.+ .|.+|.|+.|+.+++++|.|||+|.+.+++..||.|.| ..+.|-+|.|+.
T Consensus       176 ERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsG-qrllg~pv~vq~  254 (549)
T KOG0147|consen  176 ERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSG-QRLLGVPVIVQL  254 (549)
T ss_pred             HHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcC-CcccCceeEecc
Confidence            4455889999999999999999999999 99999999999999999999999999999999999999 999999999998


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCC
Q psy1680          89 ADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRS  168 (227)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~  168 (227)
                      ....+........                                ...           ...-..|-..|||+||.++. 
T Consensus       255 sEaeknr~a~~s~--------------------------------a~~-----------~k~~~~p~~rl~vgnLHfNi-  290 (549)
T KOG0147|consen  255 SEAEKNRAANASP--------------------------------ALQ-----------GKGFTGPMRRLYVGNLHFNI-  290 (549)
T ss_pred             cHHHHHHHHhccc--------------------------------ccc-----------ccccccchhhhhhcccccCc-
Confidence            7654432110000                                000           00000112238999997666 


Q ss_pred             CChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         169 NSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       169 ~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                       ++++|+.+|++||.|+.|.+++|.+||.++||||++|.+.++|.+|++.|||++|.||
T Consensus       291 -te~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr  348 (549)
T KOG0147|consen  291 -TEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGR  348 (549)
T ss_pred             -hHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCc
Confidence             7899999999999999999999999999999999999999999999999999999997

>KOG0124|consensus

Probab=99.90  E-value=1.5e-23  Score=167.92  Aligned_cols=165  Identities=16%  Similarity=0.276  Sum_probs=139.6

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecCC
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~~   91 (227)
                      ++||||.|.+.+.|+.|+..|..| +|..|.+.+|+.|++.+|||||+|.-.+.|+.|++ +|| ..++|+.|+|.....
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg-~mlGGRNiKVgrPsN  192 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNG-QMLGGRNIKVGRPSN  192 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhcc-ccccCccccccCCCC
Confidence            789999999999999999999999 99999999999999999999999999999999999 999 999999999985332


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCCCh
Q psy1680          92 KRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSM  171 (227)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~  171 (227)
                      -.....                   -.+..                           ......-+.|||..+.+++  ++
T Consensus       193 mpQAQp-------------------iID~v---------------------------qeeAk~fnRiYVaSvHpDL--Se  224 (544)
T KOG0124|consen  193 MPQAQP-------------------IIDMV---------------------------QEEAKKFNRIYVASVHPDL--SE  224 (544)
T ss_pred             Ccccch-------------------HHHHH---------------------------HHHHHhhheEEeeecCCCc--cH
Confidence            111000                   00000                           0000123579999997777  68


Q ss_pred             hhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         172 NDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       172 ~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +||+..|+.||.|..|.|.+++.++.++||+|++|.+......|+..||-+.++|.
T Consensus       225 ~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQ  280 (544)
T KOG0124|consen  225 TDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQ  280 (544)
T ss_pred             HHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccc
Confidence            99999999999999999999999999999999999999999999999999888873

>KOG0123|consensus

Probab=99.88  E-value=6.3e-22  Score=165.25  Aligned_cols=140  Identities=21%  Similarity=0.312  Sum_probs=126.4

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecCC
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~~   91 (227)
                      ..|||+   +++|+..|.++|+.+ ++..+++.+|. |  +.|||||.|.+.++|.+||. +|. ..+.|++|+|-|+..
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~-~~~~~~~~rim~s~r   74 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNF-DVLKGKPIRIMWSQR   74 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCC-cccCCcEEEeehhcc
Confidence            468998   899999999999999 99999999997 6  99999999999999999999 999 999999999999753


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCCCh
Q psy1680          92 KRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSM  171 (227)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~  171 (227)
                      ...                                                              .+||.||+++.  +.
T Consensus        75 d~~--------------------------------------------------------------~~~i~nl~~~~--~~   90 (369)
T KOG0123|consen   75 DPS--------------------------------------------------------------LVFIKNLDESI--DN   90 (369)
T ss_pred             CCc--------------------------------------------------------------eeeecCCCccc--Cc
Confidence            111                                                              28999997655  56


Q ss_pred             hhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         172 NDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       172 ~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+|.++|+.||.|.+|++..|.+ | ++|| ||+|++.+.|.+|++.+||..++|.
T Consensus        91 ~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~k  143 (369)
T KOG0123|consen   91 KSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGK  143 (369)
T ss_pred             HHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCC
Confidence            88999999999999999999965 5 9999 9999999999999999999998773

>KOG0110|consensus

Probab=99.87  E-value=6.7e-22  Score=170.01  Aligned_cols=163  Identities=27%  Similarity=0.376  Sum_probs=135.5

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCC---CeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETD---RFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~---~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      ++|||.||++.+|.++|+..|... .|..+.|...+...   .+.|||||+|.+.++|+.|++ |+| +.|+|+.|.|.+
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqg-tvldGH~l~lk~  594 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQG-TVLDGHKLELKI  594 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcC-ceecCceEEEEe
Confidence            449999999999999999999999 99999887654321   355999999999999999999 999 999999999999


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCC
Q psy1680          89 ADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRS  168 (227)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~  168 (227)
                      +..+.....+                                                ...+.......|.|+|+|+.+ 
T Consensus       595 S~~k~~~~~g------------------------------------------------K~~~~kk~~tKIlVRNipFeA-  625 (725)
T KOG0110|consen  595 SENKPASTVG------------------------------------------------KKKSKKKKGTKILVRNIPFEA-  625 (725)
T ss_pred             ccCccccccc------------------------------------------------cccccccccceeeeeccchHH-
Confidence            8832221110                                                000111235689999998766 


Q ss_pred             CChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         169 NSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       169 ~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                       +..+++++|+.||.|.+|+|++....+.++|||||+|.++.+|.+|+++|.+..|-||
T Consensus       626 -t~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGR  683 (725)
T KOG0110|consen  626 -TKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGR  683 (725)
T ss_pred             -HHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceech
Confidence             7899999999999999999999876677899999999999999999999999888776

>KOG0105|consensus

Probab=99.87  E-value=1.1e-20  Score=138.45  Aligned_cols=168  Identities=24%  Similarity=0.402  Sum_probs=126.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      ..+++|||+|||.++.+.+|+.+|-+| .|..|.+...   -....||||+|.+..+|+.||. -+| ..++|+.|+|++
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdG-Ydydg~rLRVEf   79 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDG-YDYDGCRLRVEF   79 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccc-cccCcceEEEEe
Confidence            457899999999999999999999999 9999988432   3345799999999999999999 999 999999999999


Q ss_pred             cCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCC
Q psy1680          89 ADGKRNDN--KGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPN  166 (227)
Q Consensus        89 ~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~  166 (227)
                      +..-....  .+.+.. ++++++.++....                               .++ --+...+.|..||+.
T Consensus        80 prggr~s~~~~G~y~g-ggrgGgg~gg~rg-------------------------------pps-rrSe~RVvVsGLp~S  126 (241)
T KOG0105|consen   80 PRGGRSSSDRRGSYSG-GGRGGGGGGGRRG-------------------------------PPS-RRSEYRVVVSGLPPS  126 (241)
T ss_pred             ccCCCcccccccccCC-CCCCCCCCCcccC-------------------------------Ccc-cccceeEEEecCCCC
Confidence            87543211  111111 1111111000000                               000 012346899999888


Q ss_pred             CCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccc
Q psy1680         167 RSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV  224 (227)
Q Consensus       167 ~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i  224 (227)
                      .+|  .||++...+-|.|....+.+|       |++.|+|.+.||.+.|+.+|....+
T Consensus       127 gSW--QDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~  175 (241)
T KOG0105|consen  127 GSW--QDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKF  175 (241)
T ss_pred             Cch--HHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhccccc
Confidence            866  789999999999999999888       6899999999999999999986654

>KOG4205|consensus

Probab=99.86  E-value=6.8e-22  Score=159.95  Aligned_cols=153  Identities=22%  Similarity=0.333  Sum_probs=135.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEecC
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~~   90 (227)
                      ..++|||++|++.++++.|+++|.+| +|.++.+++|+.+++++||+||+|.+.+.+..+|.... ..|+|+.|.+..+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~-h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNART-HKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccc-cccCCccccceecc
Confidence            78999999999999999999999999 99999999999999999999999999999999998666 78999999999998


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCCC
Q psy1680          91 GKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNS  170 (227)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~  170 (227)
                      ++.........                                                   ....++||+.||.++  +
T Consensus        84 ~r~~~~~~~~~---------------------------------------------------~~tkkiFvGG~~~~~--~  110 (311)
T KOG4205|consen   84 SREDQTKVGRH---------------------------------------------------LRTKKIFVGGLPPDT--T  110 (311)
T ss_pred             Ccccccccccc---------------------------------------------------cceeEEEecCcCCCC--c
Confidence            77654321110                                                   135689999997655  7


Q ss_pred             hhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHH
Q psy1680         171 MNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK  218 (227)
Q Consensus       171 ~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~  218 (227)
                      ++++++.|++||.|..+.++.|..+.+++||+||.|.+.+.+.+++..
T Consensus       111 e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~  158 (311)
T KOG4205|consen  111 EEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQ  158 (311)
T ss_pred             hHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceeccc
Confidence            899999999999999999999999999999999999999988887653

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

Probab=99.86  E-value=6.2e-20  Score=160.51  Aligned_cols=81  Identities=14%  Similarity=0.310  Sum_probs=76.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      ..++|||+|||.++++++|+++|+.| .|..+.|++++.+++++|||||+|.+.++|.+||+ +|+ ..|+|+.|+|.++
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg-~elgGr~LrV~kA  281 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNL-FDLGGQYLRVGKC  281 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCC-CeeCCeEEEEEec
Confidence            45799999999999999999999999 99999999999999999999999999999999999 999 9999999999998


Q ss_pred             CCCC
Q psy1680          90 DGKR   93 (227)
Q Consensus        90 ~~~~   93 (227)
                      ..+.
T Consensus       282 i~pP  285 (612)
T TIGR01645       282 VTPP  285 (612)
T ss_pred             CCCc
Confidence            7644

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.

>KOG0146|consensus

Probab=99.84  E-value=9.8e-21  Score=146.10  Aligned_cols=211  Identities=19%  Similarity=0.277  Sum_probs=143.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC--eEeEEE
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG--LQVRLD   87 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g--~~l~v~   87 (227)
                      +.++|||+-|...-.|+|++.+|..| .+.+|.+.+... |.+||+|||.|.+..+|+.||. |+|-..+-|  ..|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~d-g~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPD-GNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCC-CCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            56899999999999999999999999 999999998754 8899999999999999999999 998556665  468899


Q ss_pred             ecCCCCCCC--C--------CCCCC-------------------------------------------------------
Q psy1680          88 IADGKRNDN--K--------GGFNN-------------------------------------------------------  102 (227)
Q Consensus        88 ~~~~~~~~~--~--------~~~~~-------------------------------------------------------  102 (227)
                      ++...+++.  +        +.+.+                                                       
T Consensus        97 ~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~A  176 (371)
T KOG0146|consen   97 FADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLAA  176 (371)
T ss_pred             eccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhccccc
Confidence            987544321  0        00000                                                       


Q ss_pred             CC----CCCCCCCC------------CCCCCCCCCCCC----------------CCCCCCC-----------CCCCC---
Q psy1680         103 KQ----NRGGGSGG------------MGGNKYNQHQGG----------------SFNRDNM-----------RNNSR---  136 (227)
Q Consensus       103 ~~----~~~~~~~~------------~~~~~~~~~~~~----------------~~~~~~~-----------~~~~~---  136 (227)
                      .+    ......++            ...+.+......                .+....+           .....   
T Consensus       177 ~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~Aa  256 (371)
T KOG0146|consen  177 APVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAAA  256 (371)
T ss_pred             CCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhhh
Confidence            00    00000000            000001000000                0000000           00000   


Q ss_pred             --CCCCCCCCCC--------CCCCCCCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEE
Q psy1680         137 --GGGASSGGGF--------NDFSRGGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEF  206 (227)
Q Consensus       137 --~~~~~~~~~~--------~~~~~~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F  206 (227)
                        ..++.-...+        .....++.+.+|||..||...  ...+|-++|-+||.|.+.++..|+.|+.||=|+||.|
T Consensus       257 ypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEF--gDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSf  334 (371)
T KOG0146|consen  257 YPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEF--GDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSF  334 (371)
T ss_pred             cchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhh--ccHHHHHHhccccceeeeeeeehhccccccceeeEec
Confidence              0000000011        111235778999999998666  4577999999999999999999999999999999999


Q ss_pred             cCHHHHHHHHHHcCCcccc
Q psy1680         207 VDVENLRQALLKDGRITVD  225 (227)
Q Consensus       207 ~~~~~a~~Al~~l~g~~i~  225 (227)
                      +++..|++||.+|||+.|+
T Consensus       335 DNp~SaQaAIqAMNGFQIG  353 (371)
T KOG0146|consen  335 DNPASAQAAIQAMNGFQIG  353 (371)
T ss_pred             CCchhHHHHHHHhcchhhh
Confidence            9999999999999999885

>KOG0144|consensus

Probab=99.84  E-value=2e-20  Score=152.80  Aligned_cols=84  Identities=21%  Similarity=0.381  Sum_probs=76.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCe--EeEE
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGL--QVRL   86 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~--~l~v   86 (227)
                      ...++|||+-|+..+||.+++++|++| .|++|.|++|.. +.+||+|||.|.+.+.|..||+ +|+-..+.|+  +|.|
T Consensus       122 ~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~-~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVV  200 (510)
T KOG0144|consen  122 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD-GLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVV  200 (510)
T ss_pred             ccchhhhhhhccccccHHHHHHHHHhhCccchhhheeccc-ccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEE
Confidence            347899999999999999999999999 999999999954 8999999999999999999999 9986778876  8999


Q ss_pred             EecCCCCCC
Q psy1680          87 DIADGKRND   95 (227)
Q Consensus        87 ~~~~~~~~~   95 (227)
                      +++.+++.+
T Consensus       201 kFADtqkdk  209 (510)
T KOG0144|consen  201 KFADTQKDK  209 (510)
T ss_pred             EecccCCCc
Confidence            999987653

>KOG0123|consensus

Probab=99.82  E-value=1.9e-19  Score=150.45  Aligned_cols=162  Identities=18%  Similarity=0.300  Sum_probs=136.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      .......|||.||++.++.++|.++|+.| +|..|++..+.. | ++|| ||+|.+++.|.+||+ +|| ..+.++.|.|
T Consensus        72 s~rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng-~ll~~kki~v  147 (369)
T KOG0123|consen   72 SQRDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNG-MLLNGKKIYV  147 (369)
T ss_pred             hccCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcC-cccCCCeeEE
Confidence            33444449999999999999999999999 999999999865 4 8999 999999999999999 999 9999999999


Q ss_pred             EecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCC
Q psy1680          87 DIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPN  166 (227)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~  166 (227)
                      .....+.........                                                 ....-..++|.|++. 
T Consensus       148 g~~~~~~er~~~~~~-------------------------------------------------~~~~~t~v~vk~~~~-  177 (369)
T KOG0123|consen  148 GLFERKEEREAPLGE-------------------------------------------------YKKRFTNVYVKNLEE-  177 (369)
T ss_pred             eeccchhhhcccccc-------------------------------------------------hhhhhhhhheecccc-
Confidence            998776654321100                                                 001234578999964 


Q ss_pred             CCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         167 RSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       167 ~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                       +.+.+.|..+|+.+|.|.++.++++.. ++++||+||.|.++++|..|++.|++..++|
T Consensus       178 -~~~~~~l~~~f~~~g~i~s~~v~~~~~-g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~  235 (369)
T KOG0123|consen  178 -DSTDEELKDLFSAYGSITSVAVMRDSI-GKSKGFGFVNFENPEDAKKAVETLNGKIFGD  235 (369)
T ss_pred             -ccchHHHHHhhcccCcceEEEEeecCC-CCCCCccceeecChhHHHHHHHhccCCcCCc
Confidence             447889999999999999999999955 7799999999999999999999999998763

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

Probab=99.81  E-value=8.2e-19  Score=128.57  Aligned_cols=86  Identities=24%  Similarity=0.445  Sum_probs=80.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ...+++|||+|||+.+++++|+++|++| .|..+.|+.++.+++++|||||+|.+.++|+.||+ +++ ..|+|+.|+|.
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng-~~i~Gr~l~V~  109 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDG-KELNGRHIRVN  109 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCC-CEECCEEEEEE
Confidence            4567899999999999999999999999 99999999999999999999999999999999998 999 99999999999


Q ss_pred             ecCCCCCCC
Q psy1680          88 IADGKRNDN   96 (227)
Q Consensus        88 ~~~~~~~~~   96 (227)
                      ++.++....
T Consensus       110 ~a~~~~~~~  118 (144)
T PLN03134        110 PANDRPSAP  118 (144)
T ss_pred             eCCcCCCCC
Confidence            998765543

>KOG4206|consensus

Probab=99.79  E-value=7.1e-18  Score=127.83  Aligned_cols=195  Identities=18%  Similarity=0.245  Sum_probs=136.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHh----cccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCe
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVER----FFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGL   82 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~----~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~   82 (227)
                      ...+..+|||.||+..+..++|+.    +|++| .|.+|...   .+.+.+|.|||.|.+.+.|..|+. |+| +.+.|+
T Consensus         5 ~~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~---kt~KmRGQA~VvFk~~~~As~A~r~l~g-fpFygK   80 (221)
T KOG4206|consen    5 SVNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF---KTPKMRGQAFVVFKETEAASAALRALQG-FPFYGK   80 (221)
T ss_pred             ccCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec---CCCCccCceEEEecChhHHHHHHHHhcC-CcccCc
Confidence            345566999999999999999887    99999 99999886   447789999999999999999999 999 999999


Q ss_pred             EeEEEecCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcce
Q psy1680          83 QVRLDIADGKRNDN---KGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGF  159 (227)
Q Consensus        83 ~l~v~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  159 (227)
                      .++|++|..++..-   .+.+..+..+.....-.....-....+..+.      ....+.   +..+ .....++..+||
T Consensus        81 ~mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~------~~~~~~---p~p~-~~~~~ppn~ilf  150 (221)
T KOG4206|consen   81 PMRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYN------MNRMNL---PPPF-LAQMAPPNNILF  150 (221)
T ss_pred             hhheecccCccchhhccCceeccccCccccccccccCCcccccccccc------cccccC---CCCc-cccCCCCceEEE
Confidence            99999998776421   1222222111000000000000000000000      000000   0001 122246788999


Q ss_pred             eccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccc
Q psy1680         160 RNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV  224 (227)
Q Consensus       160 v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i  224 (227)
                      +.|+|...  +.+.+..+|+.|.....|+++...     ++.|||+|.+...|..|+..++|..|
T Consensus       151 ~~niP~es--~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~i  208 (221)
T KOG4206|consen  151 LTNIPSES--ESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKI  208 (221)
T ss_pred             EecCCcch--hHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhcccee
Confidence            99996444  678889999999999999998865     58999999999999999999999876

>KOG0148|consensus

Probab=99.79  E-value=2.9e-19  Score=138.11  Aligned_cols=129  Identities=17%  Similarity=0.292  Sum_probs=104.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEe
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDI   88 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~   88 (227)
                      +...++|||+||...+||+-|-.+|.+. .+..++|+.|                                   .|+|.+
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~-----------------------------------e~~v~w   47 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD-----------------------------------ELKVNW   47 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhccccccceeehh-----------------------------------hhcccc
Confidence            4567999999999999999999999999 9999999876                                   233444


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCC
Q psy1680          89 ADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRS  168 (227)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~  168 (227)
                      +...........                                                    ...--+||+.|.+.. 
T Consensus        48 a~~p~nQsk~t~----------------------------------------------------~~hfhvfvgdls~eI-   74 (321)
T KOG0148|consen   48 ATAPGNQSKPTS----------------------------------------------------NQHFHVFVGDLSPEI-   74 (321)
T ss_pred             ccCcccCCCCcc----------------------------------------------------ccceeEEehhcchhc-
Confidence            433211111000                                                    012247999996555 


Q ss_pred             CChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         169 NSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       169 ~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                       +-++|++.|.+||.|.+++|++|..|+++||||||.|-+.++|+.||+.|||.=|++|
T Consensus        75 -~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R  132 (321)
T KOG0148|consen   75 -DNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRR  132 (321)
T ss_pred             -chHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccc
Confidence             5688999999999999999999999999999999999999999999999999988876

>KOG1457|consensus

Probab=99.76  E-value=6e-17  Score=122.21  Aligned_cols=206  Identities=16%  Similarity=0.210  Sum_probs=125.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEee-cCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeC---CeEeE
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVK-DKETDRFKGFCYVEFVDVENLRQALL-KDGRITVD---GLQVR   85 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~-~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~---g~~l~   85 (227)
                      .-++|||.+||.++...+|..+|..| ..+...|.. ++...-++-+||+.|.+.+.|..||. ||| ..|+   +..|+
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNG-vrFDpE~~stLh  111 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNG-VRFDPETGSTLH  111 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcC-eeeccccCceeE
Confidence            35999999999999999999999999 777666643 33334456799999999999999999 999 9986   56888


Q ss_pred             EEecCCCCCCC-CCCCCCCCC---CCCCCCCC--CCCCCCCCCCCCCCC---------CCCCCCCC---------CCCCC
Q psy1680          86 LDIADGKRNDN-KGGFNNKQN---RGGGSGGM--GGNKYNQHQGGSFNR---------DNMRNNSR---------GGGAS  141 (227)
Q Consensus        86 v~~~~~~~~~~-~~~~~~~~~---~~~~~~~~--~~~~~~~~~~~~~~~---------~~~~~~~~---------~~~~~  141 (227)
                      +++++...... ..+.+..+.   -.-...+.  ....+..+-....+.         +.......         ..+..
T Consensus       112 iElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P  191 (284)
T KOG1457|consen  112 IELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAP  191 (284)
T ss_pred             eeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCC
Confidence            88876533211 111110000   00000000  000000000000000         00000000         00000


Q ss_pred             CC-CC---CCC-CCCCCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHH
Q psy1680         142 SG-GG---FND-FSRGGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL  216 (227)
Q Consensus       142 ~~-~~---~~~-~~~~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al  216 (227)
                      +. .+   ... -.......||||.||++++  +||+|+++|+.|.....++|.-.   |. .-.|||+|++.+.|..||
T Consensus       192 ~a~a~l~ks~q~~~~~~acstlfianl~~~~--~ed~l~~~~~~~~gf~~l~~~~~---~g-~~vaf~~~~~~~~at~am  265 (284)
T KOG1457|consen  192 SANAHLEKSSQGGSGARACSTLFIANLGPNC--TEDELKQLLSRYPGFHILKIRAR---GG-MPVAFADFEEIEQATDAM  265 (284)
T ss_pred             cccchhhhhhcccccchhhhhHhhhccCCCC--CHHHHHHHHHhCCCceEEEEecC---CC-cceEeecHHHHHHHHHHH
Confidence            00 00   000 0111234799999998877  78999999999987777766432   22 237999999999999999


Q ss_pred             HHcCCccc
Q psy1680         217 LKDGRITV  224 (227)
Q Consensus       217 ~~l~g~~i  224 (227)
                      ..|+|..|
T Consensus       266 ~~lqg~~~  273 (284)
T KOG1457|consen  266 NHLQGNLL  273 (284)
T ss_pred             HHhhccee
Confidence            99999887

>KOG0147|consensus

Probab=99.75  E-value=1.4e-17  Score=140.00  Aligned_cols=206  Identities=21%  Similarity=0.242  Sum_probs=134.7

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecCC
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~~   91 (227)
                      .+|||+||.+++++++|+.+|+.| .|..|.+++|..||+++||+||+|.+.++|.+|++ +|| +.|-|+.|+|.....
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lng-felAGr~ikV~~v~~  357 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNG-FELAGRLIKVSVVTE  357 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhcc-ceecCceEEEEEeee
Confidence            349999999999999999999999 99999999998899999999999999999999999 999 999999999987665


Q ss_pred             CCCCCCC--C---CC--CCCCCCCCCCCCCCCC----CCCCCCC----CCCC-----CCCCCCCCCCCCCCC-CCC---C
Q psy1680          92 KRNDNKG--G---FN--NKQNRGGGSGGMGGNK----YNQHQGG----SFNR-----DNMRNNSRGGGASSG-GGF---N  147 (227)
Q Consensus        92 ~~~~~~~--~---~~--~~~~~~~~~~~~~~~~----~~~~~~~----~~~~-----~~~~~~~~~~~~~~~-~~~---~  147 (227)
                      +-.....  .   +.  ...+..-+.++  ..+    +....+.    .+..     .........+..... ...   -
T Consensus       358 r~~~~~a~~~~~d~D~~d~~gl~~~~~g--~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~  435 (549)
T KOG0147|consen  358 RVDTKEAAVTQFDFDEDDRQGLSLGSGG--RNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADA  435 (549)
T ss_pred             ecccccccccccccchhhcccccccccc--HHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCcccc
Confidence            4322111  0   00  00111111111  000    0000000    0000     000000000000000 000   0


Q ss_pred             CCCCCCCCCcceeccCCCCCC--------CChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHc
Q psy1680         148 DFSRGGEGPGGFRNNNGPNRS--------NSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD  219 (227)
Q Consensus       148 ~~~~~~~~~~l~v~nl~~~~~--------~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l  219 (227)
                      .+.-..++..+.+.|+=.+.+        +..+|+.+.|++||.|.-|.+.+.     +-|+.||.|.+.+.|..|+.+|
T Consensus       436 ~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~n-----s~g~VYvrc~s~~~A~~a~~al  510 (549)
T KOG0147|consen  436 SPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKN-----SAGCVYVRCPSAEAAGTAVKAL  510 (549)
T ss_pred             ccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccC-----CCceEEEecCcHHHHHHHHHHH
Confidence            111114566777777732221        245889999999999988887444     2399999999999999999999


Q ss_pred             CCccccCC
Q psy1680         220 GRITVDGL  227 (227)
Q Consensus       220 ~g~~i~gr  227 (227)
                      ||.=++||
T Consensus       511 hgrWF~gr  518 (549)
T KOG0147|consen  511 HGRWFAGR  518 (549)
T ss_pred             hhhhhccc
Confidence            99999886

>KOG4211|consensus

Probab=99.75  E-value=4.4e-17  Score=135.46  Aligned_cols=160  Identities=19%  Similarity=0.190  Sum_probs=127.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEe
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDI   88 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~   88 (227)
                      +......|-+++||+++|++||.+||+.+.|..+.+.  +.+|+..|-|||+|.+.+++++||+.+. ..+..+-|+|..
T Consensus         6 e~~~~~~vr~rGLPwsat~~ei~~Ff~~~~I~~~~~~--r~~Gr~sGeA~Ve~~seedv~~AlkkdR-~~mg~RYIEVf~   82 (510)
T KOG4211|consen    6 EGSTAFEVRLRGLPWSATEKEILDFFSNCGIENLEIP--RRNGRPSGEAYVEFTSEEDVEKALKKDR-ESMGHRYIEVFT   82 (510)
T ss_pred             CCCcceEEEecCCCccccHHHHHHHHhcCceeEEEEe--ccCCCcCcceEEEeechHHHHHHHHhhH-HHhCCceEEEEc
Confidence            4456788889999999999999999999888886665  4668999999999999999999999999 999999999998


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCC
Q psy1680          89 ADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRS  168 (227)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~  168 (227)
                      +.......-...                     .+                         +.......+|-++.||+.+ 
T Consensus        83 ~~~~e~d~~~~~---------------------~g-------------------------~~s~~~d~vVRLRGLPfsc-  115 (510)
T KOG4211|consen   83 AGGAEADWVMRP---------------------GG-------------------------PNSSANDGVVRLRGLPFSC-  115 (510)
T ss_pred             cCCccccccccC---------------------CC-------------------------CCCCCCCceEEecCCCccC-
Confidence            876554211000                     00                         0000234578899997766 


Q ss_pred             CChhhHHhhhccccceEE-EEEeecCCCCcccceEEEEEcCHHHHHHHHHHcC
Q psy1680         169 NSMNDHGLMVTEVTTLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG  220 (227)
Q Consensus       169 ~~~~~l~~~f~~~g~i~~-v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~  220 (227)
                       +++||.++|+..-.+.. |.++.|+ .+++.|-|||.|++.+.|+.||..+.
T Consensus       116 -te~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~rhr  166 (510)
T KOG4211|consen  116 -TEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGRHR  166 (510)
T ss_pred             -cHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHHHH
Confidence             89999999998876665 5567775 48899999999999999999998764

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

Probab=99.74  E-value=6.7e-18  Score=123.75  Aligned_cols=72  Identities=18%  Similarity=0.204  Sum_probs=67.7

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+.+|||+|||+.+  ++++|+++|++||.|.+|.|++|+.|++++|||||+|.+.++|++|++.||+..|+||
T Consensus        33 ~~~~lfVgnL~~~~--te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr  104 (144)
T PLN03134         33 MSTKLFIGGLSWGT--DDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGR  104 (144)
T ss_pred             CCCEEEEeCCCCCC--CHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            46789999997665  7999999999999999999999999999999999999999999999999999999986

>KOG4212|consensus

Probab=99.72  E-value=8.2e-16  Score=126.26  Aligned_cols=209  Identities=22%  Similarity=0.269  Sum_probs=139.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC--CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~--~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      +....+.+||.|||++....+|+.+|.+-  +|..|.+..| .+++++|+|.|+|++++.+++|++ ||. +++.|++|.
T Consensus        40 ~~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk-~~~~GR~l~  117 (608)
T KOG4212|consen   40 VAARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNK-YEVNGRELV  117 (608)
T ss_pred             cccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhh-ccccCceEE
Confidence            34555779999999999999999999866  8999999998 569999999999999999999999 999 999999999


Q ss_pred             EEecCCCCCCCCC--------CCCCCCC---------CCCCCCCCCCC----CCCCCCCCCCCCCCCC--CCCCCCCCCC
Q psy1680          86 LDIADGKRNDNKG--------GFNNKQN---------RGGGSGGMGGN----KYNQHQGGSFNRDNMR--NNSRGGGASS  142 (227)
Q Consensus        86 v~~~~~~~~~~~~--------~~~~~~~---------~~~~~~~~~~~----~~~~~~~~~~~~~~~~--~~~~~~~~~~  142 (227)
                      |+.....+..+.+        ++.....         ..++.++....    +-..+.+.-.+...+.  .....++..+
T Consensus       118 vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lf  197 (608)
T KOG4212|consen  118 VKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLF  197 (608)
T ss_pred             EeccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcc
Confidence            9887654332211        1100000         00000110000    0000000000000000  0000111111


Q ss_pred             CC--CCCCC---CCCCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHH
Q psy1680         143 GG--GFNDF---SRGGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL  217 (227)
Q Consensus       143 ~~--~~~~~---~~~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~  217 (227)
                      ..  .|...   -..|..+.+||.||.+.+  ..+.|++.|.--|.|+.|.+-.|++ |.++|++.++|..+-+|..|+.
T Consensus       198 gl~~~Flr~~h~f~pPl~~k~fvanl~~~v--g~~kL~qvfgmAGkv~~vdf~idKe-G~s~G~~vi~y~hpveavqaIs  274 (608)
T KOG4212|consen  198 GLSASFLRSLHIFSPPLHNKVFVANLDYKV--GNKKLKQVFGMAGKVQSVDFSIDKE-GNSRGFAVIEYDHPVEAVQAIS  274 (608)
T ss_pred             cchhhhhhhccCCCCCccceeeeecccccc--chHHHHHHhccceeeeeeceeeccc-cccCCeeEEEecchHHHHHHHH
Confidence            11  11110   123556789999996666  4577999999999999999999977 8999999999999999999999


Q ss_pred             HcCCc
Q psy1680         218 KDGRI  222 (227)
Q Consensus       218 ~l~g~  222 (227)
                      .+++-
T Consensus       275 ml~~~  279 (608)
T KOG4212|consen  275 MLDRQ  279 (608)
T ss_pred             hhccC
Confidence            99863

>KOG1548|consensus

Probab=99.68  E-value=3.1e-16  Score=125.23  Aligned_cols=193  Identities=16%  Similarity=0.186  Sum_probs=130.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeE--------EEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCcee
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLV--------SVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITV   79 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~--------~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~   79 (227)
                      ......|||.|||.++|.+++.++|+++ -|.        .|++.++.. |..+|-|++.|...+++..|+. |++ ..|
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe-~~~  208 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDE-DEL  208 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCc-ccc
Confidence            4455779999999999999999999988 443        477888744 9999999999999999999999 999 999


Q ss_pred             CCeEeEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcce
Q psy1680          80 DGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGF  159 (227)
Q Consensus        80 ~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  159 (227)
                      .|+.|+|..|.-.....   +...+...+.  .....++...+...+           ++.   ......++.....+|.
T Consensus       209 rg~~~rVerAkfq~Kge---~~~~~k~k~k--~~~~kk~~k~q~k~~-----------dw~---pd~~~~sk~r~~~tVi  269 (382)
T KOG1548|consen  209 RGKKLRVERAKFQMKGE---YDASKKEKGK--CKDKKKLKKQQQKLL-----------DWR---PDRDDPSKARADRTVI  269 (382)
T ss_pred             cCcEEEEehhhhhhccC---cCcccccccc--cccHHHHHHHHHhhc-----------ccC---CCccccccccCCcEEE
Confidence            99999999986322211   1000000000  000000000000000           000   0001122223456788


Q ss_pred             eccCC--CC-------CCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         160 RNNNG--PN-------RSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       160 v~nl~--~~-------~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +.|+=  ..       .....++|++.|++||.|.+|.|.-.    .+.|.+-|.|.+.++|..|++.|+|+-++||
T Consensus       270 ~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~----hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgR  342 (382)
T KOG1548|consen  270 LKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDR----HPDGVVTVSFRNNEEADQCIQTMDGRWFDGR  342 (382)
T ss_pred             eeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEecc----CCCceeEEEeCChHHHHHHHHHhcCeeecce
Confidence            88882  11       12345788889999999999987643    2479999999999999999999999999997

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.68  E-value=3.8e-16  Score=131.34  Aligned_cols=81  Identities=21%  Similarity=0.386  Sum_probs=76.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      .+.+|||+|||+.+++++|+++|++| .|..+.|++|+.|+.++|||||+|.+.++|.+||. ||| ..|+|+.|+|.+.
T Consensus       268 ~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG-~~~~gr~i~V~~~  346 (352)
T TIGR01661       268 AGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNG-YTLGNRVLQVSFK  346 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCC-CEECCeEEEEEEc
Confidence            34579999999999999999999999 99999999999999999999999999999999999 999 9999999999998


Q ss_pred             CCCC
Q psy1680          90 DGKR   93 (227)
Q Consensus        90 ~~~~   93 (227)
                      ..+.
T Consensus       347 ~~~~  350 (352)
T TIGR01661       347 TNKA  350 (352)
T ss_pred             cCCC
Confidence            8764

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

>KOG0106|consensus

Probab=99.68  E-value=1e-16  Score=122.63  Aligned_cols=158  Identities=25%  Similarity=0.319  Sum_probs=118.2

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecCC
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~~   91 (227)
                      .+|||++||+.+.+.+|..+|..| .+.++.+.        .||+||+|.+..+|..|+. +++ ..|.+-.+.|.++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~-~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDG-KELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcC-ceecceeeeeecccc
Confidence            479999999999999999999999 99999885        5799999999999999998 999 999998888888876


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCCCh
Q psy1680          92 KRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSM  171 (227)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~  171 (227)
                      .....+.+          ++++... +.....                          ........++|.+++...  ..
T Consensus        73 ~~~~~g~~----------~~g~r~~-~~~~~~--------------------------~p~~s~~r~~~~~~~~r~--~~  113 (216)
T KOG0106|consen   73 KRRGRGRP----------RGGDRRS-DSRRYR--------------------------PPSRTHFRLIVRNLSLRV--SW  113 (216)
T ss_pred             cccccCCC----------CCCCccc-hhhccC--------------------------Ccccccceeeeccchhhh--hH
Confidence            54332100          0110000 000000                          000123456677774333  45


Q ss_pred             hhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         172 NDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       172 ~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+|.+.|+++|.++...+        ..+++||+|.+.++|.+|+++|+|..+.|+
T Consensus       114 qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~  161 (216)
T KOG0106|consen  114 QDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGR  161 (216)
T ss_pred             HHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCc
Confidence            889999999998866655        246899999999999999999999999875

>PF00076 RRM_1: RNA recognition motif

Probab=99.65  E-value=3.5e-16  Score=100.55  Aligned_cols=67  Identities=18%  Similarity=0.354  Sum_probs=62.5

Q ss_pred             ceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         158 GFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       158 l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      |||+|||.++  ++++|+++|+.||.|..+.+..+ .++.++|+|||+|.+.++|++|++.++|..|+|+
T Consensus         1 l~v~nlp~~~--t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~   67 (70)
T PF00076_consen    1 LYVGNLPPDV--TEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGR   67 (70)
T ss_dssp             EEEESETTTS--SHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             cEEcCCCCcC--CHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECcc
Confidence            6999997666  78999999999999999999998 6689999999999999999999999999999885

(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 ....

>KOG0110|consensus

Probab=99.65  E-value=2.7e-15  Score=129.69  Aligned_cols=200  Identities=19%  Similarity=0.197  Sum_probs=127.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ......|+|+|||..+..++|..+|..| +|..+.++..   |   -.++|.|.+..+|..|.+ +.. ..+...++.+.
T Consensus       382 ~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~~---G---~~aiv~fl~p~eAr~Afrklay-sr~k~~plyle  454 (725)
T KOG0110|consen  382 ERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPG---G---TGAIVEFLNPLEARKAFRKLAY-SRFKSAPLYLE  454 (725)
T ss_pred             hhhcceeeeccCccccccHHHHHHhhcccccceeecCcc---c---ceeeeeecCccchHHHHHHhch-hhhccCccccc
Confidence            4455789999999999999999999999 9999966521   1   259999999999999999 888 88888888887


Q ss_pred             ecCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CcceeccCCC
Q psy1680          88 IADGKRNDNKGGFNNKQNRGGGS-GGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEG-PGGFRNNNGP  165 (227)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~l~v~nl~~  165 (227)
                      ++....-...+....-....... ......+.....+..      .........++   ...-...... .+|||.||  
T Consensus       455 ~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v------~eD~d~te~ss---~a~~a~~~~~~t~lfvkNl--  523 (725)
T KOG0110|consen  455 WAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQV------EEDKDPTEESS---LARVAEDEETETKLFVKNL--  523 (725)
T ss_pred             cChhhhccCCccccccccccccccccCcceecccccccc------cccCCcccccc---chhhhhccccchhhhhhcC--
Confidence            76422111000000000000000 000000000000000      00000000000   0000001122 23999999  


Q ss_pred             CCCCChhhHHhhhccccceEEEEEeecCCCC---cccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         166 NRSNSMNDHGLMVTEVTTLVSVRLVKDKETD---RFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       166 ~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~---~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +.+++.++|...|...|.|.+|.|.+.++.-   .|.|||||+|.++++|++|++.|+|..|+|+
T Consensus       524 nf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH  588 (725)
T KOG0110|consen  524 NFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGH  588 (725)
T ss_pred             CcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCc
Confidence            6677899999999999999999887765422   3679999999999999999999999999985

>KOG0149|consensus

Probab=99.64  E-value=3.1e-16  Score=119.39  Aligned_cols=81  Identities=26%  Similarity=0.407  Sum_probs=74.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEe
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDI   88 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~   88 (227)
                      ...-++||||||++.++.+.|+++|++| +|++..|+.|+.++++|||+||+|++.++|.+||+-.. ..|+||+..+.+
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~-piIdGR~aNcnl   87 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN-PIIDGRKANCNL   87 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC-Ccccccccccch
Confidence            3455899999999999999999999999 99999999999999999999999999999999999666 799999988887


Q ss_pred             cCC
Q psy1680          89 ADG   91 (227)
Q Consensus        89 ~~~   91 (227)
                      +.-
T Consensus        88 A~l   90 (247)
T KOG0149|consen   88 ASL   90 (247)
T ss_pred             hhh
Confidence            653

>KOG0121|consensus

Probab=99.63  E-value=7.1e-16  Score=106.68  Aligned_cols=84  Identities=24%  Similarity=0.391  Sum_probs=78.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      +...+++|||+||++.++|++|.++|+.. +|..|.+-.|+.+..++|||||+|-+.++|..||. +++ +.+++++|.+
T Consensus        32 a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~Alryisg-trLddr~ir~  110 (153)
T KOG0121|consen   32 ALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISG-TRLDDRPIRI  110 (153)
T ss_pred             HHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhcc-Ccccccceee
Confidence            35678999999999999999999999999 99999999999999999999999999999999999 999 9999999999


Q ss_pred             EecCCCC
Q psy1680          87 DIADGKR   93 (227)
Q Consensus        87 ~~~~~~~   93 (227)
                      .+.-.-.
T Consensus       111 D~D~GF~  117 (153)
T KOG0121|consen  111 DWDAGFV  117 (153)
T ss_pred             eccccch
Confidence            9965433

>KOG0120|consensus

Probab=99.63  E-value=8.7e-16  Score=130.55  Aligned_cols=183  Identities=22%  Similarity=0.253  Sum_probs=138.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      ...+++||++||...++.++.++...| ++....++.+..+|.++||||.+|.+......|+. +|| ..++++.|.|..
T Consensus       287 ~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnG-m~lgd~~lvvq~  365 (500)
T KOG0120|consen  287 DSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNG-MQLGDKKLVVQR  365 (500)
T ss_pred             cccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccch-hhhcCceeEeeh
Confidence            445899999999999999999999999 99999999999999999999999999999999999 999 999999999999


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCC--C-
Q psy1680          89 ADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNG--P-  165 (227)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~--~-  165 (227)
                      +................              ...+.               ..    ......+.+..+|.+.|+=  . 
T Consensus       366 A~~g~~~~~~~~~~~~~--------------~~~~i---------------~~----~~~q~~g~~t~Vl~L~n~Vt~de  412 (500)
T KOG0120|consen  366 AIVGASNANVNFNISQS--------------QVPGI---------------PL----LMTQMAGIPTEVLCLTNVVTPDE  412 (500)
T ss_pred             hhccchhccccCCcccc--------------ccccc---------------hh----hhcccCCCcchhhhhhhcCCHHH
Confidence            87644322111100000              00000               00    0001122456677777762  1 


Q ss_pred             -----CCCCChhhHHhhhccccceEEEEEeecCCCCc---ccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         166 -----NRSNSMNDHGLMVTEVTTLVSVRLVKDKETDR---FKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       166 -----~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~---~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                           .+.+..++++..|++||.|.+|.|+++...+.   ..|-.||+|.+.+++++|+++|.|..++||
T Consensus       413 Lkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nR  482 (500)
T KOG0120|consen  413 LKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANR  482 (500)
T ss_pred             hcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCc
Confidence                 12234477888999999999999999832232   357889999999999999999999999987

>PF00076 RRM_1: RNA recognition motif

Probab=99.63  E-value=2.3e-15  Score=96.66  Aligned_cols=68  Identities=31%  Similarity=0.687  Sum_probs=64.9

Q ss_pred             EEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680          16 AFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus        16 l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      |||+|||.++|+++|+++|++| .+..+.++.+ .++..+++|||+|.+.++|.+|++ +++ ..++|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g-~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNG-KKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTT-EEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCC-CEECccCcC
Confidence            7999999999999999999999 9999999988 778999999999999999999999 999 999999885

(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 ....

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

Probab=99.61  E-value=1e-14  Score=127.67  Aligned_cols=134  Identities=16%  Similarity=0.177  Sum_probs=95.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC---CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ---KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~---~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ..++|||+||+.++++++|+++|++|   .|.+|.++        ++||||+|.+.++|.+||+ +|+ ..|+|+.|+|.
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~lnG-~~i~Gr~I~V~  302 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDELNG-KELEGSEIEVT  302 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHHhCC-CEECCEEEEEE
Confidence            45789999999999999999999999   67777765        4699999999999999999 999 99999999999


Q ss_pred             ecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCC
Q psy1680          88 IADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNR  167 (227)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~  167 (227)
                      ++.++.......+.  ++ .++++........   .            .+           ..-.+.+.+++++|++++.
T Consensus       303 ~Akp~~~~~~~~~~--rg-~gg~~~~~~~~~~---~------------~g-----------~~~sp~s~~~~~g~~~~~~  353 (578)
T TIGR01648       303 LAKPVDKKSYVRYT--RG-TGGRGKERQAARQ---S------------LG-----------QVYDPASRSLAYEDYYYHP  353 (578)
T ss_pred             EccCCCcccccccc--cc-cCCCccccccccc---c------------cC-----------cccCccccccccccccccc
Confidence            99876543211110  00 0000010000000   0            00           0011457789999997666


Q ss_pred             CCChhhHHhhhccccceE
Q psy1680         168 SNSMNDHGLMVTEVTTLV  185 (227)
Q Consensus       168 ~~~~~~l~~~f~~~g~i~  185 (227)
                        +++.++++|..+|.|.
T Consensus       354 --~~~~~~~~f~~~g~~~  369 (578)
T TIGR01648       354 --PYAPSLHFPRMPGPIR  369 (578)
T ss_pred             --cccchhhccccCcccc
Confidence              5678999999998755

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.

>KOG0122|consensus

Probab=99.61  E-value=2.9e-15  Score=114.61  Aligned_cols=81  Identities=28%  Similarity=0.443  Sum_probs=78.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      ...++|-|.||+.+++|.+|+++|.+| .|..+.|.+|+.||.++|||||.|.+.++|.+||+ ||| +-++.-.|+|+|
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG-~gyd~LILrvEw  265 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNG-YGYDNLILRVEW  265 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccC-cccceEEEEEEe
Confidence            467889999999999999999999999 99999999999999999999999999999999999 999 999999999999


Q ss_pred             cCCC
Q psy1680          89 ADGK   92 (227)
Q Consensus        89 ~~~~   92 (227)
                      ++|+
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            9875

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.61  E-value=9.7e-15  Score=121.56  Aligned_cols=83  Identities=22%  Similarity=0.413  Sum_probs=76.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC--eEeEE
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG--LQVRL   86 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g--~~l~v   86 (227)
                      ...++|||+|||..+|+++|+++|++| .|..+.|++++.++++++||||+|.+.++|++||+ |++ ..+.+  ++|.|
T Consensus       191 ~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng-~~~~g~~~~l~V  269 (346)
T TIGR01659       191 IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNN-VIPEGGSQPLTV  269 (346)
T ss_pred             cccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCC-CccCCCceeEEE
Confidence            346789999999999999999999999 99999999999999999999999999999999999 999 88866  68999


Q ss_pred             EecCCCCC
Q psy1680          87 DIADGKRN   94 (227)
Q Consensus        87 ~~~~~~~~   94 (227)
                      .++.....
T Consensus       270 ~~a~~~~~  277 (346)
T TIGR01659       270 RLAEEHGK  277 (346)
T ss_pred             EECCcccc
Confidence            99876543

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).

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.60  E-value=3.6e-15  Score=96.04  Aligned_cols=67  Identities=27%  Similarity=0.420  Sum_probs=61.5

Q ss_pred             ceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         158 GFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       158 l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      |||+|||+..  ++++|+.+|+.||.|..+.+.++++ +.++|+|||+|.+.++|.+|++.++|..|+||
T Consensus         1 v~i~nlp~~~--~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~   67 (70)
T PF14259_consen    1 VYISNLPPST--TEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGR   67 (70)
T ss_dssp             EEEESSTTT----HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CEEeCCCCCC--CHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCE
Confidence            6899997655  7899999999999999999999977 99999999999999999999999999999986

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 ....

>KOG0122|consensus

Probab=99.58  E-value=7.6e-15  Score=112.29  Aligned_cols=70  Identities=21%  Similarity=0.242  Sum_probs=65.3

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      ...+|-|.|||.+.  ++++|.++|.+||.|..|.|.+|++||.++|||||+|.+.++|.+|++.|||+=++
T Consensus       188 D~~tvRvtNLsed~--~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd  257 (270)
T KOG0122|consen  188 DEATVRVTNLSEDM--REDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYD  257 (270)
T ss_pred             ccceeEEecCcccc--ChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccc
Confidence            56789999996655  78999999999999999999999999999999999999999999999999998765

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.58  E-value=2.3e-14  Score=92.28  Aligned_cols=68  Identities=35%  Similarity=0.692  Sum_probs=62.7

Q ss_pred             EEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680          16 AFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus        16 l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      |||+|||+.+++++|+++|+.+ .|..+.+..++. +.++++|||+|.+.++|.+|+. +++ ..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~-~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNG-KEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTT-EEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCC-cEECCEEcC
Confidence            7999999999999999999999 999999999877 8999999999999999999999 888 999999874

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 ....

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

Probab=99.57  E-value=5.7e-14  Score=113.23  Aligned_cols=173  Identities=20%  Similarity=0.268  Sum_probs=123.4

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecC
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~   90 (227)
                      .++|||+|||..+++++|+++|..| .+..+.+..++.+++++|||||.|.+.++|..|++ +++ ..|.|++|.|.++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~-~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNG-KELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCC-CeECCceeEeeccc
Confidence            6999999999999999999999999 99999999999899999999999999999999999 999 99999999999976


Q ss_pred             C-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCC
Q psy1680          91 G-KRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSN  169 (227)
Q Consensus        91 ~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~  169 (227)
                      . ............           .. +...        .              .............+++.+++...  
T Consensus       194 ~~~~~~~~~~~~~~-----------~~-~~~~--------~--------------~~~~~~~~~~~~~~~~~~~~~~~--  237 (306)
T COG0724         194 PASQPRSELSNNLD-----------AS-FAKK--------L--------------SRGKALLLEKSDNLYVGNLPLKT--  237 (306)
T ss_pred             cccccccccccccc-----------hh-hhcc--------c--------------cccccccccccceeecccccccc--
Confidence            4 111000000000           00 0000        0              00001111345678888886544  


Q ss_pred             ChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCc
Q psy1680         170 SMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRI  222 (227)
Q Consensus       170 ~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~  222 (227)
                      +..++...|..+|.+..+.+.............++.+....++..+.......
T Consensus       238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  290 (306)
T COG0724         238 AEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRGNKK  290 (306)
T ss_pred             chhHHHHhccccccceeeeccCCCCCcccccccccchhHHHhhhhhhccccce
Confidence            67889999999999977777666554445555666666666666655544443

>KOG0149|consensus

Probab=99.57  E-value=3.2e-15  Score=113.90  Aligned_cols=70  Identities=21%  Similarity=0.247  Sum_probs=63.3

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      -.+|||++|+  +.+..|.|+..|+.||.|+++.|+.|+.||+|||||||+|.+.+.|.+|++--| ..||||
T Consensus        12 ~TKifVggL~--w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~-piIdGR   81 (247)
T KOG0149|consen   12 FTKIFVGGLA--WETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN-PIIDGR   81 (247)
T ss_pred             EEEEEEcCcc--cccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC-Cccccc
Confidence            3579999995  555789999999999999999999999999999999999999999999998665 778887

>KOG0126|consensus

Probab=99.54  E-value=2.3e-15  Score=110.27  Aligned_cols=82  Identities=27%  Similarity=0.525  Sum_probs=77.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      ..+.-|||+|||+..||.||.-.|++| .|+.|.+++|+.||+++||||+.|.+..+...|+. +|| +.|.|+.|+|..
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NG-iki~gRtirVDH  111 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNG-IKILGRTIRVDH  111 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCC-ceecceeEEeee
Confidence            567889999999999999999999999 99999999999999999999999999999999998 999 999999999988


Q ss_pred             cCCCC
Q psy1680          89 ADGKR   93 (227)
Q Consensus        89 ~~~~~   93 (227)
                      ....+
T Consensus       112 v~~Yk  116 (219)
T KOG0126|consen  112 VSNYK  116 (219)
T ss_pred             ccccc
Confidence            65443

>KOG0124|consensus

Probab=99.54  E-value=5.5e-13  Score=107.64  Aligned_cols=79  Identities=14%  Similarity=0.334  Sum_probs=74.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      +.-++|||..+.++.+++||+..|+.| +|..|.+-+++.++..+||+||+|.+..+...|+. +|- +.++|.-|+|..
T Consensus       208 k~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNl-FDLGGQyLRVGk  286 (544)
T KOG0124|consen  208 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNL-FDLGGQYLRVGK  286 (544)
T ss_pred             HhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcch-hhcccceEeccc
Confidence            344899999999999999999999999 99999999999999999999999999999999999 999 999999999976


Q ss_pred             cC
Q psy1680          89 AD   90 (227)
Q Consensus        89 ~~   90 (227)
                      +-
T Consensus       287 ~v  288 (544)
T KOG0124|consen  287 CV  288 (544)
T ss_pred             cc
Confidence            54

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.53  E-value=6.4e-14  Score=110.07  Aligned_cols=77  Identities=26%  Similarity=0.338  Sum_probs=71.2

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEecCC
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~~~   91 (227)
                      .++|||+|||+.+|+++|+++|+.| .|.+|.|+.++.   .+|||||+|.+.++|+.||.|+| ..|.|+.|.|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~AllLnG-~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALLLSG-ATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHHhcC-CeeCCceEEEEeccC
Confidence            5799999999999999999999999 999999998853   46899999999999999999999 999999999999875


Q ss_pred             CC
Q psy1680          92 KR   93 (227)
Q Consensus        92 ~~   93 (227)
                      ..
T Consensus        80 ~~   81 (260)
T PLN03120         80 YQ   81 (260)
T ss_pred             CC
Confidence            43

>KOG0113|consensus

Probab=99.52  E-value=3.6e-14  Score=111.51  Aligned_cols=73  Identities=22%  Similarity=0.312  Sum_probs=68.8

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .|=.||||.-|  +++++|+.|+..|+.||.|+.|+|++|..||+++|||||+|+..-+..+|.+..+|..|+||
T Consensus        99 DPy~TLFv~RL--nydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgr  171 (335)
T KOG0113|consen   99 DPYKTLFVARL--NYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGR  171 (335)
T ss_pred             Cccceeeeeec--cccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCc
Confidence            45679999999  66668999999999999999999999999999999999999999999999999999999996

>KOG0113|consensus

Probab=99.51  E-value=1.4e-13  Score=108.15  Aligned_cols=84  Identities=29%  Similarity=0.558  Sum_probs=78.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ..+-++|||+-|+.+++|..|+..|+.| +|..|.|++|+.||+++|||||+|..+.+...|-+ .+| ..|+|+.|.|.
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG-~~Idgrri~VD  176 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADG-IKIDGRRILVD  176 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccC-ceecCcEEEEE
Confidence            4667999999999999999999999999 99999999999999999999999999999999999 999 99999999998


Q ss_pred             ecCCCCC
Q psy1680          88 IADGKRN   94 (227)
Q Consensus        88 ~~~~~~~   94 (227)
                      +-..+..
T Consensus       177 vERgRTv  183 (335)
T KOG0113|consen  177 VERGRTV  183 (335)
T ss_pred             ecccccc
Confidence            8765443

>KOG0121|consensus

Probab=99.51  E-value=2.3e-14  Score=99.21  Aligned_cols=72  Identities=14%  Similarity=0.152  Sum_probs=66.8

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+.||||+||++  -++|++|+++|+++|.|..|.+-.|+.+..+-|||||+|-+.++|..||.-++|..|+.|
T Consensus        35 ~S~tvyVgNlSf--yttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr  106 (153)
T KOG0121|consen   35 KSCTVYVGNLSF--YTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDR  106 (153)
T ss_pred             hcceEEEeeeee--eecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCccccc
Confidence            578999999954  448999999999999999999999999999999999999999999999999999999875

>KOG4207|consensus

Probab=99.51  E-value=1.5e-14  Score=108.17  Aligned_cols=70  Identities=21%  Similarity=0.236  Sum_probs=66.4

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+|.|-||  ...++.++|+.+|++||.|-+|.|++|+.|..++|||||.|....||+.|+++|+|.+||||
T Consensus        14 ~SLkVdNL--TyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgR   83 (256)
T KOG4207|consen   14 TSLKVDNL--TYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGR   83 (256)
T ss_pred             eeEEecce--eccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccc
Confidence            46889999  66678999999999999999999999999999999999999999999999999999999997

>KOG0125|consensus

Probab=99.50  E-value=5.3e-14  Score=111.86  Aligned_cols=70  Identities=17%  Similarity=0.127  Sum_probs=63.6

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..++|+|.|+|+...  +-||+.+|++||.|.+|.|+.+ + ..|||||||+|++++||++|.++|+|.+|.||
T Consensus        95 ~pkRLhVSNIPFrFR--dpDL~aMF~kfG~VldVEIIfN-E-RGSKGFGFVTmen~~dadRARa~LHgt~VEGR  164 (376)
T KOG0125|consen   95 TPKRLHVSNIPFRFR--DPDLRAMFEKFGKVLDVEIIFN-E-RGSKGFGFVTMENPADADRARAELHGTVVEGR  164 (376)
T ss_pred             CCceeEeecCCcccc--CccHHHHHHhhCceeeEEEEec-c-CCCCccceEEecChhhHHHHHHHhhcceeece
Confidence            346899999988775  5889999999999999999887 3 56899999999999999999999999999998

>KOG0107|consensus

Probab=99.50  E-value=6.1e-14  Score=102.30  Aligned_cols=77  Identities=30%  Similarity=0.525  Sum_probs=71.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      -.++|||+||+..+++.||+..|..| ++..|||-+.     +.|||||+|.+..+|+.|+. |+| ..|.|..|.|+++
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG-~~~cG~r~rVE~S   82 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDG-KDICGSRIRVELS   82 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCC-ccccCceEEEEee
Confidence            47899999999999999999999999 9999999754     37999999999999999999 999 9999999999998


Q ss_pred             CCCCC
Q psy1680          90 DGKRN   94 (227)
Q Consensus        90 ~~~~~   94 (227)
                      .....
T Consensus        83 ~G~~r   87 (195)
T KOG0107|consen   83 TGRPR   87 (195)
T ss_pred             cCCcc
Confidence            86654

>KOG4207|consensus

Probab=99.50  E-value=9.4e-14  Score=103.89  Aligned_cols=84  Identities=27%  Similarity=0.407  Sum_probs=78.7

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      +...+.-..|-|.||.+-++.++|+.+|++| .|-+|.|++|+.|+.++|||||.|....+|+.||+ ++| ..|+|+.|
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG-~~ldgRel   85 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDG-AVLDGREL   85 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcc-eeecccee
Confidence            4455667899999999999999999999999 99999999999999999999999999999999999 999 99999999


Q ss_pred             EEEecCC
Q psy1680          85 RLDIADG   91 (227)
Q Consensus        85 ~v~~~~~   91 (227)
                      .|+.+.-
T Consensus        86 rVq~ary   92 (256)
T KOG4207|consen   86 RVQMARY   92 (256)
T ss_pred             eehhhhc
Confidence            9998763

>KOG1190|consensus

Probab=99.49  E-value=1.5e-12  Score=106.48  Aligned_cols=179  Identities=15%  Similarity=0.131  Sum_probs=127.3

Q ss_pred             CceEEEcCCCC-CCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          13 PYTAFVGNLPN-GITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        13 ~~~l~V~nLp~-~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      +..|.|.||.. .+|.+.|..+|.-| .|.+|+|+..+     +--|+|++++...|+.||+ |+| ..|.|++|+|.++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk-----kd~ALIQmsd~~qAqLA~~hL~g-~~l~gk~lrvt~S  370 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK-----KDNALIQMSDGQQAQLAMEHLEG-HKLYGKKLRVTLS  370 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC-----CcceeeeecchhHHHHHHHHhhc-ceecCceEEEeec
Confidence            57888999865 59999999999999 99999999764     3579999999999999999 999 9999999999999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCC
Q psy1680          90 DGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSN  169 (227)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~  169 (227)
                      +..............+-....+...-.++..                      .+..+.....+|+.+|.+.|+|+.+  
T Consensus       371 KH~~vqlp~egq~d~glT~dy~~spLhrfkk----------------------pgsKN~~ni~PpsatlHlsnip~sv--  426 (492)
T KOG1190|consen  371 KHTNVQLPREGQEDQGLTKDYGNSPLHRFKK----------------------PGSKNYQNIFPPSATLHLSNIPPSV--  426 (492)
T ss_pred             cCccccCCCCCCccccccccCCCCchhhccC----------------------cccccccccCCchhheeeccCCccc--
Confidence            8765432211000000000000000001100                      0111222234788899999998777  


Q ss_pred             ChhhHHhhhccccce-EEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         170 SMNDHGLMVTEVTTL-VSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       170 ~~~~l~~~f~~~g~i-~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      +||+++.+|..-|.. ...+...     +.+.+|.+.++++|+|..|+-.++++.+++
T Consensus       427 see~lk~~f~~~g~~vkafkff~-----kd~kmal~q~~sveeA~~ali~~hnh~lge  479 (492)
T KOG1190|consen  427 SEEDLKNLFQEPGGQVKAFKFFQ-----KDRKMALPQLESVEEAIQALIDLHNHYLGE  479 (492)
T ss_pred             chhHHHHhhhcCCceEEeeeecC-----CCcceeecccCChhHhhhhccccccccCCC
Confidence            789999999988844 4444322     235699999999999999999998887764

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.49  E-value=6.9e-14  Score=109.91  Aligned_cols=67  Identities=18%  Similarity=0.092  Sum_probs=60.5

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .++|||+|||+..  ++++|+++|+.||.|++|.|++|..   ++|||||+|.+.++|..||. |+|..|.||
T Consensus         4 ~rtVfVgNLs~~t--TE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr   70 (260)
T PLN03120          4 VRTVKVSNVSLKA--TERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQ   70 (260)
T ss_pred             CCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCc
Confidence            4689999997655  8999999999999999999999864   57999999999999999995 999999986

>KOG4212|consensus

Probab=99.48  E-value=3.6e-12  Score=105.13  Aligned_cols=84  Identities=21%  Similarity=0.277  Sum_probs=69.2

Q ss_pred             CCCCCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeC
Q psy1680           3 RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVD   80 (227)
Q Consensus         3 r~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~   80 (227)
                      |+..-...+...++||.||.+.+..+.|++.|.-. .+..+.+..|+. +.++|+|.++|..+-.|-.||. +++ .-+.
T Consensus       205 r~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKe-G~s~G~~vi~y~hpveavqaIsml~~-~g~~  282 (608)
T KOG4212|consen  205 RSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKE-GNSRGFAVIEYDHPVEAVQAISMLDR-QGLF  282 (608)
T ss_pred             hhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccc-cccCCeeEEEecchHHHHHHHHhhcc-CCCc
Confidence            33333355667899999999999999999999888 888888888877 6889999999999999999998 887 6666


Q ss_pred             CeEeEEEe
Q psy1680          81 GLQVRLDI   88 (227)
Q Consensus        81 g~~l~v~~   88 (227)
                      +++..++.
T Consensus       283 ~~~~~~Rl  290 (608)
T KOG4212|consen  283 DRRMTVRL  290 (608)
T ss_pred             cccceeec
Confidence            67666655

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.46  E-value=5.2e-13  Score=103.42  Aligned_cols=79  Identities=28%  Similarity=0.339  Sum_probs=71.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEec
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA   89 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~   89 (227)
                      ...++|||+||++.+|+++|+++|+.| .|.+|.|+++.   ..+++|||+|.+.++++.||.|+| ..|.+++|.|..+
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAllLnG-a~l~d~~I~It~~   78 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVLLSG-ATIVDQRVCITRW   78 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHhcCC-CeeCCceEEEEeC
Confidence            346899999999999999999999999 99999999884   445799999999999999999999 9999999999987


Q ss_pred             CCCC
Q psy1680          90 DGKR   93 (227)
Q Consensus        90 ~~~~   93 (227)
                      ....
T Consensus        79 ~~y~   82 (243)
T PLN03121         79 GQYE   82 (243)
T ss_pred             cccc
Confidence            6543

>KOG4211|consensus

Probab=99.45  E-value=3.5e-12  Score=106.59  Aligned_cols=204  Identities=19%  Similarity=0.226  Sum_probs=119.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEE-EEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~-v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~   88 (227)
                      .....|-+++||+.+|++||.+||+.. -+.. +.++.++ .+++.|-|||+|.+.+.|++||..|. ..|+.+-|.|..
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~rhr-e~iGhRYIEvF~  178 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGRHR-ENIGHRYIEVFR  178 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHHHH-HhhccceEEeeh
Confidence            466889999999999999999999998 3333 4455554 47799999999999999999999887 888888899877


Q ss_pred             cCCCCCCC-----------CCCCCCCCCCCC-------CCCCCCCCC----------CCCCCCCCC--CCCCCCCCCCCC
Q psy1680          89 ADGKRNDN-----------KGGFNNKQNRGG-------GSGGMGGNK----------YNQHQGGSF--NRDNMRNNSRGG  138 (227)
Q Consensus        89 ~~~~~~~~-----------~~~~~~~~~~~~-------~~~~~~~~~----------~~~~~~~~~--~~~~~~~~~~~~  138 (227)
                      +......+           .+.+......++       ...+.....          +....+...  ....-.......
T Consensus       179 Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~~~~  258 (510)
T KOG4211|consen  179 SSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGRDPN  258 (510)
T ss_pred             hHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCccccccccccccccccccc
Confidence            65321110           000000000000       000000000          000000000  000000000000


Q ss_pred             -----CCCCCCCCCCCCCCCCC-CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHH
Q psy1680         139 -----GASSGGGFNDFSRGGEG-PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENL  212 (227)
Q Consensus       139 -----~~~~~~~~~~~~~~~~~-~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a  212 (227)
                           ...............+. ..+..+.||  ...++.++..+|++.-.+ .|.|-..++ |+.+|-|.|+|.+.++|
T Consensus       259 ~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlp--y~a~~~di~nfFspl~p~-~v~i~ig~d-Gr~TGEAdveF~t~eda  334 (510)
T KOG4211|consen  259 YPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLP--YDATENDIANFFSPLNPY-RVHIEIGPD-GRATGEADVEFATGEDA  334 (510)
T ss_pred             cCCCCCcccCCCcccccCCCCCCceeeecCCC--ccCCCcchhhhcCCCCce-eEEEEeCCC-CccCCcceeecccchhh
Confidence                 00001111111111222 455666675  455789999999987655 577766644 99999999999999999


Q ss_pred             HHHHHHcC
Q psy1680         213 RQALLKDG  220 (227)
Q Consensus       213 ~~Al~~l~  220 (227)
                      .+||.+-.
T Consensus       335 v~Amskd~  342 (510)
T KOG4211|consen  335 VGAMGKDG  342 (510)
T ss_pred             HhhhccCC
Confidence            99987643

>KOG0114|consensus

Probab=99.44  E-value=7.8e-13  Score=88.34  Aligned_cols=84  Identities=21%  Similarity=0.309  Sum_probs=74.8

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeE
Q psy1680           6 KTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQ   83 (227)
Q Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~   83 (227)
                      ...+....+.|||+|||+.+|.++..++|.+| .|..|+|-..+   ..+|.|||.|++..+|.+||. |+| .-+.++.
T Consensus        11 ~rlppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg-~n~~~ry   86 (124)
T KOG0114|consen   11 IRLPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSG-YNVDNRY   86 (124)
T ss_pred             CCCChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhcc-cccCCce
Confidence            33566778999999999999999999999999 99999996554   448999999999999999999 999 9999999


Q ss_pred             eEEEecCCCC
Q psy1680          84 VRLDIADGKR   93 (227)
Q Consensus        84 l~v~~~~~~~   93 (227)
                      +.|.+..+..
T Consensus        87 l~vlyyq~~~   96 (124)
T KOG0114|consen   87 LVVLYYQPED   96 (124)
T ss_pred             EEEEecCHHH
Confidence            9999987644

>smart00361 RRM_1 RNA recognition motif

Probab=99.44  E-value=2.9e-13  Score=87.05  Aligned_cols=57  Identities=16%  Similarity=0.195  Sum_probs=50.4

Q ss_pred             hhhHHhhhc----cccceEEEE-EeecCCC--CcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         171 MNDHGLMVT----EVTTLVSVR-LVKDKET--DRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       171 ~~~l~~~f~----~~g~i~~v~-i~~d~~t--~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +++|+++|+    +||.|.+|. |..++.+  +.++|+|||+|.+.++|.+|++.|||..++||
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr   65 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGR   65 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            356666666    999999995 7777777  89999999999999999999999999999986

>KOG0114|consensus

Probab=99.43  E-value=3.5e-13  Score=90.00  Aligned_cols=68  Identities=18%  Similarity=0.144  Sum_probs=60.9

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...|||.|||+..  |.|++.++|++||.|..|+|-..+.|   +|.|||.|++..+|++|++.|+|.-+++|
T Consensus        18 nriLyirNLp~~I--TseemydlFGkyg~IrQIRiG~~k~T---rGTAFVVYedi~dAk~A~dhlsg~n~~~r   85 (124)
T KOG0114|consen   18 NRILYIRNLPFKI--TSEEMYDLFGKYGTIRQIRIGNTKET---RGTAFVVYEDIFDAKKACDHLSGYNVDNR   85 (124)
T ss_pred             heeEEEecCCccc--cHHHHHHHhhcccceEEEEecCccCc---CceEEEEehHhhhHHHHHHHhcccccCCc
Confidence            4679999997665  78999999999999999999776554   89999999999999999999999998875

>PLN03213 repressor of silencing 3; Provisional

Probab=99.43  E-value=4.9e-13  Score=111.74  Aligned_cols=78  Identities=21%  Similarity=0.388  Sum_probs=71.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCH--HHHHHHHH-hCCCceeCCeEe
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDV--ENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~--~~a~~al~-~~~~~~~~g~~l   84 (227)
                      ......+||||||++.+++++|+..|++| .|..|.|+  +.+|  +|||||+|.+.  .++.+||. ||| ..+.|+.|
T Consensus         6 s~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNG-AEWKGR~L   80 (759)
T PLN03213          6 SGGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNG-CVWKGGRL   80 (759)
T ss_pred             cCCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcC-CeecCcee
Confidence            34566899999999999999999999999 99999999  4556  89999999987  78999999 999 99999999


Q ss_pred             EEEecCC
Q psy1680          85 RLDIADG   91 (227)
Q Consensus        85 ~v~~~~~   91 (227)
                      +|..+++
T Consensus        81 KVNKAKP   87 (759)
T PLN03213         81 RLEKAKE   87 (759)
T ss_pred             EEeeccH
Confidence            9999986

>KOG0126|consensus

Probab=99.43  E-value=1.8e-14  Score=105.65  Aligned_cols=73  Identities=18%  Similarity=0.214  Sum_probs=67.7

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..+.-|||++||+.+  ||.||-..|+.||.|.+|.|++|..||+|+||||+.|++.-...-|+.-|||..|.||
T Consensus        33 kdsA~Iyiggl~~~L--tEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gR  105 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYEL--TEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGR  105 (219)
T ss_pred             ccceEEEECCCcccc--cCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecce
Confidence            345579999997666  7899999999999999999999999999999999999999999999999999999987

>smart00362 RRM_2 RNA recognition motif

Probab=99.42  E-value=7e-13  Score=84.78  Aligned_cols=67  Identities=25%  Similarity=0.359  Sum_probs=60.9

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +|+|.|||...  +.++|+++|++||.|..+.+..++  +.++|+|||+|.+.++|.+|++.++|..++|+
T Consensus         1 ~v~i~~l~~~~--~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~   67 (72)
T smart00362        1 TLFVGNLPPDV--TEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGR   67 (72)
T ss_pred             CEEEcCCCCcC--CHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCE
Confidence            48999997655  689999999999999999999886  78899999999999999999999999998874

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.41  E-value=5.6e-13  Score=103.22  Aligned_cols=68  Identities=18%  Similarity=0.189  Sum_probs=59.6

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+.+|||+||++..  ++++|+++|+.||.|.+|+|++|.   ..+++|||+|.++++|..|+ .|+|.+|.|+
T Consensus         4 ~g~TV~V~NLS~~t--TE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAl-lLnGa~l~d~   71 (243)
T PLN03121          4 GGYTAEVTNLSPKA--TEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAV-LLSGATIVDQ   71 (243)
T ss_pred             CceEEEEecCCCCC--CHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHH-hcCCCeeCCc
Confidence            35689999996555  899999999999999999999994   45689999999999999999 7888888764

>KOG0107|consensus

Probab=99.41  E-value=4.6e-13  Score=97.75  Aligned_cols=66  Identities=20%  Similarity=0.260  Sum_probs=59.9

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..+|||+||+..+  ++.||..+|..||.|.+|-|.+.+     .|||||+|+++-||..|+..|+|..|.|.
T Consensus        10 ~~kVYVGnL~~~a--~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~   75 (195)
T KOG0107|consen   10 NTKVYVGNLGSRA--TKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGS   75 (195)
T ss_pred             CceEEeccCCCCc--chHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCc
Confidence            5689999997766  789999999999999999888765     69999999999999999999999999873

>KOG0125|consensus

Probab=99.41  E-value=6.8e-13  Score=105.65  Aligned_cols=81  Identities=21%  Similarity=0.396  Sum_probs=73.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ....++|+|.|||+...+-||+.+|.+| .|.+|.|+...  .-+|||+||+|.+.++|++|-+ ||| ..+.||+|+|.
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHg-t~VEGRkIEVn  169 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHG-TVVEGRKIEVN  169 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhc-ceeeceEEEEe
Confidence            4556999999999999999999999999 99999998752  4569999999999999999998 999 99999999999


Q ss_pred             ecCCCC
Q psy1680          88 IADGKR   93 (227)
Q Consensus        88 ~~~~~~   93 (227)
                      .++.+-
T Consensus       170 ~ATarV  175 (376)
T KOG0125|consen  170 NATARV  175 (376)
T ss_pred             ccchhh
Confidence            998653

>smart00362 RRM_2 RNA recognition motif

Probab=99.41  E-value=1.7e-12  Score=82.95  Aligned_cols=70  Identities=36%  Similarity=0.659  Sum_probs=64.8

Q ss_pred             eEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        15 ~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      +|||+|||..+++++|+++|.+| .+..+.+..++  +.++++|||+|.+.++|..|+. +++ ..+.|+.|.|.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~-~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNG-TKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCC-cEECCEEEeeC
Confidence            58999999999999999999999 99999998776  6778999999999999999999 999 99999998873

>smart00360 RRM RNA recognition motif

Probab=99.40  E-value=1.1e-12  Score=83.50  Aligned_cols=66  Identities=32%  Similarity=0.450  Sum_probs=59.5

Q ss_pred             eccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         160 RNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       160 v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      |+|||...  ++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|.+|++.+++..++|+
T Consensus         1 i~~l~~~~--~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~   66 (71)
T smart00360        1 VGNLPPDV--TEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGR   66 (71)
T ss_pred             CCCCCccc--CHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCc
Confidence            46775444  7899999999999999999999988899999999999999999999999999998875

>KOG0108|consensus

Probab=99.40  E-value=9.6e-13  Score=111.43  Aligned_cols=80  Identities=33%  Similarity=0.574  Sum_probs=77.3

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecCC
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~~   91 (227)
                      +.|||||||+++++++|..+|++. .|..++++.|+.||+.+||||++|.+.+++..|++ ||| .++.|++|+|.++..
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg-~~~~gr~l~v~~~~~   97 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNG-AEFNGRKLRVNYASN   97 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCC-cccCCceEEeecccc
Confidence            899999999999999999999999 99999999999999999999999999999999999 999 999999999999876


Q ss_pred             CCC
Q psy1680          92 KRN   94 (227)
Q Consensus        92 ~~~   94 (227)
                      .+.
T Consensus        98 ~~~  100 (435)
T KOG0108|consen   98 RKN  100 (435)
T ss_pred             cch
Confidence            654

>KOG0129|consensus

Probab=99.37  E-value=1.1e-11  Score=104.20  Aligned_cols=169  Identities=15%  Similarity=0.115  Sum_probs=114.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeecC---CCCCeec---EEEEEeCCHHHHHHHHH-hCCCceeCCe
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDK---ETDRFKG---FCYVEFVDVENLRQALL-KDGRITVDGL   82 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~---~~~~~~g---~afv~f~~~~~a~~al~-~~~~~~~~g~   82 (227)
                      ..-+++||||+||+.++|+.|...|..|.-..|.+....   .--.++|   |+|+.|.++.++...|. +.  .  +..
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~--~--~~~  331 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACS--E--GEG  331 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHh--h--ccc
Confidence            445699999999999999999999999944556665321   1124456   99999999999988886 32  1  222


Q ss_pred             EeEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceecc
Q psy1680          83 QVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNN  162 (227)
Q Consensus        83 ~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~n  162 (227)
                      .+.++.+.+.-....                       .+-.+|.-.....-..++.           .-.+.+||||+.
T Consensus       332 ~~yf~vss~~~k~k~-----------------------VQIrPW~laDs~fv~d~sq-----------~lDprrTVFVGg  377 (520)
T KOG0129|consen  332 NYYFKVSSPTIKDKE-----------------------VQIRPWVLADSDFVLDHNQ-----------PIDPRRTVFVGG  377 (520)
T ss_pred             ceEEEEecCcccccc-----------------------eeEEeeEeccchhhhccCc-----------ccCccceEEecC
Confidence            333333222211100                       0000000000000000000           014678999999


Q ss_pred             CCCCCCCChhhHHhhhc-cccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHH
Q psy1680         163 NGPNRSNSMNDHGLMVT-EVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK  218 (227)
Q Consensus       163 l~~~~~~~~~~l~~~f~-~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~  218 (227)
                      ||-++  +.++|..+|+ -||.|..+-|-.|++-+.++|-|-|+|.+...-.+||.+
T Consensus       378 vprpl--~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  378 LPRPL--TAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CCCcc--hHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            98777  6788999999 799999999999998899999999999999999999874

>smart00360 RRM RNA recognition motif

Probab=99.37  E-value=3e-12  Score=81.48  Aligned_cols=69  Identities=41%  Similarity=0.711  Sum_probs=64.5

Q ss_pred             EcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          18 VGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        18 V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      |+|||..+++++|+++|++| .+..+.+..++.++.++++|||+|.+.++|..|+. +++ ..++|+.|.|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~-~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNG-KELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCC-CeeCCcEEEeC
Confidence            67999999999999999999 99999999888788999999999999999999999 999 99999998873

>PLN03213 repressor of silencing 3; Provisional

Probab=99.36  E-value=1.6e-12  Score=108.78  Aligned_cols=68  Identities=16%  Similarity=0.223  Sum_probs=60.9

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCH--HHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDV--ENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~--~~a~~Al~~l~g~~i~gr  227 (227)
                      ..-+|||+||++.+  +++||...|+.||.|.+|.|+  ++||  ||||||+|.+.  +++.+|+..|||..+.||
T Consensus         9 ~gMRIYVGNLSydV--TEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR   78 (759)
T PLN03213          9 GGVRLHVGGLGESV--GRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGG   78 (759)
T ss_pred             cceEEEEeCCCCCC--CHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCc
Confidence            44679999996555  899999999999999999999  4567  99999999987  689999999999999997

>KOG0130|consensus

Probab=99.36  E-value=2.5e-12  Score=89.99  Aligned_cols=87  Identities=21%  Similarity=0.311  Sum_probs=80.0

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeE
Q psy1680           6 KTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQ   83 (227)
Q Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~   83 (227)
                      .|+..-....|||.++...+||++|.+.|..| +|..+.+-.|+-||-.+|||+|+|.+...|+.||. +|+ ..|.|..
T Consensus        65 gPqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng-~~ll~q~  143 (170)
T KOG0130|consen   65 GPQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNG-AELLGQN  143 (170)
T ss_pred             CCccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccc-hhhhCCc
Confidence            34445667999999999999999999999999 99999999999999999999999999999999999 999 9999999


Q ss_pred             eEEEecCCCC
Q psy1680          84 VRLDIADGKR   93 (227)
Q Consensus        84 l~v~~~~~~~   93 (227)
                      |.|.|+.-+.
T Consensus       144 v~VDw~Fv~g  153 (170)
T KOG0130|consen  144 VSVDWCFVKG  153 (170)
T ss_pred             eeEEEEEecC
Confidence            9999986543

>KOG0111|consensus

Probab=99.36  E-value=1.2e-12  Score=99.00  Aligned_cols=86  Identities=21%  Similarity=0.375  Sum_probs=80.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      +....++|||++|...++|.-|...|-+| .|.+|.|+.|..+++.+||+||+|.-.++|..||. +|. .+|.|+.|+|
T Consensus         6 ~a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMne-sEL~GrtirV   84 (298)
T KOG0111|consen    6 MANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNE-SELFGRTIRV   84 (298)
T ss_pred             ccccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCch-hhhcceeEEE
Confidence            45567899999999999999999999999 99999999999999999999999999999999999 999 9999999999


Q ss_pred             EecCCCCCC
Q psy1680          87 DIADGKRND   95 (227)
Q Consensus        87 ~~~~~~~~~   95 (227)
                      .++.|.+..
T Consensus        85 N~AkP~kik   93 (298)
T KOG0111|consen   85 NLAKPEKIK   93 (298)
T ss_pred             eecCCcccc
Confidence            999987643

>KOG0130|consensus

Probab=99.33  E-value=1.6e-12  Score=91.03  Aligned_cols=70  Identities=17%  Similarity=0.170  Sum_probs=64.3

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      +=.|||.++....  ++++|.+.|..||.|++|.|..|+.||..+|||.|+|++.++|++|++++||..|-|
T Consensus        72 GwIi~VtgvHeEa--tEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~  141 (170)
T KOG0130|consen   72 GWIIFVTGVHEEA--TEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLG  141 (170)
T ss_pred             eEEEEEeccCcch--hHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhC
Confidence            3468999996554  899999999999999999999999999999999999999999999999999988755

>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=99.32  E-value=1.7e-11  Score=78.66  Aligned_cols=72  Identities=43%  Similarity=0.741  Sum_probs=66.0

Q ss_pred             eEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        15 ~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      +|+|+|||..+++++|+++|..+ .+..+.+..++.+ ..+++|||+|.+.++|..|+. +++ ..++|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~-~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNG-KELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCC-CeECCeEEEEeC
Confidence            48999999999999999999999 9999999987654 678999999999999999999 999 889999998864

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).

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

Probab=99.32  E-value=4.7e-12  Score=102.01  Aligned_cols=71  Identities=25%  Similarity=0.346  Sum_probs=66.8

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..+|||+|||..+  ++++|.++|..||.|..+.+..|+.++.++|||||+|.+.++|..|++.++|..|.||
T Consensus       115 ~~~l~v~nL~~~~--~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~  185 (306)
T COG0724         115 NNTLFVGNLPYDV--TEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGR  185 (306)
T ss_pred             CceEEEeCCCCCC--CHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCc
Confidence            5789999997555  8999999999999999999999998999999999999999999999999999999886

>KOG0120|consensus

Probab=99.31  E-value=6.6e-12  Score=107.13  Aligned_cols=176  Identities=21%  Similarity=0.265  Sum_probs=129.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-C------------eEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCC
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-K------------LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG   75 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~------------i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~   75 (227)
                      ......+++|+++|..+++++.-.+|..- -            +..+.+      +..+.|||++|.+.++|..++.+++
T Consensus       171 ~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~------n~~~nfa~ie~~s~~~at~~~~~~~  244 (500)
T KOG0120|consen  171 ATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQL------NLEKNFAFIEFRSISEATEAMALDG  244 (500)
T ss_pred             hhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeee------cccccceeEEecCCCchhhhhcccc
Confidence            34556899999999999999988887542 2            333333      3347899999999999999999999


Q ss_pred             CceeCCeEeEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy1680          76 RITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEG  155 (227)
Q Consensus        76 ~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (227)
                       ..+.|.++++.............-...  .        .+.+                  +.      ...........
T Consensus       245 -~~f~g~~~~~~r~~d~~~~p~~~~~~~--~--------~~~~------------------~~------~~~~t~~~~~~  289 (500)
T KOG0120|consen  245 -IIFEGRPLKIRRPHDYQPVPGITLSPS--Q--------LGKV------------------GL------LPASTDVPDSP  289 (500)
T ss_pred             -hhhCCCCceecccccccCCccchhhhc--c--------cccc------------------CC------cccccCccccc
Confidence             999999988876554332111000000  0        0000                  00      00000011245


Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..+||++||...  +++++.++...||.+....++.|..+|.++||||.+|-++.....|+..|||..+.++
T Consensus       290 ~ki~v~~lp~~l--~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~  359 (500)
T KOG0120|consen  290 NKIFVGGLPLYL--TEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDK  359 (500)
T ss_pred             chhhhccCcCcc--CHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCc
Confidence            679999997666  6899999999999999999999999999999999999999999999999999998763

>KOG1365|consensus

Probab=99.30  E-value=2.5e-12  Score=104.39  Aligned_cols=178  Identities=17%  Similarity=0.091  Sum_probs=120.1

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-C----eEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEE
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-K----LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLD   87 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~----i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~   87 (227)
                      .-.|-+++||+++++.++.+||..- .    ...|..+.. -.|+..|-|||.|..+++|+.||..|. ..++-|-|++.
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~khr-q~iGqRYIElF  238 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALRKHR-QNIGQRYIELF  238 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCHHHHHHHHHHHH-HHHhHHHHHHH
Confidence            3456678999999999999999743 3    345555543 458999999999999999999999777 67777777776


Q ss_pred             ecCCCCCC------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceec
Q psy1680          88 IADGKRND------NKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRN  161 (227)
Q Consensus        88 ~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~  161 (227)
                      .++..+..      ......+..+    ++...                            +..........+...|-++
T Consensus       239 RSTaaEvqqvlnr~~s~pLi~~~~----sp~~p----------------------------~~p~~~~p~~~~kdcvRLR  286 (508)
T KOG1365|consen  239 RSTAAEVQQVLNREVSEPLIPGLT----SPLLP----------------------------GGPARLVPPTRSKDCVRLR  286 (508)
T ss_pred             HHhHHHHHHHHHhhccccccCCCC----CCCCC----------------------------CCccccCCCCCCCCeeEec
Confidence            65532210      0000000000    00000                            0000001111235678889


Q ss_pred             cCCCCCCCChhhHHhhhcccc-ceEE--EEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         162 NNGPNRSNSMNDHGLMVTEVT-TLVS--VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       162 nl~~~~~~~~~~l~~~f~~~g-~i~~--v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .||+.+  +.+||.++|..|. .|..  |.++.+ ..|++.|-|||+|.+.|+|.+|..+.+...+.+|
T Consensus       287 GLPy~A--tvEdIL~FlgdFa~~i~f~gVHmv~N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~R  352 (508)
T KOG1365|consen  287 GLPYEA--TVEDILDFLGDFATDIRFQGVHMVLN-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSR  352 (508)
T ss_pred             CCChhh--hHHHHHHHHHHHhhhcccceeEEEEc-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccc
Confidence            996555  7899999999987 4444  777777 4599999999999999999999998877665443

>KOG1456|consensus

Probab=99.29  E-value=4.1e-11  Score=97.15  Aligned_cols=153  Identities=16%  Similarity=0.176  Sum_probs=122.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH---hCCCceeCCeEeE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL---KDGRITVDGLQVR   85 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~---~~~~~~~~g~~l~   85 (227)
                      ..++-.|.|++|-..++|.+|.+-++.| .|..+..+..      +..|.|+|.+.+.|+.++.   -+. ..+.|+.--
T Consensus        28 ~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~------~r~alvefedi~~akn~Vnfaa~n~-i~i~gq~Al  100 (494)
T KOG1456|consen   28 PNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPH------KRQALVEFEDIEGAKNCVNFAADNQ-IYIAGQQAL  100 (494)
T ss_pred             CCCCceEEEeccccccchhHHHHHHhcCCceEEEEeccc------cceeeeeeccccchhhheehhccCc-ccccCchhh
Confidence            4667889999999999999999999999 9999888754      5589999999999999997   344 667777777


Q ss_pred             EEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCC
Q psy1680          86 LDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGP  165 (227)
Q Consensus        86 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~  165 (227)
                      +.+++.+.-.+.+                                                  .....+...|.+.-|.+
T Consensus       101 ~NyStsq~i~R~g--------------------------------------------------~es~~pN~VLl~TIlNp  130 (494)
T KOG1456|consen  101 FNYSTSQCIERPG--------------------------------------------------DESATPNKVLLFTILNP  130 (494)
T ss_pred             cccchhhhhccCC--------------------------------------------------CCCCCCCeEEEEEeecC
Confidence            7777654433221                                                  00012455677777776


Q ss_pred             CCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccc
Q psy1680         166 NRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV  224 (227)
Q Consensus       166 ~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i  224 (227)
                      .+..|.|-|..+|.+.|.|..|.|++..  |   -.|.|||++.+.|++|.++|||..|
T Consensus       131 ~YpItvDVly~Icnp~GkVlRIvIfkkn--g---VQAmVEFdsv~~AqrAk~alNGADI  184 (494)
T KOG1456|consen  131 QYPITVDVLYTICNPQGKVLRIVIFKKN--G---VQAMVEFDSVEVAQRAKAALNGADI  184 (494)
T ss_pred             ccccchhhhhhhcCCCCceEEEEEEecc--c---eeeEEeechhHHHHHHHhhcccccc
Confidence            7777889999999999999999998862  2   3699999999999999999999876

>KOG0108|consensus

Probab=99.29  E-value=4.5e-12  Score=107.38  Aligned_cols=70  Identities=29%  Similarity=0.334  Sum_probs=66.9

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..+||+|+|+..  ++++|..+|+..|.|.+++++.|++||+++||||++|.+.++|..|++.|||.++.||
T Consensus        19 ~~v~vgnip~~~--se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr   88 (435)
T KOG0108|consen   19 SSVFVGNIPYEG--SEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGR   88 (435)
T ss_pred             cceEecCCCCcc--cHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCc
Confidence            689999996655  8999999999999999999999999999999999999999999999999999999997

>KOG0131|consensus

Probab=99.29  E-value=1.9e-12  Score=95.15  Aligned_cols=72  Identities=17%  Similarity=0.201  Sum_probs=65.7

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...||||+||+..+  +++.|+++|-..|.|.++++++|+.|+...|||||+|.+.|+|+.|++-||...|-||
T Consensus         8 qd~tiyvgnld~kv--s~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgr   79 (203)
T KOG0131|consen    8 QDATLYVGNLDEKV--SEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGR   79 (203)
T ss_pred             CCceEEEecCCHHH--HHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCc
Confidence            45689999996544  7888999999999999999999999999999999999999999999999998887765

>KOG0145|consensus

Probab=99.28  E-value=2.9e-11  Score=93.68  Aligned_cols=81  Identities=19%  Similarity=0.338  Sum_probs=76.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      .....|||-||.++++|.-|-++|.+| .|..|+|++|..|+++|||+||.+.+-++|.+||. ||| ..+.++.|.|.+
T Consensus       276 ~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNG-y~lg~rvLQVsF  354 (360)
T KOG0145|consen  276 GGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNG-YRLGDRVLQVSF  354 (360)
T ss_pred             CCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcC-ccccceEEEEEE
Confidence            446899999999999999999999999 99999999999999999999999999999999999 999 999999999988


Q ss_pred             cCCC
Q psy1680          89 ADGK   92 (227)
Q Consensus        89 ~~~~   92 (227)
                      ...+
T Consensus       355 Ktnk  358 (360)
T KOG0145|consen  355 KTNK  358 (360)
T ss_pred             ecCC
Confidence            6654

>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=99.27  E-value=2.2e-11  Score=78.19  Aligned_cols=68  Identities=32%  Similarity=0.440  Sum_probs=61.2

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +|+|.+||...  ++++|+++|+.+|.|..+.+..++.+ .++|+|||+|.+.++|..|++.+++..++|+
T Consensus         1 ~i~i~~l~~~~--~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~   68 (74)
T cd00590           1 TLFVGNLPPDV--TEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGR   68 (74)
T ss_pred             CEEEeCCCCcc--CHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            47999997665  78999999999999999999998764 7789999999999999999999999988875

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).

>KOG0111|consensus

Probab=99.27  E-value=1.4e-12  Score=98.51  Aligned_cols=72  Identities=14%  Similarity=0.178  Sum_probs=66.8

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..++|||+.|...+  ++.-|...|=+||.|.+|.++.|.++++++|||||+|+..|||.+|+.-||+.+|-||
T Consensus         9 ~KrtlYVGGladeV--tekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~Gr   80 (298)
T KOG0111|consen    9 QKRTLYVGGLADEV--TEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGR   80 (298)
T ss_pred             cceeEEeccchHHH--HHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcce
Confidence            45799999996655  6788999999999999999999999999999999999999999999999999999886

>KOG1190|consensus

Probab=99.23  E-value=3.5e-10  Score=92.82  Aligned_cols=202  Identities=13%  Similarity=0.104  Sum_probs=121.1

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC-eEeEEEecC
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG-LQVRLDIAD   90 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g-~~l~v~~~~   90 (227)
                      -+++|+++-+.++-+-|..+|++| .|..|.-...    ...-.|+|+|.+.+.|+.|-. |+|....+| +.|+|.++.
T Consensus       151 Lr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~K----nn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sk  226 (492)
T KOG1190|consen  151 LRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTK----NNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSK  226 (492)
T ss_pred             EEEEeccceeeeEHHHHHHHHhhcceeEEEEEEec----ccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhh
Confidence            567899999999999999999999 8887654322    123379999999999999998 999334455 367777765


Q ss_pred             CCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCC--CCcceecc
Q psy1680          91 GKRNDNKGGFNNKQNRGGG----SGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGG--GFNDFSRGGE--GPGGFRNN  162 (227)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~--~~~l~v~n  162 (227)
                      -..-...  +.+++++.=+    +.+...+..+..-...+.....-........+...  ...+..-..+  ..+|.|.|
T Consensus       227 lt~LnvK--ynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsn  304 (492)
T KOG1190|consen  227 LTDLNVK--YNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSN  304 (492)
T ss_pred             cccceee--ccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEec
Confidence            3221110  1111111000    00000000000000000000000000000000000  0000111122  46788999


Q ss_pred             CCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         163 NGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       163 l~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      |.... .|.|-|.-+|+-||.|..|+|+.++.     --|.|.+.+..+|.-|++.|+|..|-|+
T Consensus       305 ln~~~-VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk  363 (492)
T KOG1190|consen  305 LNEEA-VTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGK  363 (492)
T ss_pred             Cchhc-cchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCc
Confidence            96443 37899999999999999999998853     5699999999999999999999998774

>PF13893 RRM_5: RNA recognition motif

Probab=99.22  E-value=2.9e-11  Score=74.18  Aligned_cols=49  Identities=22%  Similarity=0.432  Sum_probs=44.2

Q ss_pred             HHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         174 HGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       174 l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      |+++|++||.|..+.+.++.     +++|||+|.+.++|..|++.|||..++|+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~   49 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGR   49 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            67899999999999997774     58999999999999999999999999885

(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 ....

>KOG4208|consensus

Probab=99.20  E-value=4.1e-11  Score=89.95  Aligned_cols=74  Identities=16%  Similarity=0.078  Sum_probs=64.2

Q ss_pred             CCCCCcceeccCCCCCCCChhhHHhhhccc-cceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         152 GGEGPGGFRNNNGPNRSNSMNDHGLMVTEV-TTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~-g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ......+++..+|.-.  -+.++..+|.+| |.|+.+++-|++.||+|+|||||+|++.+.|+=|-+.||++.|.|+
T Consensus        46 ~~~~g~~~~~~~p~g~--~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~  120 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGF--FETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEH  120 (214)
T ss_pred             cCCccceeecccccch--hHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhh
Confidence            3455678999996544  467788889988 6888999999999999999999999999999999999999998774

>KOG0109|consensus

Probab=99.17  E-value=8.1e-11  Score=92.56  Aligned_cols=78  Identities=17%  Similarity=0.351  Sum_probs=71.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      .+.+.+|+|+||.+.++..+|+..|.+| ++++++|++        +|+||.|.-.++|..|++ |++ .+|.|++++|+
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk--------dy~fvh~d~~eda~~air~l~~-~~~~gk~m~vq  145 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK--------DYAFVHFDRAEDAVEAIRGLDN-TEFQGKRMHVQ  145 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeeec--------ceeEEEEeeccchHHHHhcccc-cccccceeeee
Confidence            4578999999999999999999999999 999999984        599999999999999999 999 99999999999


Q ss_pred             ecCCCCCCC
Q psy1680          88 IADGKRNDN   96 (227)
Q Consensus        88 ~~~~~~~~~   96 (227)
                      +++.+-...
T Consensus       146 ~stsrlrta  154 (346)
T KOG0109|consen  146 LSTSRLRTA  154 (346)
T ss_pred             eeccccccC
Confidence            998765543

>smart00361 RRM_1 RNA recognition motif

Probab=99.16  E-value=1.4e-10  Score=74.56  Aligned_cols=59  Identities=24%  Similarity=0.374  Sum_probs=52.4

Q ss_pred             HHHHHhccc----CC-CeEEEE-EeecCCC--CCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680          27 QGDVERFFP----EQ-KLVSVR-LVKDKET--DRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus        27 ~~~l~~~f~----~~-~i~~v~-i~~~~~~--~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      +++|+++|+    .| .|..+. |+.++.+  +.++|||||.|.+.++|.+|+. ||| ..+.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g-~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNG-RYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCC-CEECCEEEEe
Confidence            567888888    99 999985 7777666  8899999999999999999999 999 9999999876

>KOG0415|consensus

Probab=99.15  E-value=5.8e-11  Score=95.70  Aligned_cols=83  Identities=25%  Similarity=0.439  Sum_probs=78.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ..+|.+.|||-.|.+-+|.++|.-+|+.| .|..|.|++|..||.+..||||+|.+.+++++|.- +++ ..|++++|+|
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdN-vLIDDrRIHV  313 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDN-VLIDDRRIHV  313 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcc-eeeccceEEe
Confidence            35788999999999999999999999999 99999999999999999999999999999999998 999 9999999999


Q ss_pred             EecCCC
Q psy1680          87 DIADGK   92 (227)
Q Consensus        87 ~~~~~~   92 (227)
                      .++..-
T Consensus       314 DFSQSV  319 (479)
T KOG0415|consen  314 DFSQSV  319 (479)
T ss_pred             ehhhhh
Confidence            998653

>KOG1456|consensus

Probab=99.14  E-value=5.4e-09  Score=85.07  Aligned_cols=186  Identities=17%  Similarity=0.141  Sum_probs=130.3

Q ss_pred             CCCCCceEEEcCCCCC-CCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           9 PTEPPYTAFVGNLPNG-ITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~-~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      ...+.+.+.|-+|... +.-+.|.++|=.| .|..|+.++.+     .|.|.|++.+...+++|+. ||+ ..+-|.+|.
T Consensus       283 g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn-~~lfG~kl~  356 (494)
T KOG1456|consen  283 GGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNN-IPLFGGKLN  356 (494)
T ss_pred             CCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhcc-CccccceEE
Confidence            4567789999999865 6667899999999 99999999764     4799999999999999999 999 999999999


Q ss_pred             EEecCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccC
Q psy1680          86 LDIADGKRNDNKGGFNNKQNRGGG--SGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNN  163 (227)
Q Consensus        86 v~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl  163 (227)
                      |..++..-......+.-..+...-  -.++..++|.+....+                      -....+|+++|.-.|.
T Consensus       357 v~~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAs----------------------KNrIq~Ps~vLHffNa  414 (494)
T KOG1456|consen  357 VCVSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQAS----------------------KNRIQPPSNVLHFFNA  414 (494)
T ss_pred             EeeccccccccCCceecCCCCcchhhcccccccccCChhHhh----------------------cccccCCcceeEEecC
Confidence            999865433221111110000000  0011111121111111                      1112367899999999


Q ss_pred             CCCCCCChhhHHhhhcccc-ceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         164 GPNRSNSMNDHGLMVTEVT-TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       164 ~~~~~~~~~~l~~~f~~~g-~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      |..+  ||+.|..+|..-+ .-.+++|..-+ +-+ .--+.+||++.++|..||.++|-..|++
T Consensus       415 P~~v--tEe~l~~i~nek~v~~~svkvFp~k-ser-SssGllEfe~~s~Aveal~~~NH~pi~~  474 (494)
T KOG1456|consen  415 PLGV--TEEQLIGICNEKDVPPTSVKVFPLK-SER-SSSGLLEFENKSDAVEALMKLNHYPIEG  474 (494)
T ss_pred             CCcc--CHHHHHHHhhhcCCCcceEEeeccc-ccc-cccceeeeehHHHHHHHHHHhccccccC
Confidence            7666  7999999999876 34567777664 233 3468999999999999999999988865

>KOG0415|consensus

Probab=99.11  E-value=1.1e-10  Score=94.17  Aligned_cols=78  Identities=18%  Similarity=0.254  Sum_probs=70.3

Q ss_pred             CCCCCCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         148 DFSRGGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       148 ~~~~~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .....||.++|||-.|.  ..++.+||.-+|+.||.|.+|.+++|..||.+--||||+|++.+++++|.-+|++..|++|
T Consensus       232 dAd~~PPeNVLFVCKLN--PVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDr  309 (479)
T KOG0415|consen  232 DADVKPPENVLFVCKLN--PVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDR  309 (479)
T ss_pred             ccccCCCcceEEEEecC--CcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccc
Confidence            33345788999999995  3447799999999999999999999999999999999999999999999999999999876

>PF13893 RRM_5: RNA recognition motif

Probab=99.10  E-value=6.1e-10  Score=68.21  Aligned_cols=54  Identities=26%  Similarity=0.593  Sum_probs=48.5

Q ss_pred             HHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          30 VERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        30 l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      |+++|++| +|..+.+....     +++|||+|.+.++|..|++ +|+ ..+.|++|+|.++
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-----RGFAFVEFASVEDAQKAIEQLNG-RQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTT-SEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCC-CEECCcEEEEEEC
Confidence            67899999 99999997653     5899999999999999999 999 9999999999985

(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 ....

>KOG0146|consensus

Probab=99.08  E-value=1.4e-10  Score=90.37  Aligned_cols=88  Identities=17%  Similarity=0.328  Sum_probs=82.4

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      .+.++.|+|||-.||.+..+.+|-++|-.| .|+..++..|+.|+.+|=|+||.|.+..+++.||. +|| +.|+=++|+
T Consensus       280 reGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNG-FQIGMKRLK  358 (371)
T KOG0146|consen  280 REGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNG-FQIGMKRLK  358 (371)
T ss_pred             hcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcc-hhhhhhhhh
Confidence            356788999999999999999999999999 99999999999999999999999999999999999 999 999999999


Q ss_pred             EEecCCCCCCC
Q psy1680          86 LDIADGKRNDN   96 (227)
Q Consensus        86 v~~~~~~~~~~   96 (227)
                      |.+.++|...+
T Consensus       359 VQLKRPkdanR  369 (371)
T KOG0146|consen  359 VQLKRPKDANR  369 (371)
T ss_pred             hhhcCccccCC
Confidence            99998877543

>KOG0226|consensus

Probab=99.05  E-value=5e-10  Score=86.63  Aligned_cols=160  Identities=18%  Similarity=0.261  Sum_probs=110.2

Q ss_pred             CceEEEcCCCCCCCHHH-H--HhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          13 PYTAFVGNLPNGITQGD-V--ERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~-l--~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      -...+++++-..+..+- |  ...|+.| ......++++.. +...+++|+.|.....-.++-. -++ +.+.-..+++.
T Consensus        96 vf~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p-~~~~~~~~~~~k~s~a~~k~~~~~~~-Kki~~~~VR~a  173 (290)
T KOG0226|consen   96 VFRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRP-QPIRPEAFESFKASDALLKAETEKEK-KKIGKPPVRLA  173 (290)
T ss_pred             cccccccccccccCCCCCCcchhhhccchhhhhhhhhhcCC-CccCcccccCcchhhhhhhhcccccc-ccccCcceeec
Confidence            35556666655544443 3  5678888 777777777754 5668899999987665555544 444 44443332221


Q ss_pred             ecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCC
Q psy1680          88 IADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNR  167 (227)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~  167 (227)
                      ..+  .                        |....-..|                         ......||.+.|+..+
T Consensus       174 ~gt--s------------------------wedPsl~ew-------------------------~~~DfRIfcgdlgNev  202 (290)
T KOG0226|consen  174 AGT--S------------------------WEDPSLAEW-------------------------DEDDFRIFCGDLGNEV  202 (290)
T ss_pred             ccc--c------------------------cCCcccccC-------------------------ccccceeecccccccc
Confidence            111  1                        000000000                         1234478999997666


Q ss_pred             CCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         168 SNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       168 ~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                        +.+-|...|.+|-.....++++|..||+++||+||.|.++.|+.+|+..|+|.-++.|
T Consensus       203 --nd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsr  260 (290)
T KOG0226|consen  203 --NDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSR  260 (290)
T ss_pred             --cHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccc
Confidence              5677899999999999999999999999999999999999999999999999988764

>KOG0105|consensus

Probab=99.04  E-value=2.9e-10  Score=84.01  Aligned_cols=68  Identities=15%  Similarity=0.160  Sum_probs=58.3

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      .+.+|||+|||.+.  -+.+|.++|.+||.|..|.|...+   ....||||+|+++-||+.|+..-+|+.++|
T Consensus         5 ~~~~iyvGNLP~di--RekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg   72 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDI--REKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDG   72 (241)
T ss_pred             ccceEEecCCCcch--hhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCc
Confidence            35689999998877  468899999999999999875442   345799999999999999999999999886

>KOG4210|consensus

Probab=99.03  E-value=4.3e-10  Score=91.18  Aligned_cols=168  Identities=24%  Similarity=0.250  Sum_probs=124.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEec
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA   89 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~   89 (227)
                      ....++|++++..++.+.++..++..+ ...............+++++.+.|...+.+..++.+.+...+.++.+.....
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            357899999999999999888888888 7777766665677888999999999999999999965513445554444333


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCC
Q psy1680          90 DGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSN  169 (227)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~  169 (227)
                      ........ ...                                             ......++...++|.+|+..+  
T Consensus       166 ~~~~~~~~-n~~---------------------------------------------~~~~~~~s~~~~~~~~~~f~~--  197 (285)
T KOG4210|consen  166 TRRGLRPK-NKL---------------------------------------------SRLSSGPSDTIFFVGELDFSL--  197 (285)
T ss_pred             cccccccc-chh---------------------------------------------cccccCccccceeeccccccc--
Confidence            32221000 000                                             000111223334499996555  


Q ss_pred             ChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         170 SMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       170 ~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++++|+..|..+|.|+.++++.++.++.++|||+|.|.....+..|+.. +...+.+|
T Consensus       198 ~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~  254 (285)
T KOG4210|consen  198 TRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGR  254 (285)
T ss_pred             chHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCc
Confidence            7899999999999999999999999999999999999999999999987 77766654

>KOG4454|consensus

Probab=99.02  E-value=6.6e-11  Score=89.52  Aligned_cols=142  Identities=16%  Similarity=0.222  Sum_probs=113.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      .+...+|||.||...++|+-|.++|-+. +|..|.|..++. ++.+ ||||.|.++-++.-|++ +|| ..+.+..+.+.
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng-~~l~~~e~q~~   82 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENG-DDLEEDEEQRT   82 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhccc-chhccchhhcc
Confidence            4567899999999999999999999999 999999988865 4445 99999999999999999 999 99988888777


Q ss_pred             ecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCC
Q psy1680          88 IADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNR  167 (227)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~  167 (227)
                      +-.....                                                             .       |.+.
T Consensus        83 ~r~G~sh-------------------------------------------------------------a-------pld~   94 (267)
T KOG4454|consen   83 LRCGNSH-------------------------------------------------------------A-------PLDE   94 (267)
T ss_pred             cccCCCc-------------------------------------------------------------c-------hhhh
Confidence            6432110                                                             0       1123


Q ss_pred             CCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcc
Q psy1680         168 SNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRIT  223 (227)
Q Consensus       168 ~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~  223 (227)
                      ..+++.+...|+.-+.+..+++.++.+ |+++.++||.+-..-..-.++..-.+..
T Consensus        95 r~~~ei~~~v~s~a~p~~~~R~~~~~d-~rnrn~~~~~~qr~~~~P~~~~~y~~l~  149 (267)
T KOG4454|consen   95 RVTEEILYEVFSQAGPIEGVRIPTDND-GRNRNFGFVTYQRLCAVPFALDLYQGLE  149 (267)
T ss_pred             hcchhhheeeecccCCCCCcccccccc-CCccCccchhhhhhhcCcHHhhhhcccC
Confidence            335677788888889999999999977 8899999999887777777776655543

>KOG4205|consensus

Probab=99.02  E-value=5.8e-10  Score=90.87  Aligned_cols=84  Identities=27%  Similarity=0.407  Sum_probs=79.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEecC
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~~   90 (227)
                      ...+|||++||.++++++++++|.+| .|..+.++.|+.+.++++|+||.|.+++++.+++.+.- +.|+++.+.|..|.
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~~f-~~~~gk~vevkrA~  174 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQKF-HDFNGKKVEVKRAI  174 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecccce-eeecCceeeEeecc
Confidence            46799999999999999999999999 99999999999999999999999999999999999888 99999999999999


Q ss_pred             CCCCCC
Q psy1680          91 GKRNDN   96 (227)
Q Consensus        91 ~~~~~~   96 (227)
                      ++....
T Consensus       175 pk~~~~  180 (311)
T KOG4205|consen  175 PKEVMQ  180 (311)
T ss_pred             chhhcc
Confidence            987644

>KOG0153|consensus

Probab=98.93  E-value=4.4e-09  Score=84.81  Aligned_cols=79  Identities=19%  Similarity=0.399  Sum_probs=70.6

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH--hCCCceeCCeEe
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL--KDGRITVDGLQV   84 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~--~~~~~~~~g~~l   84 (227)
                      .+.....+|||++|...+++.+|+++|.+| +|..+.++..      +++|||+|.+.++|+.|.+  ++. ..++|++|
T Consensus       223 PeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~-lvI~G~Rl  295 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNK-LVINGFRL  295 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcce-eeecceEE
Confidence            345666999999999999999999999999 9999999765      5699999999999999998  776 99999999


Q ss_pred             EEEecCCCC
Q psy1680          85 RLDIADGKR   93 (227)
Q Consensus        85 ~v~~~~~~~   93 (227)
                      .|.|..+++
T Consensus       296 ~i~Wg~~~~  304 (377)
T KOG0153|consen  296 KIKWGRPKQ  304 (377)
T ss_pred             EEEeCCCcc
Confidence            999998843

>KOG0116|consensus

Probab=98.92  E-value=1.1e-08  Score=86.49  Aligned_cols=83  Identities=17%  Similarity=0.265  Sum_probs=69.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEec
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA   89 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~   89 (227)
                      .....|||+|||.+++..+|+++|..| .|....|....-.++...||||+|.+..+++.||..+- ..+++++|.|+.-
T Consensus       286 ~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp-~~ig~~kl~Veek  364 (419)
T KOG0116|consen  286 ADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASP-LEIGGRKLNVEEK  364 (419)
T ss_pred             ecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCc-cccCCeeEEEEec
Confidence            344569999999999999999999999 99988876543223434899999999999999999777 9999999999987


Q ss_pred             CCCCC
Q psy1680          90 DGKRN   94 (227)
Q Consensus        90 ~~~~~   94 (227)
                      .+...
T Consensus       365 ~~~~~  369 (419)
T KOG0116|consen  365 RPGFR  369 (419)
T ss_pred             ccccc
Confidence            66443

>KOG4208|consensus

Probab=98.92  E-value=6.1e-09  Score=78.39  Aligned_cols=83  Identities=19%  Similarity=0.330  Sum_probs=75.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC--CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~--~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      ......-+||+.+|.-+.+.++..+|.++  .+..+++.+.+.||.++|||||+|.+.+.|.-|-+ +|+ ..|.++.|.
T Consensus        45 ~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNN-YLl~e~lL~  123 (214)
T KOG4208|consen   45 EQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNN-YLLMEHLLE  123 (214)
T ss_pred             ccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhh-hhhhhheee
Confidence            44566788999999999999999999999  57777888999999999999999999999999999 999 999999999


Q ss_pred             EEecCCC
Q psy1680          86 LDIADGK   92 (227)
Q Consensus        86 v~~~~~~   92 (227)
                      +++-.+.
T Consensus       124 c~vmppe  130 (214)
T KOG4208|consen  124 CHVMPPE  130 (214)
T ss_pred             eEEeCch
Confidence            9987654

>KOG4307|consensus

Probab=98.81  E-value=1.1e-07  Score=83.20  Aligned_cols=81  Identities=17%  Similarity=0.126  Sum_probs=64.3

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEE-EEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~-v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      .+......|||..||..+++.++-++|... .|++ |.|-+- -+++.++-|||.|...+.+..|.. .+. +.++.+.|
T Consensus       429 ~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~-P~~~~~~~afv~F~~~~a~~~a~~~~~k-~y~G~r~i  506 (944)
T KOG4307|consen  429 FPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRL-PTDLLRPAAFVAFIHPTAPLTASSVKTK-FYPGHRII  506 (944)
T ss_pred             CCCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccC-Ccccccchhhheeccccccchhhhcccc-cccCceEE
Confidence            455677999999999999999999999988 7777 566554 346778999999999888888877 555 66667778


Q ss_pred             EEEecC
Q psy1680          85 RLDIAD   90 (227)
Q Consensus        85 ~v~~~~   90 (227)
                      +|+...
T Consensus       507 rv~si~  512 (944)
T KOG4307|consen  507 RVDSIA  512 (944)
T ss_pred             Eeechh
Confidence            876654

>KOG0128|consensus

Probab=98.80  E-value=3.1e-10  Score=100.61  Aligned_cols=136  Identities=19%  Similarity=0.254  Sum_probs=113.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      ...++||.||+..+.+.+|...|..+ .+..+.|......++.+|+|++.|-..+.+.+|+. ... ..++         
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~-~~~g---------  735 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDS-CFFG---------  735 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhh-hhhh---------
Confidence            34789999999999999999999999 77777776667788999999999999999999998 444 2222         


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCC
Q psy1680          90 DGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSN  169 (227)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~  169 (227)
                                                                                       ...++|.|+|+..  
T Consensus       736 -----------------------------------------------------------------K~~v~i~g~pf~g--  748 (881)
T KOG0128|consen  736 -----------------------------------------------------------------KISVAISGPPFQG--  748 (881)
T ss_pred             -----------------------------------------------------------------hhhhheeCCCCCC--
Confidence                                                                             0137899997665  


Q ss_pred             ChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         170 SMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       170 ~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      |.+.++.+|+.+|.+++++++..+. |+++|.|+|.|.+..+|.+++....+..++
T Consensus       749 t~e~~k~l~~~~gn~~~~~~vt~r~-gkpkg~a~v~y~~ea~~s~~~~s~d~~~~r  803 (881)
T KOG0128|consen  749 TKEELKSLASKTGNVTSLRLVTVRA-GKPKGKARVDYNTEADASRKVASVDVAGKR  803 (881)
T ss_pred             chHHHHhhccccCCccccchhhhhc-cccccceeccCCCcchhhhhcccchhhhhh
Confidence            7899999999999999999888755 999999999999999999998887766553

>KOG4307|consensus

Probab=98.78  E-value=5.1e-08  Score=85.12  Aligned_cols=188  Identities=13%  Similarity=0.057  Sum_probs=122.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEec
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA   89 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~   89 (227)
                      ....+.+-+.++++++.+.|+++||-...+..+.|..++..+...|-++|.|....++++|+.-+. ..+-.+.+.+..+
T Consensus       308 v~d~~y~~~~gm~fn~~~nd~rkfF~g~~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~-~~~~~R~~q~~P~  386 (944)
T KOG4307|consen  308 VSDKYYNNYKGMEFNNDFNDGRKFFPGRNAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTRNP-SDDVNRPFQTGPP  386 (944)
T ss_pred             cchhheeeecccccccccchhhhhcCcccccccchhhhhcCCCcCCceEEEecCcchHHHHHhcCc-hhhhhcceeecCC
Confidence            355677778899999999999999976666666666666666668999999999999999999777 7777888888776


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCC
Q psy1680          90 DGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRD-NMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRS  168 (227)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~  168 (227)
                      ........+.+........             .+.++.+. .+.....      .++.+...-.+....|||..||... 
T Consensus       387 g~~~~~~a~~~~~~~~~~~-------------~~~~hg~p~~~pr~~~------~~gq~vp~P~~ag~~lyv~~lP~~t-  446 (944)
T KOG4307|consen  387 GNLGRNGAPPFQAGVPPPV-------------IQNNHGRPIAPPRAMV------RPGQNVPFPGGAGGALYVFQLPVMT-  446 (944)
T ss_pred             CccccccCccccccCCCCc-------------ccccCCCCCCCccccc------CCCCCCCCCCCccceEEeccCCccc-
Confidence            6544332222111110000             00000000 0000000      0011111222456789999996544 


Q ss_pred             CChhhHHhhhccccceEE-EEEeecCCCCcccceEEEEEcCHHHHHHHHHHcC
Q psy1680         169 NSMNDHGLMVTEVTTLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG  220 (227)
Q Consensus       169 ~~~~~l~~~f~~~g~i~~-v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~  220 (227)
                       ++.++.++|.....|++ |.|-+-+ +++-++-|||+|..++++..|+..-.
T Consensus       447 -~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~  497 (944)
T KOG4307|consen  447 -PIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKT  497 (944)
T ss_pred             -cccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhccc
Confidence             67788889988777776 6666664 48889999999999888777765443

>KOG1365|consensus

Probab=98.78  E-value=1.1e-07  Score=77.79  Aligned_cols=165  Identities=19%  Similarity=0.126  Sum_probs=112.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCCCeEEE-EEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEe
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQKLVSV-RLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDI   88 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v-~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~   88 (227)
                      .+.+..|-.++||+..++.+|-.+|....|... ..+.--..++..|.+.|.|.+.+.-+.|++.+. ..+.++.|.|-.
T Consensus        57 ~~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhk-hh~g~ryievYk  135 (508)
T KOG1365|consen   57 ADDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKRHK-HHMGTRYIEVYK  135 (508)
T ss_pred             cCcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHhhh-hhccCCceeeec
Confidence            344556667899999999999999976633322 222223447778999999999999999999777 788889998887


Q ss_pred             cCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCC
Q psy1680          89 ADGKRNDN--KGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPN  166 (227)
Q Consensus        89 ~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~  166 (227)
                      +....--.  ++++.            ....                               +......-.|-++.||++
T Consensus       136 a~ge~f~~iagg~s~------------e~~~-------------------------------flsk~~qvivRmRGLPfd  172 (508)
T KOG1365|consen  136 ATGEEFLKIAGGTSN------------EAAP-------------------------------FLSKENQVIVRMRGLPFD  172 (508)
T ss_pred             cCchhheEecCCccc------------cCCC-------------------------------CCCcccceEEEecCCCCC
Confidence            76433211  00000            0000                               000011224567778665


Q ss_pred             CCCChhhHHhhhccc----cceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCC
Q psy1680         167 RSNSMNDHGLMVTEV----TTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR  221 (227)
Q Consensus       167 ~~~~~~~l~~~f~~~----g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g  221 (227)
                      +  ++.|+..+|.+-    |..+.|-+++.++ |+.+|-|||.|..+++|+.||.++.+
T Consensus       173 a--t~~dVv~FF~~~cpv~~g~egvLFV~rpd-grpTGdAFvlfa~ee~aq~aL~khrq  228 (508)
T KOG1365|consen  173 A--TALDVVEFFGPPCPVTGGTEGVLFVTRPD-GRPTGDAFVLFACEEDAQFALRKHRQ  228 (508)
T ss_pred             c--chHHHHHhcCCCCcccCCccceEEEECCC-CCcccceEEEecCHHHHHHHHHHHHH
Confidence            5  789999999742    2455666666655 99999999999999999999987653

>KOG4206|consensus

Probab=98.77  E-value=1.9e-08  Score=76.88  Aligned_cols=68  Identities=15%  Similarity=0.208  Sum_probs=56.6

Q ss_pred             CCCcceeccCCCCCCCChhhHHh----hhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGL----MVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~----~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      +..||||.||....  ..++|+.    +|+.||.|.+|...+.   .+.+|.|||.|.+.+.|-.|+.+|+|+.+=|
T Consensus         8 pn~TlYInnLnekI--~~~elkrsL~~LFsqfG~ildI~a~kt---~KmRGQA~VvFk~~~~As~A~r~l~gfpFyg   79 (221)
T KOG4206|consen    8 PNGTLYINNLNEKI--KKDELKRSLYLLFSQFGKILDISAFKT---PKMRGQAFVVFKETEAASAALRALQGFPFYG   79 (221)
T ss_pred             CCceEeehhccccc--cHHHHHHHHHHHHHhhCCeEEEEecCC---CCccCceEEEecChhHHHHHHHHhcCCcccC
Confidence            34499999996544  3455555    9999999999987765   6789999999999999999999999998755

>KOG0132|consensus

Probab=98.76  E-value=1.7e-08  Score=89.07  Aligned_cols=74  Identities=24%  Similarity=0.486  Sum_probs=68.6

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecC
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~   90 (227)
                      +++||||+|+.++++.||.++|+.| +|..|.++-.      +++|||.+-..++|.+||. |.. ..+.++.|+|.|+.
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n-~kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSN-VKVADKTIKIAWAV  493 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhc-ccccceeeEEeeec
Confidence            4899999999999999999999999 9999988744      7899999999999999998 999 99999999999987


Q ss_pred             CCC
Q psy1680          91 GKR   93 (227)
Q Consensus        91 ~~~   93 (227)
                      .+-
T Consensus       494 g~G  496 (894)
T KOG0132|consen  494 GKG  496 (894)
T ss_pred             cCC
Confidence            654

>KOG0533|consensus

Probab=98.75  E-value=3.3e-08  Score=77.68  Aligned_cols=84  Identities=24%  Similarity=0.407  Sum_probs=75.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      .+..+.+|+|.|||+.++++||+++|..| .+..+.+-.++. |++.|.|-|.|...++|.+||+ +++ +.++|++|++
T Consensus        79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~-G~s~Gta~v~~~r~~DA~~avk~~~g-v~ldG~~mk~  156 (243)
T KOG0533|consen   79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRA-GRSLGTADVSFNRRDDAERAVKKYNG-VALDGRPMKI  156 (243)
T ss_pred             cCCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCC-CCCCccceeeecchHhHHHHHHHhcC-cccCCceeee
Confidence            34555889999999999999999999999 999999988855 8999999999999999999999 999 9999999999


Q ss_pred             EecCCCCC
Q psy1680          87 DIADGKRN   94 (227)
Q Consensus        87 ~~~~~~~~   94 (227)
                      ....+...
T Consensus       157 ~~i~~~~~  164 (243)
T KOG0533|consen  157 EIISSPSQ  164 (243)
T ss_pred             EEecCccc
Confidence            88766543

>KOG4209|consensus

Probab=98.67  E-value=2.9e-08  Score=78.11  Aligned_cols=72  Identities=24%  Similarity=0.243  Sum_probs=64.2

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .....+||+|+.+..  +.+++...|+.||.|..+.|+.|+.++.++||+||+|.+.+.++.|+. |||..|.|+
T Consensus        99 ~d~~sv~v~nvd~~~--t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~  170 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLV--TLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGP  170 (231)
T ss_pred             cCCceEEEecccccc--ccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccc
Confidence            455679999995544  566699999999999999999999999999999999999999999999 999998875

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

Probab=98.67  E-value=1.5e-07  Score=63.67  Aligned_cols=76  Identities=20%  Similarity=0.197  Sum_probs=65.0

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC---CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeC----CeEeE
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ---KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVD----GLQVR   85 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~---~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~----g~~l~   85 (227)
                      ++|.|+|||...|.++|.+++...   ...-+.++.|..++.+.|||||-|.+++.|.+..+ .+| ..+.    .+.+.
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g-~~w~~~~s~Kvc~   80 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNG-KKWPNFNSKKVCE   80 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcC-CccccCCCCcEEE
Confidence            689999999999999999888754   56677899998889999999999999999999998 999 7775    44667


Q ss_pred             EEecC
Q psy1680          86 LDIAD   90 (227)
Q Consensus        86 v~~~~   90 (227)
                      |.+|+
T Consensus        81 i~yAr   85 (97)
T PF04059_consen   81 ISYAR   85 (97)
T ss_pred             EehhH
Confidence            77765

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

>KOG4661|consensus

Probab=98.67  E-value=4.1e-08  Score=84.05  Aligned_cols=81  Identities=12%  Similarity=0.259  Sum_probs=72.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ..-.++|||.+|...+.-.+|+.+|++| .|+..+++...-+.-.+=|+||++++.++|.+||+ |+. +.|.|+.|.|.
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHr-TELHGrmISVE  480 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHR-TELHGRMISVE  480 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhh-hhhcceeeeee
Confidence            3445899999999999999999999999 99999999876555556799999999999999999 999 99999999999


Q ss_pred             ecCC
Q psy1680          88 IADG   91 (227)
Q Consensus        88 ~~~~   91 (227)
                      .++.
T Consensus       481 kaKN  484 (940)
T KOG4661|consen  481 KAKN  484 (940)
T ss_pred             eccc
Confidence            8864

>KOG0533|consensus

Probab=98.66  E-value=5.1e-08  Score=76.65  Aligned_cols=70  Identities=20%  Similarity=0.128  Sum_probs=63.7

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +.+|+|.|||..+  +.+||+++|+.|+.++.+-|..|+. |.+.|.|=|.|...+||.+|++.+||..++|+
T Consensus        83 ~~~v~v~NL~~~V--~~~Dl~eLF~~~~~~~r~~vhy~~~-G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~  152 (243)
T KOG0533|consen   83 STKVNVSNLPYGV--IDADLKELFAEFGELKRVAVHYDRA-GRSLGTADVSFNRRDDAERAVKKYNGVALDGR  152 (243)
T ss_pred             cceeeeecCCcCc--chHHHHHHHHHhccceEEeeccCCC-CCCCccceeeecchHhHHHHHHHhcCcccCCc
Confidence            4679999996555  7899999999999999999999955 99999999999999999999999999999985

>KOG2193|consensus

Probab=98.65  E-value=3.4e-09  Score=87.50  Aligned_cols=140  Identities=20%  Similarity=0.267  Sum_probs=113.3

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC--CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecC
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~--~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~   90 (227)
                      .++|++||.+..+..+|+.+|...  +...-.+++       .||+||.+.+..+|.+|++ +++...+.|.++.+..+-
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k-------~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv   74 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK-------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee-------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence            468999999999999999999876  444445543       4799999999999999999 888678999999999887


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCCC
Q psy1680          91 GKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNS  170 (227)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~  170 (227)
                      +++.+                                                           ++.+-+.|+|+...| 
T Consensus        75 ~kkqr-----------------------------------------------------------srk~Qirnippql~w-   94 (584)
T KOG2193|consen   75 PKKQR-----------------------------------------------------------SRKIQIRNIPPQLQW-   94 (584)
T ss_pred             hHHHH-----------------------------------------------------------hhhhhHhcCCHHHHH-
Confidence            76642                                                           335789999877644 


Q ss_pred             hhhHHhhhccccceEEEE-EeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         171 MNDHGLMVTEVTTLVSVR-LVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       171 ~~~l~~~f~~~g~i~~v~-i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                       +.|..+...||.++.|. ++.|.+|-    ..-|+|.+.+.+..|+.+++|..+.
T Consensus        95 -evld~Ll~qyg~ve~~eqvnt~~eta----vvnvty~~~~~~~~ai~kl~g~Q~e  145 (584)
T KOG2193|consen   95 -EVLDSLLAQYGTVENCEQVNTDSETA----VVNVTYSAQQQHRQAIHKLNGPQLE  145 (584)
T ss_pred             -HHHHHHHhccCCHhHhhhhccchHHH----HHHHHHHHHHHHHHHHHhhcchHhh
Confidence             67888999999999885 55565532    2347899999999999999998774

>KOG0226|consensus

Probab=98.64  E-value=2e-08  Score=77.83  Aligned_cols=83  Identities=24%  Similarity=0.444  Sum_probs=76.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      .....+||.+-|.-+++++-|-..|.+| .....++++|+-|++++||+||.|.+..++..||. ++| ..++.++|+++
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~g-kyVgsrpiklR  265 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNG-KYVGSRPIKLR  265 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcc-cccccchhHhh
Confidence            3556899999999999999999999999 89999999999999999999999999999999999 999 99999999988


Q ss_pred             ecCCCC
Q psy1680          88 IADGKR   93 (227)
Q Consensus        88 ~~~~~~   93 (227)
                      .+..+.
T Consensus       266 kS~wke  271 (290)
T KOG0226|consen  266 KSEWKE  271 (290)
T ss_pred             hhhHHh
Confidence            776655

>KOG0132|consensus

Probab=98.55  E-value=5.2e-07  Score=79.89  Aligned_cols=64  Identities=17%  Similarity=0.240  Sum_probs=57.4

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      ++||||+.|+.++  ++.||..+|++||.|.+|.++..      +|+|||...+..+|.+||.+|.+..+.+
T Consensus       421 SrTLwvG~i~k~v--~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~  484 (894)
T KOG0132|consen  421 SRTLWVGGIPKNV--TEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVAD  484 (894)
T ss_pred             eeeeeeccccchh--hHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccc
Confidence            6899999995544  89999999999999999988665      6899999999999999999999888765

>KOG4660|consensus

Probab=98.55  E-value=5.7e-08  Score=82.96  Aligned_cols=69  Identities=19%  Similarity=0.139  Sum_probs=59.8

Q ss_pred             CCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         152 GGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .-+..+|+|.|||..+  +.++|+.+|+.||.|+.|+.-+.     .+|..||+|-++-+|++|+++|++.+|.|+
T Consensus        72 ~~~~~~L~v~nl~~~V--sn~~L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~  140 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSV--SNDTLLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKALNRREIAGK  140 (549)
T ss_pred             cCccceEEEEecCCcC--CHHHHHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHHHHHHHhhhh
Confidence            4567899999997666  78999999999999999765444     479999999999999999999999999774

>KOG4209|consensus

Probab=98.50  E-value=3e-07  Score=72.38  Aligned_cols=84  Identities=26%  Similarity=0.345  Sum_probs=77.6

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRL   86 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v   86 (227)
                      ....+...+||+|+.+.+|.++++..|+.+ .+..+.|..|+.++.++||+||+|.+.+.++.++.+++ ..|.++.+.|
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~g-s~i~~~~i~v  174 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDG-SEIPGPAIEV  174 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCC-ccccccccee
Confidence            345677999999999999999999999999 99999999999999999999999999999999999999 9999999999


Q ss_pred             EecCCC
Q psy1680          87 DIADGK   92 (227)
Q Consensus        87 ~~~~~~   92 (227)
                      .+....
T Consensus       175 t~~r~~  180 (231)
T KOG4209|consen  175 TLKRTN  180 (231)
T ss_pred             eeeeee
Confidence            887654

>KOG0112|consensus

Probab=98.48  E-value=7.6e-08  Score=86.24  Aligned_cols=148  Identities=14%  Similarity=0.215  Sum_probs=113.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ...+.+||++||+..+++.+|+..|..+ .+..|.|-.-+. +.-.-|+||.|.+...+..|+. +.+ ..|..-.+.+.
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~-~~I~~g~~r~g  446 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESG-PLIGNGTHRIG  446 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCcccchhhcC-CccccCccccc
Confidence            3556899999999999999999999999 999988855422 3334599999999988888887 777 55544333333


Q ss_pred             ecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCC
Q psy1680          88 IADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNR  167 (227)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~  167 (227)
                      +..++.                                                           .+...++++.|++-.
T Consensus       447 lG~~ks-----------------------------------------------------------t~ttr~~sgglg~w~  467 (975)
T KOG0112|consen  447 LGQPKS-----------------------------------------------------------TPTTRLQSGGLGPWS  467 (975)
T ss_pred             cccccc-----------------------------------------------------------ccceeeccCCCCCCC
Confidence            332211                                                           244568899887544


Q ss_pred             CCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         168 SNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       168 ~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                        ....|..+|..||.|..|.+-..      .-||+|.|++...|++|++.|-|..|+|
T Consensus       468 --p~~~l~r~fd~fGpir~Idy~hg------q~yayi~yes~~~aq~a~~~~rgap~G~  518 (975)
T KOG0112|consen  468 --PVSRLNREFDRFGPIRIIDYRHG------QPYAYIQYESPPAAQAATHDMRGAPLGG  518 (975)
T ss_pred             --hHHHHHHHhhccCcceeeecccC------CcceeeecccCccchhhHHHHhcCcCCC
Confidence              35778999999999998866333      2499999999999999999999998875

>KOG0153|consensus

Probab=98.47  E-value=2.4e-07  Score=74.91  Aligned_cols=68  Identities=16%  Similarity=0.168  Sum_probs=55.4

Q ss_pred             CCCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHH-cCCccccC
Q psy1680         151 RGGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-DGRITVDG  226 (227)
Q Consensus       151 ~~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~-l~g~~i~g  226 (227)
                      .+....+|||++|.+  ..++.+|++.|.+||.|++|++...      +++|||+|.+.+.|+.|.++ ++...|+|
T Consensus       224 eD~~I~tLyIg~l~d--~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G  292 (377)
T KOG0153|consen  224 EDTSIKTLYIGGLND--EVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVING  292 (377)
T ss_pred             cccceeEEEeccccc--chhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecc
Confidence            345568999999965  4478999999999999999999877      46999999999999988775 44444555

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

Probab=98.40  E-value=1.2e-06  Score=59.26  Aligned_cols=68  Identities=10%  Similarity=-0.053  Sum_probs=58.4

Q ss_pred             CcceeccCCCCCCCChhhHHhhhcc--ccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTE--VTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~--~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      .||.|+|+|...  +.++|.+++..  .|...-+.|+.|..++-+.|||||-|.+++.|.+-.+..+|..+.
T Consensus         2 TTvMirNIPn~~--t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~   71 (97)
T PF04059_consen    2 TTVMIRNIPNKY--TQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWP   71 (97)
T ss_pred             eeEEEecCCCCC--CHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccc
Confidence            589999998666  56777666554  267888999999999999999999999999999999999998875

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

>KOG0116|consensus

Probab=98.31  E-value=9.4e-07  Score=74.99  Aligned_cols=70  Identities=16%  Similarity=0.269  Sum_probs=55.7

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      ...+|||.|||++.  +.++|.++|..||.|+...|....-.++...||||+|.+.+.++.|+++. -..|+|
T Consensus       287 ~~~~i~V~nlP~da--~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As-p~~ig~  356 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDA--TPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS-PLEIGG  356 (419)
T ss_pred             cccceEeecCCCCC--CHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC-ccccCC
Confidence            34569999997766  78889999999999998887765422444489999999999999999986 444444

>KOG4661|consensus

Probab=98.30  E-value=1.8e-06  Score=74.19  Aligned_cols=73  Identities=10%  Similarity=0.161  Sum_probs=63.3

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..+.+|+|..|+.  .+-..||+.+|++||.|.-.+++.+..+-.-+=|+||+..+.++|.+||+.|+-.+|.||
T Consensus       403 ~~gRNlWVSGLSs--tTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGr  475 (940)
T KOG4661|consen  403 TLGRNLWVSGLSS--TTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGR  475 (940)
T ss_pred             ccccceeeecccc--chhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcce
Confidence            4568899999953  334588999999999999999999877666778999999999999999999999888886

>KOG1457|consensus

Probab=98.29  E-value=2.1e-06  Score=65.68  Aligned_cols=70  Identities=10%  Similarity=-0.022  Sum_probs=57.1

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCC-cccceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETD-RFKGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~-~~~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      ..+||||..||.++  -..+|+-+|.+|..-+.+.|...-..+ ..+-+|||+|.+..+|.+|+.+|||..+|
T Consensus        33 ~VRTLFVSGLP~Dv--KpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFD  103 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDV--KPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFD  103 (284)
T ss_pred             ccceeeeccCCccc--CHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeec
Confidence            35899999998777  468899999999888877665432222 35689999999999999999999999886

>KOG0151|consensus

Probab=98.25  E-value=1.2e-06  Score=76.89  Aligned_cols=73  Identities=19%  Similarity=0.167  Sum_probs=60.9

Q ss_pred             CCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecC---CCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         152 GGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDK---ETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~---~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      ++....|||+||++.+  +++.|...|+.||.|-+++|+-.+   +....+.+|||.|.+..||++|++.|+|..+.+
T Consensus       171 DP~TTNlyv~Nlnpsv--~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~  246 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSV--DENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVME  246 (877)
T ss_pred             CCcccceeeecCCccc--cHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeee
Confidence            3566789999997666  789999999999999999887532   223457899999999999999999999988754

>KOG4454|consensus

Probab=98.21  E-value=9.3e-07  Score=67.36  Aligned_cols=71  Identities=13%  Similarity=0.052  Sum_probs=61.9

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +...||||.|+...+  +++-|.++|-.-|.|..|.|+.+++ ++.+ ||||.|.+.....-|++.+||..+.++
T Consensus         7 e~drtl~v~n~~~~v--~eelL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~   77 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGV--SEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEED   77 (267)
T ss_pred             chhhHHHHHhhhhhh--hHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccc
Confidence            456799999995444  7888999999999999999999977 6777 999999999999999999999988653

>KOG0151|consensus

Probab=98.17  E-value=3.9e-06  Score=73.86  Aligned_cols=82  Identities=23%  Similarity=0.342  Sum_probs=72.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecC---CCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDK---ETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~---~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      .+-.++|||+||++.++++.|...|..| ++..++|+..+   ...+.+.++||.|-+..+|++|++ |+| ..+.+..+
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg-~iv~~~e~  249 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQG-IIVMEYEM  249 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcc-eeeeeeee
Confidence            4556899999999999999999999999 99999988753   334566799999999999999999 999 99999999


Q ss_pred             EEEecCCC
Q psy1680          85 RLDIADGK   92 (227)
Q Consensus        85 ~v~~~~~~   92 (227)
                      ++-|++.-
T Consensus       250 K~gWgk~V  257 (877)
T KOG0151|consen  250 KLGWGKAV  257 (877)
T ss_pred             eecccccc
Confidence            99998643

>KOG4660|consensus

Probab=98.09  E-value=2.4e-06  Score=73.26  Aligned_cols=70  Identities=24%  Similarity=0.388  Sum_probs=61.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      .-+..+|+|-|||..+++++|+++|+.| +|..|+.-.     ..++.+||+|-+..+|+.|++ |++ ..+.|+.|.
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~-----~~~~~~~v~FyDvR~A~~Alk~l~~-~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETP-----NKRGIVFVEFYDVRDAERALKALNR-REIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccc-----ccCceEEEEEeehHhHHHHHHHHHH-HHhhhhhhc
Confidence            3456899999999999999999999999 999965543     337899999999999999999 999 999888776

>KOG4676|consensus

Probab=98.05  E-value=4.5e-06  Score=68.73  Aligned_cols=190  Identities=12%  Similarity=0.075  Sum_probs=114.6

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecC---CCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEe
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDK---ETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDI   88 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~---~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~   88 (227)
                      ...|.|.||.+++|.++++.+|.-. .|.++.++-..   .-......|||.|.+...+..|-.|.+ +.+-++.|.|..
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtn-tvfvdraliv~p   85 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTN-TVFVDRALIVRP   85 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhcc-ceeeeeeEEEEe
Confidence            3488999999999999999999888 89888776521   112345699999999999999988888 888888887766


Q ss_pred             cCCCCCCCCCCCCCCC------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC----CCCCCCCcc
Q psy1680          89 ADGKRNDNKGGFNNKQ------NRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDF----SRGGEGPGG  158 (227)
Q Consensus        89 ~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~l  158 (227)
                      .........-.+....      +.-...|-+.+.......++.           .+........++.    .-..-..++
T Consensus        86 ~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~-----------p~ailktP~Lp~~~~A~kleeirRt~  154 (479)
T KOG4676|consen   86 YGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHS-----------PNAILKTPELPPQAAAKKLEEIRRTR  154 (479)
T ss_pred             cCCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCC-----------ccceecCCCCChHhhhhhhHHHHhhh
Confidence            5432221110000000      000001111111111000100           0000000000000    001123689


Q ss_pred             eeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcC
Q psy1680         159 FRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG  220 (227)
Q Consensus       159 ~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~  220 (227)
                      +|.+|+..  +..+++...|..+|.|....+.-..    ..-+|-|+|........|+..++
T Consensus       155 ~v~sl~~~--~~l~e~~e~f~r~Gev~ya~~ask~----~s~~c~~sf~~qts~~halr~~g  210 (479)
T KOG4676|consen  155 EVQSLISA--AILPESGESFERKGEVSYAHTASKS----RSSSCSHSFRKQTSSKHALRSHG  210 (479)
T ss_pred             hhhcchhh--hcchhhhhhhhhcchhhhhhhhccC----CCcchhhhHhhhhhHHHHHHhcc
Confidence            99999544  4678899999999999888775433    35577799988888888877654

>KOG4210|consensus

Probab=97.91  E-value=1.6e-05  Score=64.82  Aligned_cols=85  Identities=31%  Similarity=0.511  Sum_probs=74.2

Q ss_pred             CCCCceEE-EcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAF-VGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~-V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~   87 (227)
                      .....++| |++|+..+++++|+.+|..+ .|..+++..++.++.++++|+|.|.....+.+++.... ..+.++++.+.
T Consensus       181 ~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~  259 (285)
T KOG4210|consen  181 SGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALNDQT-RSIGGRPLRLE  259 (285)
T ss_pred             cCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhccc-CcccCcccccc
Confidence            34556677 99999999999999999999 99999999999999999999999999999888887645 78889999999


Q ss_pred             ecCCCCCC
Q psy1680          88 IADGKRND   95 (227)
Q Consensus        88 ~~~~~~~~   95 (227)
                      ...+....
T Consensus       260 ~~~~~~~~  267 (285)
T KOG4210|consen  260 EDEPRPKS  267 (285)
T ss_pred             cCCCCccc
Confidence            98776544

>KOG1548|consensus

Probab=97.90  E-value=3.4e-05  Score=62.71  Aligned_cols=69  Identities=12%  Similarity=0.227  Sum_probs=59.8

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceE--------EEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLV--------SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~--------~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..|||.+||.+.  |.+++.++|++||.|.        .|+|-++.. |..+|-|.+.|-..+...-|++.|++..|.|+
T Consensus       135 t~VYVsgLP~Di--T~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~  211 (382)
T KOG1548|consen  135 TSVYVSGLPLDI--TVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDELRGK  211 (382)
T ss_pred             ceEEecCCCCcc--cHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCcccccCc
Confidence            459999997766  7899999999999774        367777754 88999999999999999999999999998874

>KOG1855|consensus

Probab=97.86  E-value=1.1e-05  Score=67.28  Aligned_cols=67  Identities=22%  Similarity=0.163  Sum_probs=55.8

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeec---CCCCc----------ccceEEEEEcCHHHHHHHHHHc
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKD---KETDR----------FKGFCYVEFVDVENLRQALLKD  219 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d---~~t~~----------~~g~afV~F~~~~~a~~Al~~l  219 (227)
                      -++++|.+-|||.+..  -+.|.++|+.+|.|.+|+|++.   +...+          .+-+|+|+|+..+.|.+|.+.|
T Consensus       229 l~srtivaenLP~Dh~--~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~  306 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHS--YENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELL  306 (484)
T ss_pred             cccceEEEecCCcchH--HHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhh
Confidence            3688999999987774  4889999999999999999987   33222          1457999999999999999998


Q ss_pred             CC
Q psy1680         220 GR  221 (227)
Q Consensus       220 ~g  221 (227)
                      +.
T Consensus       307 ~~  308 (484)
T KOG1855|consen  307 NP  308 (484)
T ss_pred             ch
Confidence            63

>KOG0106|consensus

Probab=97.84  E-value=9.4e-06  Score=62.70  Aligned_cols=60  Identities=15%  Similarity=0.144  Sum_probs=53.3

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      .+||++||...  .+.+|..+|..||.|..|.+..        ||+||+|++.-+|.-|+.-+||.+|.|
T Consensus         3 rv~vg~~~~~~--~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~   62 (216)
T KOG0106|consen    3 RVYIGRLPYRA--RERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCG   62 (216)
T ss_pred             ceeecccCCcc--chhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecc
Confidence            57999997666  6899999999999999887633        689999999999999999999999876

>KOG2314|consensus

Probab=97.83  E-value=2.1e-05  Score=67.72  Aligned_cols=70  Identities=13%  Similarity=0.152  Sum_probs=57.5

Q ss_pred             CCcceeccCCCC--C--CCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         155 GPGGFRNNNGPN--R--SNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       155 ~~~l~v~nl~~~--~--~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      ...|+|-+.|--  .  ..-..-|.++|+++|.|..+.++.+.+ |..+||.|++|.+..+|+.|++.|||+.|+
T Consensus        58 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   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNGKRLD  131 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhcccceec
Confidence            457888888721  1  112245678899999999999999977 559999999999999999999999999886

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

Probab=97.81  E-value=5e-05  Score=49.32  Aligned_cols=60  Identities=18%  Similarity=0.117  Sum_probs=41.4

Q ss_pred             cceeccCCCCCC--CChhhHHhhhcccc-ceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         157 GGFRNNNGPNRS--NSMNDHGLMVTEVT-TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       157 ~l~v~nl~~~~~--~~~~~l~~~f~~~g-~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      .|+|.|||.+.+  ....-|++++..|| .|.+|.          .+.|+|.|.+.+.|.+|++.|+|-.+-|
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG   66 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFG   66 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSS
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhccccccc
Confidence            589999986654  22355788888887 676662          3689999999999999999999877655

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

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

Probab=97.65  E-value=0.00011  Score=50.82  Aligned_cols=56  Identities=20%  Similarity=0.072  Sum_probs=36.3

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcC
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG  220 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~  220 (227)
                      .|.+.+++.++  +.++|++.|+.||.|..|.+.+.-      -.|+|.|.+++.|++|++++.
T Consensus         3 il~~~g~~~~~--~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~   58 (105)
T PF08777_consen    3 ILKFSGLGEPT--SREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLK   58 (105)
T ss_dssp             EEEEEE--SS----HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHH
T ss_pred             EEEEecCCCCc--CHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHH
Confidence            46777776555  589999999999999999887653      379999999999999998764

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

>KOG0128|consensus

Probab=97.63  E-value=3.7e-06  Score=75.36  Aligned_cols=161  Identities=17%  Similarity=0.096  Sum_probs=108.8

Q ss_pred             ceEEEcCCCCCCCHH-HHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEecCC
Q psy1680          14 YTAFVGNLPNGITQG-DVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~-~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~~~   91 (227)
                      ....+.++.+..... ..+..|..+ .+..|.+......-....+.++.+..+.+++.+..-.+ ..+.++...|..+.+
T Consensus       572 ~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~pa~-~~~a~~~~av~~ad~  650 (881)
T KOG0128|consen  572 REKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATVPAG-GALANRSAAVGLADA  650 (881)
T ss_pred             hhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhcccccc-cccCCccccCCCCCc
Confidence            445566676665555 456778888 89999887632212222377888888888888877555 566666666655554


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCCCh
Q psy1680          92 KRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSM  171 (227)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~  171 (227)
                      +.....                  ..+.                             ........++||.||++..  .+
T Consensus       651 ~~~~~~------------------~kvs-----------------------------~n~~R~~~~~fvsnl~~~~--~~  681 (881)
T KOG0128|consen  651 EEKEEN------------------FKVS-----------------------------PNEIRDLIKIFVSNLSPKM--SE  681 (881)
T ss_pred             hhhhhc------------------cCcC-----------------------------chHHHHHHHHHHhhcchhh--cC
Confidence            432110                  0000                             0000123578999997666  67


Q ss_pred             hhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccc
Q psy1680         172 NDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV  224 (227)
Q Consensus       172 ~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i  224 (227)
                      .+|...|++++.+..+++.--..+++.+|+|+|+|..+++|.+|+....+..+
T Consensus       682 ~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~  734 (881)
T KOG0128|consen  682 EDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFF  734 (881)
T ss_pred             chhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhh
Confidence            89999999999888887775556688999999999999999999987765543

>KOG1995|consensus

Probab=97.62  E-value=5.3e-05  Score=61.99  Aligned_cols=83  Identities=23%  Similarity=0.338  Sum_probs=73.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-Ce--------EEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCcee
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KL--------VSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITV   79 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i--------~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~   79 (227)
                      ....-+|||-+||..+++++|..+|.++ .|        ..|+|-+++.|++.|+-|.|.|.+...|+.|+. +++ ..+
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~ag-kdf  141 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAG-KDF  141 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcc-ccc
Confidence            4556899999999999999999999887 44        257788899999999999999999999999999 999 999


Q ss_pred             CCeEeEEEecCCCC
Q psy1680          80 DGLQVRLDIADGKR   93 (227)
Q Consensus        80 ~g~~l~v~~~~~~~   93 (227)
                      .+..|+|..+..+.
T Consensus       142 ~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  142 CGNTIKVSLAERRT  155 (351)
T ss_pred             cCCCchhhhhhhcc
Confidence            99999998887554

>KOG4849|consensus

Probab=97.61  E-value=3.7e-05  Score=62.58  Aligned_cols=75  Identities=16%  Similarity=0.308  Sum_probs=64.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC---CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ---KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~---~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      .....+||+||-|.+|++||.+.....   .+.+++....+.+|.+||||+|...+..++.+.|+ |.. ..|.|..-.|
T Consensus        78 Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~-k~iHGQ~P~V  156 (498)
T KOG4849|consen   78 GRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPT-KTIHGQSPTV  156 (498)
T ss_pred             CceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhccc-ceecCCCCee
Confidence            344678999999999999988776544   67888888899999999999999999999999999 888 8998875444

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

Probab=97.59  E-value=5.7e-05  Score=49.06  Aligned_cols=68  Identities=21%  Similarity=0.297  Sum_probs=45.2

Q ss_pred             ceEEEcCCCCCCCHHHHH----hcccCC--CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680          14 YTAFVGNLPNGITQGDVE----RFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~----~~f~~~--~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ..|+|.|||.+.+...|+    +++.-+  .|..|  .        .+.|+|.|.+.+.|.+|.+ ++| -.+-|+.|.|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~--------~~tAilrF~~~~~A~RA~KRmeg-EdVfG~kI~v   71 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--S--------GGTAILRFPNQEFAERAQKRMEG-EDVFGNKISV   71 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT---SSSS--EE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e--------CCEEEEEeCCHHHHHHHHHhhcc-cccccceEEE
Confidence            468999999998887655    555555  45543  2        3689999999999999999 999 9999999999


Q ss_pred             EecCCC
Q psy1680          87 DIADGK   92 (227)
Q Consensus        87 ~~~~~~   92 (227)
                      .+....
T Consensus        72 ~~~~~~   77 (90)
T PF11608_consen   72 SFSPKN   77 (90)
T ss_dssp             ESS--S
T ss_pred             EEcCCc
Confidence            997543

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

>KOG1996|consensus

Probab=97.54  E-value=0.00018  Score=57.44  Aligned_cols=59  Identities=14%  Similarity=0.050  Sum_probs=49.5

Q ss_pred             CChhhHHhhhccccceEEEEEeecCCCCccc-ceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         169 NSMNDHGLMVTEVTTLVSVRLVKDKETDRFK-GFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       169 ~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~-g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +.++++...|++||.|..|.|.-++..-..+ ---||+|.++++|.+|+--|||+.++||
T Consensus       298 elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr  357 (378)
T KOG1996|consen  298 ELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGR  357 (378)
T ss_pred             HHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecce
Confidence            3467889999999999999998886433332 2469999999999999999999999997

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

Probab=97.51  E-value=0.00019  Score=43.11  Aligned_cols=51  Identities=10%  Similarity=0.128  Sum_probs=40.0

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHH
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL  216 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al  216 (227)
                      .|-|...++..   .+.+...|..||.|+.+.+...      ....+|+|.+..+|++||
T Consensus         3 wI~V~Gf~~~~---~~~vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    3 WISVSGFPPDL---AEEVLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             EEEEEeECchH---HHHHHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            45666664322   5778889999999999988633      358999999999999996

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

Probab=97.46  E-value=0.00049  Score=47.55  Aligned_cols=69  Identities=19%  Similarity=0.285  Sum_probs=43.2

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-h--C---CCceeCCeEeEE
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-K--D---GRITVDGLQVRL   86 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~--~---~~~~~~g~~l~v   86 (227)
                      +.|+|.+++..++.++|++.|++| .|..|.+.+.      -..|+|.|.+.+.|+.|+. +  .   + ..+.+..+.+
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~-~~i~~~~~~~   74 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGK-LKIKGKEVTL   74 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS--B-TTSSSEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCc-eEEcCceEEE
Confidence            468899999999999999999999 9999998654      3489999999999999997 3  2   3 5666666665


Q ss_pred             Eec
Q psy1680          87 DIA   89 (227)
Q Consensus        87 ~~~   89 (227)
                      ...
T Consensus        75 ~vL   77 (105)
T PF08777_consen   75 EVL   77 (105)
T ss_dssp             E--
T ss_pred             EEC
Confidence            543

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

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.41  E-value=0.00037  Score=56.72  Aligned_cols=73  Identities=8%  Similarity=0.047  Sum_probs=55.1

Q ss_pred             CCCcceeccCCCCCCCChh---hH--HhhhccccceEEEEEeecCCCCccc-c-e-EEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         154 EGPGGFRNNNGPNRSNSMN---DH--GLMVTEVTTLVSVRLVKDKETDRFK-G-F-CYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~---~l--~~~f~~~g~i~~v~i~~d~~t~~~~-g-~-afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      +.+-+||-.+|+.+- .|+   -|  .++|+.||.|..|.+.+.-....+. + + .+++|.+.|||.+|+...+|..+|
T Consensus       113 QKNLvYVigi~pkva-~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~D  191 (480)
T COG5175         113 QKNLVYVIGIPPKVA-DEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLD  191 (480)
T ss_pred             ecceeEEecCCCCCC-cccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccccc
Confidence            445689999987664 233   23  5689999999999887754222221 2 2 399999999999999999999999


Q ss_pred             CC
Q psy1680         226 GL  227 (227)
Q Consensus       226 gr  227 (227)
                      ||
T Consensus       192 Gr  193 (480)
T COG5175         192 GR  193 (480)
T ss_pred             Cc
Confidence            97

>KOG1995|consensus

Probab=97.35  E-value=0.00054  Score=56.21  Aligned_cols=72  Identities=18%  Similarity=0.131  Sum_probs=62.0

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceE--------EEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccc
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLV--------SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV  224 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~--------~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i  224 (227)
                      ....+|||-.||+.+  ++++|.++|..++.|.        .|.|-+|++|+.+||-|.|.|++...|++|++-.++..+
T Consensus        64 s~~~ti~v~g~~d~~--~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf  141 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSV--CENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDF  141 (351)
T ss_pred             cccccceeeccCccc--hHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccc
Confidence            445789999997655  7899999999999773        456778999999999999999999999999999998877


Q ss_pred             cC
Q psy1680         225 DG  226 (227)
Q Consensus       225 ~g  226 (227)
                      .|
T Consensus       142 ~g  143 (351)
T KOG1995|consen  142 CG  143 (351)
T ss_pred             cC
Confidence            54

>KOG0115|consensus

Probab=97.33  E-value=0.00047  Score=54.07  Aligned_cols=60  Identities=15%  Similarity=-0.010  Sum_probs=52.3

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHc
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD  219 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l  219 (227)
                      .|+|.||+.-+  +.|.+.+.|+.||.|....+..| +.++..+-++|+|...-.|.+|+..+
T Consensus        33 ~l~V~nl~~~~--sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~   92 (275)
T KOG0115|consen   33 ELYVVNLMQGA--SNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRC   92 (275)
T ss_pred             eEEEEecchhh--hhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHh
Confidence            38999997655  56778999999999998888888 56999999999999999999999877

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=97.29  E-value=0.0009  Score=43.52  Aligned_cols=54  Identities=7%  Similarity=0.029  Sum_probs=41.4

Q ss_pred             eeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcC
Q psy1680         159 FRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG  220 (227)
Q Consensus       159 ~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~  220 (227)
                      .|..|.++..+-..||.++|++||.|. |.++-|-       -|||...+.++|..|+..+.
T Consensus        10 HVFhltFPkeWK~~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLTFPKEWKTSDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE--TT--HHHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEeCchHhhhhhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHHHHHHHHHHhc
Confidence            444455567777899999999999876 8887773       69999999999999988775

; 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.

>KOG3152|consensus

Probab=97.29  E-value=0.00013  Score=57.19  Aligned_cols=71  Identities=11%  Similarity=0.046  Sum_probs=59.9

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCC--------Cccc----ceEEEEEcCHHHHHHHHHHcCCc
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKET--------DRFK----GFCYVEFVDVENLRQALLKDGRI  222 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t--------~~~~----g~afV~F~~~~~a~~Al~~l~g~  222 (227)
                      ...||++++|+..+  ..-|+++++.||.|-.|.|.+...+        |.++    --|+|+|.+.-.|.++.+.|||.
T Consensus        74 ~GVvylS~IPp~m~--~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~  151 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMD--PVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNT  151 (278)
T ss_pred             ceEEEeccCCCccC--HHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCC
Confidence            36899999998884  5779999999999999999887665        2222    23689999999999999999999


Q ss_pred             cccCC
Q psy1680         223 TVDGL  227 (227)
Q Consensus       223 ~i~gr  227 (227)
                      .|+|+
T Consensus       152 ~Iggk  156 (278)
T KOG3152|consen  152 PIGGK  156 (278)
T ss_pred             ccCCC
Confidence            99986

>KOG4849|consensus

Probab=97.13  E-value=0.00028  Score=57.62  Aligned_cols=70  Identities=10%  Similarity=0.104  Sum_probs=59.7

Q ss_pred             CcceeccCCCCCCCChhhHHhhhcccc--ceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVT--TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g--~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      -.+||+||  .+-+|.+||.+.....|  .|.+++++.++..|.+||||.|-..+....++-++.|-.++|.|.
T Consensus        81 ~~~YvGNL--~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ  152 (498)
T KOG4849|consen   81 YCCYVGNL--LWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQ  152 (498)
T ss_pred             EEEEecce--eEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCC
Confidence            35899999  55557788877777666  677889999999999999999999999999999999999998873

>KOG0129|consensus

Probab=97.07  E-value=0.0019  Score=55.46  Aligned_cols=83  Identities=22%  Similarity=0.273  Sum_probs=67.1

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhccc-CC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCC----CceeC
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFP-EQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG----RITVD   80 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~-~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~----~~~~~   80 (227)
                      ..+.++.++||||+||.-++-++|-.+|+ -| .|+.+.|-.|+.=+-++|-|=|.|++..+..+||...=    +..+.
T Consensus       364 sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsarFvql~h~d~~  443 (520)
T KOG0129|consen  364 NQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISARFVQLDHTDID  443 (520)
T ss_pred             CcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhhheEEEeccccc
Confidence            34568889999999999999999999999 56 89999999997778999999999999999999996222    02332


Q ss_pred             CeEeEEEecC
Q psy1680          81 GLQVRLDIAD   90 (227)
Q Consensus        81 g~~l~v~~~~   90 (227)
                       ++|+|+..-
T Consensus       444 -KRVEIkPYv  452 (520)
T KOG0129|consen  444 -KRVEIKPYV  452 (520)
T ss_pred             -eeeeeccee
Confidence             366665543

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.01  E-value=0.0018  Score=52.87  Aligned_cols=78  Identities=14%  Similarity=0.336  Sum_probs=60.3

Q ss_pred             CceEEEcCCCCCCCHHH----H--HhcccCC-CeEEEEEeecCCC-CCeecE--EEEEeCCHHHHHHHHH-hCCCceeCC
Q psy1680          13 PYTAFVGNLPNGITQGD----V--ERFFPEQ-KLVSVRLVKDKET-DRFKGF--CYVEFVDVENLRQALL-KDGRITVDG   81 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~----l--~~~f~~~-~i~~v~i~~~~~~-~~~~g~--afv~f~~~~~a~~al~-~~~~~~~~g   81 (227)
                      .+-+||-+||+.+..++    |  .++|.+| .|..|.|-+...+ ....+.  .||.|.+.++|.+||. .+| ..++|
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDg-s~~DG  192 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDG-SLLDG  192 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcc-ccccC
Confidence            46789999998866655    3  3799999 9999888654312 222232  3999999999999999 999 99999


Q ss_pred             eEeEEEecCC
Q psy1680          82 LQVRLDIADG   91 (227)
Q Consensus        82 ~~l~v~~~~~   91 (227)
                      +.|+..+...
T Consensus       193 r~lkatYGTT  202 (480)
T COG5175         193 RVLKATYGTT  202 (480)
T ss_pred             ceEeeecCch
Confidence            9999887664

>KOG2202|consensus

Probab=96.86  E-value=0.00039  Score=54.54  Aligned_cols=55  Identities=18%  Similarity=0.189  Sum_probs=46.2

Q ss_pred             hhHHhhhc-cccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         172 NDHGLMVT-EVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       172 ~~l~~~f~-~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +|+..+|+ +||.|+++.+..+.. ..-.|=++|.|...++|++|++.|||.-++|+
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~-~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~  138 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLG-DHLVGNVYVKFRSEEDAEAALEDLNNRWYNGR  138 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccc-hhhhhhhhhhcccHHHHHHHHHHHcCccccCC
Confidence            56666677 899999998877643 34578899999999999999999999999886

>KOG2416|consensus

Probab=96.82  E-value=0.00093  Score=58.25  Aligned_cols=78  Identities=18%  Similarity=0.325  Sum_probs=63.8

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC--CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCcee---C
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITV---D   80 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~--~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~---~   80 (227)
                      |.....++.|||.||-.-.|..+|+.++..-  .|...||      .+.+..|||.|.+.++|..... ||| ..|   +
T Consensus       438 PsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm------DkIKShCyV~yss~eEA~atr~Alhn-V~WP~sN  510 (718)
T KOG2416|consen  438 PSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM------DKIKSHCYVSYSSVEEAAATREALHN-VQWPPSN  510 (718)
T ss_pred             CCCCCccceEeeecccccchHHHHHHHHhhccCchHHHHH------HHhhcceeEecccHHHHHHHHHHHhc-cccCCCC
Confidence            3456788999999999999999999999855  5666644      2347899999999999999998 999 776   5


Q ss_pred             CeEeEEEecCC
Q psy1680          81 GLQVRLDIADG   91 (227)
Q Consensus        81 g~~l~v~~~~~   91 (227)
                      .+.|.+.+...
T Consensus       511 PK~L~adf~~~  521 (718)
T KOG2416|consen  511 PKHLIADFVRA  521 (718)
T ss_pred             CceeEeeecch
Confidence            67888888764

>KOG2314|consensus

Probab=96.82  E-value=0.0059  Score=53.16  Aligned_cols=78  Identities=18%  Similarity=0.269  Sum_probs=61.6

Q ss_pred             CCCceEEEcCCCCCC--CHH----HHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeC-C
Q psy1680          11 EPPYTAFVGNLPNGI--TQG----DVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVD-G   81 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~--t~~----~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~-g   81 (227)
                      .-...|+|.|+|.--  ..+    -|..+|+++ ++....++.+..+| ++||.|++|.+..+|+.|++ +|| ..|+ .
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G-~~ldkn  133 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNG-KRLDKN  133 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhccc-ceeccc
Confidence            455788999998542  222    366789999 99999999887755 89999999999999999999 999 7664 5


Q ss_pred             eEeEEEecC
Q psy1680          82 LQVRLDIAD   90 (227)
Q Consensus        82 ~~l~v~~~~   90 (227)
                      ++..|..-+
T Consensus       134 Htf~v~~f~  142 (698)
T KOG2314|consen  134 HTFFVRLFK  142 (698)
T ss_pred             ceEEeehhh
Confidence            677775543

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

Probab=96.55  E-value=0.0048  Score=36.94  Aligned_cols=51  Identities=16%  Similarity=0.339  Sum_probs=41.1

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHH
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL   71 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al   71 (227)
                      +.|-|.|.++...+ ++..+|..| +|.++.+..      ...+.+|.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            46778899987664 456689999 999988862      2569999999999999985

>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=96.51  E-value=0.005  Score=42.00  Aligned_cols=66  Identities=11%  Similarity=0.032  Sum_probs=41.3

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEE-EeecCC------CCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVR-LVKDKE------TDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~-i~~d~~------t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      -|.|...|+.   ..+.+.+.|++||.|.+.. +.++..      ......+--|+|+++.+|.+||.. ||..|+|
T Consensus         8 wVtVFGfp~~---~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g   80 (100)
T PF05172_consen    8 WVTVFGFPPS---ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSG   80 (100)
T ss_dssp             EEEEE---GG---GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETT
T ss_pred             EEEEEccCHH---HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcC
Confidence            4666666543   3578999999999998774 222100      011245889999999999999976 4455655

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.

>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=96.48  E-value=0.0099  Score=40.57  Aligned_cols=78  Identities=15%  Similarity=0.195  Sum_probs=51.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEE-EeecC------CCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVR-LVKDK------ETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL   82 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~-i~~~~------~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~   82 (227)
                      ...+-|.|-|.|+.. -..|.++|++| .|.+.. +.++.      .......+-.|.|.+..+|.+||..|| ..+.|.
T Consensus         4 ~~~~wVtVFGfp~~~-~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG-~i~~g~   81 (100)
T PF05172_consen    4 DSETWVTVFGFPPSA-SNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNG-TIFSGS   81 (100)
T ss_dssp             GGCCEEEEE---GGG-HHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTT-EEETTC
T ss_pred             cCCeEEEEEccCHHH-HHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCC-eEEcCc
Confidence            345668888999884 46678899999 887764 11100      001224699999999999999999999 999886


Q ss_pred             -EeEEEecC
Q psy1680          83 -QVRLDIAD   90 (227)
Q Consensus        83 -~l~v~~~~   90 (227)
                       .+-|.+.+
T Consensus        82 ~mvGV~~~~   90 (100)
T PF05172_consen   82 LMVGVKPCD   90 (100)
T ss_dssp             EEEEEEE-H
T ss_pred             EEEEEEEcH
Confidence             45566653

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.

>KOG2416|consensus

Probab=96.41  E-value=0.002  Score=56.19  Aligned_cols=70  Identities=14%  Similarity=0.103  Sum_probs=54.8

Q ss_pred             CCCCCCCCCCcceeccCCCCCCCChhhHHhhhcc-ccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccc
Q psy1680         147 NDFSRGGEGPGGFRNNNGPNRSNSMNDHGLMVTE-VTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV  224 (227)
Q Consensus       147 ~~~~~~~~~~~l~v~nl~~~~~~~~~~l~~~f~~-~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i  224 (227)
                      ..+++.++++.|+|.||=-+  .|.-+|+.+... +|.|++. || |    +.+..|||.|.+.++|.+...+|+|..+
T Consensus       436 pSPsR~~~SnvlhI~nLvRP--FTlgQLkelL~rtgg~Vee~-Wm-D----kIKShCyV~yss~eEA~atr~AlhnV~W  506 (718)
T KOG2416|consen  436 PSPSRKEPSNVLHIDNLVRP--FTLGQLKELLGRTGGNVEEF-WM-D----KIKSHCYVSYSSVEEAAATREALHNVQW  506 (718)
T ss_pred             CCCCCCCccceEeeeccccc--chHHHHHHHHhhccCchHHH-HH-H----HhhcceeEecccHHHHHHHHHHHhcccc
Confidence            34456678899999999433  478999999994 5566655 32 3    3467899999999999999999999865

>KOG3152|consensus

Probab=96.28  E-value=0.0017  Score=51.04  Aligned_cols=71  Identities=11%  Similarity=0.196  Sum_probs=59.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCC--------CCee----cEEEEEeCCHHHHHHHHH-hCCCc
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKET--------DRFK----GFCYVEFVDVENLRQALL-KDGRI   77 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~--------~~~~----g~afv~f~~~~~a~~al~-~~~~~   77 (227)
                      ..-.||+++||+.+...-|+++|+.| .|-.|.+-....+        +.+.    .-|+|+|.+...|..+.. ||+ .
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn-~  151 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNN-T  151 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCC-C
Confidence            45789999999999999999999999 9999988765444        2222    347899999999999988 999 9


Q ss_pred             eeCCeE
Q psy1680          78 TVDGLQ   83 (227)
Q Consensus        78 ~~~g~~   83 (227)
                      .|+|+.
T Consensus       152 ~Iggkk  157 (278)
T KOG3152|consen  152 PIGGKK  157 (278)
T ss_pred             ccCCCC
Confidence            888874

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.20  E-value=0.018  Score=41.85  Aligned_cols=73  Identities=25%  Similarity=0.341  Sum_probs=50.6

Q ss_pred             CCCCceEEEcCCCC------CCCH---HHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCcee
Q psy1680          10 TEPPYTAFVGNLPN------GITQ---GDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV   79 (227)
Q Consensus        10 ~~~~~~l~V~nLp~------~~t~---~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~   79 (227)
                      .++..+|.|.=+.+      ...+   .+|-+.|..| .+.-++++-        +.-+|+|.+-++|.+|+.++| .++
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~--------~~mwVTF~dg~sALaals~dg-~~v   94 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG--------DTMWVTFRDGQSALAALSLDG-IQV   94 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET--------TCEEEEESSCHHHHHHHHGCC-SEE
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC--------CeEEEEECccHHHHHHHccCC-cEE
Confidence            45667777764441      2222   2566778888 888777763        358999999999999999999 999


Q ss_pred             CCeEeEEEecCC
Q psy1680          80 DGLQVRLDIADG   91 (227)
Q Consensus        80 ~g~~l~v~~~~~   91 (227)
                      +|+.|.|++.++
T Consensus        95 ~g~~l~i~LKtp  106 (146)
T PF08952_consen   95 NGRTLKIRLKTP  106 (146)
T ss_dssp             TTEEEEEEE---
T ss_pred             CCEEEEEEeCCc
Confidence            999999998765

; PDB: 1UFW_A 2DNR_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.10  E-value=0.027  Score=34.73  Aligned_cols=53  Identities=23%  Similarity=0.449  Sum_probs=43.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC----CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ----KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL   72 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~----~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~   72 (227)
                      ....|+|+|+. +++-++|+.+|..|    ....|.++-|.       -|-|.|.+.+.|.+||.
T Consensus         4 rpeavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~   60 (62)
T PF10309_consen    4 RPEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALV   60 (62)
T ss_pred             eeceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHH
Confidence            35689999995 56778899999887    56788888763       48899999999999986

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=95.96  E-value=0.021  Score=43.31  Aligned_cols=80  Identities=14%  Similarity=0.094  Sum_probs=47.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccC-C-Ce---EEEE--EeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPE-Q-KL---VSVR--LVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG   81 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~-~-~i---~~v~--i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g   81 (227)
                      .....+|.|++||+++|++++.+.++. + ..   ..+.  ..........-.-|||.|.+.+++...+. ++| ..|.+
T Consensus         4 ~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g-~~F~D   82 (176)
T PF03467_consen    4 EKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDG-HVFVD   82 (176)
T ss_dssp             -----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTT-EEEE-
T ss_pred             cccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCC-cEEEC
Confidence            345679999999999999999998887 4 33   2332  11111111234579999999999999988 999 66643


Q ss_pred             e-----EeEEEecC
Q psy1680          82 L-----QVRLDIAD   90 (227)
Q Consensus        82 ~-----~l~v~~~~   90 (227)
                      .     +..|.+|-
T Consensus        83 ~kg~~~~~~VE~Ap   96 (176)
T PF03467_consen   83 SKGNEYPAVVEFAP   96 (176)
T ss_dssp             TTS-EEEEEEEE-S
T ss_pred             CCCCCcceeEEEcc
Confidence            2     34455554

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=95.85  E-value=0.036  Score=34.16  Aligned_cols=55  Identities=20%  Similarity=0.183  Sum_probs=43.8

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccc---cceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHc
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEV---TTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD  219 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~---g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l  219 (227)
                      ...|+|..+. .+  +.+||+.+|..|   .....|.++-|.       -|-|.|.+.+.|.+||.+|
T Consensus         5 peavhirGvd-~l--sT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-EL--STDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CC--CHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            3468888883 33  568999999998   135578888884       4889999999999999875

>KOG1855|consensus

Probab=95.85  E-value=0.066  Score=45.35  Aligned_cols=66  Identities=26%  Similarity=0.300  Sum_probs=54.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeec---CCCC--C--------eecEEEEEeCCHHHHHHHHH-hC
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKD---KETD--R--------FKGFCYVEFVDVENLRQALL-KD   74 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~---~~~~--~--------~~g~afv~f~~~~~a~~al~-~~   74 (227)
                      +-++++|.+-|||.+-.-+-|.++|..+ .|..|+|..-   +.+.  .        .+-+|+|+|...+.|.+|-+ ++
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            4478999999999998889999999999 9999998765   3322  1        24589999999999999999 54


Q ss_pred             C
Q psy1680          75 G   75 (227)
Q Consensus        75 ~   75 (227)
                      .
T Consensus       308 ~  308 (484)
T KOG1855|consen  308 P  308 (484)
T ss_pred             h
Confidence            4

>KOG2068|consensus

Probab=95.84  E-value=0.0074  Score=49.38  Aligned_cols=71  Identities=8%  Similarity=-0.013  Sum_probs=53.6

Q ss_pred             CcceeccCCCCCCCChhhH--HhhhccccceEEEEEeecCCCCc---ccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDH--GLMVTEVTTLVSVRLVKDKETDR---FKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l--~~~f~~~g~i~~v~i~~d~~t~~---~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +-+||..|++... .++.|  ...|+.||.|..|.+.+++-+..   ..--++|+|...|+|..||...+|..++||
T Consensus        78 nlvyvvgl~~~~a-de~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~  153 (327)
T KOG2068|consen   78 NLVYVVGLPLDLA-DESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGR  153 (327)
T ss_pred             hhhhhhCCCcccc-chhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhh
Confidence            4567878875553 45555  45799999999999998862111   112379999999999999999999999886

>KOG4676|consensus

Probab=95.78  E-value=0.008  Score=50.10  Aligned_cols=67  Identities=18%  Similarity=0.272  Sum_probs=54.8

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCC---cccceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETD---RFKGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~---~~~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      .|-|.||.+.+  +.|++.-+|+-.|.|..+.|....+.-   ...-.|||.|.+...+..|..+.|-..||
T Consensus         9 vIqvanispsa--t~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvd   78 (479)
T KOG4676|consen    9 VIQVANISPSA--TKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVD   78 (479)
T ss_pred             eeeecccCchh--hHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeee
Confidence            78999997666  789999999999999999998754322   23568999999999999998887766554

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=95.71  E-value=0.044  Score=35.78  Aligned_cols=56  Identities=11%  Similarity=0.195  Sum_probs=40.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hC
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KD   74 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~   74 (227)
                      ...+..+|. +|..|...||.++|+.|.-+.|.++-|       .-|||.....+.|..++. +.
T Consensus         7 ~RdHVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~d-------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    7 SRDHVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWIND-------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             SGCCEEEEE---TT--HHHHHHHCCCCCCEEEEEECT-------TEEEEEECCCHHHHHHHHHHT
T ss_pred             CcceEEEEe-CchHhhhhhHHHHhccCCcEEEEEEcC-------CcEEEEeecHHHHHHHHHHhc
Confidence            345666776 999999999999999994445666554       269999999999999987 44

; 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.

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.64  E-value=0.042  Score=39.93  Aligned_cols=67  Identities=24%  Similarity=0.270  Sum_probs=45.8

Q ss_pred             CCCCCcceeccCCCCCCCC-------hhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccc
Q psy1680         152 GGEGPGGFRNNNGPNRSNS-------MNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV  224 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~~-------~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i  224 (227)
                      +||..|+.|.-+.+.....       .++|.+.|+.||.+.-+++.-+        .-+|+|.+-+.|-+|+. ++|..|
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v   94 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQV   94 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEE
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEE
Confidence            3677788888776222111       2467888999998888887665        47999999999999875 566777


Q ss_pred             cCC
Q psy1680         225 DGL  227 (227)
Q Consensus       225 ~gr  227 (227)
                      +|+
T Consensus        95 ~g~   97 (146)
T PF08952_consen   95 NGR   97 (146)
T ss_dssp             TTE
T ss_pred             CCE
Confidence            764

; PDB: 1UFW_A 2DNR_A.

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=95.57  E-value=0.18  Score=35.09  Aligned_cols=66  Identities=14%  Similarity=0.123  Sum_probs=48.3

Q ss_pred             CceEE-EcCCCCCCCHHHHHhcccCC--CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC
Q psy1680          13 PYTAF-VGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG   81 (227)
Q Consensus        13 ~~~l~-V~nLp~~~t~~~l~~~f~~~--~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g   81 (227)
                      ...|. +...|..++-++|..+.+.+  .|.+++|++|..  .++=.+++.|.+.++|...-. +|| ..++.
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNG-k~Fns   81 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNG-KPFNS   81 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCC-CccCC
Confidence            34444 44444555556777777777  688999998743  345589999999999999998 999 87764

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0112|consensus

Probab=95.35  E-value=0.019  Score=52.65  Aligned_cols=76  Identities=16%  Similarity=0.256  Sum_probs=65.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC--eEe
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG--LQV   84 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g--~~l   84 (227)
                      ....++.+|+++|...+....|...|..| .|..|.+-..      ..||+|.|.+...++.|++ +.+ ..|++  +++
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg------q~yayi~yes~~~aq~a~~~~rg-ap~G~P~~r~  523 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG------QPYAYIQYESPPAAQAATHDMRG-APLGGPPRRL  523 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC------CcceeeecccCccchhhHHHHhc-CcCCCCCccc
Confidence            45678999999999999999999999999 9988877432      4699999999999999999 999 88876  578


Q ss_pred             EEEecCC
Q psy1680          85 RLDIADG   91 (227)
Q Consensus        85 ~v~~~~~   91 (227)
                      .|.++.+
T Consensus       524 rvdla~~  530 (975)
T KOG0112|consen  524 RVDLASP  530 (975)
T ss_pred             ccccccC
Confidence            8888764

>KOG2202|consensus

Probab=95.08  E-value=0.0077  Score=47.44  Aligned_cols=61  Identities=18%  Similarity=0.245  Sum_probs=46.5

Q ss_pred             HHHhccc-CC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecCC
Q psy1680          29 DVERFFP-EQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        29 ~l~~~f~-~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~~   91 (227)
                      ++...|+ +| +|..+.|-.. ..-...|-++|.|...++|++|++ ||+ ..+.|++|...+..-
T Consensus        84 d~f~E~~~kygEiee~~Vc~N-l~~hl~GNVYV~f~~Ee~ae~a~~~lnn-Rw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDN-LGDHLVGNVYVKFRSEEDAEAALEDLNN-RWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhcc-cchhhhhhhhhhcccHHHHHHHHHHHcC-ccccCCcceeeecCc
Confidence            3444444 77 7877755433 223447899999999999999999 999 999999999888653

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=94.83  E-value=0.32  Score=33.82  Aligned_cols=67  Identities=9%  Similarity=0.032  Sum_probs=49.0

Q ss_pred             CcceeccCCCCCCCChhhHHhhhcccc-ceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVT-TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g-~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      ..+.+--.|+.. .+.++|..+.+++- .|..++|++|..  .++-.+.++|.+.++|..-.+..||+.++
T Consensus        13 ~~~~~l~vp~~~-~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   13 STLCCLAVPPYM-TPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             ceEEEEEeCccc-ccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            344444444333 35677776666665 777889999843  35567899999999999999999999875

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG1996|consensus

Probab=94.22  E-value=0.15  Score=41.20  Aligned_cols=62  Identities=18%  Similarity=0.157  Sum_probs=49.3

Q ss_pred             HHHHhcccCC-CeEEEEEeecCCCCCeec-EEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecC
Q psy1680          28 GDVERFFPEQ-KLVSVRLVKDKETDRFKG-FCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        28 ~~l~~~f~~~-~i~~v~i~~~~~~~~~~g-~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~   90 (227)
                      +++.+.+++| .|..|.|...+..-...- --||+|...++|.+|+- +|| ..|+|+.++..+..
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnG-RyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNG-RYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCC-ceecceeeeheecc
Confidence            3577889999 999888876644332222 47999999999999998 999 99999999877654

>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=93.89  E-value=0.12  Score=39.10  Aligned_cols=70  Identities=13%  Similarity=0.030  Sum_probs=44.9

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhcc-ccce---EEEEEeecCCCCc--ccceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTE-VTTL---VSVRLVKDKETDR--FKGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~-~g~i---~~v~i~~d~~t~~--~~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      ....|.|++||+.+  |++++++.+++ ++.-   ..+.-......-.  .-.-|+|.|.+.+++..-...++|+.+-
T Consensus         6 ~~~KvVIR~LPP~L--teeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~   81 (176)
T PF03467_consen    6 EGTKVVIRRLPPNL--TEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFV   81 (176)
T ss_dssp             ---EEEEEEE-TTS---HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE
T ss_pred             cCceEEEeCCCCCC--CHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEE
Confidence            34589999999888  78999988887 6644   2333112211111  1246999999999999999999997763

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.80  E-value=0.2  Score=36.16  Aligned_cols=65  Identities=12%  Similarity=-0.066  Sum_probs=48.4

Q ss_pred             CCCCCcceeccCCCCCCCCh--hhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcc
Q psy1680         152 GGEGPGGFRNNNGPNRSNSM--NDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRIT  223 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~~~--~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~  223 (227)
                      ++|=.||.|+=|..+...++  ..+.+..+.||.|.+|.++=..       .|.|.|.+...|=+|+.+.+...
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGrq-------savVvF~d~~SAC~Av~Af~s~~  149 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGRQ-------SAVVVFKDITSACKAVSAFQSRA  149 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCCc-------eEEEEehhhHHHHHHHHhhcCCC
Confidence            45667888887765554322  3445567889999999876442       59999999999999999887643

>KOG0804|consensus

Probab=93.59  E-value=0.2  Score=42.77  Aligned_cols=66  Identities=17%  Similarity=0.246  Sum_probs=57.9

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC--CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG   81 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~--~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g   81 (227)
                      +..|+|-.+|..++-.||-.|+..+  .|.+++|++|..  ..+=..+|.|.+..+|...-+ +|| ..|+.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~--pnrymvLIkFr~q~da~~Fy~efNG-k~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGM--PNRYMVLIKFRDQADADTFYEEFNG-KQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCC--CceEEEEEEeccchhHHHHHHHcCC-CcCCC
Confidence            7899999999999999999999988  799999999643  234578999999999999998 999 88865

>KOG2193|consensus

Probab=93.34  E-value=0.084  Score=44.70  Aligned_cols=60  Identities=13%  Similarity=0.130  Sum_probs=44.0

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcc
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRIT  223 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~  223 (227)
                      +.+|++||++..  +.+||..+|...-.--+=.++..      .||+||...+..-|.+|++.++|..
T Consensus         2 nklyignL~p~~--~psdl~svfg~ak~~~~g~fl~k------~gyafvd~pdq~wa~kaie~~sgk~   61 (584)
T KOG2193|consen    2 NKLYIGNLSPQV--TPSDLESVFGDAKIPGSGQFLVK------SGYAFVDCPDQQWANKAIETLSGKV   61 (584)
T ss_pred             CcccccccCCCC--ChHHHHHHhccccCCCCcceeee------cceeeccCCchhhhhhhHHhhchhh
Confidence            368999998766  78999999986410011111111      4899999999999999999998853

>KOG4574|consensus

Probab=93.15  E-value=0.047  Score=49.97  Aligned_cols=52  Identities=17%  Similarity=0.142  Sum_probs=45.7

Q ss_pred             CCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccc
Q psy1680         167 RSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV  224 (227)
Q Consensus       167 ~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i  224 (227)
                      +..+-..|..+|+.||.|.++..++|.      ..|.|+|.+.+.|..|+++++|+++
T Consensus       308 v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkev  359 (1007)
T KOG4574|consen  308 VNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEV  359 (1007)
T ss_pred             ccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcc
Confidence            344567789999999999999988885      4899999999999999999999875

>KOG0115|consensus

Probab=93.08  E-value=0.091  Score=41.58  Aligned_cols=58  Identities=22%  Similarity=0.191  Sum_probs=51.5

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL   72 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~   72 (227)
                      ..|||.||+..+..+.|.+-|+.| +|....++.| ..++..+-++|.|...-.+.+|+.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~r   90 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAAR   90 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHH
Confidence            789999999999999999999999 8887766666 447778899999999999999998

>KOG2068|consensus

Probab=92.98  E-value=0.051  Score=44.60  Aligned_cols=78  Identities=19%  Similarity=0.316  Sum_probs=59.7

Q ss_pred             ceEEEcCCCCCCCHH-HHH--hcccCC-CeEEEEEeecCC----CCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680          14 YTAFVGNLPNGITQG-DVE--RFFPEQ-KLVSVRLVKDKE----TDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~-~l~--~~f~~~-~i~~v~i~~~~~----~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      +.+||-+|+.....+ .|+  ++|.+| .|..|.+.+++.    .+-.. -++|.|...++|..||. .+| +.++|+.+
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~-s~yITy~~~eda~rci~~v~g-~~~dg~~l  155 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTC-SVYITYEEEEDADRCIDDVDG-FVDDGRAL  155 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCC-cccccccchHhhhhHHHHhhh-HHhhhhhh
Confidence            567888888775544 444  689999 999998887652    12222 38999999999999999 999 99999998


Q ss_pred             EEEecCCCC
Q psy1680          85 RLDIADGKR   93 (227)
Q Consensus        85 ~v~~~~~~~   93 (227)
                      +..+...+-
T Consensus       156 ka~~gttky  164 (327)
T KOG2068|consen  156 KASLGTTKY  164 (327)
T ss_pred             HHhhCCCcc
Confidence            877766543

>KOG0804|consensus

Probab=92.81  E-value=0.34  Score=41.49  Aligned_cols=68  Identities=9%  Similarity=0.005  Sum_probs=56.1

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhcccc-ceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVT-TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g-~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      ++..|+|--+|.-.  +--||..|+.++- .|..++|++|..  ..+-.+.++|.+.++|..-.+.+||..++
T Consensus        73 ~~~mLcilaVP~~m--t~~Dll~F~~~~~~~I~~irivRd~~--pnrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   73 SSTMLCILAVPAYM--TSHDLLRFCASFIKQISDIRIVRDGM--PNRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CCcEEEEEeccccc--cHHHHHHHHHHHhhhhheeEEeecCC--CceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            47789999997555  5678888888775 889999999754  33456899999999999999999999886

>KOG2253|consensus

Probab=90.56  E-value=0.41  Score=42.86  Aligned_cols=63  Identities=16%  Similarity=0.017  Sum_probs=51.6

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      ++..++||+|+....  ..+=++.+...+|.|.++....         |||++|..+..+.+|+..+.-..++|
T Consensus        38 ~~~~~vfv~~~~~~~--s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~  100 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLV--SQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDD  100 (668)
T ss_pred             CCCceeEecchhhhh--hHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCc
Confidence            567789999995444  4555688899999888875433         89999999999999999999888876

>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=89.66  E-value=1  Score=34.36  Aligned_cols=60  Identities=18%  Similarity=0.222  Sum_probs=43.7

Q ss_pred             CHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hC--CCceeCCeEeEEEecCCC
Q psy1680          26 TQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KD--GRITVDGLQVRLDIADGK   92 (227)
Q Consensus        26 t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~--~~~~~~g~~l~v~~~~~~   92 (227)
                      ....|+.+|..+ .+.....++.      -+=..|.|.+.+.|..|.. ++  + ..+.|..+++.++...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~-~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDG-TSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--T-SEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccc-cccCCCceEEEEcccc
Confidence            347799999999 8777766643      3458899999999999999 88  8 9999999999988543

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.

>KOG2135|consensus

Probab=89.39  E-value=0.28  Score=42.25  Aligned_cols=76  Identities=13%  Similarity=0.160  Sum_probs=60.8

Q ss_pred             CCCCCceEEEcCCCCCC-CHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGI-TQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~-t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v   86 (227)
                      .....+.|-+.-.|+.. |.++|...|.+| .|..|.+-..      -.-|.|+|.+..+|-.|-..++ ..|+++.|+|
T Consensus       368 ~~~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~s~~-avlnnr~iKl  440 (526)
T KOG2135|consen  368 AVVDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYASHG-AVLNNRFIKL  440 (526)
T ss_pred             hhcccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhcccc-ceecCceeEE
Confidence            34455566666666653 557899999999 9999888543      3479999999999988888888 9999999999


Q ss_pred             EecCC
Q psy1680          87 DIADG   91 (227)
Q Consensus        87 ~~~~~   91 (227)
                      .|-.+
T Consensus       441 ~whnp  445 (526)
T KOG2135|consen  441 FWHNP  445 (526)
T ss_pred             EEecC
Confidence            99776

>KOG4285|consensus

Probab=88.55  E-value=1.1  Score=36.56  Aligned_cols=49  Identities=12%  Similarity=0.154  Sum_probs=38.2

Q ss_pred             hhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         171 MNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       171 ~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      ..-|..+|++||.|.......+      -.+-.|.|.+.-+|.+||.+ ||+.|+|
T Consensus       210 ~s~vL~~F~~cG~Vvkhv~~~n------gNwMhirYssr~~A~KALsk-ng~ii~g  258 (350)
T KOG4285|consen  210 VSIVLNLFSRCGEVVKHVTPSN------GNWMHIRYSSRTHAQKALSK-NGTIIDG  258 (350)
T ss_pred             hhHHHHHHHhhCeeeeeecCCC------CceEEEEecchhHHHHhhhh-cCeeecc
Confidence            3557889999999987765422      35789999999999999986 4566665

>KOG2591|consensus

Probab=85.92  E-value=3.3  Score=36.68  Aligned_cols=55  Identities=9%  Similarity=0.033  Sum_probs=42.3

Q ss_pred             CcceeccCCCCCCCChhhHHhhhcc--ccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHc
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTE--VTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD  219 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~--~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l  219 (227)
                      ..+.++.+|...  -+|+++.+|..  |..+.+|.+--+-       -=||+|++..||+.|.+.|
T Consensus       176 cIvilREIpett--p~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykyl  232 (684)
T KOG2591|consen  176 CIVILREIPETT--PIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYL  232 (684)
T ss_pred             eEEEEeecCCCC--hHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHH
Confidence            457888886444  56889999985  6788889875542       2589999999999997654

>KOG4483|consensus

Probab=83.80  E-value=2.6  Score=35.73  Aligned_cols=57  Identities=19%  Similarity=0.290  Sum_probs=49.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC--CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHh
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK   73 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~--~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~   73 (227)
                      .+-.+.|=|-++|....-+||...|+.|  .-.+|.|+-|.       .+|..|.+...|..||.+
T Consensus       388 ~dlpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt-------halaVFss~~~AaeaLt~  446 (528)
T KOG4483|consen  388 SDLPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT-------HALAVFSSVNRAAEALTL  446 (528)
T ss_pred             ccccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc-------eeEEeecchHHHHHHhhc
Confidence            4456888899999998888999999999  67888888764       699999999999999985

>KOG2591|consensus

Probab=83.38  E-value=3  Score=36.96  Aligned_cols=71  Identities=17%  Similarity=0.263  Sum_probs=53.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccC--C-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCC-ceeCCeE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPE--Q-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGR-ITVDGLQ   83 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~--~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~-~~~~g~~   83 (227)
                      +....|.|+++-||.++-.++++.+|..  + +++.|..-..       .-=||+|.+..+|+.|.+ |.-+ .+|.|++
T Consensus       171 p~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N-------~nWyITfesd~DAQqAykylreevk~fqgKp  243 (684)
T KOG2591|consen  171 PNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN-------DNWYITFESDTDAQQAYKYLREEVKTFQGKP  243 (684)
T ss_pred             cCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec-------CceEEEeecchhHHHHHHHHHHHHHhhcCcc
Confidence            4456688999999999999999999975  4 7777765322       236899999999999987 4321 4667776


Q ss_pred             eEE
Q psy1680          84 VRL   86 (227)
Q Consensus        84 l~v   86 (227)
                      |..
T Consensus       244 ImA  246 (684)
T KOG2591|consen  244 IMA  246 (684)
T ss_pred             hhh
Confidence            543

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=82.29  E-value=8.8  Score=23.98  Aligned_cols=54  Identities=19%  Similarity=0.323  Sum_probs=41.0

Q ss_pred             CCCHHHHHhcccCCCeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680          24 GITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus        24 ~~t~~~l~~~f~~~~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      .++-++++.-+..|....|..  |      +--=||.|.+..+|+++.. .++ ..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~~~I~~--d------~tGfYIvF~~~~Ea~rC~~~~~~-~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRWDRIRD--D------RTGFYIVFNDSKEAERCFRAEDG-TLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCcceEEe--c------CCEEEEEECChHHHHHHHHhcCC-CEEEEEEEEe
Confidence            367788998898886666554  2      1246899999999999999 888 8877776654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG2253|consensus

Probab=81.29  E-value=0.94  Score=40.70  Aligned_cols=72  Identities=19%  Similarity=0.218  Sum_probs=56.6

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      ..+.++..+|||+|+...+..+-++.+...+ -|..+...         .|+|..|..+.....|+. +.- ..++|..+
T Consensus        34 ~~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~---------~fgf~~f~~~~~~~ra~r~~t~-~~~~~~kl  103 (668)
T KOG2253|consen   34 FQPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRD---------KFGFCEFLKHIGDLRASRLLTE-LNIDDQKL  103 (668)
T ss_pred             ccCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhh---------hhcccchhhHHHHHHHHHHhcc-cCCCcchh
Confidence            3466788999999999999988888877776 55554443         299999999999999998 666 78888776


Q ss_pred             EEEe
Q psy1680          85 RLDI   88 (227)
Q Consensus        85 ~v~~   88 (227)
                      .+..
T Consensus       104 ~~~~  107 (668)
T KOG2253|consen  104 IENV  107 (668)
T ss_pred             hccc
Confidence            6554

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=80.56  E-value=2.4  Score=28.20  Aligned_cols=32  Identities=16%  Similarity=0.312  Sum_probs=25.7

Q ss_pred             EEEEeCCHHHHHHHHH--hCCCceeCCeEeEEEec
Q psy1680          57 CYVEFVDVENLRQALL--KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        57 afv~f~~~~~a~~al~--~~~~~~~~g~~l~v~~~   89 (227)
                      |+|+|.+..-|++.+.  .+. ..+++..+.|...
T Consensus         1 AlITF~e~~VA~~i~~~~~~~-v~l~~~~~~V~v~   34 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHP-VPLEDCCVRVKVS   34 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEE-EEECCEEEEEEEE
Confidence            6899999999999998  455 7788887776654

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>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=80.41  E-value=4.7  Score=25.66  Aligned_cols=57  Identities=21%  Similarity=0.386  Sum_probs=32.2

Q ss_pred             CCCCHHHHHhcccCC-C-----eEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          23 NGITQGDVERFFPEQ-K-----LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        23 ~~~t~~~l~~~f~~~-~-----i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      ..++..+|..++..- .     |-.|.|.        ..|+||+.... .|..++. +++ ..+.|+++.|+.|
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~--------~~~S~vev~~~-~a~~v~~~l~~-~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIF--------DNFSFVEVPEE-VAEKVLEALNG-KKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE---------SS-EEEEE-TT--HHHHHHHHTT---SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEe--------eeEEEEEECHH-HHHHHHHHhcC-CCCCCeeEEEEEC
Confidence            346777777777554 3     4456664        34999999874 6888888 999 9999999999864

; PDB: 2G0C_A 3MOJ_B.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	227
2dng_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		9e-25
2dng_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		1e-08
1wi8_A	104	Solution Structure Of The Rna Binding Domain Of Euk		2e-08
2j76_E	100	Solution Structure And Rna Interactions Of The Rna		4e-08
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		1e-07
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-04
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		1e-04
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		3e-04
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		3e-04
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		5e-04
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		5e-04
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		8e-04

>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 4h Length = 103

Iteration: 1
 Score =  110 bits (274), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 52/97 (53%), Positives = 72/97 (74%), Gaps = 1/97 (1%)
Query: 2  GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEF 61
          G + K LPTEPPYTA+VGNLP    QGD++  F +  + SVRLV+DK+TD+FKGFCYVEF
Sbjct: 4  GSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEF 63
Query: 62 VDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKG 98
           +V++L++AL  DG +  D   +R+DIA+G++ D  G
Sbjct: 64 DEVDSLKEALTYDGALLGD-RSLRVDIAEGRKQDKSG 99

>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 4h Length = 103

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/43 (58%), Positives = 36/43 (83%)
Query: 183 TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVD 225
           ++ SVRLV+DK+TD+FKGFCYVEF +V++L++AL  DG +  D
Sbjct: 40  SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGD 82

>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic Initiation Factor 4b Length = 104

Iteration: 1
 Score = 55.8 bits (133), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 31/92 (33%), Positives = 53/92 (57%), Gaps = 2/92 (2%)
Query: 8   LPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKE-TDRFKGFCYVEFVDVEN 66
           LP  PPYTAF+GNLP  +T+  ++ FF    + +VRL ++    +R KGF Y EF +  +
Sbjct: 10  LPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEF-EDLD 68
Query: 67  LRQALLKDGRITVDGLQVRLDIADGKRNDNKG 98
              + L     ++   ++R+D+AD  ++ + G
Sbjct: 69  SLLSALSLNEESLGNKRIRVDVADQAQDKDSG 100

>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna Recognition Motif From Eukaryotic Translation Initiation Factor 4b Length = 100

Iteration: 1
 Score = 54.7 bits (130), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 30/84 (35%), Positives = 49/84 (58%), Gaps = 2/84 (2%)
Query: 8  LPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKE-TDRFKGFCYVEFVDVEN 66
          LP  PPYTAF+GNLP  +T+  ++ FF    + +VRL ++    +R KGF Y EF +  +
Sbjct: 14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEF-EDLD 72
Query: 67 LRQALLKDGRITVDGLQVRLDIAD 90
             + L     ++   ++R+D+AD
Sbjct: 73 SLLSALSLNEESLGNRRIRVDVAD 96

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 31/84 (36%), Positives = 52/84 (61%), Gaps = 2/84 (2%)
Query: 17 FVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          FVG L     +  +E+ F +   +S V +VKD+ET R +GF +V F ++++ + A++   
Sbjct: 16 FVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMN 75
Query: 76 RITVDGLQVRLDIADGKRNDNKGG 99
            +VDG Q+R+D A GK +DN+ G
Sbjct: 76 GKSVDGRQIRVDQA-GKSSDNRSG 98

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 14 YTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 72
          +  FVG+L   IT  D++  F P  K+   R+VKD  T + KG+ +V F +  +   A++
Sbjct: 16 FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 75
Query: 73 KDGRITVDGLQVRLDIA 89
            G   + G Q+R + A
Sbjct: 76 HMGGQWLGGRQIRTNWA 92

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 1/81 (1%)
Query: 15 TAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
          + FVGN+P   T+  ++  F E   +VS RLV D+ET + KG+ + E+ D E    A+  
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 74 DGRITVDGLQVRLDIADGKRN 94
                 G  +R+D A  ++N
Sbjct: 70 LNGREFSGRALRVDNAASEKN 90

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 14 YTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 72
          +  FVG+L   IT  D++  F P  ++   R+VKD  T + KG+ +V F +  +   A+ 
Sbjct: 16 FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 75
Query: 73 KDGRITVDGLQVRLDIA 89
          + G   + G Q+R + A
Sbjct: 76 QMGGQWLGGRQIRTNWA 92

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/50 (40%), Positives = 32/50 (64%), Gaps = 1/50 (2%)
Query: 15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVD 63
          T +V NLP  +T  D+ R F +  K+V V ++KDK+T + KG  ++ F+D
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLD 67

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/82 (35%), Positives = 43/82 (52%), Gaps = 6/82 (7%)
Query: 10 TEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 69
          ++P  T FV  L    T+  ++  F     V  R+V D+ET   KGF +V+F   E+ + 
Sbjct: 12 SQPSKTLFVKGLSEDTTEETLKESF--DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKA 69
Query: 70 A--LLKDGRITVDGLQVRLDIA 89
          A   ++DG I  DG +V LD A
Sbjct: 70 AKEAMEDGEI--DGNKVTLDWA 89

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/102 (26%), Positives = 48/102 (47%), Gaps = 1/102 (0%)
Query: 2   GRNQKTLPTEPPYTAFVGNLPNGITQGDV-ERFFPEQKLVSVRLVKDKETDRFKGFCYVE 60
           G    + P+ P  + +VG+L   +T+  + E+F P   ++S+R+ +D  T R  G+ YV 
Sbjct: 4   GSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVN 63
Query: 61  FVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNN 102
           F    +  +AL       + G  VR+  +    +  K G  N
Sbjct: 64  FQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN 105

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 40.4 bits (93), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 26/97 (26%), Positives = 47/97 (48%), Gaps = 1/97 (1%)
Query: 7   TLPTEPPYTAFVGNLPNGITQGDV-ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVE 65
           + P+ P  + +VG+L   +T+  + E+F P   ++S+R+ +D  T R  G+ YV F    
Sbjct: 4   SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 63
Query: 66  NLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNN 102
           +  +AL       + G  VR+  +    +  K G  N
Sbjct: 64  DAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN 100

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	227
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	100.0
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	100.0
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	100.0
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	100.0
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	100.0
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.98
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.97
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.97
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.96
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.89
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.86
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.86
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.85
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.84
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.84
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.83
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.83
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.83
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.82
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.82
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.82
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.82
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.82
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.82
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.82
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.82
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.81
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.81
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.81
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.81
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.81
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.81
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.81
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.81
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.81
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.81
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.8
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.8
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.8
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.8
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.8
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.8
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.8
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.8
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.8
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.8
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.8
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.8
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.8
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.8
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.8
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.8
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.79
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.79
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.79
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.79
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.79
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.79
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.79
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.79
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.79
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.79
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.79
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.79
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.79
2div_A	99	TRNA selenocysteine associated protein; structural	99.79
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.78
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.78
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.78
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.78
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.78
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.78
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.78
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.78
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.78
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.78
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.78
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.78
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.78
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.78
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.78
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.78
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.78
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.78
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.78
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.78
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.78
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.77
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.77
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.77
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.77
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.77
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.77
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.77
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.77
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.77
2div_A	99	TRNA selenocysteine associated protein; structural	99.77
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.77
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.77
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.77
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.77
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.77
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.77
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.77
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.77
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.77
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.77
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.77
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.77
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.77
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.77
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.77
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.76
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.76
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.76
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.76
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.76
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.76
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.76
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.76
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.76
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.76
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.76
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.76
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.76
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.76
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.76
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.76
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.76
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.76
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.76
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.76
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.76
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.76
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.75
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.75
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.75
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.75
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.75
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.75
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.75
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.75
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.75
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.75
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.75
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.75
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.75
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.75
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.75
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.75
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.75
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.75
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.75
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.74
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.74
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.74
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.74
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.74
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.74
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.74
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.74
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.74
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.74
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.74
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.74
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.74
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.74
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.74
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.74
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.74
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.74
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.74
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.74
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.74
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.74
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.74
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.59
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.73
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.73
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.73
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.73
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.73
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.73
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.73
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.73
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.73
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.73
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.73
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.73
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.73
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.73
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.73
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.73
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.73
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.73
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.73
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.73
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.73
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.72
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.72
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.72
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.72
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.72
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.72
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.72
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.72
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.72
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.72
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.72
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.72
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.72
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.72
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.72
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.72
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.71
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.71
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.71
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.71
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.71
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.71
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.71
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.71
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.71
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.7
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.7
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.7
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.7
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.7
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.7
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.7
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.7
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.7
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.7
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.7
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.7
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.7
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.69
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.69
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.69
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.69
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.69
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.69
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.69
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.69
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.69
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.69
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.69
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.69
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.69
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.69
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.69
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.69
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.69
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.69
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.68
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.68
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.68
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.68
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.68
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.68
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.68
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.68
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.68
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.68
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.67
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.67
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.67
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.67
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.67
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.67
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.67
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.67
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.67
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.67
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.66
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.47
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.66
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.66
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.65
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.65
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.65
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.65
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.65
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.65
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.65
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.65
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.65
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.65
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.65
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.64
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.64
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.64
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.64
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.64
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.64
1x5p_A	97	Negative elongation factor E; structure genomics,	99.64
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.64
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.64
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.63
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.63
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.62
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.62
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.62
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.62
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.62
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.62
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.62
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.62
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.62
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.62
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.61
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.61
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.61
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.61
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.61
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.61
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.61
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.61
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.61
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.6
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.6
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.6
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.6
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.6
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.59
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.59
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.59
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.59
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.58
1x5p_A	97	Negative elongation factor E; structure genomics,	99.58
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.58
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.57
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.57
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.57
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.57
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.57
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.56
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.56
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.56
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.55
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.54
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.54
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.53
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.5
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.5
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.49
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.47
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.47
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.46
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.46
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.46
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.46
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.43
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.42
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.41
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.4
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.38
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.26
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.26
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.26
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.19
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.11
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.09
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.07
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.01
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.0
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.99
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.72
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.71
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.57
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.88
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.8
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.55
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.42
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.37
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.35
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.17
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.0
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.95
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.93
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.9
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.9
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.65
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.0
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.71
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	94.47
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	94.2
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	93.88
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	93.66
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	81.78
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	80.99

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=100.00  E-value=8.4e-36  Score=229.30  Aligned_cols=168  Identities=18%  Similarity=0.287  Sum_probs=144.3

Q ss_pred             CCCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeE
Q psy1680           5 QKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQ   83 (227)
Q Consensus         5 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~   83 (227)
                      ..+....+.++|||+|||+++|+++|+++|++| .|..|.|++++.+++++|||||+|.+.++|.+||++++ ..+.|+.
T Consensus         5 ~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~-~~~~g~~   83 (196)
T 1l3k_A            5 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP-HKVDGRV   83 (196)
T ss_dssp             ---CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCS-CEETTEE
T ss_pred             cCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCC-CEECCEE
Confidence            445566778999999999999999999999999 99999999999999999999999999999999999988 9999999


Q ss_pred             eEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccC
Q psy1680          84 VRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNN  163 (227)
Q Consensus        84 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl  163 (227)
                      |.|.++.++......                                                   ....+..+|||+||
T Consensus        84 l~v~~~~~~~~~~~~---------------------------------------------------~~~~~~~~l~V~nL  112 (196)
T 1l3k_A           84 VEPKRAVSREDSQRP---------------------------------------------------GAHLTVKKIFVGGI  112 (196)
T ss_dssp             CEEEECCC--------------------------------------------------------------CCSEEEEECC
T ss_pred             eeeecccCccccccc---------------------------------------------------ccCCCcceEEEeCC
Confidence            999998765432110                                                   00124578999999


Q ss_pred             CCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         164 GPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       164 ~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      |..+  ++++|+++|++||.|..|.|++++.+|.++|||||+|.+.++|.+|++. +|..|+||
T Consensus       113 p~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~  173 (196)
T 1l3k_A          113 KEDT--EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGH  173 (196)
T ss_dssp             TTTC--CHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTE
T ss_pred             CCCC--CHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCE
Confidence            7655  7999999999999999999999999999999999999999999999987 68898885

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=3.3e-36  Score=235.06  Aligned_cols=160  Identities=21%  Similarity=0.278  Sum_probs=140.4

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      .+..+.++|||+|||+++|+++|+++|++| .|..|.|++++.+++++|||||+|.+.++|.+||+ +++ ..+.|+.|+
T Consensus        10 ~p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~-~~~~g~~i~   88 (213)
T 4f02_A           10 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNF-DVIKGKPVR   88 (213)
T ss_dssp             -----CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT-CEETTEECE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhh-hhcCCcccc
Confidence            345677899999999999999999999999 99999999999999999999999999999999999 999 999999999


Q ss_pred             EEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCC
Q psy1680          86 LDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGP  165 (227)
Q Consensus        86 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~  165 (227)
                      +.++........                                                       ....+|||+|||.
T Consensus        89 ~~~~~~~~~~~~-------------------------------------------------------~~~~~l~v~nl~~  113 (213)
T 4f02_A           89 IMWSQRDPSLRK-------------------------------------------------------SGVGNIFIKNLDK  113 (213)
T ss_dssp             EEECCCCTHHHH-------------------------------------------------------HCTTEEEEESCCT
T ss_pred             cccccccccccc-------------------------------------------------------cccccceECCccc
Confidence            998765432110                                                       1245799999976


Q ss_pred             CCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         166 NRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       166 ~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+  ++++|+++|++||.|.+|+|++|.  +.++|||||+|.+.++|.+|++.|||..|+||
T Consensus       114 ~~--t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~  171 (213)
T 4f02_A          114 SI--DNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDR  171 (213)
T ss_dssp             TC--CHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             cc--HHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCE
Confidence            55  799999999999999999999985  56899999999999999999999999999986

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=100.00  E-value=2.2e-35  Score=221.08  Aligned_cols=156  Identities=16%  Similarity=0.281  Sum_probs=143.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      +.++|||+|||+++++++|+++|++| .|..+.+++++.+++++|||||+|.+.++|.+|++ +++ ..+.|+.|.|.++
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~-~~~~g~~l~v~~~   79 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNG-LRLQTKTIKVSYA   79 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT-CEETTEECEEEEC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCC-CccCCceEEEEec
Confidence            36899999999999999999999999 99999999999899999999999999999999999 999 9999999999998


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCC
Q psy1680          90 DGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSN  169 (227)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~  169 (227)
                      .+....                                                         ....+|||+|||...  
T Consensus        80 ~~~~~~---------------------------------------------------------~~~~~l~v~nl~~~~--  100 (167)
T 1fxl_A           80 RPSSAS---------------------------------------------------------IRDANLYVSGLPKTM--  100 (167)
T ss_dssp             CCCCGG---------------------------------------------------------GTTCEEEEESCCTTC--
T ss_pred             CCCccc---------------------------------------------------------CCCCcEEECCCCCcC--
Confidence            754321                                                         134579999997655  


Q ss_pred             ChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         170 SMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       170 ~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++++|+++|++||.|..+++++++.+|.++|||||+|.+.++|.+|++.|||..|+||
T Consensus       101 t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  158 (167)
T 1fxl_A          101 TQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA  158 (167)
T ss_dssp             CHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             CHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCC
Confidence            7899999999999999999999998999999999999999999999999999999985

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=100.00  E-value=3.3e-35  Score=220.53  Aligned_cols=155  Identities=18%  Similarity=0.310  Sum_probs=143.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      ++++|||+|||+++++++|+++|++| .|..+.+++++.+++++|||||+|.+.++|.+|++ +++ ..+.|+.|.|.++
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~-~~~~g~~l~v~~~   80 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNG-ITVRNKRLKVSYA   80 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTT-CEETTEECEEEEC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCC-CEeCCcEEEEEec
Confidence            57899999999999999999999999 99999999999999999999999999999999998 999 9999999999998


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCC
Q psy1680          90 DGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSN  169 (227)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~  169 (227)
                      .++...                                                         .+..+|||+|||...  
T Consensus        81 ~~~~~~---------------------------------------------------------~~~~~l~v~nl~~~~--  101 (168)
T 1b7f_A           81 RPGGES---------------------------------------------------------IKDTNLYVTNLPRTI--  101 (168)
T ss_dssp             CCCSST---------------------------------------------------------TTTCEEEEESCCTTC--
T ss_pred             CCCccc---------------------------------------------------------CCCCCEEEeCCCCCC--
Confidence            754321                                                         235689999997655  


Q ss_pred             ChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         170 SMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       170 ~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      ++++|+++|++||.|..+.+++++.++.++|+|||+|.+.++|.+|++.|||..|+|
T Consensus       102 t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  158 (168)
T 1b7f_A          102 TDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEG  158 (168)
T ss_dssp             CHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTT
T ss_pred             CHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecC
Confidence            789999999999999999999999899999999999999999999999999999987

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=5.6e-35  Score=218.65  Aligned_cols=155  Identities=17%  Similarity=0.297  Sum_probs=140.4

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecCC
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~~   91 (227)
                      ++|||+|||.++|+++|+++|++| .|..+.++.++. ++++|||||+|.+.++|.+|++ +++ ..+.|+.|.|.++.+
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~~-~~~~g~~i~v~~~~~   78 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNG-KQIENNIVKINWAFQ   78 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC--CCEEEEEEEESSHHHHHHHHHHHTT-CEETTEECEEEECCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC-CCCCCEEEEEeCCHHHHHHHHHHcCC-CccCCCeeEEEEcCC
Confidence            589999999999999999999999 999999999865 7789999999999999999997 999 999999999999865


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCCCh
Q psy1680          92 KRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSM  171 (227)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~  171 (227)
                      ......                                                       .+..+|||+|||...  ++
T Consensus        79 ~~~~~~-------------------------------------------------------~~~~~l~v~nl~~~~--t~  101 (166)
T 3md3_A           79 SQQSSS-------------------------------------------------------DDTFNLFVGDLNVNV--DD  101 (166)
T ss_dssp             CCCCCC-------------------------------------------------------TTCEEEEEESCCTTC--CH
T ss_pred             CCCCCC-------------------------------------------------------CCCceEEECCCCCCC--CH
Confidence            443111                                                       245689999997655  78


Q ss_pred             hhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         172 NDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       172 ~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++|+++|++||.|.++.+++++.+|.++|+|||+|.+.++|.+|++.|||..|+||
T Consensus       102 ~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  157 (166)
T 3md3_A          102 ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGR  157 (166)
T ss_dssp             HHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             HHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCc
Confidence            99999999999999999999999999999999999999999999999999999985

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=100.00  E-value=8.9e-34  Score=221.16  Aligned_cols=168  Identities=15%  Similarity=0.201  Sum_probs=141.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      .+.++|||+|||.++|+++|+++|++| .|..|.|++++.+++++|||||+|.+.++|.+||+ +++ ..+.|+.|.|.+
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~-~~~~g~~l~v~~  104 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNS-VMLGGRNIKVGR  104 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSS-CCCC-CCCEEEC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccC-CeeCCeeEEEec
Confidence            345899999999999999999999999 99999999998899999999999999999999999 999 999999999988


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCC
Q psy1680          89 ADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRS  168 (227)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~  168 (227)
                      +...........                                              ..........+|||+|||..+ 
T Consensus       105 ~~~~~~~~~~~~----------------------------------------------~~~~~~~~~~~l~v~nlp~~~-  137 (216)
T 2qfj_A          105 PSNIGQAQPIID----------------------------------------------QLAEEARAFNRIYVASVHQDL-  137 (216)
T ss_dssp             CSCCGGGHHHHH----------------------------------------------HHHHHHTTSCEEEEECCCTTC-
T ss_pred             CCCccccchhhh----------------------------------------------hhhcccCCCcEEEEeCCCCcC-
Confidence            764432100000                                              000000245689999997655 


Q ss_pred             CChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         169 NSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       169 ~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                       ++++|+++|++||.|..|+|++++.+|.++|||||+|.+.++|.+|++.|||..|+||
T Consensus       138 -t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~  195 (216)
T 2qfj_A          138 -SDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQ  195 (216)
T ss_dssp             -CHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSS
T ss_pred             -CHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCc
Confidence             7999999999999999999999999999999999999999999999999999999986

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=100.00  E-value=6.3e-35  Score=218.91  Aligned_cols=154  Identities=18%  Similarity=0.337  Sum_probs=139.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEecC
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~~   90 (227)
                      ++++|||+|||+++|+++|+++|++| .|..+.+++++.+++++|||||+|.+.++|.+||+ ++ ..++|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~-~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK-TQ-HILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH-SC-CEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh-cc-cccCCeEccccccc
Confidence            57899999999999999999999999 99999999999999999999999999999999998 46 78999999998876


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCCC
Q psy1680          91 GKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNS  170 (227)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~  170 (227)
                      ++...                                                         .+..+|||+|||...  +
T Consensus        80 ~~~~~---------------------------------------------------------~~~~~l~V~nlp~~~--t  100 (167)
T 2cjk_A           80 PRDEQ---------------------------------------------------------DKTGKIFVGGIGPDV--R  100 (167)
T ss_dssp             CHHHH---------------------------------------------------------HHCEEEEEEEECTTC--C
T ss_pred             chhhc---------------------------------------------------------cCCCeEEECCCCCCC--C
Confidence            43221                                                         124579999997655  7


Q ss_pred             hhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         171 MNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       171 ~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +++|+++|++||.|.+|.+++++.+|.++|||||+|.+.++|.+|++ ++|..|+||
T Consensus       101 ~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~  156 (167)
T 2cjk_A          101 PKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDR  156 (167)
T ss_dssp             HHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSS
T ss_pred             HHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCe
Confidence            89999999999999999999999999999999999999999999998 899999986

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=100.00  E-value=2.5e-33  Score=211.51  Aligned_cols=154  Identities=18%  Similarity=0.298  Sum_probs=135.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCC--CeecEEEEEeCCHHHHHHHHH-hCCCceeC---CeEe
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETD--RFKGFCYVEFVDVENLRQALL-KDGRITVD---GLQV   84 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~--~~~g~afv~f~~~~~a~~al~-~~~~~~~~---g~~l   84 (227)
                      ++++|||+|||+++|+++|+++|++| .|..+.|++++.++  +++|||||+|.+.++|.+|++ +++ ..+.   ++.+
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~-~~~~~~~~~~~   80 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHN-MKVLPGMHHPI   80 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTT-TCCCTTCSSCC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcC-cEEccCCccce
Confidence            57899999999999999999999999 99999999998877  899999999999999999998 999 7765   5677


Q ss_pred             EEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCC
Q psy1680          85 RLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNG  164 (227)
Q Consensus        85 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~  164 (227)
                      .+.++.+.....                                                        .+..+|||+|||
T Consensus        81 ~~~~~~~~~~~~--------------------------------------------------------~~~~~l~v~nl~  104 (175)
T 3nmr_A           81 QMKPADSEKNNA--------------------------------------------------------VEDRKLFIGMIS  104 (175)
T ss_dssp             EEEECGGGCCSC--------------------------------------------------------GGGSEEEEESCC
T ss_pred             EEcccccccccc--------------------------------------------------------CCCCeEEEcCCC
Confidence            777765433211                                                        245689999997


Q ss_pred             CCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         165 PNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       165 ~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      ...  ++++|+++|++||.|.+|+|++++ +|.++|||||+|.+.++|.+|++.|||..+.
T Consensus       105 ~~~--t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~  162 (175)
T 3nmr_A          105 KKC--TENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTM  162 (175)
T ss_dssp             TTC--CHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCC
T ss_pred             CcC--CHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCccc
Confidence            655  789999999999999999999996 4999999999999999999999999998775

>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=100.00  E-value=8.2e-33  Score=214.40  Aligned_cols=187  Identities=12%  Similarity=0.046  Sum_probs=137.8

Q ss_pred             CCCceEEEcCCC-CCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          11 EPPYTAFVGNLP-NGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        11 ~~~~~l~V~nLp-~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      .++++|||+||| ..+++++|+++|++| .|..|+|++++     +|||||+|.+.++|+.||+ ||| ..+.|+.|.|.
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng-~~~~g~~l~v~   75 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNN-NFMFGQKMNVC   75 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTT-CEETTEECEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCC-CEECCceEEEE
Confidence            457899999999 899999999999999 99999998752     7999999999999999999 999 99999999999


Q ss_pred             ecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCC
Q psy1680          88 IADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNR  167 (227)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~  167 (227)
                      ++..+..........    ..  ++.....+.....   .        +.....   ........+++.+|||+|||+..
T Consensus        76 ~s~~~~~~p~~~~~~----~~--~~~~~~~~~~~~~---~--------r~~~~~---~~~~~~~~~p~~~l~v~NLp~~~  135 (205)
T 3tyt_A           76 VSKQPAIMPGQSYGL----ED--GSCSYKDFSESRN---N--------RFSTPE---QAAKNRIQHPSNVLHFFNAPLEV  135 (205)
T ss_dssp             ECSCSCCCCCSCCBC----TT--SCBSEEECTTCTT---C--------SCSSHH---HHTTSCCCCCCSEEEEEEECTTC
T ss_pred             EccCCccCCCccccc----cc--CCccccccCCCcc---c--------cccCcc---cccccccCCCcceEEEeCCCCCC
Confidence            987544311100000    00  0000000000000   0        000000   00000112567899999997665


Q ss_pred             CCChhhHHhhhccccce--EEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         168 SNSMNDHGLMVTEVTTL--VSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       168 ~~~~~~l~~~f~~~g~i--~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                        ++++|+++|++||.|  .+|+++.+.  +.++|+|||+|.+.++|.+||+.|||..|+|+
T Consensus       136 --t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~  193 (205)
T 3tyt_A          136 --TEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNP  193 (205)
T ss_dssp             --CHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCS
T ss_pred             --CHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCC
Confidence              789999999999998  899998875  56679999999999999999999999999885

>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=100.00  E-value=8.3e-33  Score=208.31  Aligned_cols=150  Identities=25%  Similarity=0.363  Sum_probs=131.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC------------CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCcee
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ------------KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV   79 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~------------~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~   79 (227)
                      +.++|||+|||+++|+++|+++|++|            .|..+.+.      +++|||||+|.+.++|.+||.+++ ..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~~~~~-~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAMAFDG-IIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHGGGTT-CEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHHHhCC-cEe
Confidence            57899999999999999999999988            34444443      348999999999999999999999 999


Q ss_pred             CCeEeEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcce
Q psy1680          80 DGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGF  159 (227)
Q Consensus        80 ~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  159 (227)
                      .|+.|.|.++.+....                                                         ....+||
T Consensus        76 ~g~~i~v~~~~~~~~~---------------------------------------------------------~~~~~l~   98 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQPL---------------------------------------------------------PGAHKLF   98 (172)
T ss_dssp             TTEECEEECCSSCCCC---------------------------------------------------------TTTTCEE
T ss_pred             cCceeeecCCcccCCC---------------------------------------------------------CCCCEEE
Confidence            9999999986543221                                                         1256899


Q ss_pred             eccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         160 RNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       160 v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      |+|||...  ++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        99 v~nlp~~~--t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  164 (172)
T 2g4b_A           99 IGGLPNYL--NDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK  164 (172)
T ss_dssp             EECCCTTC--CHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTE
T ss_pred             EEcCCCcC--CHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCe
Confidence            99997655  7899999999999999999999998999999999999999999999999999999986

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=100.00  E-value=2.2e-33  Score=216.12  Aligned_cols=177  Identities=23%  Similarity=0.273  Sum_probs=135.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEE-----EeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVR-----LVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQV   84 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~-----i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l   84 (227)
                      ..+++|||+|||+++|+++|+++|++| .|..+.     .+.+...++++|||||+|.+.++|.+||.+++ ..+.|+.|
T Consensus         2 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al~l~g-~~~~g~~i   80 (198)
T 2yh0_A            2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDG-IIFQGQSL   80 (198)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTTTEEEEEESCSHHHHHHGGGTT-EEETTEEE
T ss_pred             CceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCCCEEEEEeCCHHHHHHHHHhcC-CEEcCceE
Confidence            357899999999999999999999988 433211     11111224558999999999999999999999 99999999


Q ss_pred             EEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCC
Q psy1680          85 RLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNG  164 (227)
Q Consensus        85 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~  164 (227)
                      .|.++.++.........              ... ..         +             .........+..+|||+|||
T Consensus        81 ~v~~~~~~~~~~~~~~~--------------~~~-~~---------~-------------~~~~~~~~~~~~~l~v~nl~  123 (198)
T 2yh0_A           81 KIRRPHDYQPLPGMSEN--------------PSV-YV---------P-------------GVVSTVVPDSAHKLFIGGLP  123 (198)
T ss_dssp             EEECCCCCCCCCCSSSC--------------SSC-CC---------T-------------TSSCCCSSCCCCEEEEECCC
T ss_pred             EEeCCCCCCCCCCCcCC--------------CcC-CC---------C-------------CCccCCCCCCCCEEEEeCCC
Confidence            99998765432210000              000 00         0             00001112456899999997


Q ss_pred             CCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         165 PNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       165 ~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...  ++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|.+|++.|||..|+||
T Consensus       124 ~~~--~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~  184 (198)
T 2yh0_A          124 NYL--NDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK  184 (198)
T ss_dssp             TTC--CHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTE
T ss_pred             CCC--CHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            655  7899999999999999999999998999999999999999999999999999999985

>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=100.00  E-value=3.3e-33  Score=211.24  Aligned_cols=156  Identities=21%  Similarity=0.326  Sum_probs=134.9

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRL   86 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v   86 (227)
                      .+..+.++|||+|||.++|+++|+++|++| .+.. .++.+..+++++|||||+|.+.++|.+||++++ ..+.|+.|.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g-~~~~g~~l~v   85 (175)
T 1fje_B            8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTG-LKVFGNEIKL   85 (175)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGG-EEETTEEEEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHhcCC-CEeCCeEEEE
Confidence            356778999999999999999999999999 7655 444555678889999999999999999999999 9999999999


Q ss_pred             EecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCC
Q psy1680          87 DIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPN  166 (227)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~  166 (227)
                      .++.++.....                                                       .+..+|||+|||..
T Consensus        86 ~~~~~~~~~~~-------------------------------------------------------~~~~~l~v~nlp~~  110 (175)
T 1fje_B           86 EKPKGRDSKKV-------------------------------------------------------RAARTLLAKNLSFN  110 (175)
T ss_dssp             ECCCCSSCSTT-------------------------------------------------------GGGGEEEEESCCSS
T ss_pred             ecCCCcccccc-------------------------------------------------------ccCCEEEEeCCCCC
Confidence            99876543111                                                       24668999999765


Q ss_pred             CCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         167 RSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       167 ~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .  ++++|+++|++||.|..+     ..++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus       111 ~--t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  164 (175)
T 1fje_B          111 I--TEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGR  164 (175)
T ss_dssp             C--CHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTE
T ss_pred             C--CHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCe
Confidence            5  789999999999988766     46789999999999999999999999999999986

>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=99.98  E-value=1.2e-31  Score=217.67  Aligned_cols=161  Identities=17%  Similarity=0.191  Sum_probs=144.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ..+.++|||+|||..+++++|+++|++| .|..+.++.++.++.++|||||+|.+.++|.+|++ +++ ..++|+.|.|.
T Consensus        92 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~-~~~~g~~i~v~  170 (284)
T 3smz_A           92 QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG-KPLGPRTLYVH  170 (284)
T ss_dssp             CCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT-CEETTEECEEE
T ss_pred             cCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCC-CEeCCcEEEEE
Confidence            3456899999999999999999999999 99999999999999999999999999999999997 999 99999999999


Q ss_pred             ecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCC
Q psy1680          88 IADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNR  167 (227)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~  167 (227)
                      ++.++.....                                                      ..+..+|||+|||..+
T Consensus       171 ~a~~~~~~~~------------------------------------------------------~~~~~~l~v~nlp~~~  196 (284)
T 3smz_A          171 WTDAGQLTPA------------------------------------------------------LLHSRCLCVDRLPPGF  196 (284)
T ss_dssp             ECCGGGCCTT------------------------------------------------------TTSCSEEEEECCCTTC
T ss_pred             ECCCCCCCcc------------------------------------------------------cCCccEEEEecCCccc
Confidence            9876443111                                                      0245689999997653


Q ss_pred             CCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         168 SNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       168 ~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                       +++++|+++|++||.|.+|.|++++ +|.++|+|||+|.+.++|.+|++.|||..|+||
T Consensus       197 -~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  254 (284)
T 3smz_A          197 -NDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGS  254 (284)
T ss_dssp             -CCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             -CCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCe
Confidence             2689999999999999999999996 699999999999999999999999999999985

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.97  E-value=4.7e-30  Score=208.14  Aligned_cols=208  Identities=16%  Similarity=0.199  Sum_probs=140.8

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHH----hcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVE----RFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG   81 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~----~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g   81 (227)
                      .+..++++|||+|||.++|+++|+    ++|++| .|..|.|++   +++++|||||+|.+.++|.+||+ +++ ..|.|
T Consensus         4 ~~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g   79 (282)
T 3pgw_A            4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQG-FPFYD   79 (282)
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcC-CeeCC
Confidence            356778999999999999999976    899999 999999875   57889999999999999999998 999 99999


Q ss_pred             eEeEEEecCCCCCC---CCCCCCCCCC-----------------------CCCCCCCCCCC-------------------
Q psy1680          82 LQVRLDIADGKRND---NKGGFNNKQN-----------------------RGGGSGGMGGN-------------------  116 (227)
Q Consensus        82 ~~l~v~~~~~~~~~---~~~~~~~~~~-----------------------~~~~~~~~~~~-------------------  116 (227)
                      +.|.|.++..+...   ..+....+..                       ...+.+.....                   
T Consensus        80 ~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g  159 (282)
T 3pgw_A           80 KPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPG  159 (282)
T ss_pred             cEEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCC
Confidence            99999998765421   0000000000                       00000000000                   


Q ss_pred             --CCCCCCCCCCCCCCCCCC-----CCCCCCCCC---CCCCCCCCCCCCCcceeccCCCCCCCChhhHHhhhccccceEE
Q psy1680         117 --KYNQHQGGSFNRDNMRNN-----SRGGGASSG---GGFNDFSRGGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVS  186 (227)
Q Consensus       117 --~~~~~~~~~~~~~~~~~~-----~~~~~~~~~---~~~~~~~~~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~  186 (227)
                        .+....+... .......     .........   .........++..+|||+|||..+  ++++|+++|++||.|.+
T Consensus       160 ~~~~~~~p~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~--~~~~l~~~F~~~G~i~~  236 (282)
T 3pgw_A          160 QPPYMPPPGMIP-PPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEET--NELMLSMLFNQFPGFKE  236 (282)
T ss_pred             CCCCCCCCCCCC-CCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcC--CHHHHHHHHHhcCCeEE
Confidence              0000000000 0000000     000000000   000112234567889999997655  78999999999999999


Q ss_pred             EEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcccc-CC
Q psy1680         187 VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVD-GL  227 (227)
Q Consensus       187 v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~-gr  227 (227)
                      |+|++++     +|||||+|.+.++|.+|++.|||..|+ ||
T Consensus       237 v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~  273 (282)
T 3pgw_A          237 VRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNN  273 (282)
T ss_pred             EEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCC
Confidence            9999764     589999999999999999999999998 75

>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=99.97  E-value=2.3e-30  Score=204.11  Aligned_cols=184  Identities=15%  Similarity=0.130  Sum_probs=137.6

Q ss_pred             CCCCCceEEEcCCCC-CCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           9 PTEPPYTAFVGNLPN-GITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~-~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      +..++++|||+|||+ ++++++|+++|++| .|..|.|++++     +|||||+|.+.++|.+||+ +++ ..+.|+.|.
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g-~~~~g~~l~  103 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNG-HKLHGKPIR  103 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTT-CBCSSSBCE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCC-CeECCeEEE
Confidence            456789999999999 99999999999999 99999999875     7899999999999999998 999 999999999


Q ss_pred             EEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCC
Q psy1680          86 LDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGP  165 (227)
Q Consensus        86 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~  165 (227)
                      |.++.++.............        ....+.....   .+....           .........++..+|||+|||.
T Consensus       104 v~~a~~~~~~~~~~~~~~~~--------~~~~~~~~~~---~~~~~~-----------~~~~~~~~~~~~~~l~V~nlp~  161 (229)
T 2adc_A          104 ITLSKHQNVQLPREGQEDQG--------LTKDYGNSPL---HRFKKP-----------GSKNFQNIFPPSATLHLSNIPP  161 (229)
T ss_dssp             EECCSCCCCCCCCSSSSTTT--------TEEECTTCSS---CCCCST-----------TSGGGTTCCCSCSEEEEECCCT
T ss_pred             EEEecCccccCccccccccc--------cccccccCcc---cccCCc-----------cccccccCCCCCCEEEEeCCCc
Confidence            99998654321100000000        0000000000   000000           0000011124678999999976


Q ss_pred             CCCCChhhHHhhhcccc-ceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcccc-CC
Q psy1680         166 NRSNSMNDHGLMVTEVT-TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVD-GL  227 (227)
Q Consensus       166 ~~~~~~~~l~~~f~~~g-~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~-gr  227 (227)
                      ..  ++++|+++|++|| .|..|+|+++     ++|+|||+|.+.++|.+|++.|||..|+ ||
T Consensus       162 ~~--t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~  218 (229)
T 2adc_A          162 SV--SEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENH  218 (229)
T ss_dssp             TC--CHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             cC--CHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCC
Confidence            55  7899999999999 9999999764     2699999999999999999999999998 75

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.97  E-value=1.9e-30  Score=199.91  Aligned_cols=181  Identities=15%  Similarity=0.155  Sum_probs=135.8

Q ss_pred             CCceEEEcCCCC-CCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          12 PPYTAFVGNLPN-GITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        12 ~~~~l~V~nLp~-~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      .+++|||+|||+ ++++++|+++|++| .|..|.+++++     +|||||+|.+.++|.+|++ +++ ..+.|+.|.|.+
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~-~~~~g~~l~v~~   75 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNG-HKLHGKPIRITL   75 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTT-CCCSSCCCEEEE
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCC-CeecCeEEEEEE
Confidence            368999999999 99999999999999 99999998774     7899999999999999999 999 999999999999


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCC
Q psy1680          89 ADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRS  168 (227)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~  168 (227)
                      +.+..............        ....+....   ..+....           .........+++.+|||+|||... 
T Consensus        76 a~~~~~~~~~~~~~~~~--------~~~~~~~~~---~~r~~~~-----------~~~~~~~~~~~~~~l~v~nl~~~~-  132 (198)
T 1qm9_A           76 SKHQNVQLPREGQEDQG--------LTKDYGNSP---LHRFKKP-----------GSKNFQNIFPPSATLHLSNIPPSV-  132 (198)
T ss_dssp             CCCCSCCCSSSSSSSSS--------CEEESSCCC---TTSSSSC-----------CCCCCSCCCCCCCEEEECCCCTTC-
T ss_pred             ecCCCcCCCCcCCcccc--------ccccccCCc---hhhccCc-----------cccccccCCCCccEEEEeCCCCCC-
Confidence            88654322100000000        000000000   0000000           000011122567899999997655 


Q ss_pred             CChhhHHhhhcccc-ceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcccc-CC
Q psy1680         169 NSMNDHGLMVTEVT-TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVD-GL  227 (227)
Q Consensus       169 ~~~~~l~~~f~~~g-~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~-gr  227 (227)
                       ++++|+++|++|| .|.+|+|+++.     +|+|||+|.+.++|.+|++.|||..|+ ||
T Consensus       133 -~~~~l~~~f~~~G~~v~~v~i~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~  187 (198)
T 1qm9_A          133 -SEEDLKVLFSSNGGVVKGFKFFQKD-----RKMALIQMGSVEEAVQALIDLHNHDLGENH  187 (198)
T ss_dssp             -CHHHHHHHHHHTTSCCCEEEESSTT-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCC
T ss_pred             -CHHHHHHHHHHcCCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCC
Confidence             7899999999999 99999997753     699999999999999999999999998 75

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.97  E-value=1.2e-30  Score=212.56  Aligned_cols=163  Identities=14%  Similarity=0.196  Sum_probs=133.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC--CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~--~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ...++|||+|||..+++++|+++|++|  .|..+.++.++. +.++|||||+|.+.++|.+|+. +++ ..+.|+.|.|.
T Consensus       115 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~v~  192 (292)
T 2ghp_A          115 LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNG-LKIEGYTLVTK  192 (292)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTT-CEETTEECEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCC-CEeCCcEEEEE
Confidence            357899999999999999999999999  789999998865 7889999999999999999999 999 99999999999


Q ss_pred             ecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCC
Q psy1680          88 IADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNR  167 (227)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~  167 (227)
                      ++.++......                                                  .....+..+|||+|||...
T Consensus       193 ~a~~~~~~~~~--------------------------------------------------~~~~~~~~~l~v~nlp~~~  222 (292)
T 2ghp_A          193 VSNPLEKSKRT--------------------------------------------------DSATLEGREIMIRNLSTEL  222 (292)
T ss_dssp             ECCCC-----------------------------------------------------------CCTTTEEEEEEECTTT
T ss_pred             ECCCCcccccc--------------------------------------------------cccCCCCceEEEECCCccc
Confidence            98865542210                                                  0001356789999997661


Q ss_pred             CCChhhHHhhhccccceEEEEEeecCC-CCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         168 SNSMNDHGLMVTEVTTLVSVRLVKDKE-TDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       168 ~~~~~~l~~~f~~~g~i~~v~i~~d~~-t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                       .++++|+++|++||.|..|+|+++.. ||.++|||||+|.+.++|.+|+ .|||..|+||
T Consensus       223 -~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~  281 (292)
T 2ghp_A          223 -LDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNR  281 (292)
T ss_dssp             -CCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTE
T ss_pred             -CCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCc
Confidence             37899999999999999999999977 6999999999999999999999 9999999985

>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=99.97  E-value=5.5e-30  Score=205.73  Aligned_cols=139  Identities=25%  Similarity=0.325  Sum_probs=127.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ....++|||+|||+++|+++|+++|++| .|..|.|.++      +|||||+|.+.++|.+|+. +++ ..+.|+.|.|.
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g-~~i~g~~l~v~   91 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDG-TILKSRPLRIR   91 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTT-CEETTEECEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCC-cEECCceeEee
Confidence            4556899999999999999999999999 9999999654      7899999999999999999 999 99999999999


Q ss_pred             ecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCC
Q psy1680          88 IADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNR  167 (227)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~  167 (227)
                      ++.+                                                               +.+|||+|||..+
T Consensus        92 ~a~~---------------------------------------------------------------~~~l~v~nl~~~~  108 (261)
T 3sde_A           92 FATH---------------------------------------------------------------GAALTVKNLSPVV  108 (261)
T ss_dssp             ECCC---------------------------------------------------------------SSEEEEESCCTTC
T ss_pred             eccc---------------------------------------------------------------CCcccccCCCCCC
Confidence            9752                                                               3369999997655


Q ss_pred             CCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCC
Q psy1680         168 SNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR  221 (227)
Q Consensus       168 ~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g  221 (227)
                        ++++|+++|+.||.|..|.|++| .+|.++|||||+|.+.++|.+|++.||+
T Consensus       109 --t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~  159 (261)
T 3sde_A          109 --SNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGD  159 (261)
T ss_dssp             --CHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHH
T ss_pred             --CHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcC
Confidence              78999999999999999999999 5799999999999999999999999943

>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=99.97  E-value=1.1e-29  Score=206.16  Aligned_cols=145  Identities=15%  Similarity=0.207  Sum_probs=132.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      .+.++|||+|||.++|+++|+++|++|.|..+.+      ++++|||||+|.+.++|.+|++ +++ ..+.|+.|.|.++
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~Gi~~~~~------~~~~g~afV~f~~~~~A~~A~~~l~~-~~~~g~~i~v~~~   92 (284)
T 3smz_A           20 RNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINAFHQ-SRLRERELSVQLQ   92 (284)
T ss_dssp             HCCCEEEEECCCTTCCHHHHHHHTTTSCEEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTT-CEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCEEEEE------ecCCCEEEEEeCCHHHHHHHHHHcCC-CeeCCeEEEEEec
Confidence            4578999999999999999999999998777777      4458999999999999999998 999 9999999999874


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCC
Q psy1680          90 DGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSN  169 (227)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~  169 (227)
                      .                                                               +..+|||+|||...  
T Consensus        93 ~---------------------------------------------------------------~~~~l~v~nlp~~~--  107 (284)
T 3smz_A           93 P---------------------------------------------------------------TDALLCVANLPPSL--  107 (284)
T ss_dssp             C---------------------------------------------------------------CSCEEEEESCCTTC--
T ss_pred             C---------------------------------------------------------------CCCEEEEcCCCCcC--
Confidence            2                                                               23479999997665  


Q ss_pred             ChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         170 SMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       170 ~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++++|+++|++||.|.+|.+++++.+|.++|||||+|.+.++|.+|++.|+|..|+||
T Consensus       108 t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~  165 (284)
T 3smz_A          108 TQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR  165 (284)
T ss_dssp             CHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            7899999999999999999999999999999999999999999999999999999885

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.96  E-value=1.3e-29  Score=206.44  Aligned_cols=149  Identities=17%  Similarity=0.259  Sum_probs=127.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLD   87 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~   87 (227)
                      ...+.++|||+|||+++|+++|+++|+.| .|..|.|+.++.+  ++|||||+|.+.++|.+||++++ ..+.|+.|.|.
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~~~~-~~~~g~~i~v~  113 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAITKTH-KVVGQNEIIVS  113 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHTTTT-CEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHHhCC-cEeCCcEEEEE
Confidence            35667999999999999999999999999 9999999998643  47999999999999999999999 99999999999


Q ss_pred             ecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCC
Q psy1680          88 IADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNR  167 (227)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~  167 (227)
                      ++.                                                                ..+|||+|||...
T Consensus       114 ~~~----------------------------------------------------------------~~~l~v~nlp~~~  129 (292)
T 2ghp_A          114 HLT----------------------------------------------------------------ECTLWMTNFPPSY  129 (292)
T ss_dssp             ECC----------------------------------------------------------------SCEEEEECCCTTC
T ss_pred             ECC----------------------------------------------------------------CCEEEEECCCCCC
Confidence            851                                                                3479999997665


Q ss_pred             CCChhhHHhhhcccc-ceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         168 SNSMNDHGLMVTEVT-TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       168 ~~~~~~l~~~f~~~g-~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                        ++++|+++|+.|| .|..|.|++++. +.++|||||+|.+.++|.+|++.|+|..|+|+
T Consensus       130 --t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~  187 (292)
T 2ghp_A          130 --TQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGY  187 (292)
T ss_dssp             --CHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             --CHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence              7899999999999 999999999976 88999999999999999999999999999885

>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=99.89  E-value=5.9e-23  Score=152.59  Aligned_cols=138  Identities=16%  Similarity=0.113  Sum_probs=100.0

Q ss_pred             EEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy1680          41 SVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYN  119 (227)
Q Consensus        41 ~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  119 (227)
                      .+.|+.+..  +++|||||+|.+.++|++|++ +++ ....+..+.+...............                  
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~------------------   60 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAATAEKVFKQYAN-DNGVDGEWTYDDATKTFTVTEGSHH------------------   60 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHH-HHTCCCEEEEETTTTEEEEECCCCC------------------
T ss_pred             cEEEEecCc--cccchhHHHHHHHHhHHHHHHhhcc-cCCCCCcccccCccccccccccccc------------------
Confidence            456666643  689999999999999999997 665 3322222222221111000000000                  


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCccc
Q psy1680         120 QHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFK  199 (227)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~  199 (227)
                                                ........+..+|||+|||+..  ++++|+++|+.||.|.+|+|++|+.+|.++
T Consensus        61 --------------------------~~~~~~~~~~~~l~v~nl~~~~--~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~  112 (158)
T 2kn4_A           61 --------------------------HHHHMDVEGMTSLKVDNLTYRT--SPDTLRRVFEKYGRVGDVYIPRDRYTKESR  112 (158)
T ss_dssp             --------------------------SSCCCCCCBCCEEEEESCCTTC--CHHHHHHHHHHHSCEEEEECCCCSSCTTSC
T ss_pred             --------------------------cccccCCCCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEeecCCCCccc
Confidence                                      0000011346789999997665  799999999999999999999999999999


Q ss_pred             ceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         200 GFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       200 g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      |||||+|.+.++|.+|++.|||..|+||
T Consensus       113 g~afV~f~~~~~a~~A~~~l~g~~~~g~  140 (158)
T 2kn4_A          113 GFAFVRFHDKRDAEDAMDAMDGAVLDGR  140 (158)
T ss_dssp             CEEEEEESBHHHHHHHHHHSTTEESSSS
T ss_pred             eEEEEEECCHHHHHHHHHHhCCCEECCe
Confidence            9999999999999999999999999986

>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=99.86  E-value=1e-21  Score=138.34  Aligned_cols=80  Identities=20%  Similarity=0.343  Sum_probs=73.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      .+.+|||+|||+++|+++|+++|++| .|..|.|++++  +.++|||||+|.+.++|++||+ +++ ..|+|+.|.|.++
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~-~~~~g~~i~V~~a   80 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNG-MLLNDRKVFVGRF   80 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTT-CEETTEECEEEES
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCC-CEECCEEEEEEEC
Confidence            35789999999999999999999999 99999999985  4579999999999999999998 999 9999999999998


Q ss_pred             CCCCC
Q psy1680          90 DGKRN   94 (227)
Q Consensus        90 ~~~~~   94 (227)
                      .++..
T Consensus        81 ~~~~~   85 (115)
T 4f25_A           81 KSRKE   85 (115)
T ss_dssp             SCCCC
T ss_pred             CCccc
Confidence            86554

>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=99.86  E-value=2.9e-21  Score=132.29  Aligned_cols=80  Identities=20%  Similarity=0.412  Sum_probs=76.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      ...++|||+|||+++|+++|+++|++| .|..+.|++++.+++++|||||+|.+.++|.+|++ +|+ ..|+|++|+|.+
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng-~~~~gr~l~V~~   95 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNG-LRLQSKTIKVSY   95 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTT-CEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCC-CEECCEEEEEEE
Confidence            446899999999999999999999999 99999999999999999999999999999999998 999 999999999999


Q ss_pred             cCC
Q psy1680          89 ADG   91 (227)
Q Consensus        89 ~~~   91 (227)
                      ++|
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            875

>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=99.85  E-value=4.7e-21  Score=141.10  Aligned_cols=127  Identities=20%  Similarity=0.175  Sum_probs=99.9

Q ss_pred             CCeecEEEEEeCCHHHHHHHHH-h-CCCceeCCeEeEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy1680          51 DRFKGFCYVEFVDVENLRQALL-K-DGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNR  128 (227)
Q Consensus        51 ~~~~g~afv~f~~~~~a~~al~-~-~~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (227)
                      ...+|+++|+|.+.++|++|++ + ++ ..++| .+.+.++..+..........            ..            
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng-~~~~G-~~~~~~a~~~~~~~~~~~~~------------~~------------   63 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYAND-NGVDG-EWTYDDATKTFTVTEGSHHH------------HH------------   63 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHH-HTCCC-EEEEETTTTEEEEECSSSSC------------CC------------
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcC-CCCCC-ceecccccCccccccccccc------------cc------------
Confidence            4668999999999999999998 8 99 99999 99999876533211000000            00            


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcC
Q psy1680         129 DNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVD  208 (227)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~  208 (227)
                                       ........+..+|||+|||+..  ++++|+++|++||.|.+|+|+++     ++|||||+|.+
T Consensus        64 -----------------~~~~~~~~~~~~l~V~nl~~~~--t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~  119 (150)
T 2i2y_A           64 -----------------HMHRDSCPLDCKVYVGNLGNNG--NKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFED  119 (150)
T ss_dssp             -----------------CSCSSSSTTSCEEEEESCCSCC--SCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESS
T ss_pred             -----------------cccccCCCCCCEEEEeCCCCCC--CHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECC
Confidence                             0001111456799999997665  78999999999999999999987     47999999999


Q ss_pred             HHHHHHHHHHcCCccccCC
Q psy1680         209 VENLRQALLKDGRITVDGL  227 (227)
Q Consensus       209 ~~~a~~Al~~l~g~~i~gr  227 (227)
                      .++|.+|++.|||..|+||
T Consensus       120 ~~~a~~A~~~l~g~~~~g~  138 (150)
T 2i2y_A          120 PRDAADAVRELDGRTLCGC  138 (150)
T ss_dssp             HHHHHHHHHHHSSSCSSSS
T ss_pred             HHHHHHHHHHcCCCEECCe
Confidence            9999999999999999986

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.84  E-value=5.9e-21  Score=130.72  Aligned_cols=72  Identities=15%  Similarity=0.280  Sum_probs=67.8

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+.+|||+|||+.+  ++++|+++|++||.|.+|+|++|+.+|.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        18 ~gt~lfV~nLp~~~--te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr   89 (99)
T 4fxv_A           18 QGTNLIVNYLPQNM--TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSK   89 (99)
T ss_dssp             CCSEEEEESCCTTC--CHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCEEEEeCCCCCC--CHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            45689999997665  7999999999999999999999999999999999999999999999999999999986

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.84  E-value=1.2e-19  Score=127.52  Aligned_cols=90  Identities=28%  Similarity=0.425  Sum_probs=83.1

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeE
Q psy1680           6 KTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQ   83 (227)
Q Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~   83 (227)
                      ...+..+.++|||+|||..+++++|+++|++| .|..|.|++++.++.++|||||+|.+.++|++||+ +++ ..|+|+.
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~   86 (115)
T 2dgo_A            8 QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG-QWLGGRQ   86 (115)
T ss_dssp             SCCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTT-CEETTEE
T ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCC-CEECCEE
Confidence            34456778999999999999999999999999 99999999998899999999999999999999998 999 9999999


Q ss_pred             eEEEecCCCCCCC
Q psy1680          84 VRLDIADGKRNDN   96 (227)
Q Consensus        84 l~v~~~~~~~~~~   96 (227)
                      |.|.++.++....
T Consensus        87 l~V~~a~~~~~~~   99 (115)
T 2dgo_A           87 IRTNWATRKPPAP   99 (115)
T ss_dssp             CEEEESSCCCCCS
T ss_pred             EEEEEccCCCCCC
Confidence            9999998876543

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.83  E-value=4.9e-20  Score=128.48  Aligned_cols=83  Identities=11%  Similarity=0.141  Sum_probs=78.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ..+.++|||+|||+++++++|+++|++| .|..|.|++|+.|++++|||||+|.+.++|++||+ +|+ ..+.|+.|.|.
T Consensus         3 ~~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng-~~~~gr~i~V~   81 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHL-TSVMGNIIHAQ   81 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT-CEETTEECEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCC-CEECCeEEEEE
Confidence            3567899999999999999999999999 99999999999999999999999999999999999 999 99999999999


Q ss_pred             ecCCCC
Q psy1680          88 IADGKR   93 (227)
Q Consensus        88 ~~~~~~   93 (227)
                      ++....
T Consensus        82 ~a~~~~   87 (110)
T 3s8s_A           82 LDIKGQ   87 (110)
T ss_dssp             ECSTTH
T ss_pred             ECCCCc
Confidence            987543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=2.1e-19  Score=123.88  Aligned_cols=88  Identities=25%  Similarity=0.371  Sum_probs=82.1

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      .....+.++|||+|||..+++++|+++|++| .|..|.|+.++.++.++|||||+|.+.++|.+||+ +++ ..|+|+.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~l   87 (103)
T 2cq0_A            9 NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG-FGYDHLIL   87 (103)
T ss_dssp             CCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTT-CEETTEEC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCC-CeeCCcEE
Confidence            3456778999999999999999999999999 99999999999999999999999999999999999 999 99999999


Q ss_pred             EEEecCCCCCC
Q psy1680          85 RLDIADGKRND   95 (227)
Q Consensus        85 ~v~~~~~~~~~   95 (227)
                      .|.++.++...
T Consensus        88 ~v~~a~~~~~~   98 (103)
T 2cq0_A           88 NVEWAKPSTNS   98 (103)
T ss_dssp             EEEESSCCCCS
T ss_pred             EEEECCCCCCC
Confidence            99999877653

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.83  E-value=1.5e-20  Score=131.08  Aligned_cols=73  Identities=12%  Similarity=-0.016  Sum_probs=68.8

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++..+|||+|||+.+  ++++|+++|++||.|.+|+|++|+.|++++|||||+|.+.++|.+|++.|||..|+||
T Consensus         4 ~p~~~lfV~nL~~~~--te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr   76 (110)
T 3s8s_A            4 IPLKEVTFARLNDNV--RETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGN   76 (110)
T ss_dssp             SCCCEEEEESCCTTC--CHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCcEEEEECCCCCC--CHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCe
Confidence            467899999997655  7999999999999999999999999999999999999999999999999999999986

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.82  E-value=2.4e-19  Score=123.55  Aligned_cols=90  Identities=54%  Similarity=0.993  Sum_probs=83.6

Q ss_pred             CCCCCCCCCceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEe
Q psy1680           5 QKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQV   84 (227)
Q Consensus         5 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l   84 (227)
                      ..+.+..+.++|||+|||.++++++|+++|++|.|..|.|++++.+++++|||||+|.+.++|.+||.+++ ..|.|+.|
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~gi~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g-~~~~g~~l   85 (103)
T 2dng_A            7 GKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDG-ALLGDRSL   85 (103)
T ss_dssp             CCCCCSSSCEEEEEESCCTTCCHHHHHHHTTTSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTT-CEETTEEC
T ss_pred             CCCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhCCceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCC-CeECCeEE
Confidence            45566788899999999999999999999999999999999999999999999999999999999999999 99999999


Q ss_pred             EEEecCCCCCC
Q psy1680          85 RLDIADGKRND   95 (227)
Q Consensus        85 ~v~~~~~~~~~   95 (227)
                      .|.++.++...
T Consensus        86 ~V~~a~~~~~~   96 (103)
T 2dng_A           86 RVDIAEGRKQD   96 (103)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEecCCCCC
Confidence            99999876653

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=1.5e-19  Score=122.70  Aligned_cols=85  Identities=27%  Similarity=0.440  Sum_probs=80.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ..++++|||+|||..+++++|+++|++| .|..+.|+.++.+++++|||||+|.+.++|.+||+ +++ ..+.|+.|+|.
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~V~   80 (95)
T 2dnz_A            2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNG-FELAGRPMRVG   80 (95)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTT-CCSSSSCCEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCC-CeeCCcEEEEE
Confidence            4578999999999999999999999999 99999999999999999999999999999999999 999 99999999999


Q ss_pred             ecCCCCCC
Q psy1680          88 IADGKRND   95 (227)
Q Consensus        88 ~~~~~~~~   95 (227)
                      ++.++...
T Consensus        81 ~a~~~~~~   88 (95)
T 2dnz_A           81 HVTERLDG   88 (95)
T ss_dssp             ESSCCCCC
T ss_pred             EcccccCC
Confidence            99877653

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=2.3e-19  Score=122.78  Aligned_cols=88  Identities=20%  Similarity=0.386  Sum_probs=82.0

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRL   86 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v   86 (227)
                      .+..+.++|||+|||..+++++|+++|++| .|..|.|+.++.+++++|||||+|.+.++|.+||++++ ..|+|+.|.|
T Consensus         5 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~-~~~~g~~l~V   83 (99)
T 2dgs_A            5 SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHF-HDIMGKKVEV   83 (99)
T ss_dssp             CCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCC-CBSSSCBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCC-CEECCeEEEE
Confidence            355778999999999999999999999999 99999999999999999999999999999999999999 9999999999


Q ss_pred             EecCCCCCCC
Q psy1680          87 DIADGKRNDN   96 (227)
Q Consensus        87 ~~~~~~~~~~   96 (227)
                      .++.++....
T Consensus        84 ~~a~~~~~~~   93 (99)
T 2dgs_A           84 KRAEPRDSKS   93 (99)
T ss_dssp             EECCCCCCCC
T ss_pred             EECCCCcccC
Confidence            9998876543

>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=99.82  E-value=1.8e-19  Score=119.12  Aligned_cols=80  Identities=20%  Similarity=0.403  Sum_probs=76.6

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecC
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~   90 (227)
                      +++|||+|||.++++++|+++|++| .|..+.+++++.+++++|||||+|.+.++|.+|++ +++ ..++|+.|+|.++.
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g-~~~~g~~l~v~~a~   79 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQG-QDLNGRPLRINWAA   79 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTT-CEETTEECEEEECC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcC-CeeCCcEEEEEecC
Confidence            4689999999999999999999999 99999999999999999999999999999999999 999 99999999999998


Q ss_pred             CCC
Q psy1680          91 GKR   93 (227)
Q Consensus        91 ~~~   93 (227)
                      +++
T Consensus        80 ~~~   82 (83)
T 3md1_A           80 KLE   82 (83)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            764

>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=99.82  E-value=1e-19  Score=121.42  Aligned_cols=83  Identities=29%  Similarity=0.474  Sum_probs=75.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      +..+.++|||+|||.++++++|+++|++| .|..+.++.++.+++++|||||+|.+.++|.+|++ +++ ..++|+.|.|
T Consensus         2 p~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~l~v   80 (87)
T 3bs9_A            2 PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG-QWLGGRQIRT   80 (87)
T ss_dssp             ----CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT-CEETTEECEE
T ss_pred             CCCCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCC-CEECCeEEEE
Confidence            34678999999999999999999999999 99999999999899999999999999999999999 999 9999999999


Q ss_pred             EecCCC
Q psy1680          87 DIADGK   92 (227)
Q Consensus        87 ~~~~~~   92 (227)
                      .++.++
T Consensus        81 ~~a~~k   86 (87)
T 3bs9_A           81 NWATRK   86 (87)
T ss_dssp             EEEC--
T ss_pred             EecCCC
Confidence            999765

>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=99.82  E-value=1.8e-19  Score=124.60  Aligned_cols=89  Identities=22%  Similarity=0.375  Sum_probs=82.7

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      +.+..+.++|||+|||..+++++|+++|++| .|..|.|+.++.+++++|||||+|.+.++|.+||+ +++ ..|.|+.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l   87 (105)
T 1x5u_A            9 ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDM-IKLYGKPI   87 (105)
T ss_dssp             CCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSS-CBCSSCBC
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCC-CeECCeEE
Confidence            3456778999999999999999999999999 99999999999899999999999999999999999 999 99999999


Q ss_pred             EEEecCCCCCCC
Q psy1680          85 RLDIADGKRNDN   96 (227)
Q Consensus        85 ~v~~~~~~~~~~   96 (227)
                      .|.++.++....
T Consensus        88 ~v~~a~~~~~~~   99 (105)
T 1x5u_A           88 RVNKASAHNKNL   99 (105)
T ss_dssp             EEEETTTTSCCC
T ss_pred             EEEECCCCCcCC
Confidence            999998876543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.82  E-value=1.4e-20  Score=126.94  Aligned_cols=81  Identities=21%  Similarity=0.432  Sum_probs=75.1

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC--CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-h-CCCceeCCeEeEEEe
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-K-DGRITVDGLQVRLDI   88 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~--~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~-~~~~~~~g~~l~v~~   88 (227)
                      +++|||+|||+++|+++|+++|++|  .|.+|.|++++.++.++|||||+|.+.++|.+||+ + ++ ..++|++|.|.+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~-~~~~gr~i~V~~   79 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHS-LNILGQKVSMHY   79 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTE-EEETTEEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCC-eEECCEEEEEEE
Confidence            5789999999999999999999999  58999999999999999999999999999999998 5 45 789999999999


Q ss_pred             cCCCCC
Q psy1680          89 ADGKRN   94 (227)
Q Consensus        89 ~~~~~~   94 (227)
                      +.++..
T Consensus        80 a~~~~~   85 (91)
T 2lxi_A           80 SDPKPK   85 (91)
T ss_dssp             CCSCCC
T ss_pred             cCCCCC
Confidence            987664

>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=99.82  E-value=1.8e-19  Score=125.75  Aligned_cols=90  Identities=22%  Similarity=0.356  Sum_probs=83.2

Q ss_pred             CCCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hC------CC
Q psy1680           5 QKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KD------GR   76 (227)
Q Consensus         5 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~------~~   76 (227)
                      ..+....+.++|||+|||+.+++++|+++|++| .|..|.|++++.++.++|||||+|.+.++|.+||+ ++      + 
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~-   85 (111)
T 1x4h_A            7 GLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGG-   85 (111)
T ss_dssp             CCCCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCC-
T ss_pred             CCCCcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCC-
Confidence            344566788999999999999999999999999 99999999999999999999999999999999999 99      9 


Q ss_pred             ceeCCeEeEEEecCCCCCC
Q psy1680          77 ITVDGLQVRLDIADGKRND   95 (227)
Q Consensus        77 ~~~~g~~l~v~~~~~~~~~   95 (227)
                      ..|+|+.|.|.++.++...
T Consensus        86 ~~~~g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           86 LKLDGRQLKVDLAVTRDEA  104 (111)
T ss_dssp             EESSSCEEEEECCCCCCCC
T ss_pred             cEEcCEEEEEEECCCCccC
Confidence            9999999999999877653

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=1.2e-18  Score=122.26  Aligned_cols=86  Identities=17%  Similarity=0.199  Sum_probs=79.1

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      ..+..+.++|||+|||..+++++|+++|++| .|..|.|+.++ +++++|||||+|.+.++|.+||+ +++ ..|+|+.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l   86 (114)
T 2do0_A            9 LQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNG-QLLFDRPM   86 (114)
T ss_dssp             CCCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTT-CEETTEEC
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCC-CEeCCCEE
Confidence            3456778999999999999999999999999 99999999987 59999999999999999999999 999 99999999


Q ss_pred             EEEecCCCCC
Q psy1680          85 RLDIADGKRN   94 (227)
Q Consensus        85 ~v~~~~~~~~   94 (227)
                      .|.++.....
T Consensus        87 ~v~~a~~~~~   96 (114)
T 2do0_A           87 HVKMDERALP   96 (114)
T ss_dssp             EEEECSCCCC
T ss_pred             EEEEcccCCC
Confidence            9999876443

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.9e-19  Score=123.80  Aligned_cols=89  Identities=20%  Similarity=0.324  Sum_probs=82.5

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      .....+.++|||+|||..+++++|+++|++| .|..|.|+.++.+++++|||||+|.+.++|.+||+ +++ ..|+|+.|
T Consensus         6 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~l   84 (102)
T 2cqb_A            6 SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE-SELFGRTI   84 (102)
T ss_dssp             SCSCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTT-EEETTEEE
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCC-CEECCcEE
Confidence            3456778999999999999999999999999 99999999999999999999999999999999998 999 99999999


Q ss_pred             EEEecCCCCCCC
Q psy1680          85 RLDIADGKRNDN   96 (227)
Q Consensus        85 ~v~~~~~~~~~~   96 (227)
                      .|.++.++....
T Consensus        85 ~V~~a~~~~~~~   96 (102)
T 2cqb_A           85 RVNLAKPMRIKE   96 (102)
T ss_dssp             EEEECCCCCCCC
T ss_pred             EEEeCCCCCCCC
Confidence            999998876543

>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=99.81  E-value=4.2e-19  Score=122.55  Aligned_cols=92  Identities=36%  Similarity=0.716  Sum_probs=84.1

Q ss_pred             CCCCCCCCCCceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeecCCC-CCeecEEEEEeCCHHHHHHHHHhCCCceeCCe
Q psy1680           4 NQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKET-DRFKGFCYVEFVDVENLRQALLKDGRITVDGL   82 (227)
Q Consensus         4 ~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~~~-~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~   82 (227)
                      .+.+.+..+.++|||+|||+++++++|+++|++|.|..|.|+.++.+ ++++|||||+|.+.++|.+||.+++ ..|.|+
T Consensus         6 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~Gi~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g-~~~~g~   84 (104)
T 1wi8_A            6 SGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNE-ESLGNK   84 (104)
T ss_dssp             CCCCCCSSSCEEEEEESCCSSCCHHHHHHHTTTSCEEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGT-CEETTE
T ss_pred             CCCCCCCCCCCEEEEeCCCCcCCHHHHHHHHHHCCceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCC-CEeCCc
Confidence            34556778889999999999999999999999999999999999887 9999999999999999999999999 999999


Q ss_pred             EeEEEecCCCCCCC
Q psy1680          83 QVRLDIADGKRNDN   96 (227)
Q Consensus        83 ~l~v~~~~~~~~~~   96 (227)
                      .|.|.++.++....
T Consensus        85 ~l~V~~a~~~~~~~   98 (104)
T 1wi8_A           85 RIRVDVADQAQDKD   98 (104)
T ss_dssp             ECEEEECCCCCCCC
T ss_pred             EEEEEEccCCCCCC
Confidence            99999998876543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.81  E-value=7.7e-20  Score=123.97  Aligned_cols=82  Identities=21%  Similarity=0.354  Sum_probs=75.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-C--eEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCc----eeC
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-K--LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRI----TVD   80 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~--i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~----~~~   80 (227)
                      ....-.+|||+|||+++|+++|+++|++| .  +.+|+|++|+.+++++|||||+|.+.++|.+||+ +|+ .    .++
T Consensus         5 ~~~~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            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQS-LHPPLKID   83 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHS-SSSCEEET
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcC-CCCCceEC
Confidence            44566899999999999999999999999 5  6789999999999999999999999999999999 888 5    599


Q ss_pred             CeEeEEEecCC
Q psy1680          81 GLQVRLDIADG   91 (227)
Q Consensus        81 g~~l~v~~~~~   91 (227)
                      |++|.|.+++.
T Consensus        84 Gr~i~V~~Aks   94 (95)
T 2lkz_A           84 GKTIGVDFAKS   94 (95)
T ss_dssp             TEEEEEEECCC
T ss_pred             CEEEEEEEccC
Confidence            99999999864

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=4.8e-19  Score=121.36  Aligned_cols=85  Identities=22%  Similarity=0.429  Sum_probs=79.4

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      ....+.++|||+|||..+++++|+++|++| .|..+.|+.++ +++++|||||+|.+.++|.+||+ +++ ..++|+.|.
T Consensus        12 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~   89 (100)
T 2do4_A           12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDG-MTIKENIIK   89 (100)
T ss_dssp             SSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTT-EESSSCEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCC-CEECCEEEE
Confidence            345678999999999999999999999999 99999999997 89999999999999999999998 999 999999999


Q ss_pred             EEecCCCCC
Q psy1680          86 LDIADGKRN   94 (227)
Q Consensus        86 v~~~~~~~~   94 (227)
                      |.++.++..
T Consensus        90 v~~a~~~~~   98 (100)
T 2do4_A           90 VAISNSGPS   98 (100)
T ss_dssp             EEECCCCSC
T ss_pred             EEECCCCCC
Confidence            999987654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=7.3e-19  Score=121.11  Aligned_cols=89  Identities=21%  Similarity=0.343  Sum_probs=81.1

Q ss_pred             CCCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCe
Q psy1680           5 QKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGL   82 (227)
Q Consensus         5 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~   82 (227)
                      .......+.++|||+|||+.+|+++|+++|++| .|..|.|+.+  ++.++|||||+|.+.++|.+||+ +++ ..+.|+
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~   83 (103)
T 2d9p_A            7 GDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNG-RIVATK   83 (103)
T ss_dssp             CCCCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTT-CBSSSS
T ss_pred             CCccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCC-CEeCCc
Confidence            344456788999999999999999999999999 9999999988  78999999999999999999999 999 999999


Q ss_pred             EeEEEecCCCCCCC
Q psy1680          83 QVRLDIADGKRNDN   96 (227)
Q Consensus        83 ~l~v~~~~~~~~~~   96 (227)
                      .|.|.++.++....
T Consensus        84 ~l~V~~a~~~~~~~   97 (103)
T 2d9p_A           84 PLYVALAQRKEERQ   97 (103)
T ss_dssp             BCEEEECSSCCCCC
T ss_pred             EEEEEEecccccCC
Confidence            99999998876543

>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=99.81  E-value=3.5e-19  Score=121.79  Aligned_cols=86  Identities=24%  Similarity=0.311  Sum_probs=80.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ...+.++|||+|||..+++++|+++|++| .|..+.|+.++.+++++|||||+|.+.++|.+||+ +++ ..+.|+.|.|
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~V   82 (99)
T 1whw_A            4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDG-QVFQGRMLHV   82 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTT-EESSSCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCC-CEECCcEEEE
Confidence            35678999999999999999999999999 99999999998899999999999999999999997 999 9999999999


Q ss_pred             EecCCCCCC
Q psy1680          87 DIADGKRND   95 (227)
Q Consensus        87 ~~~~~~~~~   95 (227)
                      .++.++...
T Consensus        83 ~~a~~~~~~   91 (99)
T 1whw_A           83 LPSTIKKEA   91 (99)
T ss_dssp             EECCCCSTT
T ss_pred             EEcCCCccc
Confidence            999887653

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=1.7e-19  Score=124.25  Aligned_cols=88  Identities=24%  Similarity=0.361  Sum_probs=81.8

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeE
Q psy1680           6 KTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQ   83 (227)
Q Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~   83 (227)
                      .+....+.++|||+|||..+++++|+++|++| .|..+.|+.++.+++++|||||+|.+.++|++||+ +++ ..|+|+.
T Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~   84 (103)
T 2dnm_A            6 SGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG-AELDGRE   84 (103)
T ss_dssp             CSSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSS-CCBTTBC
T ss_pred             CCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCC-CEECCcE
Confidence            34456778999999999999999999999999 99999999999999999999999999999999999 999 9999999


Q ss_pred             eEEEecCCCCC
Q psy1680          84 VRLDIADGKRN   94 (227)
Q Consensus        84 l~v~~~~~~~~   94 (227)
                      |.|.++.++..
T Consensus        85 l~V~~a~~~~~   95 (103)
T 2dnm_A           85 LRVQVARYGRR   95 (103)
T ss_dssp             CEEEECSSCCS
T ss_pred             EEEEECCcCCC
Confidence            99999987654

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=2.1e-19  Score=123.59  Aligned_cols=89  Identities=29%  Similarity=0.530  Sum_probs=82.5

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      .....+.++|||+|||.++++++|+++|++| .|..+.|+.++.+++++|||||+|.+.++|.+||+ +++ ..|+|+.|
T Consensus         6 ~~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~l   84 (102)
T 1x5s_A            6 SGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNG-KSVDGRQI   84 (102)
T ss_dssp             CCCCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTT-CCTTSCCC
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCC-CEECCeEE
Confidence            3456778999999999999999999999999 99999999999999999999999999999999998 999 99999999


Q ss_pred             EEEecCCCCCCC
Q psy1680          85 RLDIADGKRNDN   96 (227)
Q Consensus        85 ~v~~~~~~~~~~   96 (227)
                      +|.++.++....
T Consensus        85 ~v~~a~~~~~~~   96 (102)
T 1x5s_A           85 RVDQAGKSSDNR   96 (102)
T ss_dssp             EEEEEECCCCCC
T ss_pred             EEEECCCCCCCC
Confidence            999998776543

>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=99.81  E-value=3e-19  Score=125.50  Aligned_cols=87  Identities=18%  Similarity=0.313  Sum_probs=81.0

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      ....+.++|||+|||.++++++|+++|++| .|..|.|+.++.+++++|||||+|.+.++|++||+ +++ ..|+|+.|+
T Consensus        20 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~   98 (115)
T 2cpz_A           20 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNG-FQIGMKRLK   98 (115)
T ss_dssp             CCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTT-CEETTEECE
T ss_pred             cCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCC-CEECCEEEE
Confidence            345667999999999999999999999999 99999999999899999999999999999999998 999 999999999


Q ss_pred             EEecCCCCCC
Q psy1680          86 LDIADGKRND   95 (227)
Q Consensus        86 v~~~~~~~~~   95 (227)
                      |.++.++...
T Consensus        99 V~~a~~~~~~  108 (115)
T 2cpz_A           99 VQLKRSKNDS  108 (115)
T ss_dssp             EECCCCSCCC
T ss_pred             EEEcCCCCcC
Confidence            9999877653

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.4e-18  Score=122.31  Aligned_cols=88  Identities=18%  Similarity=0.340  Sum_probs=79.9

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeE
Q psy1680           6 KTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQ   83 (227)
Q Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~   83 (227)
                      .+....+.++|||+|||..+++++|+++|++| .|..|.|++++.+++++|||||+|.+.++|++||+ +++  .|.|+.
T Consensus        10 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~--~~~g~~   87 (116)
T 2cqd_A           10 GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP--IIDGRK   87 (116)
T ss_dssp             CCCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC--EETTEE
T ss_pred             CCcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC--cCCCEE
Confidence            34456778999999999999999999999999 99999999999999999999999999999999999 675  799999


Q ss_pred             eEEEecCCCCCC
Q psy1680          84 VRLDIADGKRND   95 (227)
Q Consensus        84 l~v~~~~~~~~~   95 (227)
                      |.|.++.++...
T Consensus        88 l~V~~a~~~~~~   99 (116)
T 2cqd_A           88 ANVNLAYLGAKP   99 (116)
T ss_dssp             CEEEESTTTCCC
T ss_pred             EEEEEcccCCCc
Confidence            999999765443

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.80  E-value=4e-19  Score=121.57  Aligned_cols=86  Identities=24%  Similarity=0.372  Sum_probs=80.1

Q ss_pred             CCCCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEE--------EEEeecCCCCCeecEEEEEeCCHHHHHHHHH-h
Q psy1680           4 NQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVS--------VRLVKDKETDRFKGFCYVEFVDVENLRQALL-K   73 (227)
Q Consensus         4 ~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~--------v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~   73 (227)
                      ...+.+..+.++|||+|||.++++++|+++|++| .|..        +.|+.++.+++++|||||+|.+.++|.+|++ +
T Consensus         4 ~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l   83 (99)
T 2la6_A            4 HHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWF   83 (99)
T ss_dssp             SCSCCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHh
Confidence            3455667888999999999999999999999999 9999        9999999999999999999999999999998 9


Q ss_pred             CCCceeCCeEeEEEecC
Q psy1680          74 DGRITVDGLQVRLDIAD   90 (227)
Q Consensus        74 ~~~~~~~g~~l~v~~~~   90 (227)
                      ++ ..+.|+.|+|.+++
T Consensus        84 ~g-~~~~g~~l~V~~A~   99 (99)
T 2la6_A           84 DG-KEFSGNPIKVSFAT   99 (99)
T ss_dssp             TT-CBSSSSBCEEEECC
T ss_pred             CC-CEeCCcEEEEEecC
Confidence            99 99999999999874

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=2.8e-19  Score=121.56  Aligned_cols=84  Identities=18%  Similarity=0.316  Sum_probs=79.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEE-EEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSV-RLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v-~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      .+.++|||+|||..+++++|+++|++| .|..+ .|++++.++.++|||||+|.+.++|.+||+ +++ ..++|+.|.|.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~l~v~   81 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNG-QYLCNRPITVS   81 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTT-CEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCC-CEECCEEEEEE
Confidence            568999999999999999999999999 99999 999998999999999999999999999999 999 99999999999


Q ss_pred             ecCCCCCC
Q psy1680          88 IADGKRND   95 (227)
Q Consensus        88 ~~~~~~~~   95 (227)
                      ++.++...
T Consensus        82 ~a~~~~~~   89 (96)
T 1x5t_A           82 YAFKKDSK   89 (96)
T ss_dssp             ESCCCCCC
T ss_pred             EecccCCC
Confidence            99876653

>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=99.80  E-value=4.2e-19  Score=124.98  Aligned_cols=85  Identities=20%  Similarity=0.430  Sum_probs=79.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      +..+.++|||+|||.++++++|+++|++| .|..|.|+.++ +++++|||||+|.+.++|++||+ +++ ..|+|+.|.|
T Consensus         3 e~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g-~~~~g~~l~V   80 (116)
T 2fy1_A            3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNG-KSLHGKAIKV   80 (116)
T ss_dssp             TTCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSS-CBCSSSBCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCC-CEECCEEEEE
Confidence            45678999999999999999999999999 99999999997 89999999999999999999999 999 9999999999


Q ss_pred             EecCCCCCC
Q psy1680          87 DIADGKRND   95 (227)
Q Consensus        87 ~~~~~~~~~   95 (227)
                      .++.++...
T Consensus        81 ~~a~~~~~~   89 (116)
T 2fy1_A           81 EQAKKPSFQ   89 (116)
T ss_dssp             EECCCSSCS
T ss_pred             EECCCCCCC
Confidence            999876643

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=4e-19  Score=120.53  Aligned_cols=84  Identities=24%  Similarity=0.409  Sum_probs=78.9

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      .....+.++|||+|||..+++++|+++|++| .|..+.|+.++.+++++|||||+|.+.++|.+||+ +++ ..++|+.|
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~l   87 (95)
T 2cqc_A            9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG-MELDGRRI   87 (95)
T ss_dssp             CCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTT-EEETTEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCC-CEECCEEE
Confidence            3456778999999999999999999999999 99999999999999999999999999999999999 999 99999999


Q ss_pred             EEEecCC
Q psy1680          85 RLDIADG   91 (227)
Q Consensus        85 ~v~~~~~   91 (227)
                      .|.+++.
T Consensus        88 ~v~~a~~   94 (95)
T 2cqc_A           88 RVSGPSS   94 (95)
T ss_dssp             EEECCSC
T ss_pred             EEEecCC
Confidence            9999864

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.80  E-value=3.8e-19  Score=123.65  Aligned_cols=86  Identities=26%  Similarity=0.447  Sum_probs=80.8

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      +....++++|||+|||..+++++|+++|++| .|..+.|+.++.+++++|||||+|.+.++|.+|++ +++ ..++|+.|
T Consensus        20 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g-~~i~g~~l   98 (108)
T 2jrs_A           20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNG-FELAGRPM   98 (108)
T ss_dssp             CCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTT-CCSSSSCC
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCC-CEECCEEE
Confidence            3456778999999999999999999999999 99999999999999999999999999999999998 999 99999999


Q ss_pred             EEEecCCCC
Q psy1680          85 RLDIADGKR   93 (227)
Q Consensus        85 ~v~~~~~~~   93 (227)
                      .|.++.++.
T Consensus        99 ~V~~a~~k~  107 (108)
T 2jrs_A           99 KVGHVTERT  107 (108)
T ss_dssp             EEECSCSSC
T ss_pred             EEEEcccCC
Confidence            999998764

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=5.6e-19  Score=123.72  Aligned_cols=88  Identities=23%  Similarity=0.305  Sum_probs=81.5

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeE--------EEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCC
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLV--------SVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGR   76 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~--------~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~   76 (227)
                      +....+.++|||+|||..+++++|+++|++| .|.        .|.|+.++.+++++|||||+|.+.++|.+||+ +++ 
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g-   87 (113)
T 2cpe_A            9 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDG-   87 (113)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTT-
T ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCC-
Confidence            3456788999999999999999999999999 998        69999999999999999999999999999999 999 


Q ss_pred             ceeCCeEeEEEecCCCCCC
Q psy1680          77 ITVDGLQVRLDIADGKRND   95 (227)
Q Consensus        77 ~~~~g~~l~v~~~~~~~~~   95 (227)
                      ..|.|+.|.|.++.++...
T Consensus        88 ~~~~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           88 KDFQGSKLKVSLARKKPPM  106 (113)
T ss_dssp             CEETTEECEEECSSCCCCS
T ss_pred             CccCCCEEEEEECCCCCCC
Confidence            9999999999999876653

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=5.6e-19  Score=119.58  Aligned_cols=83  Identities=28%  Similarity=0.422  Sum_probs=78.0

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      .....+.++|||+|||..+++++|+++|++| .|..+.|+.++.+++++|||||+|.+.++|.+|++ +++ ..+.|+.|
T Consensus        10 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~l   88 (94)
T 2e5h_A           10 GGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINN-KQLFGRVI   88 (94)
T ss_dssp             CSCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTT-EEETTEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCC-CeeCCcEE
Confidence            3455778999999999999999999999999 99999999999999999999999999999999998 999 99999999


Q ss_pred             EEEecC
Q psy1680          85 RLDIAD   90 (227)
Q Consensus        85 ~v~~~~   90 (227)
                      +|.+++
T Consensus        89 ~v~~ak   94 (94)
T 2e5h_A           89 KASIAI   94 (94)
T ss_dssp             EEEECC
T ss_pred             EEEecC
Confidence            999874

>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=99.80  E-value=5.5e-19  Score=117.94  Aligned_cols=81  Identities=23%  Similarity=0.385  Sum_probs=76.0

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRL   86 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v   86 (227)
                      ....+.++|||+|||+.+++++|+++|++| .|..+.|+.++.+++++|||||+|.+.++|.+||++++ ..++|+.|.|
T Consensus         6 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~-~~~~g~~i~v   84 (87)
T 3s7r_A            6 KNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKE-HRLDGRVIDP   84 (87)
T ss_dssp             -CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSC-EEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCC-CEECCEEEEE
Confidence            456778999999999999999999999999 99999999999999999999999999999999999888 8999999999


Q ss_pred             Eec
Q psy1680          87 DIA   89 (227)
Q Consensus        87 ~~~   89 (227)
                      ++|
T Consensus        85 ~~A   87 (87)
T 3s7r_A           85 KKA   87 (87)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            875

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.80  E-value=6.5e-19  Score=127.92  Aligned_cols=86  Identities=19%  Similarity=0.381  Sum_probs=80.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      .....++|||+|||.++++++|+++|+.| .|..|.|++++.+++++|||||+|.+.++|.+||+ +++ ..|.|+.|.|
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~v  116 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG-FNILNKRLKV  116 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTT-EECSSCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCC-CEECCeEEEE
Confidence            34566999999999999999999999999 99999999999999999999999999999999999 999 9999999999


Q ss_pred             EecCCCCCC
Q psy1680          87 DIADGKRND   95 (227)
Q Consensus        87 ~~~~~~~~~   95 (227)
                      .++.++...
T Consensus       117 ~~a~~~~~~  125 (139)
T 1u6f_A          117 ALAASGHQR  125 (139)
T ss_dssp             EESSCCCCC
T ss_pred             EECCCCCCC
Confidence            999877654

>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=99.80  E-value=3.8e-19  Score=120.97  Aligned_cols=82  Identities=18%  Similarity=0.415  Sum_probs=78.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      ++++|||+|||..+++++|+++|++| .|..+.|+.++.+++++|||||+|.+.++|.+|++ +++ ..++|+.|.|.++
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g-~~~~g~~l~V~~a   79 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNG-YQLGSRFLKCGYS   79 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTT-CEETTEECEEEEC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCC-CeECCeEEEEEEc
Confidence            47899999999999999999999999 99999999999999999999999999999999998 999 9999999999999


Q ss_pred             CCCCC
Q psy1680          90 DGKRN   94 (227)
Q Consensus        90 ~~~~~   94 (227)
                      .++..
T Consensus        80 ~~~~~   84 (96)
T 2x1f_A           80 SNSDI   84 (96)
T ss_dssp             SCSSG
T ss_pred             CCCCC
Confidence            87654

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.80  E-value=1.9e-19  Score=128.55  Aligned_cols=89  Identities=19%  Similarity=0.291  Sum_probs=82.0

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeE
Q psy1680           6 KTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQ   83 (227)
Q Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~   83 (227)
                      .+....+.++|||+|||..+|+++|+++|++| .|..|.|+.++.++.++|||||+|.+.++|.+||+ |++ ..|+|+.
T Consensus        15 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~   93 (126)
T 3ex7_B           15 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNG-QDLMGQP   93 (126)
T ss_dssp             CBCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTT-CBSSSSB
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCC-CeeCCeE
Confidence            34456677899999999999999999999999 99999999999899999999999999999999998 999 9999999


Q ss_pred             eEEEecCCCCCC
Q psy1680          84 VRLDIADGKRND   95 (227)
Q Consensus        84 l~v~~~~~~~~~   95 (227)
                      |.|.++.++...
T Consensus        94 l~v~~a~~~~~~  105 (126)
T 3ex7_B           94 ISVDWCFVRGPP  105 (126)
T ss_dssp             CEEEESEESSSC
T ss_pred             EEEEEecCCCCC
Confidence            999999876554

>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=99.80  E-value=7.7e-19  Score=120.79  Aligned_cols=85  Identities=21%  Similarity=0.270  Sum_probs=77.3

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeE
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVR   85 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~   85 (227)
                      .......++|||+|||+++|+++|+++|++| .+ .|.|++++ +++++|||||+|.+.++|++||++++ ..|+++.|+
T Consensus         9 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~-~~~~gr~i~   85 (102)
T 1wez_A            9 SFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDK-ANMQHRYVE   85 (102)
T ss_dssp             SCCCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSS-CCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCC-CeECCcEEE
Confidence            3455677999999999999999999999999 65 99999997 89999999999999999999999999 999999999


Q ss_pred             EEecCCCCC
Q psy1680          86 LDIADGKRN   94 (227)
Q Consensus        86 v~~~~~~~~   94 (227)
                      |..+.+...
T Consensus        86 V~~~~~~~~   94 (102)
T 1wez_A           86 LFLNSTAGT   94 (102)
T ss_dssp             EEEECCCCC
T ss_pred             EEECCCCCC
Confidence            999876553

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.80  E-value=3.7e-19  Score=118.19  Aligned_cols=81  Identities=21%  Similarity=0.367  Sum_probs=76.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ...+.++|||+|||+++++++|+++|++| .|..+.+++++.+++++|||||+|.+.++|.+|++ +++ ..++|+.|+|
T Consensus         3 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~v   81 (85)
T 3mdf_A            3 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE-SELFGRTIRV   81 (85)
T ss_dssp             CCCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTT-CEETTEECEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCC-CEECCcEEEE
Confidence            35678999999999999999999999999 99999999999999999999999999999999998 999 9999999999


Q ss_pred             EecC
Q psy1680          87 DIAD   90 (227)
Q Consensus        87 ~~~~   90 (227)
                      .+++
T Consensus        82 ~~ak   85 (85)
T 3mdf_A           82 NLAK   85 (85)
T ss_dssp             EECC
T ss_pred             EEcC
Confidence            9874

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.80  E-value=2.4e-20  Score=126.51  Aligned_cols=71  Identities=21%  Similarity=0.321  Sum_probs=64.6

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccc--eEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCc----cccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTT--LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRI----TVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~--i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~----~i~gr  227 (227)
                      -+||||+|||+..  |+++|+++|++||.  |.+|+|++|+.||.++|||||+|.+.++|.+|++.|||.    .|+||
T Consensus         9 m~tlfV~nL~~~~--tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr   85 (95)
T 2lkz_A            9 MDTIILRNIAPHT--VVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK   85 (95)
T ss_dssp             CCEEEEESCCTTC--CHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTE
T ss_pred             cCEEEEeCCCCcC--CHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCE
Confidence            4689999997655  89999999999994  679999999999999999999999999999999999997    48886

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.80  E-value=1.5e-20  Score=126.78  Aligned_cols=71  Identities=15%  Similarity=0.211  Sum_probs=64.7

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhcccc-ceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHc-CCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVT-TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD-GRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g-~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l-~g~~i~gr  227 (227)
                      +++|||+|||+.+  |+++|+++|++|| .|.+|+|++|+.||.++|||||+|.+.++|.+|++.+ ++..|+||
T Consensus         1 S~~i~v~nLp~~~--te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr   73 (91)
T 2lxi_A            1 SNIVMLRMLPQAA--TEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQ   73 (91)
T ss_dssp             CCEEEEETCCSSC--CHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTE
T ss_pred             CCEEEEeCCCCCC--CHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCE
Confidence            4689999997665  8999999999999 8999999999999999999999999999999999987 56678885

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=8.7e-19  Score=121.50  Aligned_cols=89  Identities=22%  Similarity=0.381  Sum_probs=82.1

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeec-CCCCCeecEEEEEeCCHHHHHHHHH-h-CCCceeCC
Q psy1680           6 KTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKD-KETDRFKGFCYVEFVDVENLRQALL-K-DGRITVDG   81 (227)
Q Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~-~~~~~~~g~afv~f~~~~~a~~al~-~-~~~~~~~g   81 (227)
                      .+....+.++|||+|||..+++++|+++|++| .|..|.|+.+ +.+++++|||||+|.+.++|.+||+ + ++ ..|.|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~-~~~~g   86 (107)
T 2cph_A            8 QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHS-THLYG   86 (107)
T ss_dssp             SSCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTC-CBSSS
T ss_pred             ccccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccC-CeECC
Confidence            34456778999999999999999999999999 9999999998 7889999999999999999999999 8 89 99999


Q ss_pred             eEeEEEecCCCCCC
Q psy1680          82 LQVRLDIADGKRND   95 (227)
Q Consensus        82 ~~l~v~~~~~~~~~   95 (227)
                      +.|.|.++.++...
T Consensus        87 ~~l~v~~a~~~~~~  100 (107)
T 2cph_A           87 RRLVLEWADSEVTV  100 (107)
T ss_dssp             CBCEEEECCCCCCC
T ss_pred             CEEEEEeCCCCCCC
Confidence            99999999887654

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=4.3e-19  Score=120.17  Aligned_cols=73  Identities=19%  Similarity=0.224  Sum_probs=68.3

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++..+|||+|||...  ++++|+++|++||.|..|.|++++.++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        14 ~~~~~l~V~nlp~~~--t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   86 (94)
T 2e5h_A           14 PSKSTVYVSNLPFSL--TNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGR   86 (94)
T ss_dssp             CCTTSEEEESCCTTS--CHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTE
T ss_pred             CCCCEEEEECCCCCC--CHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCc
Confidence            467899999997655  7999999999999999999999999999999999999999999999999999999885

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=3.5e-19  Score=123.31  Aligned_cols=84  Identities=20%  Similarity=0.325  Sum_probs=79.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ...+.++|||+|||..+++++|+++|++| .|..|.|+.++.++.++|||||+|.+.++|.+||+ +++ ..++|+.|.|
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~V   97 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNG-QDLMGQPISV   97 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTT-CBSSSSBCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcC-CEECCcEEEE
Confidence            34567899999999999999999999999 99999999999999999999999999999999999 999 9999999999


Q ss_pred             EecCCCC
Q psy1680          87 DIADGKR   93 (227)
Q Consensus        87 ~~~~~~~   93 (227)
                      .++.++.
T Consensus        98 ~~a~~~~  104 (106)
T 1p27_B           98 DWCFVRG  104 (106)
T ss_dssp             EESEESS
T ss_pred             EeecCCC
Confidence            9997654

>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=99.79  E-value=3.7e-19  Score=124.06  Aligned_cols=88  Identities=17%  Similarity=0.242  Sum_probs=81.0

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeE
Q psy1680           6 KTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQ   83 (227)
Q Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~   83 (227)
                      .+....+.++|||+|||..+++++|+++|++| .|..+.|+.++.++.++|||||+|.+.++|.+||. +++ ..|+|+.
T Consensus        19 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g-~~~~g~~   97 (110)
T 1oo0_B           19 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNG-AEIMGQT   97 (110)
T ss_dssp             CBCCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTT-CEETTEE
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCC-CEECCcE
Confidence            33445677999999999999999999999999 99999999999999999999999999999999999 999 9999999


Q ss_pred             eEEEecCCCCC
Q psy1680          84 VRLDIADGKRN   94 (227)
Q Consensus        84 l~v~~~~~~~~   94 (227)
                      |.|.++.++..
T Consensus        98 l~V~~a~~~~~  108 (110)
T 1oo0_B           98 IQVDWCFVKGP  108 (110)
T ss_dssp             CEEEESEESSC
T ss_pred             EEEEEcccCCC
Confidence            99999987553

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=6.2e-19  Score=120.33  Aligned_cols=84  Identities=25%  Similarity=0.351  Sum_probs=78.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCC---CCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKE---TDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~---~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      .+.++|||+|||.++++++|+++|++| .|..|.|+.++.   +++++|||||+|.+.++|.+||+ |++ ..|+|+.|.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~   81 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQG-HTVDGHKLE   81 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTT-CEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCC-CeeCCeEEE
Confidence            567999999999999999999999999 999999999876   66999999999999999999999 999 999999999


Q ss_pred             EEecCCCCCC
Q psy1680          86 LDIADGKRND   95 (227)
Q Consensus        86 v~~~~~~~~~   95 (227)
                      |.++.++...
T Consensus        82 V~~a~~~~~~   91 (98)
T 2cpf_A           82 VRISERATKP   91 (98)
T ss_dssp             EECSSCSSCC
T ss_pred             EEEccCCCCC
Confidence            9999876653

>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=99.79  E-value=1e-18  Score=129.42  Aligned_cols=87  Identities=23%  Similarity=0.384  Sum_probs=81.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ...+.++|||+|||..+|+++|+++|++| .|..|.|+.++.++.++|||||+|.+.++|++||+ |++ ..|+|+.|.|
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g-~~~~g~~l~V  113 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYING-TRLDDRIIRT  113 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTT-SEETTEECEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCC-CEECCeEEEE
Confidence            34578999999999999999999999999 99999999999999999999999999999999999 999 9999999999


Q ss_pred             EecCCCCCCC
Q psy1680          87 DIADGKRNDN   96 (227)
Q Consensus        87 ~~~~~~~~~~   96 (227)
                      .++.++....
T Consensus       114 ~~a~~~~~~~  123 (156)
T 1h2v_Z          114 DWDAGFKEGR  123 (156)
T ss_dssp             EEESCCCTTC
T ss_pred             EECCCCCCcC
Confidence            9998766543

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=6.7e-19  Score=121.48  Aligned_cols=85  Identities=29%  Similarity=0.468  Sum_probs=79.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccC-C-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCce-eCCeEe
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPE-Q-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRIT-VDGLQV   84 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~-~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~-~~g~~l   84 (227)
                      +..+.++|||+|||.++|+++|+++|++ | .|..|.|+.++ +++++|||||+|.+.++|.+||+ +++ .. ++|+.|
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g-~~~~~g~~l   82 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQG-AVGLGSKPV   82 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTT-CCSSSSSCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccC-CcccCCEeE
Confidence            4567899999999999999999999999 9 99999999998 89999999999999999999999 999 88 999999


Q ss_pred             EEEecCCCCCC
Q psy1680          85 RLDIADGKRND   95 (227)
Q Consensus        85 ~v~~~~~~~~~   95 (227)
                      .|.++.++...
T Consensus        83 ~v~~a~~~~~~   93 (104)
T 2dhg_A           83 RLSVAIPKASR   93 (104)
T ss_dssp             CCCBCCCCCSC
T ss_pred             EEEEccCCCcC
Confidence            99999876653

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=6.4e-19  Score=121.81  Aligned_cols=89  Identities=24%  Similarity=0.351  Sum_probs=82.3

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeE
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVR   85 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~   85 (227)
                      .....+.++|||+|||+.+++++|+++|++| .|..|.|+.++.+++++|||||+|.+.++|.+||+.++ ..|+|+.|.
T Consensus        10 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~   88 (105)
T 2dh8_A           10 NSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRP-HTLDGRNID   88 (105)
T ss_dssp             CCCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCS-EEETTEEEB
T ss_pred             cCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCC-CeECCEEEE
Confidence            3456778999999999999999999999999 99999999999999999999999999999999999888 999999999


Q ss_pred             EEecCCCCCCC
Q psy1680          86 LDIADGKRNDN   96 (227)
Q Consensus        86 v~~~~~~~~~~   96 (227)
                      |.++.++....
T Consensus        89 V~~a~~~~~~~   99 (105)
T 2dh8_A           89 PKPCTPRGMQP   99 (105)
T ss_dssp             CCCSCCSSCCT
T ss_pred             EEEccCCCCCC
Confidence            99998776543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.79  E-value=9.1e-20  Score=125.05  Aligned_cols=74  Identities=14%  Similarity=0.088  Sum_probs=67.4

Q ss_pred             CCCcceeccCCCCC----CCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC-C
Q psy1680         154 EGPGGFRNNNGPNR----SNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG-L  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~----~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g-r  227 (227)
                      .+++|||+|||...    +.++++|+++|++||.|.+|+|++|+.||+++|||||+|.+.++|.+|++.|||..|+| |
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            46789999997500    44789999999999999999999999999999999999999999999999999999998 5

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.79  E-value=6.2e-19  Score=122.07  Aligned_cols=88  Identities=18%  Similarity=0.352  Sum_probs=81.6

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCcee---CC
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITV---DG   81 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~---~g   81 (227)
                      +.+..+.++|||+|||.++++++|+++|++| .|..|.|+.++.+++++|||||+|.+.++|.+||+ +++ ..+   .|
T Consensus         7 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g-~~~~~~~g   85 (106)
T 2dgp_A            7 GMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHE-QKTLPGMN   85 (106)
T ss_dssp             SCCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTT-TCCCTTCS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcC-CcccCCCC
Confidence            4456778999999999999999999999999 99999999999999999999999999999999999 999 887   89


Q ss_pred             eEeEEEecCCCCCC
Q psy1680          82 LQVRLDIADGKRND   95 (227)
Q Consensus        82 ~~l~v~~~~~~~~~   95 (227)
                      +.|.|.++.++...
T Consensus        86 ~~l~v~~a~~~~~~   99 (106)
T 2dgp_A           86 RPIQVKPADSESRG   99 (106)
T ss_dssp             SCCEEEECCCCSCC
T ss_pred             ceEEEEECCccccc
Confidence            99999999876653

>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=99.79  E-value=1.7e-18  Score=119.62  Aligned_cols=85  Identities=19%  Similarity=0.260  Sum_probs=78.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC---eE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG---LQ   83 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g---~~   83 (227)
                      ...+.++|||+|||..+++++|+++|++| .|..|.|+.++ +++++|||||+|.+.++|.+||+ +++ ..+.+   +.
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g-~~~~gg~~~~   88 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHG-SQTMPGASSS   88 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSS-CCCCTTCSSC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcC-CccCCCCCcc
Confidence            34668999999999999999999999999 99999999997 79999999999999999999999 999 99888   99


Q ss_pred             eEEEecCCCCCC
Q psy1680          84 VRLDIADGKRND   95 (227)
Q Consensus        84 l~v~~~~~~~~~   95 (227)
                      |.|.++.++...
T Consensus        89 l~V~~a~~~~~~  100 (105)
T 2dnh_A           89 LVVKFADTDKES  100 (105)
T ss_dssp             CEEEESCSSCCC
T ss_pred             EEEEECccCccc
Confidence            999999877654

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=2.8e-18  Score=117.94  Aligned_cols=86  Identities=31%  Similarity=0.451  Sum_probs=77.4

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      .....+.++|||+|||.++++++|+++|+.|  ..+.++.++.+++++|||||+|.+.++|.+||+ +++ ..|.|+.|.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~--~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~l~   85 (102)
T 2fc8_A            9 NARSQPSKTLFVKGLSEDTTEETLKESFDGS--VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMED-GEIDGNKVT   85 (102)
T ss_dssp             SSSSCCCSSEEEECCCTTCCHHHHHHTSTTC--SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTT-CEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCccCHHHHHHHhcCC--eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCC-CeECCeEEE
Confidence            3456778999999999999999999999987  356778888889999999999999999999999 999 999999999


Q ss_pred             EEecCCCCCC
Q psy1680          86 LDIADGKRND   95 (227)
Q Consensus        86 v~~~~~~~~~   95 (227)
                      |.++.++...
T Consensus        86 V~~a~~~~~~   95 (102)
T 2fc8_A           86 LDWAKPKGEG   95 (102)
T ss_dssp             EEECCCCCSS
T ss_pred             EEEecCCCCC
Confidence            9999887653

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=5.1e-19  Score=120.01  Aligned_cols=73  Identities=18%  Similarity=0.234  Sum_probs=68.4

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++..+|||+|||...  ++++|+++|++||.|..|.|++++.++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        13 ~~~~~l~v~nlp~~~--t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   85 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYT--TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR   85 (95)
T ss_dssp             CGGGCEEEESCCSSC--CHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCEEEEECCCCCC--CHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            567899999997665  7899999999999999999999999999999999999999999999999999999885

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=7.9e-19  Score=120.03  Aligned_cols=84  Identities=23%  Similarity=0.436  Sum_probs=79.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeE-EEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeE--
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLV-SVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQ--   83 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~-~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~--   83 (227)
                      ...+.++|||+|||+++++++|+++|++| .|. .+.|++++.+++++|||||+|.+.++|++|++ +|+ ..+.|+.  
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~~~   83 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKING-KPLPGATPA   83 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTT-SEESSCSSC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcC-CccCCCCcc
Confidence            45678999999999999999999999999 999 99999999999999999999999999999999 999 9999999  


Q ss_pred             --eEEEecCCCC
Q psy1680          84 --VRLDIADGKR   93 (227)
Q Consensus        84 --l~v~~~~~~~   93 (227)
                        |+|.++.+..
T Consensus        84 ~~l~v~~a~~~~   95 (99)
T 2div_A           84 KRFKLNYATYSG   95 (99)
T ss_dssp             EECCEEETTCCS
T ss_pred             eeEEEeecCCCC
Confidence              9999987654

>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=99.78  E-value=1.4e-19  Score=121.70  Aligned_cols=69  Identities=12%  Similarity=0.125  Sum_probs=63.9

Q ss_pred             cceeccCCCCCCCChhhHHhhhcccc--ceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVT--TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g--~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +|||+|||...  ++++|+++|++||  .|.+|+|++|+.+|+++|||||+|.+.++|.+|++.|||..|+||
T Consensus         3 ~l~V~nL~~~~--t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr   73 (90)
T 3p5t_L            3 ALYIGNLTWWT--TDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQ   73 (90)
T ss_dssp             -CEEESCCTTC--CHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSC
T ss_pred             EEEEeCCCCCC--CHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCE
Confidence            79999997655  8999999999999  999999999999999999999999999999999999999999997

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=1.1e-18  Score=119.52  Aligned_cols=72  Identities=21%  Similarity=0.237  Sum_probs=67.2

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|..|+|++++ ++.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        15 ~~~~~l~v~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   86 (100)
T 2do4_A           15 LEKHKLFISGLPFSC--TKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKEN   86 (100)
T ss_dssp             CCCSCEEEESCCTTC--CHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSC
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            567899999997655  799999999999999999999998 899999999999999999999999999999986

>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=1.3e-19  Score=127.19  Aligned_cols=83  Identities=18%  Similarity=0.221  Sum_probs=77.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-Ce-EEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KL-VSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i-~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v   86 (227)
                      ...+.++|||+|||+++|+++|+++|++| .| ..|.|+.++ +++++|||||+|.+.++|.+||++++ ..|+|+.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~-~~~~gr~i~v   88 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERLHR-KKLNGREAFV   88 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGGCS-EEETTEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHhCC-CccCCeEEEE
Confidence            45667999999999999999999999999 88 889999998 89999999999999999999999999 9999999999


Q ss_pred             EecCCCC
Q psy1680          87 DIADGKR   93 (227)
Q Consensus        87 ~~~~~~~   93 (227)
                      .++.++.
T Consensus        89 ~~a~~~~   95 (114)
T 2cpy_A           89 HVVTLED   95 (114)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9998654

>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=99.78  E-value=8.5e-19  Score=121.15  Aligned_cols=73  Identities=18%  Similarity=0.203  Sum_probs=68.5

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|++||.|..|.|++++.++.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        13 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   85 (105)
T 1x5u_A           13 NQDATVYVGGLDEKV--SEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGK   85 (105)
T ss_dssp             CTTTEEEEECCCTTC--CHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSC
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            467899999997655  7999999999999999999999999999999999999999999999999999999986

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=7e-19  Score=121.19  Aligned_cols=73  Identities=21%  Similarity=0.251  Sum_probs=68.4

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|++||.|..|.|++++.++.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        13 ~~~~~l~V~nlp~~~--t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   85 (103)
T 2cq0_A           13 DDNATIRVTNLSEDT--RETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHL   85 (103)
T ss_dssp             SSSEEEEEESCCTTC--CHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCc
Confidence            567899999997655  7999999999999999999999999999999999999999999999999999999885

>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=99.78  E-value=4.8e-18  Score=116.95  Aligned_cols=87  Identities=21%  Similarity=0.381  Sum_probs=78.9

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeE
Q psy1680           6 KTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQ   83 (227)
Q Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~   83 (227)
                      ......+.++|||+|||..+++++|+++|++| .|..|.|+.++.  .++|||||+|.+.++|.+||. +++ ..|+|+.
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~   84 (103)
T 2cq3_A            8 NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHG-TVVEGRK   84 (103)
T ss_dssp             CSCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTT-CEETTEE
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCC-CEECCEE
Confidence            34456778999999999999999999999999 999999998864  379999999999999999999 999 9999999


Q ss_pred             eEEEecCCCCCC
Q psy1680          84 VRLDIADGKRND   95 (227)
Q Consensus        84 l~v~~~~~~~~~   95 (227)
                      |.|.++.++...
T Consensus        85 l~v~~a~~~~~~   96 (103)
T 2cq3_A           85 IEVNNATARVMT   96 (103)
T ss_dssp             CEEEECCSSCCC
T ss_pred             EEEEEcccCCCC
Confidence            999999887653

>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=99.78  E-value=8.9e-19  Score=119.55  Aligned_cols=85  Identities=18%  Similarity=0.217  Sum_probs=78.3

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      ......++|||+|||+.+++++|+++|++| .|..+.++.++.+++++|||||+|.+.++|++||+ +++ ..|+|+.|+
T Consensus        10 ~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g-~~~~g~~l~   88 (98)
T 2cqp_A           10 SGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLND-RPIGSRKVK   88 (98)
T ss_dssp             CCCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTT-CEETTEECE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCC-CeeCCeEEE
Confidence            345667999999999999999999999999 99888888888999999999999999999999998 999 999999999


Q ss_pred             EEecCCCC
Q psy1680          86 LDIADGKR   93 (227)
Q Consensus        86 v~~~~~~~   93 (227)
                      |.++..+.
T Consensus        89 V~~a~~~~   96 (98)
T 2cqp_A           89 LVLGSGPS   96 (98)
T ss_dssp             EEESSCSS
T ss_pred             EEEcCCCC
Confidence            99987543

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=5.8e-19  Score=124.27  Aligned_cols=85  Identities=21%  Similarity=0.385  Sum_probs=79.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEec
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA   89 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~   89 (227)
                      .+.++|||+|||.++++++|+++|++| .|..|.|+.++.+++++|||||+|.+.++|.+||+.++ ..|+|+.|.|.++
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~-~~~~g~~l~V~~a  103 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARP-HSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCS-EEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCC-cEECCEEEEEEEC
Confidence            344899999999999999999999999 99999999999999999999999999999999999988 9999999999999


Q ss_pred             CCCCCCC
Q psy1680          90 DGKRNDN   96 (227)
Q Consensus        90 ~~~~~~~   96 (227)
                      .++....
T Consensus       104 ~~~~~~~  110 (116)
T 1x4b_A          104 VAREESG  110 (116)
T ss_dssp             SSCCCCC
T ss_pred             CCCccCC
Confidence            8876543

>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=99.78  E-value=7.3e-19  Score=126.04  Aligned_cols=85  Identities=27%  Similarity=0.454  Sum_probs=80.1

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      ....+.++|||+|||..+++++|+++|++| .|..|.|++++.+++++|||||+|.+.++|++||+ +++ ..|+|+.|.
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng-~~i~g~~l~  119 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG-MELDGRRIR  119 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTT-CCSSSSCCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCC-CEECCEEEE
Confidence            345677999999999999999999999999 99999999999999999999999999999999999 999 999999999


Q ss_pred             EEecCCCC
Q psy1680          86 LDIADGKR   93 (227)
Q Consensus        86 v~~~~~~~   93 (227)
                      |.++.+++
T Consensus       120 V~~a~~~~  127 (129)
T 2kxn_B          120 VDFSITKR  127 (129)
T ss_dssp             ESCCSSSS
T ss_pred             EEEecCCC
Confidence            99998765

>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=99.78  E-value=1e-18  Score=125.28  Aligned_cols=74  Identities=18%  Similarity=0.224  Sum_probs=69.2

Q ss_pred             CCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         152 GGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..+..+|||+|||..+  ++++|+++|++||.|..|.|++|+.++.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        43 ~~~~~~l~V~nLp~~~--te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~  116 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYT--TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR  116 (129)
T ss_dssp             CCCSSCBCEETCTTSC--CHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSS
T ss_pred             CCCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            3567899999997665  7999999999999999999999999999999999999999999999999999999986

>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=99.78  E-value=4.4e-18  Score=117.14  Aligned_cols=87  Identities=22%  Similarity=0.356  Sum_probs=80.2

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeE
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVR   85 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~   85 (227)
                      ..+..+.++|||+|||..+++++|+++|++| .|..|.|+.++.+++++|||||+|.+.++|.+||. ++ ..|+|+.|.
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~-~~~~g~~l~   86 (103)
T 2cqg_A            9 KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QR-HMIDGRWCD   86 (103)
T ss_dssp             SCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SC-EEETTEEEE
T ss_pred             CCccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH-cC-CeeCCeEEE
Confidence            3456778999999999999999999999999 99999999999999999999999999999999998 57 899999999


Q ss_pred             EEecCCCCCC
Q psy1680          86 LDIADGKRND   95 (227)
Q Consensus        86 v~~~~~~~~~   95 (227)
                      |.++.++...
T Consensus        87 v~~a~~~~~~   96 (103)
T 2cqg_A           87 CKLPNSKQSQ   96 (103)
T ss_dssp             EECCCTTCCC
T ss_pred             EEecCCCCcC
Confidence            9999887653

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.78  E-value=4.7e-19  Score=117.67  Aligned_cols=73  Identities=15%  Similarity=0.145  Sum_probs=68.3

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||...  ++++|+++|++||.|.+|.|++++.++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus         5 ~~~~~l~V~nl~~~~--~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   77 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEV--DDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGR   77 (85)
T ss_dssp             CCSSEEEEECCCTTC--CHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEECCCCCC--CHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            467899999997655  7899999999999999999999999999999999999999999999999999999985

>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=99.78  E-value=3.2e-18  Score=117.85  Aligned_cols=87  Identities=22%  Similarity=0.403  Sum_probs=78.6

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeE
Q psy1680           6 KTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQ   83 (227)
Q Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~   83 (227)
                      ...+..+.++|||+|||..+++++|+++|++| .|..|.|+.++.+  ++|||||+|.+.++|.+||+ +++ ..|.|+.
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~   84 (103)
T 2cqi_A            8 MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNG-RKILGKE   84 (103)
T ss_dssp             CCCCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTT-EEETTEE
T ss_pred             CCCCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCC-CCcCCCe
Confidence            34456778999999999999999999999999 9999999988654  58999999999999999999 999 9999999


Q ss_pred             eEEEecCCCCCC
Q psy1680          84 VRLDIADGKRND   95 (227)
Q Consensus        84 l~v~~~~~~~~~   95 (227)
                      |.|.++.++...
T Consensus        85 l~V~~a~~~~~~   96 (103)
T 2cqi_A           85 VKVNWATTPSSQ   96 (103)
T ss_dssp             EEEEECCCTTCC
T ss_pred             EEEEECCCCccc
Confidence            999999876653

>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=99.78  E-value=1.2e-18  Score=122.37  Aligned_cols=73  Identities=19%  Similarity=0.160  Sum_probs=68.2

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++..+|||+|||..+  ++++|+++|+.||.|.+|+|++++.++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        23 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   95 (115)
T 2cpz_A           23 PEGANLFIYHLPQEF--GDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMK   95 (115)
T ss_dssp             STTCCEEEESCCSSC--CHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCcEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            456899999997655  7899999999999999999999999999999999999999999999999999999885

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.78  E-value=2.8e-19  Score=117.77  Aligned_cols=70  Identities=11%  Similarity=0.104  Sum_probs=64.1

Q ss_pred             CcceeccCCCCCCC----ChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSN----SMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~----~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++|||+|||...++    ++++|+++|++||.|.+|.|+  +.+|.++|||||+|.+.++|.+|++.|||..|+||
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~   75 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   75 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSS
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCc
Confidence            57999999876654    679999999999999999988  46799999999999999999999999999999986

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.78  E-value=1.1e-19  Score=124.61  Aligned_cols=82  Identities=18%  Similarity=0.263  Sum_probs=77.5

Q ss_pred             CCCCceEEEcCCCC------CCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC
Q psy1680          10 TEPPYTAFVGNLPN------GITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG   81 (227)
Q Consensus        10 ~~~~~~l~V~nLp~------~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g   81 (227)
                      ...+++|||+|||.      ++++++|+++|++| .|..|.|++++.|++++|||||+|.+.++|.+||+ +|+ ..+.|
T Consensus         3 ~~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng-~~~~g   81 (100)
T 3ns6_A            3 LGSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG-KRLDL   81 (100)
T ss_dssp             SCGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTT-CBSSS
T ss_pred             CCcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCC-cccCC
Confidence            34578999999999      99999999999999 99999999999999999999999999999999998 999 99999


Q ss_pred             -eEeEEEecCCC
Q psy1680          82 -LQVRLDIADGK   92 (227)
Q Consensus        82 -~~l~v~~~~~~   92 (227)
                       +.|.|.++.++
T Consensus        82 ~r~l~V~~a~~~   93 (100)
T 3ns6_A           82 KHRLFLYTMKDV   93 (100)
T ss_dssp             SCBCEEEESHHH
T ss_pred             CeEEEEEECchh
Confidence             99999998764

>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=99.78  E-value=2.1e-18  Score=119.58  Aligned_cols=82  Identities=22%  Similarity=0.350  Sum_probs=76.8

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      +....+.++|||+|||+.+++++|+++|++| .|..+.|+.++ +++++|||||+|.+.++|.+||+ |++ ..|.|+.|
T Consensus        23 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l  100 (107)
T 3ulh_A           23 GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNG-VPLDGRPM  100 (107)
T ss_dssp             -CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTT-CEETTEEC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCC-CEeCCcEE
Confidence            3455778999999999999999999999999 99999999998 89999999999999999999999 999 99999999


Q ss_pred             EEEecC
Q psy1680          85 RLDIAD   90 (227)
Q Consensus        85 ~v~~~~   90 (227)
                      .|.++.
T Consensus       101 ~V~~a~  106 (107)
T 3ulh_A          101 NIQLVT  106 (107)
T ss_dssp             EEEEEC
T ss_pred             EEEEeC
Confidence            999975

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=6.7e-19  Score=121.22  Aligned_cols=71  Identities=10%  Similarity=0.172  Sum_probs=66.0

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||+.+  ++++|+++|++||.|.+|+|++|+. |.++|||||+|.+.++|.+|++ ++|..|+||
T Consensus         9 ~~~~~lfV~~Lp~~~--te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr   79 (103)
T 1s79_A            9 VKNRSVYIKGFPTDA--TLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKET   79 (103)
T ss_dssp             SGGGCEEEECCCTTC--CHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTT
T ss_pred             CCCCEEEEECCCCCC--CHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCE
Confidence            456899999997665  8999999999999999999999987 9999999999999999999999 899999986

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.78  E-value=2.1e-18  Score=116.31  Aligned_cols=85  Identities=20%  Similarity=0.262  Sum_probs=78.0

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      .+..+.++|||+|||..+++++|+++|++| .|..+.|+++  +++++|||||+|.+.++|.+|++ +++ ..++|+.|.
T Consensus         3 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g-~~~~g~~l~   79 (92)
T 2dgv_A            3 SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNG-MKLSGREID   79 (92)
T ss_dssp             CSSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTT-CCBTTBCCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCC-CEECCcEEE
Confidence            456778999999999999999999999999 9999999874  68899999999999999999999 999 999999999


Q ss_pred             EEecCCCCCC
Q psy1680          86 LDIADGKRND   95 (227)
Q Consensus        86 v~~~~~~~~~   95 (227)
                      |.++.+....
T Consensus        80 v~~a~~~~~~   89 (92)
T 2dgv_A           80 VRIDRNASGP   89 (92)
T ss_dssp             CEECSCCSSC
T ss_pred             EEEcCCCCCC
Confidence            9999876543

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.78  E-value=7e-19  Score=120.77  Aligned_cols=75  Identities=32%  Similarity=0.575  Sum_probs=70.4

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecCC
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~~   91 (227)
                      ++|||+|||.++|+++|+++|++| .|..+.++.+     ++|||||+|.+.++|.+|++ +++ ..++|+.|.|.++.+
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~V~~a~~   74 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDG-KVICGSRVRVELSTG   74 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHH-SCSSSCCCEEEESSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCC-CeECCcEEEEEEccC
Confidence            589999999999999999999999 9999999876     58999999999999999999 999 999999999999987


Q ss_pred             CCC
Q psy1680          92 KRN   94 (227)
Q Consensus        92 ~~~   94 (227)
                      +..
T Consensus        75 ~~~   77 (101)
T 2hvz_A           75 MPR   77 (101)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            664

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=2.9e-19  Score=118.76  Aligned_cols=73  Identities=19%  Similarity=0.265  Sum_probs=68.0

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .++.+|||+|||...  ++++|+++|++||.|.+|.|++++.++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus         3 ~~~~~l~v~nlp~~~--t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   75 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGT--TDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQ   75 (85)
T ss_dssp             CCCCEEEEESCCTTC--CHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEE
T ss_pred             CCCcEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeE
Confidence            357799999997655  7999999999999999999999999999999999999999999999999999999875

>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=99.77  E-value=1.5e-18  Score=115.94  Aligned_cols=82  Identities=22%  Similarity=0.401  Sum_probs=76.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCC-eecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDR-FKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~-~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ...++|||+|||.++++++|+++|++| .|..+.|+.++.++. ++|||||+|.+.++|.+|++ +|+ ..++|+.|.|.
T Consensus         2 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~v~   80 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDG-GQIDGQEITAT   80 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTT-CEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCC-CeECCeEEEEE
Confidence            357899999999999999999999999 999999999887665 89999999999999999999 999 99999999999


Q ss_pred             ecCCCC
Q psy1680          88 IADGKR   93 (227)
Q Consensus        88 ~~~~~~   93 (227)
                      ++.+.+
T Consensus        81 ~a~~~~   86 (88)
T 4a8x_A           81 AVLAPW   86 (88)
T ss_dssp             EECCCC
T ss_pred             ECCCCC
Confidence            997654

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=9.8e-19  Score=118.62  Aligned_cols=73  Identities=22%  Similarity=0.277  Sum_probs=68.3

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +++.+|||+|||..+  ++++|+++|++||.|..|.|++++.++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus         3 ~~~~~l~v~nlp~~~--t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   75 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNI--TEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGR   75 (95)
T ss_dssp             SCCCEEEEESCCTTC--CHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSS
T ss_pred             CCCcEEEEeCCCCCC--CHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCc
Confidence            457899999997655  7999999999999999999999999999999999999999999999999999999986

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.77  E-value=2.1e-19  Score=129.85  Aligned_cols=73  Identities=18%  Similarity=0.161  Sum_probs=67.9

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|..|.|++++.++.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        45 ~~~~~l~V~nLp~~~--te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~  117 (135)
T 2lea_A           45 EGMTSLKVDNLTYRT--SPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGR  117 (135)
T ss_dssp             GGCCCEEEECCCSSC--HHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSS
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            346789999997655  8999999999999999999999999999999999999999999999999999999986

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.77  E-value=2.2e-18  Score=119.93  Aligned_cols=85  Identities=21%  Similarity=0.357  Sum_probs=76.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLD   87 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~   87 (227)
                      ...+.++|||+|||.++++++|+++|++| .|..|.|++++.+++++|||||+|.+.++|.+||+..+ ..++|+.|.|.
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSC-EEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCC-CcCCCEEEEEE
Confidence            35667999999999999999999999999 99999999999999999999999999999999999668 99999999999


Q ss_pred             ecCCCCC
Q psy1680          88 IADGKRN   94 (227)
Q Consensus        88 ~~~~~~~   94 (227)
                      ++.++..
T Consensus       100 ~a~~~~~  106 (109)
T 2rs2_A          100 VAFPRRA  106 (109)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9987654

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=4.3e-18  Score=114.52  Aligned_cols=83  Identities=20%  Similarity=0.308  Sum_probs=77.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEe
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDI   88 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~   88 (227)
                      +....++|||+|||+++++++|+++|++|.|..+.|+++ .+++++|||||+|.+.++|.+||.+++ ..|+|+.|.|.+
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~~~g-~~~~gr~i~v~~   83 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALKCNR-EYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTSCCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHHSCS-EEETTEEEEEEE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhCCceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHHhCC-ceeCCcEEEEEE
Confidence            456779999999999999999999999998889999998 789999999999999999999999999 999999999999


Q ss_pred             cCCCC
Q psy1680          89 ADGKR   93 (227)
Q Consensus        89 ~~~~~   93 (227)
                      +.++.
T Consensus        84 a~~~~   88 (91)
T 2dgw_A           84 EKSGP   88 (91)
T ss_dssp             ESSCC
T ss_pred             CCcCC
Confidence            98764

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=9.1e-19  Score=120.36  Aligned_cols=73  Identities=22%  Similarity=0.362  Sum_probs=68.3

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|++||.|..|.|++++.++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        10 ~~~~~l~v~nLp~~~--t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   82 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDT--NEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGR   82 (102)
T ss_dssp             CCCSEEEEESCCTTC--CHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSC
T ss_pred             CCCCEEEEECCCCCC--CHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCe
Confidence            467899999997655  7999999999999999999999999999999999999999999999999999999986

>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=99.77  E-value=1.8e-18  Score=120.72  Aligned_cols=73  Identities=23%  Similarity=0.343  Sum_probs=68.4

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcC------CccccC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG------RITVDG  226 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~------g~~i~g  226 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|.+|+|++|+.++.++|||||+|.+.++|.+|++.||      |..|+|
T Consensus        13 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDS--EEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCEEEESCCTTC--CHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCCEEEEECCCCCC--CHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            467899999997665  799999999999999999999999999999999999999999999999999      999988


Q ss_pred             C
Q psy1680         227 L  227 (227)
Q Consensus       227 r  227 (227)
                      +
T Consensus        91 ~   91 (111)
T 1x4h_A           91 R   91 (111)
T ss_dssp             C
T ss_pred             E
Confidence            6

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.77  E-value=1.5e-18  Score=122.44  Aligned_cols=81  Identities=21%  Similarity=0.354  Sum_probs=76.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      +..+.++|||+|||.++++++|+++|++| .|..+.|++++.+++++|||||+|.+.++|++||+ +|+ ..|+|+.|+|
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~l~V  114 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNG-FQVGTKRLKV  114 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCC-CEETTEECCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCC-CEECCEEEEE
Confidence            45667999999999999999999999999 99999999999999999999999999999999999 999 9999999999


Q ss_pred             EecC
Q psy1680          87 DIAD   90 (227)
Q Consensus        87 ~~~~   90 (227)
                      .+++
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            9874

>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=99.77  E-value=6.4e-19  Score=119.86  Aligned_cols=72  Identities=15%  Similarity=0.238  Sum_probs=67.3

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      |+++|||+|||...  ++++|+++|+.||.|.+|+|++++.+|.++|||||+|.+.++|.+|++.|||..|+||
T Consensus         1 P~~~l~V~nLp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   72 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQ--TEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSR   72 (96)
T ss_dssp             CCSEEEEESCCTTC--CHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCcEEEEECCCCCC--CHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            46789999997655  7999999999999999999999999999999999999999999999999999999985

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=8.4e-19  Score=119.88  Aligned_cols=73  Identities=22%  Similarity=0.338  Sum_probs=68.4

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceE-EEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLV-SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~-~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|++||.|. +|+|++++.++.++|||||+|.+.++|++|++.|||..|+|+
T Consensus         7 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   80 (99)
T 2div_A            7 GMAASLWMGDLEPYM--DENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGA   80 (99)
T ss_dssp             SSSSEEEECSCCTTC--CHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSC
T ss_pred             CCccEEEEeCCCCCC--CHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCC
Confidence            467899999997655  7999999999999999 999999999999999999999999999999999999999986

>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=99.77  E-value=5.2e-18  Score=118.03  Aligned_cols=85  Identities=26%  Similarity=0.449  Sum_probs=76.3

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      +.+..+.++|||+|||.++|+++|+++|++| .|..|.|+.+   +.+++||||+|.+.++|++||+ +++ ..|+|+.|
T Consensus        16 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~l   91 (109)
T 1x4a_A           16 GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDG-YDYDGYRL   91 (109)
T ss_dssp             CCCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTT-CEETTEEC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCC-CEECCeEE
Confidence            3456678999999999999999999999999 9999999654   5678999999999999999998 999 99999999


Q ss_pred             EEEecCCCCCC
Q psy1680          85 RLDIADGKRND   95 (227)
Q Consensus        85 ~v~~~~~~~~~   95 (227)
                      .|.++.++...
T Consensus        92 ~V~~a~~~~~~  102 (109)
T 1x4a_A           92 RVEFPRSGRGT  102 (109)
T ss_dssp             EEECCCCCCCC
T ss_pred             EEEEcccCCCC
Confidence            99999876543

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.77  E-value=7.2e-19  Score=117.29  Aligned_cols=72  Identities=19%  Similarity=0.252  Sum_probs=67.0

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +..+|||+|||...  ++++|+++|++||.|.+|.|++++.++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus         5 ~~~~l~v~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   76 (87)
T 3bs9_A            5 SHFHVFVGDLSPEI--TTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGR   76 (87)
T ss_dssp             -CEEEEEESCCTTC--CHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CceEEEEeCCCCCC--CHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            56789999997655  7999999999999999999999999999999999999999999999999999999985

>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=99.77  E-value=1.7e-18  Score=117.36  Aligned_cols=83  Identities=27%  Similarity=0.397  Sum_probs=76.4

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      +.+..+.++|||+|||+.+++++|+++|++| .|..+.|+.++. ++++|||||+|.+.++|.+||+ +++ ..++|+.|
T Consensus        10 ~~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l   87 (95)
T 2ywk_A           10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNG-IRLYGRPI   87 (95)
T ss_dssp             --CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTT-CEETTEEC
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCC-CEECCCEE
Confidence            3456778999999999999999999999999 999999999976 8999999999999999999999 999 99999999


Q ss_pred             EEEecCC
Q psy1680          85 RLDIADG   91 (227)
Q Consensus        85 ~v~~~~~   91 (227)
                      .|.+++.
T Consensus        88 ~V~~a~~   94 (95)
T 2ywk_A           88 NVSGPSS   94 (95)
T ss_dssp             EEECCCC
T ss_pred             EEEEcCC
Confidence            9999763

>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=99.77  E-value=2.1e-18  Score=115.48  Aligned_cols=81  Identities=30%  Similarity=0.444  Sum_probs=76.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEecC
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~~   90 (227)
                      ..++|||+|||.++++++|+++|++| .|..+.++.++.+++++|||||+|.+.++|++|+.+++ ..+.|+.|.|.++.
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g-~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDE-SLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTT-CEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCC-CEECCcEEEEEEcc
Confidence            35899999999999999999999999 99999999999899999999999999999999999999 99999999999987


Q ss_pred             CCC
Q psy1680          91 GKR   93 (227)
Q Consensus        91 ~~~   93 (227)
                      ++.
T Consensus        84 ~~~   86 (89)
T 3ucg_A           84 TNR   86 (89)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            643

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=9.3e-19  Score=120.56  Aligned_cols=73  Identities=16%  Similarity=0.120  Sum_probs=68.3

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|..|.|++++.++.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        11 ~~~~~l~V~nLp~~~--t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   83 (103)
T 2dnm_A           11 DGMITLKVDNLTYRT--SPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGR   83 (103)
T ss_dssp             SCCCEEEEESCCTTC--CHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTB
T ss_pred             CCCeEEEEeCCCCCC--CHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            456899999997655  7999999999999999999999999999999999999999999999999999999985

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.77  E-value=2.8e-18  Score=121.06  Aligned_cols=74  Identities=20%  Similarity=0.192  Sum_probs=68.8

Q ss_pred             CCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         152 GGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .++..+|||+|||...  ++++|+++|++||.|.+|+|++++.++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        37 ~~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  110 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEF--TDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTK  110 (118)
T ss_dssp             CCCSEEEEEECSCTTC--CHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTE
T ss_pred             CCCCCEEEEeCCCCCC--CHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            3567899999997655  7999999999999999999999999999999999999999999999999999999985

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.77  E-value=5.8e-19  Score=126.97  Aligned_cols=85  Identities=25%  Similarity=0.397  Sum_probs=78.7

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEE--EEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCc----ee
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVS--VRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRI----TV   79 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~--v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~----~~   79 (227)
                      ....+.++|||+|||+++|+++|+++|++| .|..  |+|++|+.+++++|||||+|.+. +|.+||. +++ .    .+
T Consensus        18 ~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g-~~~~~~~   95 (131)
T 2m2b_A           18 SSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQA-LHPPLTI   95 (131)
T ss_dssp             CCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTT-CCCSCCG
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcC-CCCCccC
Confidence            345677999999999999999999999999 9966  99999999999999999999999 9999999 999 8    99


Q ss_pred             CCeEeEEEecCCCCC
Q psy1680          80 DGLQVRLDIADGKRN   94 (227)
Q Consensus        80 ~g~~l~v~~~~~~~~   94 (227)
                      +|+.|.|.++.++..
T Consensus        96 ~gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           96 DGKTINVEFAKGSKR  110 (131)
T ss_dssp             GGCCCCCEECCCSCC
T ss_pred             CCEEEEEEECCCCCC
Confidence            999999999987654

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.77  E-value=1.6e-18  Score=118.58  Aligned_cols=73  Identities=19%  Similarity=0.227  Sum_probs=68.5

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEE--------EEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccc
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVS--------VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV  224 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~--------v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i  224 (227)
                      ++..+|||+|||...  ++++|+++|++||.|..        |+|++++.+|.++|||||+|.+.++|.+|++.|||..|
T Consensus        11 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A           11 SDNNTIFVQGLGENV--TIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             CCCSEEEEECCCSSC--CHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            567899999997655  79999999999999999        99999999999999999999999999999999999999


Q ss_pred             cCC
Q psy1680         225 DGL  227 (227)
Q Consensus       225 ~gr  227 (227)
                      +||
T Consensus        89 ~g~   91 (99)
T 2la6_A           89 SGN   91 (99)
T ss_dssp             SSS
T ss_pred             CCc
Confidence            986

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.8e-18  Score=118.29  Aligned_cols=72  Identities=18%  Similarity=0.204  Sum_probs=67.2

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|..|.|++++.++.++|||||+|.+.++|.+|++ |+|..|+|+
T Consensus         8 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~   79 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNC--GETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGK   79 (99)
T ss_dssp             SSCCEEEEESCCSSC--CHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSC
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCe
Confidence            467899999997655  899999999999999999999999999999999999999999999999 999999986

>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=99.77  E-value=8.8e-18  Score=116.69  Aligned_cols=82  Identities=18%  Similarity=0.257  Sum_probs=74.8

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC--
Q psy1680           6 KTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG--   81 (227)
Q Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g--   81 (227)
                      .+.+....++|||+|||+++++++|+++|++| .|..|.|+.+       |||||+|.+.++|++||+ ||+ ..|.|  
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g-~~~~g~~   79 (108)
T 1x4c_A            8 GPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDN-TKFRSHE   79 (108)
T ss_dssp             SCCCCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSS-EEEECTT
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCc-CCccCCc
Confidence            34456778999999999999999999999999 9999999875       899999999999999999 999 99999  


Q ss_pred             ---eEeEEEecCCCCCC
Q psy1680          82 ---LQVRLDIADGKRND   95 (227)
Q Consensus        82 ---~~l~v~~~~~~~~~   95 (227)
                         +.|.|.++.++...
T Consensus        80 ~~~~~i~V~~a~~~~~~   96 (108)
T 1x4c_A           80 GETAYIRVKVDGPRSPS   96 (108)
T ss_dssp             SCEEEEEEEESSCCSCC
T ss_pred             CcceEEEEEeCCCCCCC
Confidence               99999999886653

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.77  E-value=1.7e-18  Score=121.65  Aligned_cols=73  Identities=21%  Similarity=0.274  Sum_probs=68.1

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|..|.|++++.++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        13 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   85 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEI--TTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGR   85 (115)
T ss_dssp             TTCEEEEEESCCTTC--CHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTE
T ss_pred             CCCcEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            467899999997655  7999999999999999999999999999999999999999999999999999999885

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=6.8e-19  Score=116.95  Aligned_cols=80  Identities=20%  Similarity=0.324  Sum_probs=74.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ..+.++|||+|||+++++++|+++|++| .|..+.|+.++.+++++|||||+|.+.++|.+|++ +|+ ..+.|+.|++.
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~~~~~   80 (85)
T 1x4e_A            2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA-SGVQAQMAKQS   80 (85)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHH-HTCCEESCCSS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcC-CeEeeEEEeec
Confidence            4578999999999999999999999999 99999999999999999999999999999999999 999 99999998876


Q ss_pred             ecC
Q psy1680          88 IAD   90 (227)
Q Consensus        88 ~~~   90 (227)
                      ++.
T Consensus        81 ~~~   83 (85)
T 1x4e_A           81 GPS   83 (85)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.77  E-value=4.1e-18  Score=117.58  Aligned_cols=85  Identities=19%  Similarity=0.190  Sum_probs=77.3

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEE-EEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVR   85 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~-v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~   85 (227)
                      .+....++|||+|||+++|+++|+++|++| .|.. |.|+.+ .+++++|||||+|.+.++|.+||..++ ..++|+.|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~-~~~~gr~i~   87 (104)
T 1wg5_A           10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKKHK-ERIGHRYIE   87 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTTTT-CCSSSSCCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHhCc-chhCCcEEE
Confidence            345678999999999999999999999999 8887 888888 789999999999999999999999888 999999999


Q ss_pred             EEecCCCCC
Q psy1680          86 LDIADGKRN   94 (227)
Q Consensus        86 v~~~~~~~~   94 (227)
                      |.++.++..
T Consensus        88 v~~~~~~~~   96 (104)
T 1wg5_A           88 IFKSSRAEV   96 (104)
T ss_dssp             EEEECTTTS
T ss_pred             EEECCHHHH
Confidence            999876553

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.77  E-value=2.7e-18  Score=119.01  Aligned_cols=73  Identities=18%  Similarity=0.214  Sum_probs=68.1

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeec-CCCCcccceEEEEEcCHHHHHHHHHHc-CCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKD-KETDRFKGFCYVEFVDVENLRQALLKD-GRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d-~~t~~~~g~afV~F~~~~~a~~Al~~l-~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|..|+|+++ +.++.++|||||+|.+.++|.+|++.| ||..|+|+
T Consensus        13 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~   87 (107)
T 2cph_A           13 QTTSKILVRNIPFQA--NQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGR   87 (107)
T ss_dssp             SCCCCEEEESCCTTC--CHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSC
T ss_pred             CCCCEEEEeCCCCcC--CHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCC
Confidence            567899999997655  79999999999999999999999 789999999999999999999999999 99999986

>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=99.77  E-value=1.1e-18  Score=119.31  Aligned_cols=73  Identities=21%  Similarity=0.179  Sum_probs=68.2

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|.+|.|++++.++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus         6 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   78 (99)
T 1whw_A            6 SGSGRLFVRNLSYTS--SEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGR   78 (99)
T ss_dssp             CSCEEEEEECCCTTC--CHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSC
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            457899999997655  7999999999999999999999998999999999999999999999999999999986

>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=99.76  E-value=5.7e-19  Score=121.78  Aligned_cols=85  Identities=33%  Similarity=0.524  Sum_probs=79.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ...+.++|||+|||..+++++|+++|++| .|..+.|+.++.++.++|||||+|.+.++|.+|++ +++ ..+.|+.|.|
T Consensus         4 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~v   82 (104)
T 1p1t_A            4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNG-REFSGRALRV   82 (104)
T ss_dssp             SHHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSS-BSCSSSCBEE
T ss_pred             cCCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCC-CeeCCcEEEE
Confidence            34556899999999999999999999999 99999999999999999999999999999999998 999 9999999999


Q ss_pred             EecCCCCC
Q psy1680          87 DIADGKRN   94 (227)
Q Consensus        87 ~~~~~~~~   94 (227)
                      .++.++..
T Consensus        83 ~~a~~~~~   90 (104)
T 1p1t_A           83 DNAASEKN   90 (104)
T ss_dssp             EETTCTTH
T ss_pred             EeCCCccc
Confidence            99987654

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.76  E-value=1.1e-18  Score=115.37  Aligned_cols=70  Identities=14%  Similarity=0.170  Sum_probs=65.9

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+|||+|||...  ++++|+++|++||.|.+|.|++++.++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus         2 ~~l~V~nlp~~~--t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~   71 (83)
T 3md1_A            2 FNLFVGDLNVNV--DDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGR   71 (83)
T ss_dssp             EEEEEECCCTTC--CHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             eEEEEeCCCCCC--CHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCc
Confidence            479999997655  7999999999999999999999999999999999999999999999999999999885

>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=99.76  E-value=1.2e-18  Score=118.23  Aligned_cols=81  Identities=17%  Similarity=0.206  Sum_probs=74.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      .++.++|||+|||+.+++++|+++|++| .|..+.++.++.+++++|||||+|.+.++|++||+ +++ ..|+|+.|+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g-~~~~gr~l~v~   90 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLND-RPIGSRKVKLS   90 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTT-CEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCC-CeECCcEEEEE
Confidence            4456999999999999999999999999 99889999988999999999999999999999999 999 99999999999


Q ss_pred             ecCC
Q psy1680          88 IADG   91 (227)
Q Consensus        88 ~~~~   91 (227)
                      ++..
T Consensus        91 ~a~s   94 (95)
T 2ek1_A           91 GPSS   94 (95)
T ss_dssp             CCC-
T ss_pred             eccC
Confidence            8753

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.76  E-value=1.6e-18  Score=120.41  Aligned_cols=73  Identities=21%  Similarity=0.220  Sum_probs=68.4

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +++.+|||+|||...  ++++|+++|++||.|..|.|++++.+|.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        24 ~~~~~l~V~nLp~~~--te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~   96 (108)
T 2jrs_A           24 AGPMRLYVGSLHFNI--TEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGR   96 (108)
T ss_dssp             SSCEEEEEECCCSSC--CHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSS
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            467899999997655  8999999999999999999999999999999999999999999999999999999986

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=8e-19  Score=120.66  Aligned_cols=73  Identities=15%  Similarity=0.145  Sum_probs=68.2

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|..|.|++++.++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        10 ~~~~~l~V~nLp~~~--t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   82 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEV--DDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGR   82 (102)
T ss_dssp             CCCSCEEEESCCSSC--CHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            467899999997655  7999999999999999999999999999999999999999999999999999999885

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.4e-18  Score=119.57  Aligned_cols=81  Identities=14%  Similarity=0.339  Sum_probs=75.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLD   87 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~   87 (227)
                      ...+.++|||+|||+++|+++|+++|++| .|..|.|++++. ++++|||||+|.+.++|.+||.+++ ..++|+.|.|.
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~~~~-~~~~gr~l~V~   84 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLIL   84 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHTSSC-CCCTTTTCEEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHHcCC-CEECCEEEEEE
Confidence            34567999999999999999999999999 999999999987 9999999999999999999999999 99999999999


Q ss_pred             ecCC
Q psy1680          88 IADG   91 (227)
Q Consensus        88 ~~~~   91 (227)
                      ++..
T Consensus        85 ~~~~   88 (103)
T 1s79_A           85 FKDD   88 (103)
T ss_dssp             EHHH
T ss_pred             EchH
Confidence            8764

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.9e-18  Score=121.62  Aligned_cols=73  Identities=12%  Similarity=0.140  Sum_probs=67.2

Q ss_pred             CCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         152 GGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..+..+|||+|||..+  ++++|+++|+.||.|..|+|++++.++.++|||||+|.+.++|.+|++.+++ .|+||
T Consensus        14 ~~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~   86 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHT--TDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGR   86 (116)
T ss_dssp             SCSSSEEEEECCCSSC--CHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTE
T ss_pred             CCCCCEEEEeCCCCCC--CHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCE
Confidence            3567899999997655  7999999999999999999999999999999999999999999999999998 78875

>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=99.76  E-value=3.5e-18  Score=118.87  Aligned_cols=84  Identities=17%  Similarity=0.266  Sum_probs=77.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-C-eEEEEEe-ecCCCCCeecEEEEEeCCHHHHHHHHH-hC--CCceeCCeE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-K-LVSVRLV-KDKETDRFKGFCYVEFVDVENLRQALL-KD--GRITVDGLQ   83 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~-i~~v~i~-~~~~~~~~~g~afv~f~~~~~a~~al~-~~--~~~~~~g~~   83 (227)
                      ..+.++|||+|||..+++++|+++|++| . |..+.|+ .++.+++++|||||+|.+.++|.+|++ ++  + ..++|+.
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~-~~~~g~~   83 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGR-IQLWGHQ   83 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCC-SCBTTBC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCC-ceecCCe
Confidence            4567999999999999999999999999 7 9999998 788889999999999999999999999 87  6 8999999


Q ss_pred             eEEEecCCCCC
Q psy1680          84 VRLDIADGKRN   94 (227)
Q Consensus        84 l~v~~~~~~~~   94 (227)
                      |.|.++.++..
T Consensus        84 l~V~~a~~~~~   94 (109)
T 2dis_A           84 IAVDWAEPEID   94 (109)
T ss_dssp             CEEEESCSSCS
T ss_pred             EEEEEcCCCCC
Confidence            99999987665

>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=99.76  E-value=4e-18  Score=115.92  Aligned_cols=82  Identities=13%  Similarity=0.201  Sum_probs=75.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHH----hcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCe
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVE----RFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGL   82 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~----~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~   82 (227)
                      +....++|||+|||+.+++++|+    ++|++| .|..|.|+.++.+   +|||||+|.+.++|.+||+ +|+ ..++|+
T Consensus         5 ~~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g-~~~~gr   80 (96)
T 2dgx_A            5 SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHR-YKIGSK   80 (96)
T ss_dssp             CCSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTT-EEETTE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCC-CEECCe
Confidence            44567899999999999999999    999999 9999999998765   7899999999999999999 999 999999


Q ss_pred             EeEEEecCCCCC
Q psy1680          83 QVRLDIADGKRN   94 (227)
Q Consensus        83 ~l~v~~~~~~~~   94 (227)
                      .|+|.++.++..
T Consensus        81 ~l~V~~a~~~~~   92 (96)
T 2dgx_A           81 KILVSLATGASG   92 (96)
T ss_dssp             EEEEEECCCSSC
T ss_pred             EEEEEEcCCCCC
Confidence            999999987654

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=8.1e-18  Score=117.46  Aligned_cols=87  Identities=17%  Similarity=0.273  Sum_probs=78.3

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHH---hcccCC-CeEEEEEeecCCCC---CeecEEEEEeCCHHHHHHHHH-hCCCce
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVE---RFFPEQ-KLVSVRLVKDKETD---RFKGFCYVEFVDVENLRQALL-KDGRIT   78 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~---~~f~~~-~i~~v~i~~~~~~~---~~~g~afv~f~~~~~a~~al~-~~~~~~   78 (227)
                      .......++|||+|||+++++++|+   ++|++| .|..+.|++++.++   +++|||||+|.+.++|++||+ ||+ ..
T Consensus         9 ~~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng-~~   87 (111)
T 2cpi_A            9 SVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNN-VV   87 (111)
T ss_dssp             CCCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTT-EE
T ss_pred             cccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCC-CE
Confidence            3445667999999999999999999   999999 99999999887644   566999999999999999999 999 99


Q ss_pred             eCCeEeEEEecCCCCC
Q psy1680          79 VDGLQVRLDIADGKRN   94 (227)
Q Consensus        79 ~~g~~l~v~~~~~~~~   94 (227)
                      |+|+.|.|.++.++..
T Consensus        88 ~~gr~l~V~~a~~k~~  103 (111)
T 2cpi_A           88 VDGRTLKASLGTTKYC  103 (111)
T ss_dssp             ETTEEEEEESCCCCSC
T ss_pred             ECCEEEEEEecccccc
Confidence            9999999999987763

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=2e-18  Score=119.29  Aligned_cols=73  Identities=22%  Similarity=0.254  Sum_probs=67.6

Q ss_pred             CCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         152 GGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..+..+|||+|||..+  ++++|+++|+.||.|..|.|++++.++.++|||||+|.+.++|.+||+. ++..|+|+
T Consensus        13 ~~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~   85 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWST--TQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGR   85 (105)
T ss_dssp             SSSSSEECCBSCCTTC--CHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTE
T ss_pred             CCCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCE
Confidence            3567899999997655  7999999999999999999999999999999999999999999999999 99999885

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2.2e-18  Score=119.31  Aligned_cols=73  Identities=19%  Similarity=0.155  Sum_probs=68.2

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .++.+|||+|||..+  ++++|+++|+.||.|.+|.|++++.++.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        21 ~~~~~l~V~nlp~~~--t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   93 (106)
T 1p27_B           21 VEGWILFVTGVHEEA--TEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ   93 (106)
T ss_dssp             TTBEEEEEECCCTTC--CHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCc
Confidence            456789999997655  7999999999999999999999999999999999999999999999999999999986

>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=2.9e-18  Score=119.08  Aligned_cols=82  Identities=22%  Similarity=0.292  Sum_probs=75.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEec
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA   89 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~   89 (227)
                      ....++|||+|||+++|+++|+++|++|.|..|.|++++. ++++|||||+|.+.++|++||.+++ ..|+|+.|.|..+
T Consensus        13 ~~~~~~v~V~nLp~~~te~dl~~~F~~~~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al~~~~-~~~~gr~i~V~~a   90 (109)
T 2dnn_A           13 NPDDLYVSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALKRNR-MLMIQRYVEVSPA   90 (109)
T ss_dssp             CHHHHEEEEECCCSSCCHHHHHHHTTTSCCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHHHTTT-EEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhccCCeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCC-CeECCeEEEEEEC
Confidence            3445899999999999999999999999888999999976 9999999999999999999999999 9999999999888


Q ss_pred             CCCC
Q psy1680          90 DGKR   93 (227)
Q Consensus        90 ~~~~   93 (227)
                      .++.
T Consensus        91 ~~~~   94 (109)
T 2dnn_A           91 TERQ   94 (109)
T ss_dssp             CHHH
T ss_pred             Cccc
Confidence            6543

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.76  E-value=6.1e-19  Score=118.54  Aligned_cols=80  Identities=13%  Similarity=0.214  Sum_probs=69.7

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC---CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ---KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~---~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      .+|||+|||+++|+++|+++|++|   .|..+.|+.++.+++++|||||+|.+.++|++||+ +|+ ..++|+.|.|.++
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g-~~~~gr~i~V~~~   80 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPK-RELHGQNPVVTPS   80 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGG-SCSSSCCCEECCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCC-CeeCCEEEEEEEC
Confidence            579999999999999999999999   38899999999999999999999999999999998 999 9999999999999


Q ss_pred             CCCCC
Q psy1680          90 DGKRN   94 (227)
Q Consensus        90 ~~~~~   94 (227)
                      .++..
T Consensus        81 ~~~~~   85 (90)
T 3p5t_L           81 NKLEH   85 (90)
T ss_dssp             -----
T ss_pred             CCCcc
Confidence            87654

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.76  E-value=1.3e-18  Score=122.32  Aligned_cols=69  Identities=17%  Similarity=0.190  Sum_probs=63.4

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +.+|||+|||+.+  ++++|+++|++||.|.+|+|++|.  +.++|||||+|.+.++|.+|++.|+|..|+||
T Consensus         5 ~~~lfV~nLp~~~--te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~   73 (115)
T 4f25_A            5 SGNIFIKNLDKSI--DNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDR   73 (115)
T ss_dssp             CCEEEEESCCTTC--CHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             CCEEEECCCCCCC--CHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            4579999997655  899999999999999999999986  56899999999999999999999999999985

>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=99.76  E-value=1.4e-18  Score=117.89  Aligned_cols=72  Identities=21%  Similarity=0.172  Sum_probs=66.7

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||+..  ++++|+++|++||.|.+|.|++++. +.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        14 ~~~~~l~v~nlp~~~--~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   85 (95)
T 2ywk_A           14 EADRTVFVGNLEARV--REEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGR   85 (95)
T ss_dssp             TGGGEEEEECCCTTC--CHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEECCCCCC--CHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCC
Confidence            467899999997655  7899999999999999999999976 99999999999999999999999999999885

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=1.4e-17  Score=114.24  Aligned_cols=83  Identities=18%  Similarity=0.395  Sum_probs=74.6

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      +....+.++|||+|||..+++++|+++|++| .|   .++.+ .+++++|||||+|.+.++|++||. +++ ..|.|+.|
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~l   83 (101)
T 2fc9_A            9 STWSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNK-REIEGRAI   83 (101)
T ss_dssp             CCCSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSS-EEETTEEE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCC-CEeCCeEE
Confidence            3356678999999999999999999999999 77   55666 678999999999999999999999 999 99999999


Q ss_pred             EEEecCCCCC
Q psy1680          85 RLDIADGKRN   94 (227)
Q Consensus        85 ~v~~~~~~~~   94 (227)
                      .|.++.++..
T Consensus        84 ~v~~a~~~~~   93 (101)
T 2fc9_A           84 RLELQGPRGS   93 (101)
T ss_dssp             EEEECSSCCC
T ss_pred             EEEEcCCCCC
Confidence            9999987654

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.76  E-value=1.6e-18  Score=115.64  Aligned_cols=72  Identities=21%  Similarity=0.264  Sum_probs=65.3

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||+..  ++++|+++|++||.|.+|+|++++.++.++|||||+|.+.++|.+|++. ++..|+||
T Consensus         9 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~~g~   80 (87)
T 3s7r_A            9 EDAGKMFVGGLSWDT--SKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-KEHRLDGR   80 (87)
T ss_dssp             SCTTEEEEECCCTTC--CHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-SCEEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-CCCEECCE
Confidence            467899999997655  7999999999999999999999999999999999999999999999976 66778775

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.76  E-value=1.8e-18  Score=124.40  Aligned_cols=72  Identities=25%  Similarity=0.346  Sum_probs=66.8

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEE--EEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCc----cccC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVS--VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRI----TVDG  226 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~--v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~----~i~g  226 (227)
                      .+.++|||+|||+.+  ++++|+++|++||.|..  |+|++|+.||+++|||||+|.+. +|.+|++.|||.    .|+|
T Consensus        21 ~~~~~lfV~nL~~~~--te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           21 NANDTIILRNLNPHS--TMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CCCCEEEECSCCTTC--CSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            567899999997655  78999999999999977  99999999999999999999999 999999999999    9988


Q ss_pred             C
Q psy1680         227 L  227 (227)
Q Consensus       227 r  227 (227)
                      |
T Consensus        98 r   98 (131)
T 2m2b_A           98 K   98 (131)
T ss_dssp             C
T ss_pred             E
Confidence            6

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.76  E-value=9.5e-19  Score=113.46  Aligned_cols=74  Identities=27%  Similarity=0.372  Sum_probs=71.1

Q ss_pred             eEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEec
Q psy1680          15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA   89 (227)
Q Consensus        15 ~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~   89 (227)
                      +|||+|||+++++++|+++|++| .|..+.++.++.+++++|||||+|.+.++|++|+++++ ..++|++|.|.++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHF-HEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSC-CCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCC-CEECCEEEEEEeC
Confidence            58999999999999999999999 99999999998899999999999999999999999999 9999999999875

>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=99.76  E-value=1.3e-17  Score=116.86  Aligned_cols=83  Identities=13%  Similarity=0.301  Sum_probs=76.5

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCcee------
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITV------   79 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~------   79 (227)
                      ....+.++|||+|||.++++++|+++|++| .|..+.|+.++ ++.++|||||+|.+.++|.+||+ +|+ ..+      
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g-~~~~~~~~~   97 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNG-KFIKTPPGV   97 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBT-CCCCCCTTS
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCC-CEEcCCccc
Confidence            345677999999999999999999999999 99999999998 89999999999999999999999 999 998      


Q ss_pred             --CCeEeEEEecCCC
Q psy1680          80 --DGLQVRLDIADGK   92 (227)
Q Consensus        80 --~g~~l~v~~~~~~   92 (227)
                        .+++|.|.++.++
T Consensus        98 ~~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           98 SAPTEPLLCKFSGPS  112 (114)
T ss_dssp             CCCSSCBEEEECCCS
T ss_pred             cCCCCceeEEccCCC
Confidence              5788999998864

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=6.1e-18  Score=116.44  Aligned_cols=71  Identities=17%  Similarity=0.125  Sum_probs=66.0

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||+.+  ++++|+++|++||.|..|.|+++  ++.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        13 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   83 (103)
T 2d9p_A           13 YQVVNLYVKNLDDGI--DDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATK   83 (103)
T ss_dssp             SSCCCEEEECCCTTC--CHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            467899999997655  78999999999999999999998  799999999999999999999999999999886

>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=99.75  E-value=2.2e-18  Score=119.29  Aligned_cols=73  Identities=15%  Similarity=0.120  Sum_probs=67.2

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccc---cCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV---DGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i---~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|++||.|.+|+|++|+.++.++|||||+|.+.++|.+|++.|||..+   +||
T Consensus        11 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~   86 (106)
T 2dgp_A           11 HDAIKLFIGQIPRNL--DEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNR   86 (106)
T ss_dssp             TTCEEEEEESCCTTC--CHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSS
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCc
Confidence            457899999997655  8999999999999999999999999999999999999999999999999999887   654

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.75  E-value=9.8e-18  Score=119.32  Aligned_cols=85  Identities=21%  Similarity=0.330  Sum_probs=79.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ...+.++|||+|||..+++++|+++|++| .|..|.|+.++ +++++|||||+|.+.++|.+|++ +++ ..++|+.|.|
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g-~~~~g~~l~V  108 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKG-VPLDGRPMDI  108 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTT-EESSSCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCC-CEECCcEEEE
Confidence            45667999999999999999999999999 99999999998 89999999999999999999999 999 9999999999


Q ss_pred             EecCCCCCC
Q psy1680          87 DIADGKRND   95 (227)
Q Consensus        87 ~~~~~~~~~   95 (227)
                      .++.+....
T Consensus       109 ~~a~~~~~~  117 (124)
T 2kt5_A          109 QLVASQIDL  117 (124)
T ss_dssp             EEECCTTCC
T ss_pred             EEeCCCCCC
Confidence            999876543

>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=99.75  E-value=5.4e-18  Score=116.10  Aligned_cols=80  Identities=10%  Similarity=0.110  Sum_probs=71.5

Q ss_pred             CCCCCceEEEcCCCC-CCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCC-ceeCCeEe
Q psy1680           9 PTEPPYTAFVGNLPN-GITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGR-ITVDGLQV   84 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~-~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~-~~~~g~~l   84 (227)
                      ...++++|||+|||+ .+|+++|+++|++| .|..|.|+++      ++||||+|.+.++|..||+ +++. ..|.|++|
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   84 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   84 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEE
Confidence            456789999999999 99999999999999 9999999875      5899999999999999998 7751 45999999


Q ss_pred             EEEecCCCCC
Q psy1680          85 RLDIADGKRN   94 (227)
Q Consensus        85 ~v~~~~~~~~   94 (227)
                      .|.++..++.
T Consensus        85 ~V~~a~~~~~   94 (102)
T 1x4d_A           85 RVHLSQKYKR   94 (102)
T ss_dssp             EEEEECCCTT
T ss_pred             EEEECCCCCC
Confidence            9999986654

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.75  E-value=1.4e-17  Score=114.60  Aligned_cols=79  Identities=22%  Similarity=0.360  Sum_probs=72.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ...+.++|||+|||.++|+++|+++|++| .|..|.|+        ++||||+|.+.++|.+||+ |++ ..|.|+.|.|
T Consensus         7 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~v   77 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNG-KDLEGENIEI   77 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTT-EEETTEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCC-CccCCCEEEE
Confidence            34567999999999999999999999999 99999987        4599999999999999999 999 9999999999


Q ss_pred             EecCCCCCCC
Q psy1680          87 DIADGKRNDN   96 (227)
Q Consensus        87 ~~~~~~~~~~   96 (227)
                      .++.++....
T Consensus        78 ~~a~~~~~~~   87 (103)
T 2dgu_A           78 VFAKPPDQKR   87 (103)
T ss_dssp             EECCCCCCCC
T ss_pred             EEcCCCcccc
Confidence            9998776543

>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=99.75  E-value=1.1e-17  Score=115.25  Aligned_cols=84  Identities=14%  Similarity=0.199  Sum_probs=73.1

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCC-ceeCCeE
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGR-ITVDGLQ   83 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~-~~~~g~~   83 (227)
                      +....++++|||+|||+.+++++|+++|++| .|..|.|+++      +|||||+|.+.++|.+|++ +++. ..+.|++
T Consensus         9 ~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~   82 (104)
T 1wex_A            9 HHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQ   82 (104)
T ss_dssp             CCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSB
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEE
Confidence            3445778999999999999999999999999 9999998764      7899999999999999998 7651 4599999


Q ss_pred             eEEEecCCCCCCC
Q psy1680          84 VRLDIADGKRNDN   96 (227)
Q Consensus        84 l~v~~~~~~~~~~   96 (227)
                      |.|.++.++....
T Consensus        83 l~V~~a~~~~~~~   95 (104)
T 1wex_A           83 AFFNYSTSKRITR   95 (104)
T ss_dssp             CEEEECSSSSCCC
T ss_pred             EEEEEccCccccC
Confidence            9999998766543

>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=99.75  E-value=5.4e-18  Score=126.64  Aligned_cols=86  Identities=17%  Similarity=0.251  Sum_probs=79.1

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      ....+.++|||+|||+.+++++|+++|++| .|..|.|+.++.++.++|||||+|.+.++|.+||. |++ ..|.|+.|.
T Consensus        67 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g-~~~~g~~l~  145 (165)
T 1rk8_A           67 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNG-AEIMGQTIQ  145 (165)
T ss_dssp             CCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTT-CEETTEECE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCC-CEECCEEEE
Confidence            345667899999999999999999999999 99999999999999999999999999999999999 999 999999999


Q ss_pred             EEecCCCCC
Q psy1680          86 LDIADGKRN   94 (227)
Q Consensus        86 v~~~~~~~~   94 (227)
                      |.++.++..
T Consensus       146 V~~a~~~~~  154 (165)
T 1rk8_A          146 VDWCFVKGP  154 (165)
T ss_dssp             EEESEECC-
T ss_pred             EEEecCCCC
Confidence            999987654

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.75  E-value=3.6e-18  Score=117.62  Aligned_cols=71  Identities=35%  Similarity=0.559  Sum_probs=65.8

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.|| |.+|.|++++.++.++|||||+|.+.++|.+|+ .|||..|+||
T Consensus        13 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~   83 (103)
T 2dng_A           13 EPPYTAYVGNLPFNT--VQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDR   83 (103)
T ss_dssp             SSCEEEEEESCCTTC--CHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTE
T ss_pred             CCCeEEEEeCCCCCC--CHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCe
Confidence            456899999997655  7999999999997 999999999999999999999999999999999 9999999885

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=1.8e-18  Score=118.06  Aligned_cols=73  Identities=25%  Similarity=0.246  Sum_probs=67.1

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCC---CCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKE---TDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~---t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||...  ++++|+++|++||.|..|.|++++.   |+.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus         3 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   78 (98)
T 2cpf_A            3 SGSSGLFIKNLNFST--TEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGH   78 (98)
T ss_dssp             CCCCCEEEESCCTTC--CHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCe
Confidence            457799999997655  8999999999999999999999987   679999999999999999999999999999885

>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=99.75  E-value=6.9e-18  Score=116.54  Aligned_cols=71  Identities=13%  Similarity=0.091  Sum_probs=66.0

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      ++..+|||+|||..+  ++++|+++|+.||.|..|.|++++ ++.++|||||+|.+.++|.+|++.|||..|.|
T Consensus        13 ~~~~~l~v~nLp~~~--t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   83 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQ--SEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMP   83 (105)
T ss_dssp             CCCCEEEEESCCTTC--CHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCT
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCC
Confidence            467899999997655  799999999999999999999997 69999999999999999999999999999887

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=1.3e-18  Score=118.68  Aligned_cols=73  Identities=11%  Similarity=-0.056  Sum_probs=67.4

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +...+|||+|||..+  ++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        13 ~~~~~l~v~nLp~~~--t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~   85 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTV--SIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSR   85 (98)
T ss_dssp             CSSEEEEEESCCTTC--CHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCe
Confidence            456789999997655  7999999999999999999999999999999999999999999999999999999985

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=7.1e-18  Score=118.22  Aligned_cols=72  Identities=15%  Similarity=0.070  Sum_probs=66.6

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|.+|.|++++ ++.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        13 ~~~~~l~V~nlp~~~--~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   84 (114)
T 2do0_A           13 RLGSTVFVANLDYKV--GWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDR   84 (114)
T ss_dssp             CCCSCEEEESCCTTC--CHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCC
Confidence            567899999997655  899999999999999999999997 599999999999999999999999999999885

>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=99.75  E-value=6.5e-19  Score=119.49  Aligned_cols=73  Identities=11%  Similarity=-0.051  Sum_probs=66.7

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++..+|||+|||..+  ++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        13 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr   85 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTV--SIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSR   85 (95)
T ss_dssp             --CEEEEEECCCTTC--CHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCc
Confidence            356799999997655  8999999999999999999999999999999999999999999999999999999986

>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=99.75  E-value=3.9e-18  Score=117.64  Aligned_cols=71  Identities=23%  Similarity=0.320  Sum_probs=65.8

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCC-CcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKET-DRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t-~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.|| |.+|.|++++.+ +.++|||||+|.+.++|.+|| .|||..|+||
T Consensus        13 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~   84 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDV--TEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNK   84 (104)
T ss_dssp             SSCEEEEEESCCSSC--CHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTE
T ss_pred             CCCCEEEEeCCCCcC--CHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCc
Confidence            456899999997655  7999999999999 999999999998 999999999999999999999 9999999885

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.75  E-value=6.6e-18  Score=119.21  Aligned_cols=83  Identities=19%  Similarity=0.286  Sum_probs=76.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-C---eEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEe
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-K---LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQV   84 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~---i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l   84 (227)
                      +....++|||+|||+++|+++|+++|+.| .   |..|.|+.++. ++++|||||+|.+.++|++||++++ ..|+|+.|
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~g-~~~~gr~i   90 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALKKDR-ESMGHRYI   90 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGGGTT-EEETTEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCC-CeECCeEE
Confidence            45667999999999999999999999999 7   89999999977 9999999999999999999999999 99999999


Q ss_pred             EEEecCCCC
Q psy1680          85 RLDIADGKR   93 (227)
Q Consensus        85 ~v~~~~~~~   93 (227)
                      +|.++..+.
T Consensus        91 ~V~~a~~~~   99 (118)
T 2db1_A           91 EVFKSHRTE   99 (118)
T ss_dssp             EEEEECHHH
T ss_pred             EEEECCHHH
Confidence            999987543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=3.7e-18  Score=117.12  Aligned_cols=81  Identities=16%  Similarity=0.219  Sum_probs=72.8

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hC--CCceeCCeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KD--GRITVDGLQ   83 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~--~~~~~~g~~   83 (227)
                      ....+.++|||+|||+++|+++|+++|++| .|..|.|+++      +|||||+|.+.++|..|++ ++  + ..|.|++
T Consensus        11 ~~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~-~~l~Gr~   83 (105)
T 1sjq_A           11 GSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVT-PVLRGQP   83 (105)
T ss_dssp             -CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSC-CEETTEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCC-ceECCEE
Confidence            456788999999999999999999999999 9999999875      7999999999999999998 75  5 7899999


Q ss_pred             eEEEecCCCCCC
Q psy1680          84 VRLDIADGKRND   95 (227)
Q Consensus        84 l~v~~~~~~~~~   95 (227)
                      |.|.++.++...
T Consensus        84 l~V~~A~~~~~~   95 (105)
T 1sjq_A           84 IYIQFSNHKELK   95 (105)
T ss_dssp             CCBCCCSSSSCC
T ss_pred             EEEEEcCCCCCC
Confidence            999999876543

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=6.3e-18  Score=116.53  Aligned_cols=72  Identities=18%  Similarity=0.169  Sum_probs=66.9

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhcc-ccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcc-ccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTE-VTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRIT-VDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~-~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~-i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|++ ||.|.+|.|++++ ++.++|||||+|.+.++|.+|++.|+|.. |+||
T Consensus         7 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~   80 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDV--DDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSK   80 (104)
T ss_dssp             SCCCCEEEECCCTTC--CHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSS
T ss_pred             CCCcEEEEeCCCCCC--CHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCE
Confidence            456799999997665  79999999999 9999999999998 89999999999999999999999999999 9886

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.75  E-value=1.8e-18  Score=124.94  Aligned_cols=87  Identities=25%  Similarity=0.379  Sum_probs=80.6

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      +.+..+.++|||+|||..+|+++|+++|++| .|..|.|+.++.+++++|||||+|.+.++|++||+ +++ ..|.|+.|
T Consensus        41 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g-~~i~g~~l  119 (135)
T 2lea_A           41 PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG-AVLDGREL  119 (135)
T ss_dssp             CSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTT-CCSSSSCC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCC-CEECCEEE
Confidence            3445667899999999999999999999999 99999999998899999999999999999999999 999 99999999


Q ss_pred             EEEecCCCCC
Q psy1680          85 RLDIADGKRN   94 (227)
Q Consensus        85 ~v~~~~~~~~   94 (227)
                      .|.++.++..
T Consensus       120 ~V~~a~~~~~  129 (135)
T 2lea_A          120 RVQMARYGRP  129 (135)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEECCCCCC
Confidence            9999987654

>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=99.75  E-value=2.4e-18  Score=122.58  Aligned_cols=85  Identities=16%  Similarity=0.239  Sum_probs=77.2

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRL   86 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v   86 (227)
                      .+....++|||+|||+++|+++|+++|+.| .|..+.++.+..+++++|||||+|.+.++|.+||.+|+ ..|+|+.|.|
T Consensus        20 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g-~~~~gr~i~V   98 (124)
T 1wel_A           20 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHK-QYMGNRFIQV   98 (124)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCS-BCSTTSCBEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCC-CeECCcEEEE
Confidence            345677999999999999999999999999 98887777777889999999999999999999999999 9999999999


Q ss_pred             EecCCCC
Q psy1680          87 DIADGKR   93 (227)
Q Consensus        87 ~~~~~~~   93 (227)
                      .++.++.
T Consensus        99 ~~a~~~~  105 (124)
T 1wel_A           99 HPITKKG  105 (124)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9987643

>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=99.75  E-value=3.5e-17  Score=112.05  Aligned_cols=82  Identities=13%  Similarity=0.179  Sum_probs=73.2

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-h--CCCceeCCe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-K--DGRITVDGL   82 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~--~~~~~~~g~   82 (227)
                      .....++++|||+|||+.+++++|+++|++| .|..|.|+++      +|||||+|.+.++|.+|++ +  ++ ..+.|+
T Consensus         9 ~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~-~~~~Gr   81 (101)
T 2cq1_A            9 KMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVT-PHLRNQ   81 (101)
T ss_dssp             CCCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSC-CEETTE
T ss_pred             CccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCC-ceECCc
Confidence            3456778999999999999999999999999 9999998865      7999999999999999998 5  56 789999


Q ss_pred             EeEEEecCCCCCC
Q psy1680          83 QVRLDIADGKRND   95 (227)
Q Consensus        83 ~l~v~~~~~~~~~   95 (227)
                      +|.|.++.++...
T Consensus        82 ~l~V~~a~~~~~~   94 (101)
T 2cq1_A           82 PIYIQYSNHKELK   94 (101)
T ss_dssp             ECEEEECSCSSCC
T ss_pred             EEEEEEcCcccCc
Confidence            9999999876653

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.2e-18  Score=118.41  Aligned_cols=73  Identities=14%  Similarity=0.206  Sum_probs=67.9

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEE-EEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSV-RLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v-~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .++.+|||+|||..+  ++++|+++|++||.|..| +|++++.++.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus         3 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   76 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEI--DEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNR   76 (96)
T ss_dssp             SCCCEEEEECCCTTC--CHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            356799999997665  799999999999999999 9999999999999999999999999999999999999885

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.74  E-value=2.4e-18  Score=127.25  Aligned_cols=72  Identities=8%  Similarity=0.103  Sum_probs=66.6

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhcccc--ceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVT--TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g--~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||..+  ++++|+++|+.||  .|.+|+|++|+.+|+++|||||+|.+.++|.+||+.|||..|+||
T Consensus        54 ~~~~lfVgnLp~~~--te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr  127 (156)
T 3n9u_C           54 RRAAVYVGSFSWWT--TDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGE  127 (156)
T ss_dssp             --CEEEEECCCTTC--CHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTE
T ss_pred             CCCEEEEeCCCCCC--CHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            45789999997655  8999999999999  999999999999999999999999999999999999999999986

>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=99.74  E-value=3.2e-18  Score=119.25  Aligned_cols=73  Identities=16%  Similarity=0.089  Sum_probs=68.1

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|.+|.|++++.+|.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        24 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   96 (110)
T 1oo0_B           24 VEGWILFVTSIHEEA--QEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQ   96 (110)
T ss_dssp             TTBEEEEEESCCTTC--CHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            456789999997655  7899999999999999999999999999999999999999999999999999999885

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.74  E-value=7.8e-18  Score=114.37  Aligned_cols=78  Identities=18%  Similarity=0.227  Sum_probs=70.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCce--eCCeEe
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRIT--VDGLQV   84 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~--~~g~~l   84 (227)
                      ..+++++|||+|||..+|+++|+++|++| .|..+.++++      +|||||+|.+.++|..|++ +++ ..  +.|++|
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~-~~~~i~Gr~i   89 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAAD-NQIYIAGHPA   89 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHH-SCEEETTEEE
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcC-CCceeCCcEE
Confidence            45678999999999999999999999999 9999999854      7899999999999999999 887 64  889999


Q ss_pred             EEEecCCCC
Q psy1680          85 RLDIADGKR   93 (227)
Q Consensus        85 ~v~~~~~~~   93 (227)
                      .|.++++++
T Consensus        90 ~V~~S~~k~   98 (100)
T 3r27_A           90 FVNYSTSQK   98 (100)
T ss_dssp             EEEECSCSC
T ss_pred             EEEeccccc
Confidence            999998764

>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=99.74  E-value=6.2e-18  Score=121.95  Aligned_cols=82  Identities=18%  Similarity=0.263  Sum_probs=76.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-C---eEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEe
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-K---LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQV   84 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~---i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l   84 (227)
                      +....++|||+|||+++|+++|+++|++| .   |..|.|++++. ++++|||||+|.+.++|++||++++ ..|+|+.|
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~~~g-~~l~gr~i  117 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALKKDR-ESMGHRYI  117 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHTTTE-EESSSSEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCC-CEECCEEE
Confidence            45667999999999999999999999999 8   88999999987 9999999999999999999999999 99999999


Q ss_pred             EEEecCCC
Q psy1680          85 RLDIADGK   92 (227)
Q Consensus        85 ~v~~~~~~   92 (227)
                      .|.++.++
T Consensus       118 ~V~~a~~~  125 (136)
T 2hgl_A          118 EVFKSHRT  125 (136)
T ss_dssp             EEEECCHH
T ss_pred             EEEECChH
Confidence            99998654

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.74  E-value=3.2e-18  Score=117.25  Aligned_cols=85  Identities=39%  Similarity=0.757  Sum_probs=74.9

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeecC-CCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDK-ETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRL   86 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~-~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v   86 (227)
                      .+....++|||+|||.++++++|+++|++|.|..+.|++++ .+++++|||||+|.+.++|.+||.+++ ..|+|+.|.|
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~Gi~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g-~~~~g~~l~V   92 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNE-ESLGNRRIRV   92 (100)
T ss_dssp             ------CEEEESCCSSCCSSSHHHHHSCSSCEEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTT-CCBTTBCCCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCC-CEECCeEEEE
Confidence            34577799999999999999999999999998899999987 689999999999999999999999999 9999999999


Q ss_pred             EecCCCC
Q psy1680          87 DIADGKR   93 (227)
Q Consensus        87 ~~~~~~~   93 (227)
                      .++.++.
T Consensus        93 ~~a~~~~   99 (100)
T 2j76_E           93 DVADQAQ   99 (100)
T ss_dssp             EECCCSC
T ss_pred             EeccCCC
Confidence            9997654

>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=99.74  E-value=1.6e-18  Score=121.67  Aligned_cols=81  Identities=28%  Similarity=0.517  Sum_probs=76.7

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEecCC
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~~~   91 (227)
                      .++|||+|||..+++++|+++|++| .|..|.|+.++.+++++|||||+|.+.++|.+||.+++ ..|+|+.|.|.++.+
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g-~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTG-QRLLGVPIIVQASQA  103 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTT-EEETTEEEEEEEHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCC-CEeCCeEEEEEecCC
Confidence            4799999999999999999999999 99999999999999999999999999999999999999 999999999999876


Q ss_pred             CCC
Q psy1680          92 KRN   94 (227)
Q Consensus        92 ~~~   94 (227)
                      +..
T Consensus       104 ~~~  106 (114)
T 2cq4_A          104 EKN  106 (114)
T ss_dssp             HHH
T ss_pred             Ccc
Confidence            543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.74  E-value=8e-18  Score=122.14  Aligned_cols=73  Identities=15%  Similarity=0.145  Sum_probs=68.4

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||...  ++++|+++|++||.|..|+|++++.++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        61 ~~~~~l~v~nlp~~~--~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~  133 (140)
T 2ku7_A           61 TTKRVLYVGGLAEEV--DDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGR  133 (140)
T ss_dssp             SSCCEEEEECCCTTC--CHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTE
T ss_pred             CCCcEEEEEeCCCCC--CHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            467899999997655  7899999999999999999999999999999999999999999999999999999985

>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=99.74  E-value=1.4e-18  Score=119.83  Aligned_cols=72  Identities=26%  Similarity=0.277  Sum_probs=67.5

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +.++|||+|||..+  ++++|+++|+.||.|..|.|++++.+|.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus         7 ~~~~l~V~nlp~~~--~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   78 (104)
T 1p1t_A            7 SLRSVFVGNIPYEA--TEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGR   78 (104)
T ss_dssp             HHSCEEEESCCTTS--CHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSS
T ss_pred             CccEEEEeCCCCcC--CHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCc
Confidence            45799999997655  7999999999999999999999999999999999999999999999999999999986

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.74  E-value=5e-18  Score=117.37  Aligned_cols=85  Identities=16%  Similarity=0.253  Sum_probs=76.3

Q ss_pred             CCCCCCCCceEEEcCCCCCC------CHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCc
Q psy1680           6 KTLPTEPPYTAFVGNLPNGI------TQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRI   77 (227)
Q Consensus         6 ~~~~~~~~~~l~V~nLp~~~------t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~   77 (227)
                      .+......++|||+|||+.+      |+++|+++|++| .|..+.|+  +.+|+++|||||+|.+.++|.+||. +|| .
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g-~   84 (105)
T 2nlw_A            8 PQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADG-Y   84 (105)
T ss_dssp             CCSCCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSS-E
T ss_pred             CCCCCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCC-c
Confidence            34455667999999999999      789999999999 99999988  4678999999999999999999999 999 9


Q ss_pred             eeCCe-EeEEEecCCCC
Q psy1680          78 TVDGL-QVRLDIADGKR   93 (227)
Q Consensus        78 ~~~g~-~l~v~~~~~~~   93 (227)
                      .|+|+ +|.|.++....
T Consensus        85 ~~~g~~~l~V~~a~~~~  101 (105)
T 2nlw_A           85 KLDKQHTFRVNLFTDFD  101 (105)
T ss_dssp             ECSTTCEEEEECSCCCC
T ss_pred             ccCCCceEEEEEcchHh
Confidence            99998 99999987654

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.74  E-value=6.5e-19  Score=120.93  Aligned_cols=84  Identities=26%  Similarity=0.439  Sum_probs=76.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEe
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDI   88 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~   88 (227)
                      ..+.++|||+|||.++|+++|+++|++| .|.. .++.++.+++++|||||+|.+.++|.+||++++ ..+.|+.|.|.+
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g-~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTG-LKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGG-CCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHhcCC-cEECCcEEEEEE
Confidence            3478999999999999999999999999 8877 677777888999999999999999999999999 999999999999


Q ss_pred             cCCCCCC
Q psy1680          89 ADGKRND   95 (227)
Q Consensus        89 ~~~~~~~   95 (227)
                      +.++...
T Consensus        92 a~~~~~~   98 (101)
T 1fj7_A           92 PKGRDGT   98 (101)
T ss_dssp             CSCCCCS
T ss_pred             cCCCCCC
Confidence            9876653

>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=99.74  E-value=1.3e-17  Score=117.21  Aligned_cols=81  Identities=16%  Similarity=0.228  Sum_probs=73.2

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hC--CCceeCCeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KD--GRITVDGLQ   83 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~--~~~~~~g~~   83 (227)
                      ...+++++|||+|||+++|+++|+++|++| .|..|.|+++      +|||||+|.+.++|.+|++ ++  + ..|.|++
T Consensus        26 ~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~-~~l~Gr~   98 (119)
T 2ad9_A           26 SAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVT-PVLRGQP   98 (119)
T ss_dssp             SCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHC-CCBTTBC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCC-ceECCeE
Confidence            456778999999999999999999999999 9999999876      7999999999999999998 76  5 6899999


Q ss_pred             eEEEecCCCCCC
Q psy1680          84 VRLDIADGKRND   95 (227)
Q Consensus        84 l~v~~~~~~~~~   95 (227)
                      |.|.++.++...
T Consensus        99 l~V~~a~~k~~~  110 (119)
T 2ad9_A           99 IYIQFSNHKELK  110 (119)
T ss_dssp             CEEEECSSSSCC
T ss_pred             EEEEEccCCCCC
Confidence            999999876653

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.74  E-value=2e-17  Score=120.04  Aligned_cols=73  Identities=16%  Similarity=0.137  Sum_probs=68.3

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+.++|||+|||..+  ++++|+++|+.||.|.+|.|++++.++.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        40 ~~~~~l~V~nLp~~~--~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~  112 (139)
T 1u6f_A           40 DVLRNLMVNYIPTTV--DEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNK  112 (139)
T ss_dssp             TTTSEEEEESCSTTC--CHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSC
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCe
Confidence            456899999997655  7899999999999999999999999999999999999999999999999999999886

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.74  E-value=1.8e-18  Score=112.18  Aligned_cols=68  Identities=18%  Similarity=0.196  Sum_probs=63.8

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +|||+|||+..  ++++|+++|++||.|.+|.|++++.++.++|||||+|.+.++|++|++ ++|..|+||
T Consensus         1 ~l~v~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~   68 (75)
T 2mss_A            1 KIFVGGLSVNT--TVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNK   68 (75)
T ss_dssp             CEEEECCCSSC--CHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSC
T ss_pred             CEEEecCCCCC--CHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCE
Confidence            48999997655  799999999999999999999999999999999999999999999998 999999986

>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=99.74  E-value=7.9e-18  Score=124.75  Aligned_cols=85  Identities=26%  Similarity=0.397  Sum_probs=79.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      .....++|||+|||+++++++|+++|++| .|..+.|+.++.+++++|||||+|.+.++|.+||+ +++ ..|+|+.|.|
T Consensus        66 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~v  144 (158)
T 2kn4_A           66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG-AVLDGRELRV  144 (158)
T ss_dssp             CCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTT-EESSSSEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCC-CEECCeEEEE
Confidence            34567999999999999999999999999 99999999999999999999999999999999998 999 9999999999


Q ss_pred             EecCCCCC
Q psy1680          87 DIADGKRN   94 (227)
Q Consensus        87 ~~~~~~~~   94 (227)
                      .++.++..
T Consensus       145 ~~a~~~~~  152 (158)
T 2kn4_A          145 QMARYGRP  152 (158)
T ss_dssp             EEECCSSC
T ss_pred             EECCCCCC
Confidence            99987654

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.74  E-value=1.4e-17  Score=118.54  Aligned_cols=81  Identities=22%  Similarity=0.386  Sum_probs=76.8

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEecCC
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~~~   91 (227)
                      .++|||+|||.++++++|+++|++| .|..|.|+.++.++.++|||||+|.+.++|.+||++++ ..|+|+.|.|.++.+
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g-~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDE-TVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTT-CEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCC-CeECCeEEEEEECCC
Confidence            4899999999999999999999999 99999999999999999999999999999999999999 999999999999876


Q ss_pred             CCC
Q psy1680          92 KRN   94 (227)
Q Consensus        92 ~~~   94 (227)
                      ...
T Consensus       115 ~~~  117 (124)
T 2jwn_A          115 NMP  117 (124)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            443

>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=99.74  E-value=5e-18  Score=116.70  Aligned_cols=70  Identities=16%  Similarity=0.102  Sum_probs=62.9

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||+.+  ++++|+++|++|| +.+|+|++|+ +++++|||||+|.+.++|++||+ +|+..|+||
T Consensus        13 ~~~~~l~V~nLp~~~--te~~l~~~F~~~G-~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr   82 (102)
T 1wez_A           13 TTGHCVHMRGLPYRA--TENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHR   82 (102)
T ss_dssp             SSSCEEEEESCCTTC--CHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSS
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHHcC-ceEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCc
Confidence            456789999997655  8999999999999 4599999997 89999999999999999999995 799999986

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.74  E-value=4e-18  Score=117.85  Aligned_cols=72  Identities=11%  Similarity=0.089  Sum_probs=65.3

Q ss_pred             CCCcceeccCCCCCCC----ChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSN----SMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~----~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+++|||+|||...+.    ++++|+++|++||.|.+|.|+  +.+|.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            4678999999876644    689999999999999999998  47799999999999999999999999999999986

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.74  E-value=1.1e-17  Score=121.31  Aligned_cols=80  Identities=21%  Similarity=0.381  Sum_probs=75.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ...+.++|||+|||..+++++|+++|++| .|..+.|++++.+++++|||||+|.+.++|.+|++ +++ ..|+|+.|+|
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~v  137 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE-SELFGRTIRV  137 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTE-EEETTEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCC-CEECCEEEEE
Confidence            45678999999999999999999999999 99999999999999999999999999999999998 999 9999999999


Q ss_pred             Eec
Q psy1680          87 DIA   89 (227)
Q Consensus        87 ~~~   89 (227)
                      .+|
T Consensus       138 ~~A  140 (140)
T 2ku7_A          138 NLA  140 (140)
T ss_dssp             EC-
T ss_pred             EeC
Confidence            875

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.74  E-value=4.9e-18  Score=126.87  Aligned_cols=73  Identities=16%  Similarity=0.089  Sum_probs=67.4

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+.+|+.||.|..|.|++++.+|.++|||||+|.+.++|.+||+.|||..|+|+
T Consensus        70 ~~~~~l~V~nLp~~~--t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~  142 (165)
T 1rk8_A           70 VEGWILFVTSIHEEA--QEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQ  142 (165)
T ss_dssp             C-CEEEEEESCCTTC--CHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            456789999997655  7999999999999999999999999999999999999999999999999999999885

>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=99.74  E-value=5.6e-18  Score=119.19  Aligned_cols=72  Identities=15%  Similarity=0.217  Sum_probs=66.8

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|++||.|.+|.|+++. ++.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus         5 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~   76 (116)
T 2fy1_A            5 DHPGKLFIGGLNRET--NEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGK   76 (116)
T ss_dssp             CSCCEEEEECCTTTC--CHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSS
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            356789999997655  899999999999999999999997 899999999999999999999999999999986

>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=99.74  E-value=3.2e-18  Score=114.35  Aligned_cols=72  Identities=15%  Similarity=0.177  Sum_probs=66.4

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCc-ccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDR-FKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~-~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+.+|||+|||...  ++++|+++|++||.|.+|.|++++.++. ++|||||+|.+.++|.+|++.|||..|+||
T Consensus         3 ~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   75 (88)
T 4a8x_A            3 KPTKVHIGRLTRNV--TKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQ   75 (88)
T ss_dssp             CCCEEEEECCCTTC--CHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCEEEEeCCCCCC--CHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCe
Confidence            45689999997655  7999999999999999999999988776 999999999999999999999999999985

>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=99.74  E-value=5.1e-18  Score=120.63  Aligned_cols=82  Identities=21%  Similarity=0.283  Sum_probs=74.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCCCeE--EEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQKLV--SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~--~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v   86 (227)
                      +....++|||+|||+++|+++|+++|++|.|.  .|.|++++. |+++|||||+|.+.++|++||++++ ..|+|+.|.|
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~-~~l~gR~I~V  115 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGKHK-ERIGHRYIEV  115 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTSCEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTTTT-CCBTTBCCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHCC-CEECCEEEEE
Confidence            34567899999999999999999999999666  899999977 9999999999999999999999888 9999999999


Q ss_pred             EecCCC
Q psy1680          87 DIADGK   92 (227)
Q Consensus        87 ~~~~~~   92 (227)
                      ..+.++
T Consensus       116 ~~a~~~  121 (126)
T 2hgm_A          116 FKSSQE  121 (126)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            988643

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.59  E-value=1.7e-19  Score=127.03  Aligned_cols=87  Identities=25%  Similarity=0.373  Sum_probs=80.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEE--------EEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCce
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVS--------VRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRIT   78 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~--------v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~   78 (227)
                      +..+.++|||+|||..+++++|+++|++| .|..        +.|+.++.+++++|||||+|.+.++|.+||+ +++ ..
T Consensus         3 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g-~~   81 (116)
T 2lcw_A            3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDG-KE   81 (116)
Confidence            45678999999999999999999999999 9988        8999998899999999999999999999999 999 99


Q ss_pred             eCCeEeEEEecCCCCCCC
Q psy1680          79 VDGLQVRLDIADGKRNDN   96 (227)
Q Consensus        79 ~~g~~l~v~~~~~~~~~~   96 (227)
                      +.|+.|.|.++.++....
T Consensus        82 ~~g~~l~V~~a~~~~~~~   99 (116)
T 2lcw_A           82 FSGNPIKVSFATRRADFN   99 (116)
Confidence            999999999998876543

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.73  E-value=7.2e-18  Score=124.66  Aligned_cols=80  Identities=15%  Similarity=0.250  Sum_probs=74.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-C--eEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-K--LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~--i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ..++|||+|||+++|+++|+++|++| .  |..|.|+.|+.+++++|||||+|.+.++|.+||+ +++ ..|+|+.|.|.
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng-~~~~Gr~l~V~  132 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPG-KVLNGEKVDVR  132 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTT-CEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCC-CEECCeEeEEE
Confidence            45899999999999999999999999 3  8999999999999999999999999999999999 899 99999999999


Q ss_pred             ecCCC
Q psy1680          88 IADGK   92 (227)
Q Consensus        88 ~~~~~   92 (227)
                      ++.++
T Consensus       133 ~a~~~  137 (156)
T 3n9u_C          133 PATRQ  137 (156)
T ss_dssp             ECCHH
T ss_pred             EcCCC
Confidence            98754

>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=99.73  E-value=6.4e-18  Score=120.59  Aligned_cols=73  Identities=19%  Similarity=0.155  Sum_probs=68.1

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|.+|.|++++.++.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        20 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   92 (126)
T 3ex7_B           20 VEGWILFVTGVHEEA--TEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ   92 (126)
T ss_dssp             SSSEEEEEESCCTTC--CHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCe
Confidence            456799999997655  7999999999999999999999999999999999999999999999999999999985

>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=99.73  E-value=1.1e-17  Score=115.36  Aligned_cols=71  Identities=15%  Similarity=0.047  Sum_probs=64.7

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEE-EEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~-v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ....+|||+|||+.+  ++++|+++|+.||.|.. |+|+++ .+|+++|||||+|.+.++|.+||+. ++..|+||
T Consensus        13 ~~~~~l~V~nLp~~~--te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr   84 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGC--SKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHR   84 (104)
T ss_dssp             SCCCEEEEESCCTTC--CHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSS
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCc
Confidence            356789999997655  89999999999999987 889999 7899999999999999999999998 99999986

>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=99.73  E-value=6.5e-18  Score=117.09  Aligned_cols=72  Identities=21%  Similarity=0.160  Sum_probs=67.1

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|++||.|.+|.|++++ ++.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        27 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   98 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGV--SDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGR   98 (107)
T ss_dssp             CCSEEEEEESCCTTC--CHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            467899999997655  789999999999999999999998 899999999999999999999999999999885

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.7e-17  Score=114.15  Aligned_cols=71  Identities=18%  Similarity=0.151  Sum_probs=64.7

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|..|.|++++.  .++|||||+|.+.++|.+|++.|||..|+||
T Consensus        13 ~~~~~l~V~nlp~~~--t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   83 (103)
T 2cq3_A           13 STPKRLHVSNIPFRF--RDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGR   83 (103)
T ss_dssp             CCCCEEEEESCCTTC--CHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            467899999997655  7999999999999999999999864  3899999999999999999999999999885

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=6.9e-18  Score=118.12  Aligned_cols=73  Identities=15%  Similarity=0.156  Sum_probs=67.6

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceE--------EEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccc
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLV--------SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV  224 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~--------~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i  224 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|.        .|+|++++.++.++|||||+|.+.++|.+|++.|||..|
T Consensus        13 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           13 SDNSAIYVQGLNDSV--TLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCEEEEECCCTTC--CHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCEEEEcCCCCCC--CHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            467899999997655  7899999999999999        699999999999999999999999999999999999999


Q ss_pred             cCC
Q psy1680         225 DGL  227 (227)
Q Consensus       225 ~gr  227 (227)
                      +||
T Consensus        91 ~g~   93 (113)
T 2cpe_A           91 QGS   93 (113)
T ss_dssp             TTE
T ss_pred             CCC
Confidence            885

>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=99.73  E-value=2.1e-17  Score=114.90  Aligned_cols=70  Identities=17%  Similarity=0.192  Sum_probs=63.2

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|++||.|..|.|..+   +.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        20 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   89 (109)
T 1x4a_A           20 NNDCRIYVGNLPPDI--RTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGY   89 (109)
T ss_dssp             CCSSEEEEESCCTTC--CHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            467899999997655  89999999999999999999665   56899999999999999999999999999885

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=3.2e-18  Score=118.90  Aligned_cols=68  Identities=21%  Similarity=0.120  Sum_probs=62.7

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..+|||+|||+.+  ++++|+++|+.| .|.+|+|++|+. |+++|||||+|.+.++|.+|| .+|+..|+||
T Consensus        16 ~~~v~V~nLp~~~--te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr   83 (109)
T 2dnn_A           16 DLYVSVHGMPFSA--MENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQR   83 (109)
T ss_dssp             HHEEEEECCCSSC--CHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTE
T ss_pred             CCEEEEeCCCCCC--CHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCe
Confidence            4689999997655  899999999999 899999999976 999999999999999999999 7999999986

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.5e-17  Score=115.72  Aligned_cols=82  Identities=22%  Similarity=0.402  Sum_probs=75.6

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      ....+.++|||+|||.++++++|+++|++| .|..+.|+.++  +.++|||||+|.+.++|++|++ +++ ..++|+.|.
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g-~~~~g~~l~  100 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHG-TVVEGRKIE  100 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTT-CEETTEECE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCC-CEECCEEEE
Confidence            345677999999999999999999999999 99999999885  3489999999999999999999 999 999999999


Q ss_pred             EEecCCC
Q psy1680          86 LDIADGK   92 (227)
Q Consensus        86 v~~~~~~   92 (227)
                      |.++.++
T Consensus       101 V~~a~~~  107 (109)
T 2err_A          101 VNNATAR  107 (109)
T ss_dssp             EEECCCS
T ss_pred             EEECCCC
Confidence            9999865

>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=99.73  E-value=5.8e-18  Score=113.34  Aligned_cols=70  Identities=21%  Similarity=0.273  Sum_probs=65.7

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .++|||+|||...  ++++|+++|+.||.|.+|.|++++.++.++|||||+|.+.++|.+|+ .|||..|+||
T Consensus         6 ~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~   75 (89)
T 3ucg_A            6 ARSIYVGNVDYGA--TAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGR   75 (89)
T ss_dssp             HTEEEEESCCTTC--CHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTE
T ss_pred             CCEEEEeCCCCCC--CHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCc
Confidence            4689999997665  79999999999999999999999999999999999999999999999 9999999885

>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=99.73  E-value=1.7e-18  Score=125.27  Aligned_cols=84  Identities=21%  Similarity=0.258  Sum_probs=74.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEe
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDI   88 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~   88 (227)
                      .....++|||+|||+++|+++|+++|++|.+..|.|++++. ++++|||||+|.+.++|++||++++ ..|+++.|+|..
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~Gi~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al~~~g-~~l~gR~i~V~~  119 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPD-GRVTGEADVEFATHEEAVAAMSKDR-ANMQHRYIELFL  119 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCCCSEEECCCSSS-SCSSCCCEEECSHHHHHHHHTTCCS-CSSSSCCCCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECCC-CCCceEEEEEeCCHHHHHHHHhhCC-CEECCEEEEEEE
Confidence            45667899999999999999999999999445999999976 9999999999999999999999999 999999999999


Q ss_pred             cCCCCC
Q psy1680          89 ADGKRN   94 (227)
Q Consensus        89 ~~~~~~   94 (227)
                      +.++..
T Consensus       120 a~~~~~  125 (139)
T 2hgn_A          120 NSTTGA  125 (139)
T ss_dssp             CCCSCC
T ss_pred             CCCCCC
Confidence            887654

>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=99.73  E-value=1.4e-17  Score=114.58  Aligned_cols=71  Identities=14%  Similarity=0.201  Sum_probs=64.5

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|++||.|.+|.|++++.  .++|||||+|.+.++|.+|++.|+|..|+||
T Consensus        13 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   83 (103)
T 2cqi_A           13 GQPRTLYVGNLSRDV--TEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGK   83 (103)
T ss_dssp             CCCCEEEEESCCTTC--CHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCEEEEeCCCccC--CHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCC
Confidence            567899999997655  7999999999999999999999864  3689999999999999999999999999885

>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=99.73  E-value=5.7e-18  Score=116.00  Aligned_cols=71  Identities=23%  Similarity=0.321  Sum_probs=63.9

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecC-CCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDK-ETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~-~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ....+|||+|||...  ++++|+++|+.|| |.+|+|++++ .+|+++|||||+|.+.++|.+|+ .|||..|+||
T Consensus        17 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~   88 (100)
T 2j76_E           17 SPPYTAFLGNLPYDV--TEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNR   88 (100)
T ss_dssp             ---CEEEESCCSSCC--SSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTB
T ss_pred             CCCcEEEEeCCCCCC--CHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCe
Confidence            456899999997665  7899999999999 9999999998 68999999999999999999999 9999999986

>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=99.73  E-value=2.3e-17  Score=113.56  Aligned_cols=71  Identities=20%  Similarity=0.223  Sum_probs=63.7

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|..|.|++++.++.++|||||+|.+.++|.+||+.  +..|+||
T Consensus        13 ~~~~~l~v~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~   83 (103)
T 2cqg_A           13 QKTSDLIVLGLPWKT--TEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGR   83 (103)
T ss_dssp             CCCCCEEEESCCSSC--CHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTE
T ss_pred             CCCCEEEEEcCCCcC--CHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc--CCeeCCe
Confidence            467899999997655  7999999999999999999999999999999999999999999999994  5666664

>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=99.73  E-value=1.4e-17  Score=116.27  Aligned_cols=73  Identities=12%  Similarity=0.043  Sum_probs=65.7

Q ss_pred             CCCCcceeccCCCCCCCChhhHH---hhhccccceEEEEEeecCCCC---cccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHG---LMVTEVTTLVSVRLVKDKETD---RFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~---~~f~~~g~i~~v~i~~d~~t~---~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      .+.++|||+|||+.+  ++++|+   ++|++||.|..|.|++++.++   .++|||||+|.+.++|.+|++.|||..|+|
T Consensus        13 ~~~~~l~V~nLp~~~--~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   90 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRL--ADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG   90 (111)
T ss_dssp             CCSSCEEEEEECTTT--CCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             cCCCEEEEECCCCCC--CHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECC
Confidence            457899999997665  789999   999999999999999998755   456999999999999999999999999998


Q ss_pred             C
Q psy1680         227 L  227 (227)
Q Consensus       227 r  227 (227)
                      |
T Consensus        91 r   91 (111)
T 2cpi_A           91 R   91 (111)
T ss_dssp             E
T ss_pred             E
Confidence            6

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.73  E-value=1.3e-17  Score=113.21  Aligned_cols=83  Identities=24%  Similarity=0.388  Sum_probs=73.6

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeE
Q psy1680           6 KTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQ   83 (227)
Q Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~   83 (227)
                      ......+.++|||+|||..+++++|+++|++| .|..+     ..++.++|||||+|.+.++|.+|+. +++ ..++|+.
T Consensus         9 ~~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~   82 (96)
T 1fjc_A            9 TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQG-AEIDGRS   82 (96)
T ss_dssp             TTSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTE-EEETTEE
T ss_pred             ccccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCC-CEECCeE
Confidence            33455678999999999999999999999999 77665     3568899999999999999999999 999 9999999


Q ss_pred             eEEEecCCCCC
Q psy1680          84 VRLDIADGKRN   94 (227)
Q Consensus        84 l~v~~~~~~~~   94 (227)
                      |.|.++.++..
T Consensus        83 l~v~~a~~~~~   93 (96)
T 1fjc_A           83 VSLYYTGEKGG   93 (96)
T ss_dssp             EEEEECSSSCC
T ss_pred             EEEEEcCCCCC
Confidence            99999987654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.73  E-value=4.7e-18  Score=119.97  Aligned_cols=71  Identities=21%  Similarity=0.243  Sum_probs=65.1

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccc---eEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTT---LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~---i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ....+|||+|||+.+  ++++|+++|+.||.   |..|+|++++. |+++|||||+|.+.++|.+||+ +||..|+||
T Consensus        15 ~~~~~l~V~nLp~~~--te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr   88 (118)
T 2db1_A           15 GEGYVVKLRGLPWSC--SIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHR   88 (118)
T ss_dssp             CCCCEEEEESCCTTC--CHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTE
T ss_pred             CCCcEEEEeCCCCCC--CHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCe
Confidence            356789999997655  89999999999998   89999999987 9999999999999999999999 999999986

>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=99.73  E-value=3.8e-18  Score=123.09  Aligned_cols=71  Identities=21%  Similarity=0.218  Sum_probs=65.5

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccc---eEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTT---LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~---i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ....+|||+|||+.+  |+++|+++|+.||.   |.+|+|++|+. |+++|||||+|.+.++|.+||+ +||..|+||
T Consensus        42 ~~~~~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           42 GEGFVVKLRGLPWSC--SVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHR  115 (136)
T ss_dssp             CTTCEEEEESCCTTC--CHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSS
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCE
Confidence            356789999997655  89999999999998   89999999988 9999999999999999999999 999999987

>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=99.73  E-value=6.6e-18  Score=120.26  Aligned_cols=71  Identities=10%  Similarity=0.038  Sum_probs=64.8

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||+.+  ++++|+++|+.||.|..+.++.+..+|+++|||||+|.+.++|.+||+ |||..|+||
T Consensus        24 ~~~~l~V~nLp~~~--te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr   94 (124)
T 1wel_A           24 AGFCVYLKGLPFEA--ENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNR   94 (124)
T ss_dssp             CCCEEEEECCCTTC--CHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTS
T ss_pred             CCcEEEEeCCCCCC--CHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCc
Confidence            45789999997655  799999999999999987777777889999999999999999999999 999999986

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.73  E-value=1.5e-17  Score=111.97  Aligned_cols=71  Identities=14%  Similarity=0.039  Sum_probs=65.1

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||...  ++++|+++|++||.|..|.|+++  ++.++|||||+|.+.++|.+|++.|+|..|+|+
T Consensus         6 ~~~~~l~V~nlp~~~--t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~   76 (92)
T 2dgv_A            6 SGACQIFVRNLPFDF--TWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGR   76 (92)
T ss_dssp             SSCCEEEECSCCTTC--CHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTB
T ss_pred             CCCcEEEEeCCCCCC--CHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            457899999997655  78999999999999999999984  689999999999999999999999999999986

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=3.5e-18  Score=111.27  Aligned_cols=69  Identities=16%  Similarity=0.198  Sum_probs=64.3

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+|||+|||...  ++++|+++|++||.|.+|.+++++.++.++|||||+|.+.++|.+|++.++ ..|+||
T Consensus         1 ~~l~v~nlp~~~--t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~   69 (77)
T 1uaw_A            1 CKMFIGGLSWQT--TQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSK   69 (77)
T ss_dssp             CCEEEESCCSSC--CSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSC
T ss_pred             CEEEEeCCCCCC--CHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCE
Confidence            379999997665  789999999999999999999999999999999999999999999999999 888886

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.72  E-value=6.8e-18  Score=117.45  Aligned_cols=72  Identities=17%  Similarity=0.223  Sum_probs=64.1

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||...  ++++|+++|+.||.|.+|+|++++.+|.++|||||+|.+.++|.+|++.++ ..|+||
T Consensus        23 ~~~~~lfV~nLp~~~--te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~l~g~   94 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQT--TQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSK   94 (109)
T ss_dssp             ---CCEEEESCCTTC--CHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSC-EEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCC-CcCCCE
Confidence            467899999997655  899999999999999999999999999999999999999999999999875 888875

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=4.8e-17  Score=109.15  Aligned_cols=78  Identities=18%  Similarity=0.410  Sum_probs=72.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ...+.++|||+|||.++++++|+++|++| .|..+.++        ++||||+|.+.++|++|++ +++ ..++|+.|.|
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~l~v   74 (90)
T 2dnq_A            4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHH-YKLHGVNINV   74 (90)
T ss_dssp             CSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTT-CBCSSCBCEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcC-CccCCcEEEE
Confidence            45678999999999999999999999999 99999997        5799999999999999998 999 9999999999


Q ss_pred             EecCCCCCC
Q psy1680          87 DIADGKRND   95 (227)
Q Consensus        87 ~~~~~~~~~   95 (227)
                      .++.++...
T Consensus        75 ~~a~~~~~~   83 (90)
T 2dnq_A           75 EASKNKSKA   83 (90)
T ss_dssp             ECSSCCCCC
T ss_pred             EECCCCCCC
Confidence            999877654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=8.2e-18  Score=115.37  Aligned_cols=67  Identities=7%  Similarity=-0.049  Sum_probs=60.0

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcC--CccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG--RITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~--g~~i~gr  227 (227)
                      ++..+|||+|||+.+  ++++|+++|++||.|++|+|+++      +|||||+|++.++|.+|++.|+  +..|+||
T Consensus        14 ~~~~~LfV~nLp~~v--te~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr   82 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDV--TEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQ   82 (105)
T ss_dssp             CCCCEEEECSCCTTS--CHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCE
Confidence            567899999997665  89999999999999999999986      6999999999999999999886  4788875

>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=99.72  E-value=1.9e-18  Score=116.01  Aligned_cols=79  Identities=30%  Similarity=0.505  Sum_probs=72.0

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecCC
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~~   91 (227)
                      ++|||+|||.++++++|+++|++| .|..+.+++++.+++++|||||+|.+.+ |.+|+. +++ ..++|+.|.|.++.+
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g-~~~~g~~l~V~~a~~   79 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDN-TDFMGRTIRVTEANP   79 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCS-SCCSSSSCSEEEC--
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCC-CEECCeEEEEEEcCC
Confidence            589999999999999999999999 9999999999999999999999999999 999999 999 999999999999987


Q ss_pred             CCC
Q psy1680          92 KRN   94 (227)
Q Consensus        92 ~~~   94 (227)
                      +..
T Consensus        80 ~~~   82 (90)
T 2ki2_A           80 KKS   82 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            654

>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=99.72  E-value=6.9e-18  Score=118.35  Aligned_cols=71  Identities=21%  Similarity=0.316  Sum_probs=66.1

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||..+  ++++|+++|+.||.|..|.|++++.++.++|||||+|.+.++|.+|+ .|||..|+|+
T Consensus        24 ~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~   94 (114)
T 2cq4_A           24 DARTVFCMQLAARI--RPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGV   94 (114)
T ss_dssp             HHTEEEEESCCTTC--CHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTE
T ss_pred             CCCEEEEeCCCCCC--CHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCe
Confidence            34789999997655  79999999999999999999999999999999999999999999999 9999999885

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=6.2e-18  Score=118.70  Aligned_cols=87  Identities=22%  Similarity=0.335  Sum_probs=73.4

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      .+..+.++|||+|||..+|+++|+++|++| .|..+.+..+..+++++|||||+|.+.++|.+||+ +++ ..|.|+.|.
T Consensus        20 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g-~~~~g~~l~   98 (115)
T 2cpx_A           20 NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNG-YKLYGKILV   98 (115)
T ss_dssp             CCCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTT-CBCSSCBCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCC-CEeCCcEEE
Confidence            345677999999999999999999999999 88433222222368889999999999999999999 999 999999999


Q ss_pred             EEecCCCCCC
Q psy1680          86 LDIADGKRND   95 (227)
Q Consensus        86 v~~~~~~~~~   95 (227)
                      |.++.++...
T Consensus        99 v~~a~~~~~~  108 (115)
T 2cpx_A           99 IEFGKNKKQR  108 (115)
T ss_dssp             EEECCCCSCC
T ss_pred             EEEccCCCCC
Confidence            9999877653

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.72  E-value=6.8e-18  Score=114.66  Aligned_cols=70  Identities=17%  Similarity=0.051  Sum_probs=61.0

Q ss_pred             CCCCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcc--ccCC
Q psy1680         150 SRGGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRIT--VDGL  227 (227)
Q Consensus       150 ~~~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~--i~gr  227 (227)
                      ...+|+++|||+|||+..  ++++|+++|++||.|++|+++++      ||||||+|++.++|.+|++.|+|..  |+||
T Consensus        16 ~~~~ps~~l~V~NLp~~~--te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr   87 (100)
T 3r27_A           16 HKTPASPVVHIRGLIDGV--VEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGH   87 (100)
T ss_dssp             -CCCCCSEEEEESCCTTC--CHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTE
T ss_pred             ccCCCCcEEEEeCCCCCC--CHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCc
Confidence            344688999999997665  79999999999999999999864      6999999999999999999998875  6675

>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=99.72  E-value=4.3e-17  Score=111.36  Aligned_cols=82  Identities=27%  Similarity=0.362  Sum_probs=74.3

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      +....+.++|||+|||..+++++|+++|++| .|..+.++++      +|||||+|.+.++|.+|++ +++ ..|+|+.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g-~~~~g~~l   81 (99)
T 2cpj_A            9 EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDN-MPLRGKQL   81 (99)
T ss_dssp             SCCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTT-CCBTTBCC
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCC-CEeCCceE
Confidence            3445677999999999999999999999999 9999999854      7899999999999999998 999 99999999


Q ss_pred             EEEecCCCCCC
Q psy1680          85 RLDIADGKRND   95 (227)
Q Consensus        85 ~v~~~~~~~~~   95 (227)
                      .|.++.++...
T Consensus        82 ~v~~a~~~~~~   92 (99)
T 2cpj_A           82 RVRFACHSASL   92 (99)
T ss_dssp             EEEESSCCSCC
T ss_pred             EEEEcCCCCCC
Confidence            99999876643

>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=99.72  E-value=5.1e-18  Score=119.04  Aligned_cols=71  Identities=14%  Similarity=0.088  Sum_probs=65.2

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccce-EEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTL-VSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i-~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||+.+  ++++|+++|+.||.| ..|+|++|+ +|+++|||||+|.+.++|.+||+. ||..|+||
T Consensus        13 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr   84 (114)
T 2cpy_A           13 SAKVCAHITNIPFSI--TKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGR   84 (114)
T ss_dssp             SCCCEEEEESCCTTS--CHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTE
T ss_pred             CCccEEEEeCcCCcC--CHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCe
Confidence            456789999997655  899999999999999 899999998 899999999999999999999998 99999886

>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=99.72  E-value=4.5e-17  Score=108.04  Aligned_cols=79  Identities=16%  Similarity=0.310  Sum_probs=72.1

Q ss_pred             CCCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-h-CCCceeCC
Q psy1680           5 QKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-K-DGRITVDG   81 (227)
Q Consensus         5 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~-~~~~~~~g   81 (227)
                      ..+....+.++|||+|||..+++++|+++|++| .|..+.++++      +|||||+|.+.++|.+|++ + ++ ..++|
T Consensus         4 ~~~~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~-~~~~g   76 (85)
T 2ytc_A            4 GSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNK-LIVNG   76 (85)
T ss_dssp             CCCCSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTT-CEETT
T ss_pred             CCCCCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCC-eeECC
Confidence            345566788999999999999999999999999 9999999864      7899999999999999999 8 99 99999


Q ss_pred             eEeEEEecC
Q psy1680          82 LQVRLDIAD   90 (227)
Q Consensus        82 ~~l~v~~~~   90 (227)
                      ++|.|.+++
T Consensus        77 ~~l~v~~ak   85 (85)
T 2ytc_A           77 RRLNVKWGR   85 (85)
T ss_dssp             EECCEEECC
T ss_pred             CEEEEEecC
Confidence            999999874

>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=99.72  E-value=6.7e-17  Score=113.23  Aligned_cols=71  Identities=10%  Similarity=0.133  Sum_probs=65.7

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|..|+|++++ ++.++|||||+|.+.++|.+|++.|||..|+|
T Consensus        23 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~   93 (114)
T 1x5o_A           23 QDPTNLYISNLPLSM--DEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKT   93 (114)
T ss_dssp             CCTTEEEEESCCTTC--CHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCC
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcC
Confidence            456789999997655  799999999999999999999998 89999999999999999999999999999965

>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=99.72  E-value=2.6e-18  Score=111.36  Aligned_cols=74  Identities=23%  Similarity=0.480  Sum_probs=70.8

Q ss_pred             eEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEec
Q psy1680          15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA   89 (227)
Q Consensus        15 ~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~   89 (227)
                      +|||+|||.++++++|+++|++| .|..+.++.++.+++++|||||+|.+.++|.+|+++++ ..++|+.|.|.++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~-~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKY-HNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSS-CCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEC
Confidence            58999999999999999999999 99999999999999999999999999999999999888 9999999999875

>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=99.72  E-value=6.3e-18  Score=117.25  Aligned_cols=85  Identities=15%  Similarity=0.220  Sum_probs=78.0

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-C---eEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-K---LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL   82 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~---i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~   82 (227)
                      ..+....++|||+|||+++|+++|+++|+.| .   |..|.|+.++. ++++|||||+|.+.++|.+||.+++ ..++|+
T Consensus         5 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~-~~~~gr   82 (107)
T 2lmi_A            5 EEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALEKHR-MYMGQR   82 (107)
T ss_dssp             CCCCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHTTTT-CCSSSS
T ss_pred             cCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHHhCc-ceeCCe
Confidence            3456778999999999999999999999998 6   89999999987 9999999999999999999999999 999999


Q ss_pred             EeEEEecCCCC
Q psy1680          83 QVRLDIADGKR   93 (227)
Q Consensus        83 ~l~v~~~~~~~   93 (227)
                      .|.|.++.++.
T Consensus        83 ~i~V~~a~~~~   93 (107)
T 2lmi_A           83 YVEVYEINNED   93 (107)
T ss_dssp             CCCCEECCHHH
T ss_pred             EEEEEECCHHH
Confidence            99999987643

>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=99.72  E-value=3.8e-18  Score=114.51  Aligned_cols=69  Identities=20%  Similarity=0.277  Sum_probs=64.9

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++|||+|||...  ++++|+++|+.||.|.+|.|++++.++.++|||||+|.+.+ |.+|++.|||..|+||
T Consensus         2 ~~l~V~nLp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~   70 (90)
T 2ki2_A            2 RNIYVGNLVYSA--TSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGR   70 (90)
T ss_dssp             EEEEEEEECTTS--SHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSS
T ss_pred             cEEEECCCCCCC--CHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCe
Confidence            379999997655  79999999999999999999999999999999999999999 9999999999999986

>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=99.72  E-value=1.7e-18  Score=147.95  Aligned_cols=72  Identities=11%  Similarity=0.180  Sum_probs=67.5

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +..+|||+|||+.+  ++++|..+|+.||.|+.|.|+.++.++.++|||||+|.+.++|.+||+.|||..|+|+
T Consensus       101 ~~~~lfV~nL~~~~--te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr  172 (437)
T 3pgw_S          101 AFKTLFVARVNYDT--TESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGR  172 (437)
T ss_pred             CCCEEEEeCCCCCC--CHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCE
Confidence            56789999997655  7899999999999999999999999999999999999999999999999999999885

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.72  E-value=8.2e-17  Score=114.51  Aligned_cols=72  Identities=21%  Similarity=0.157  Sum_probs=67.0

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .++.+|||+|||...  ++++|+++|+.||.|.+|.|++++ +|.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        33 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~  104 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGV--SDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGR  104 (124)
T ss_dssp             SSCEEEEEESCCSSC--CHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSC
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            456799999997655  799999999999999999999998 899999999999999999999999999999986

>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=99.71  E-value=1.4e-17  Score=114.11  Aligned_cols=67  Identities=9%  Similarity=-0.043  Sum_probs=59.2

Q ss_pred             CCCCcceeccCCC-CCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCc--cccCC
Q psy1680         153 GEGPGGFRNNNGP-NRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRI--TVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~-~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~--~i~gr  227 (227)
                      .++.+|||+|||+ .+  ++++|+++|++||.|.+|.|+++      +|||||+|++.++|.+|++.||+.  .|+||
T Consensus        13 ~p~~~l~V~nLp~~~~--te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr   82 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKN--LRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGK   82 (102)
T ss_dssp             CCCCEEEEESCCCSSS--HHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTE
T ss_pred             CCCCEEEEeCCCCCcC--CHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCc
Confidence            4678999999976 55  89999999999999999999876      489999999999999999998864  47775

>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=99.71  E-value=2.4e-17  Score=114.51  Aligned_cols=80  Identities=16%  Similarity=0.198  Sum_probs=71.2

Q ss_pred             CCCCCceEEEcCCCCC-CCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hC--CCceeCCeE
Q psy1680           9 PTEPPYTAFVGNLPNG-ITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KD--GRITVDGLQ   83 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~-~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~--~~~~~~g~~   83 (227)
                      ...++++|||+|||++ +++++|+++|++| .|..|.|++.      +|||||+|.+.++|..|++ ++  + ..|.|++
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~-~~l~Gr~   93 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKA-LWFQGRC   93 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSC-CCSSSSC
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCC-ceECCEE
Confidence            3567899999999998 9999999999999 9999999743      7899999999999999998 75  4 5699999


Q ss_pred             eEEEecCCCCCC
Q psy1680          84 VRLDIADGKRND   95 (227)
Q Consensus        84 l~v~~~~~~~~~   95 (227)
                      |.|.++..++..
T Consensus        94 l~V~~a~~~~~~  105 (112)
T 1x4f_A           94 VKVDLSEKYKKL  105 (112)
T ss_dssp             CEEEEECSCSSS
T ss_pred             EEEEECcccccc
Confidence            999999876653

>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=99.71  E-value=9.8e-17  Score=137.01  Aligned_cols=84  Identities=21%  Similarity=0.422  Sum_probs=79.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ..+.++|||+|||+.+|+++|+++|++| .|..|.|+.++.++.++|||||+|.+.++|.+||. ||+ ..|.|+.|.|.
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng-~~i~gr~i~V~  177 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADG-KKIDGRRVLVD  177 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCC-CEECCEEEEEE
Confidence            3456899999999999999999999999 99999999999999999999999999999999998 999 99999999999


Q ss_pred             ecCCCCC
Q psy1680          88 IADGKRN   94 (227)
Q Consensus        88 ~~~~~~~   94 (227)
                      ++.++..
T Consensus       178 ~a~~~~~  184 (437)
T 3pgw_S          178 VERGRTV  184 (437)
T ss_pred             EeCCCCC
Confidence            9987654

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=6.6e-17  Score=110.00  Aligned_cols=79  Identities=19%  Similarity=0.379  Sum_probs=72.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeC--CeEe
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVD--GLQV   84 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~--g~~l   84 (227)
                      ...+.++|||+|||.++++++|+++|++| .|..+.++.+      +|||||+|.+.++|++|++ +|+ ..+.  |+.|
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g-~~~~~~g~~l   85 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRG-FPLGGPDRRL   85 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTT-CBCSSSSCBC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCC-CEeCCCCcEE
Confidence            45667999999999999999999999999 9999999754      7899999999999999999 999 9999  9999


Q ss_pred             EEEecCCCCC
Q psy1680          85 RLDIADGKRN   94 (227)
Q Consensus        85 ~v~~~~~~~~   94 (227)
                      .|.++.++..
T Consensus        86 ~V~~a~~~~~   95 (97)
T 1why_A           86 RVDFAKSGPS   95 (97)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEECCCCCC
Confidence            9999987653

>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=99.71  E-value=2.1e-17  Score=122.28  Aligned_cols=73  Identities=14%  Similarity=0.136  Sum_probs=68.0

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|++||.|..|.|++++.++.++|||||+|.+.++|.+||+.|||..|+|+
T Consensus        37 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~  109 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYT--TEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDR  109 (156)
T ss_dssp             TTCCEEEEESCCTTC--CHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCe
Confidence            356899999997655  7999999999999999999999999999999999999999999999999999999875

>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=99.71  E-value=4.4e-17  Score=111.56  Aligned_cols=68  Identities=7%  Similarity=-0.037  Sum_probs=59.8

Q ss_pred             CCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHc--CCccccCC
Q psy1680         152 GGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD--GRITVDGL  227 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l--~g~~i~gr  227 (227)
                      .+++.+|||+|||..+  ++++|+++|++||.|.+|.|+++      +|||||+|.+.++|.+|++.|  ++..|+||
T Consensus        12 ~~p~~~l~V~nLp~~~--te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr   81 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEV--TETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQ   81 (101)
T ss_dssp             SSCCSEEEEESCCTTC--CHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTE
T ss_pred             CCCCCEEEEeCCCCCC--CHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCc
Confidence            3577899999997655  89999999999999999999876      799999999999999999976  46778775

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=1.4e-16  Score=107.25  Aligned_cols=79  Identities=16%  Similarity=0.321  Sum_probs=72.3

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      ....+.++|||+|||..+++++|+++|++| .|..+.++        ++||||+|.+.++|.+|++ +++ ..+.|+.|.
T Consensus         5 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~   75 (92)
T 2dgt_A            5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDN-TEFQGKRMH   75 (92)
T ss_dssp             CCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--------SSEEEEEESCHHHHHHHHHHHTT-EEETTEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--------CCEEEEEECCHHHHHHHHHHhCC-CeeCCcEEE
Confidence            345678999999999999999999999999 99999997        3499999999999999998 999 999999999


Q ss_pred             EEecCCCCCC
Q psy1680          86 LDIADGKRND   95 (227)
Q Consensus        86 v~~~~~~~~~   95 (227)
                      |.++.++...
T Consensus        76 V~~a~~~~~~   85 (92)
T 2dgt_A           76 VQLSTSRLRT   85 (92)
T ss_dssp             EEESSCCCSC
T ss_pred             EEEccCCCCC
Confidence            9999877653

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=1.1e-17  Score=108.96  Aligned_cols=75  Identities=23%  Similarity=0.420  Sum_probs=70.8

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEec
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA   89 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~   89 (227)
                      ++|||+|||.++++++|+++|++| .|..+.++.++.+++++|||||+|.+.++|.+|++..+ ..++|+.|.|.++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            479999999999999999999999 99999999999999999999999999999999999555 8999999999886

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.71  E-value=4e-17  Score=107.30  Aligned_cols=73  Identities=12%  Similarity=0.123  Sum_probs=68.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      ..+..|||+||++.+|+++|+++|.+| +|..+.++.      ++|||||+|.+.++|.+|++ ||+ ..+.|++|+|..
T Consensus         5 ~~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~-~~l~gr~I~V~~   77 (89)
T 2wbr_A            5 WGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNN-CVLANTTIFAES   77 (89)
T ss_dssp             CCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTT-EEETTEEEEEEC
T ss_pred             CccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcC-CEECCcEEEEEE
Confidence            357889999999999999999999999 999999975      48999999999999999999 999 999999999999


Q ss_pred             cC
Q psy1680          89 AD   90 (227)
Q Consensus        89 ~~   90 (227)
                      +.
T Consensus        78 A~   79 (89)
T 2wbr_A           78 PS   79 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            84

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.70  E-value=3.3e-17  Score=113.00  Aligned_cols=75  Identities=11%  Similarity=-0.047  Sum_probs=65.8

Q ss_pred             CCCCcceeccCCCC---CCCChhhHHhhhccccceEEEEEeecCCC-CcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPN---RSNSMNDHGLMVTEVTTLVSVRLVKDKET-DRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~---~~~~~~~l~~~f~~~g~i~~v~i~~d~~t-~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .++++|+|.||..+   .++++++|+++|++||.|.+|.|++++.+ +.++|+|||+|.+.++|.+|++.|||+.++||
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            46789999999632   23478999999999999999999999765 68999999999999999999999999999997

>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=99.70  E-value=5.5e-18  Score=109.79  Aligned_cols=68  Identities=19%  Similarity=0.299  Sum_probs=63.1

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +|||+|||...  ++++|+++|++||.|.+|.+++++.++.++|||||+|.+.++|.+|++. ++..|+||
T Consensus         1 ~l~v~nLp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~   68 (75)
T 1iqt_A            1 KIFVGGLSPDT--PEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLS   68 (75)
T ss_dssp             CEEESCCCSSC--CHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTB
T ss_pred             CEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCE
Confidence            58999997655  7999999999999999999999999999999999999999999999996 78888885

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.70  E-value=3.8e-17  Score=116.50  Aligned_cols=82  Identities=15%  Similarity=0.294  Sum_probs=73.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHH----hcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCe
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVE----RFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGL   82 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~----~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~   82 (227)
                      +..+.++|||+|||+.+++++|+    ++|++| .|..|.+.+   +++++|||||+|.+.++|..|+. +|| ..|.|+
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng-~~l~gr  100 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQG-YPFQGN  100 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTT-CCCTTS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCC-CEeCCC
Confidence            35667999999999999999876    699999 999988853   57889999999999999999998 999 999999


Q ss_pred             EeEEEecCCCCC
Q psy1680          83 QVRLDIADGKRN   94 (227)
Q Consensus        83 ~l~v~~~~~~~~   94 (227)
                      +|.|.++..+..
T Consensus       101 ~l~V~~a~~~~~  112 (127)
T 2a3j_A          101 PLVITFSETPQS  112 (127)
T ss_dssp             CCEEEECCCCCH
T ss_pred             EEEEEEccCcch
Confidence            999999987654

>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=99.70  E-value=2.3e-17  Score=112.10  Aligned_cols=69  Identities=13%  Similarity=0.028  Sum_probs=63.3

Q ss_pred             CCCcceeccCCCCCCCChhhHH----hhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHG----LMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~----~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||...  ++++|+    ++|++||.|.+|+|++|+.+   +|||||+|.+.++|.+|++.|||..|+||
T Consensus         8 ~~~~l~V~nL~~~~--~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr   80 (96)
T 2dgx_A            8 NGADVQVSNIDYRL--SRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSK   80 (96)
T ss_dssp             SCEEEEEESCCTTS--CHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCEEEEECCCCCC--CHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCe
Confidence            45689999997655  789999    99999999999999999875   89999999999999999999999999986

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=3.7e-17  Score=112.56  Aligned_cols=70  Identities=13%  Similarity=0.102  Sum_probs=60.3

Q ss_pred             CCCCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCc--cccCC
Q psy1680         150 SRGGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRI--TVDGL  227 (227)
Q Consensus       150 ~~~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~--~i~gr  227 (227)
                      ...+++.+|||+|||..+  ++++|+++|++||.|.+|.|+++      +|||||+|.+.++|.+|++.|++.  .|+||
T Consensus        10 ~~~~p~~~l~V~nLp~~~--te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr   81 (104)
T 1wex_A           10 HKVSVSPVVHVRGLCESV--VEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQ   81 (104)
T ss_dssp             CCCCCCSEEEEESCCSSC--CHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSS
T ss_pred             CcCCCCCEEEEeCCCCCC--CHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCE
Confidence            334678899999997655  79999999999999999999875      699999999999999999988654  47775

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.70  E-value=1.5e-16  Score=118.06  Aligned_cols=84  Identities=19%  Similarity=0.408  Sum_probs=78.9

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeE
Q psy1680           6 KTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQ   83 (227)
Q Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~   83 (227)
                      ......+.++|||+|||..+++++|+++|++| .|..+.++.++.++.++|||||+|.+.++|.+|+. +++ ..++|++
T Consensus        80 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~  158 (166)
T 3md3_A           80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQG-QDLNGRP  158 (166)
T ss_dssp             CCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTT-CEETTEE
T ss_pred             CCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCC-CccCCcE
Confidence            34456678999999999999999999999999 99999999999999999999999999999999999 999 9999999


Q ss_pred             eEEEecC
Q psy1680          84 VRLDIAD   90 (227)
Q Consensus        84 l~v~~~~   90 (227)
                      |.|.+++
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=99.70  E-value=1.2e-17  Score=114.73  Aligned_cols=83  Identities=24%  Similarity=0.447  Sum_probs=76.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLD   87 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~   87 (227)
                      .....++|||+|||.++++++|+++|++| .|..+.|+.++ +++++|||||+|.+.++|++||. ++ ..++|+.|.|.
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~-~~-~~~~g~~l~v~   81 (102)
T 2xs2_A            5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE-SQ-INFHGKKLKLG   81 (102)
T ss_dssp             CEEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT-CC-CEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh-CC-CeECCEEEEEE
Confidence            44567999999999999999999999999 99999999998 89999999999999999999999 98 99999999999


Q ss_pred             ecCCCCC
Q psy1680          88 IADGKRN   94 (227)
Q Consensus        88 ~~~~~~~   94 (227)
                      ++.++..
T Consensus        82 ~a~~~~~   88 (102)
T 2xs2_A           82 PAIRKQN   88 (102)
T ss_dssp             EEEECC-
T ss_pred             ECCcCcc
Confidence            9886654

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.70  E-value=2.4e-17  Score=128.10  Aligned_cols=73  Identities=18%  Similarity=0.176  Sum_probs=67.0

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .|..+|||+|||+.+  ++++|+++|++||.|.+|+|++|+.|++++|||||+|.+.++|.+|++.+++..+.||
T Consensus        13 ~p~~tlfVgnLp~~~--te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~   85 (213)
T 4f02_A           13 YPMASLYVGDLHPDV--TEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGK   85 (213)
T ss_dssp             --CCEEEEESCCTTC--CHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCcEEEEeCCCCCC--CHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCc
Confidence            356789999997655  8999999999999999999999999999999999999999999999999999998875

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=3.2e-17  Score=110.21  Aligned_cols=70  Identities=19%  Similarity=0.229  Sum_probs=64.5

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ....+|||+|||...  ++++|+++|+.| .|..|+|+++ .+|+++|||||+|.+.++|.+|++ |||..|+||
T Consensus         8 ~~~~~l~v~nLp~~~--t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr   77 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNV--TEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGR   77 (91)
T ss_dssp             CCCCEEEEECCCSSC--CHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTE
T ss_pred             CCccEEEEECCCCCC--CHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCc
Confidence            356789999997655  799999999999 8999999999 789999999999999999999999 999999986

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=6e-17  Score=110.21  Aligned_cols=80  Identities=21%  Similarity=0.346  Sum_probs=71.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ..+..++|||+|||..+++++|+++|++| .|. +.++.+    +++|||||+|.+.++|.+|++ +|+ ..++|+.|.|
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~V   88 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQG-LRLGTDTLRV   88 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTT-CCSSSSCCEE
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCC-CEECCcEEEE
Confidence            45667999999999999999999999999 886 666654    568999999999999999998 999 9999999999


Q ss_pred             EecCCCCC
Q psy1680          87 DIADGKRN   94 (227)
Q Consensus        87 ~~~~~~~~   94 (227)
                      .++.+++.
T Consensus        89 ~~a~~~~~   96 (97)
T 2e5j_A           89 ALARQQRD   96 (97)
T ss_dssp             EECCCCCC
T ss_pred             EEcCCCCC
Confidence            99987653

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=2.6e-17  Score=116.67  Aligned_cols=81  Identities=21%  Similarity=0.185  Sum_probs=74.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-Ce----EEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEe
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KL----VSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQV   84 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i----~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l   84 (227)
                      ....++|||+|||+++|+++|+++|++| .|    ..|.|+.+ .+++++|||||+|.+.++|++||+.++ ..|+++.|
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~~~-~~l~gR~i   97 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRKHK-DLLGKRYI   97 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTTTT-EESSSCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHhCC-CeeCCeEE
Confidence            4567999999999999999999999999 75    68999998 479999999999999999999999999 99999999


Q ss_pred             EEEecCCC
Q psy1680          85 RLDIADGK   92 (227)
Q Consensus        85 ~v~~~~~~   92 (227)
                      .|..+.++
T Consensus        98 ~V~~a~~~  105 (123)
T 2dha_A           98 ELFRSTAA  105 (123)
T ss_dssp             CCEEECHH
T ss_pred             EEEECCHH
Confidence            99988654

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=1.3e-16  Score=107.04  Aligned_cols=77  Identities=17%  Similarity=0.456  Sum_probs=71.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ...+.++|||+|||..+|+++|+++|++| .|..+.++        ++||||+|.+.++|.+||+ +++ ..++|+.|.|
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~--------~~~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~v   75 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQLNG-KEVKGKRINV   75 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESCHHHHHHHHHHHTT-CEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhCC-CEECCcEEEE
Confidence            45678999999999999999999999999 99999997        3499999999999999999 999 9999999999


Q ss_pred             EecCCCCC
Q psy1680          87 DIADGKRN   94 (227)
Q Consensus        87 ~~~~~~~~   94 (227)
                      .++.++..
T Consensus        76 ~~a~~~~~   83 (90)
T 2dnp_A           76 ELSTKGQK   83 (90)
T ss_dssp             EESCCCCC
T ss_pred             EECCCCCC
Confidence            99987654

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.70  E-value=3.6e-17  Score=111.25  Aligned_cols=83  Identities=19%  Similarity=0.388  Sum_probs=73.9

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHH----hcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVE----RFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG   81 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~----~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g   81 (227)
                      .+..++++|||+|||.++++++|+    ++|++| .|..+.+++   ++.++|||||+|.+.++|.+|++ +++ ..++|
T Consensus         3 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g   78 (97)
T 1nu4_A            3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQG-FPFYD   78 (97)
T ss_dssp             ---CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTT-CEETT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCC-CEECC
Confidence            345778999999999999999999    999999 999998874   47788999999999999999999 999 99999


Q ss_pred             eEeEEEecCCCCC
Q psy1680          82 LQVRLDIADGKRN   94 (227)
Q Consensus        82 ~~l~v~~~~~~~~   94 (227)
                      +.|.|.++.++..
T Consensus        79 ~~l~v~~a~~~~~   91 (97)
T 1nu4_A           79 KPMRIQYAKTDSD   91 (97)
T ss_dssp             EECEEEECSSCCT
T ss_pred             cEEEEEEccCCCc
Confidence            9999999987653

>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=99.69  E-value=2.2e-17  Score=114.52  Aligned_cols=71  Identities=10%  Similarity=0.067  Sum_probs=65.0

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccc---eEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTT---LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~---i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ....+|||+|||+.+  ++++|+++|+.||.   |.+|+|++|+. |+++|||||+|.+.++|.+||+ ++|..|+||
T Consensus         9 ~~~~~l~V~nLp~~~--te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr   82 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSC--TMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQR   82 (107)
T ss_dssp             SSCCEEEEECCCSSC--CSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSS
T ss_pred             CCccEEEEeCCCCCC--CHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCe
Confidence            356789999997655  78999999999998   89999999988 9999999999999999999999 999999986

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.69  E-value=1.2e-16  Score=110.99  Aligned_cols=77  Identities=17%  Similarity=0.323  Sum_probs=70.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ...+.++|||+|||.++++++|+++|++| .|..+.++        +|||||+|.+.++|.+|++ +++ ..++|+.|.|
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g-~~~~g~~l~V   97 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHG-KSFANQPLEV   97 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTT-CEETTEECEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCC-CEECCeEEEE
Confidence            45677999999999999999999999999 99999987        6899999999999999999 999 9999999999


Q ss_pred             EecCCCCC
Q psy1680          87 DIADGKRN   94 (227)
Q Consensus        87 ~~~~~~~~   94 (227)
                      .++.++..
T Consensus        98 ~~a~~~~~  105 (108)
T 2jvo_A           98 VYSKLPAK  105 (108)
T ss_dssp             ESCSCCC-
T ss_pred             EEecCCCC
Confidence            99987654

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=4e-17  Score=114.64  Aligned_cols=68  Identities=9%  Similarity=-0.016  Sum_probs=60.4

Q ss_pred             CCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCC--ccccCC
Q psy1680         152 GGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR--ITVDGL  227 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g--~~i~gr  227 (227)
                      .+++.+|||+|||+.+  ++++|+++|++||.|++|+|+++      +|||||+|++.++|.+|++.+++  ..|+||
T Consensus        28 ~~ps~~LfVgNLp~~v--te~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr   97 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDV--TEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQ   97 (119)
T ss_dssp             SSCCSEEEEESCCTTC--CHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTB
T ss_pred             CCCCCEEEEeCCCCCC--CHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCe
Confidence            3577899999997665  89999999999999999999886      69999999999999999998874  578775

>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=99.69  E-value=2.9e-17  Score=114.16  Aligned_cols=73  Identities=18%  Similarity=0.139  Sum_probs=66.1

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccc-eEEEEEe-ecCCCCcccceEEEEEcCHHHHHHHHHHcC--CccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTT-LVSVRLV-KDKETDRFKGFCYVEFVDVENLRQALLKDG--RITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~-i~~v~i~-~d~~t~~~~g~afV~F~~~~~a~~Al~~l~--g~~i~gr  227 (227)
                      .+..+|||+|||...  ++++|+++|+.||. |.+|.|+ +++.++.++|||||+|.+.++|.+|++.|+  +..|+||
T Consensus         6 ~~~~~l~V~nLp~~~--t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~   82 (109)
T 2dis_A            6 SGNCRLFIGGIPKMK--KREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGH   82 (109)
T ss_dssp             CCSEEEEEECCCTTS--CHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTB
T ss_pred             cCCCEEEEeCCCCcC--CHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCC
Confidence            456789999997655  79999999999998 9999998 898899999999999999999999999996  5889885

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.69  E-value=2.2e-17  Score=108.64  Aligned_cols=71  Identities=20%  Similarity=0.337  Sum_probs=65.7

Q ss_pred             CceEEEcCCCCCC------CHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCe-E
Q psy1680          13 PYTAFVGNLPNGI------TQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGL-Q   83 (227)
Q Consensus        13 ~~~l~V~nLp~~~------t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~-~   83 (227)
                      +++|||+|||..+      ++++|+++|++| .|..+.|+  +.+++++|||||+|.+.++|.+|++ +|| ..++|+ +
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng-~~~~g~~~   77 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADG-YKLDKQHT   77 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSS-CCCSSSSC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcC-cccCCcee
Confidence            4789999999999      779999999999 99999987  4678999999999999999999999 999 999999 8


Q ss_pred             eEE
Q psy1680          84 VRL   86 (227)
Q Consensus        84 l~v   86 (227)
                      |+|
T Consensus        78 l~V   80 (81)
T 2krb_A           78 FRV   80 (81)
T ss_dssp             CCC
T ss_pred             EEe
Confidence            876

>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=99.69  E-value=1.5e-16  Score=110.54  Aligned_cols=78  Identities=21%  Similarity=0.460  Sum_probs=72.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ....++|||+|||..+++++|+++|++| .|..|.|+.+      +|||||+|.+.++|.+||. +++ ..|+|+.|.|.
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~v~   94 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNG-TTIEGHVVKCY   94 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTT-CEETTEECEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCC-CEECCcEEEEE
Confidence            4567899999999999999999999999 9999999876      7899999999999999998 999 99999999999


Q ss_pred             ecCCCCC
Q psy1680          88 IADGKRN   94 (227)
Q Consensus        88 ~~~~~~~   94 (227)
                      ++.++..
T Consensus        95 ~a~~~~~  101 (109)
T 1x4g_A           95 WGKESPD  101 (109)
T ss_dssp             CCCCCCS
T ss_pred             ecCCCCC
Confidence            9987654

>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=99.69  E-value=1.6e-16  Score=108.01  Aligned_cols=68  Identities=15%  Similarity=0.240  Sum_probs=61.3

Q ss_pred             CCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcccc--CC
Q psy1680         152 GGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVD--GL  227 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~--gr  227 (227)
                      .++..+|||+|||...  ++++|+++|++||.|.+|.++++      +|||||+|.+.++|.+|++.|||..|+  |+
T Consensus        14 ~~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~   83 (97)
T 1why_A           14 ANPTTRLWVGGLGPNT--SLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDR   83 (97)
T ss_dssp             CCCCSCEEEECCCSSC--CHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSC
T ss_pred             CCCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCc
Confidence            3567899999997665  79999999999999999999765      689999999999999999999999998  65

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.69  E-value=8.2e-17  Score=112.97  Aligned_cols=82  Identities=21%  Similarity=0.330  Sum_probs=74.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      +..++++|||+|||..+++++|+++|++| .|..+.|+.+   +.++|||||+|.+.++|.+|+. +|+ ..++|+.|.|
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~l~v   79 (115)
T 3lqv_A            4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSG-FNVSNRYLVV   79 (115)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTT-CBSSSCBCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCC-CEECCeEEEE
Confidence            45678999999999999999999999999 9999999876   4458999999999999999999 999 9999999999


Q ss_pred             EecCCCCC
Q psy1680          87 DIADGKRN   94 (227)
Q Consensus        87 ~~~~~~~~   94 (227)
                      .++.++..
T Consensus        80 ~~a~~~~~   87 (115)
T 3lqv_A           80 LYYNANRA   87 (115)
T ss_dssp             EECCHHHH
T ss_pred             EEecCChh
Confidence            99976543

>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=99.69  E-value=5.4e-17  Score=113.98  Aligned_cols=78  Identities=19%  Similarity=0.293  Sum_probs=65.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeE---
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQ---   83 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~---   83 (227)
                      +....++|||+|||+++++++|+++|++| .|..|.|+.+       |||||+|.+.++|++||+ ||+ ..|+|+.   
T Consensus        12 ~~r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g-~~~~gr~~~~   83 (115)
T 3beg_B           12 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDN-TKFRSHEGET   83 (115)
T ss_dssp             -----CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTT-CBCCCTTSCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCC-CEECCcEeee
Confidence            34667999999999999999999999999 9999999865       899999999999999999 999 9999998   


Q ss_pred             --eEEEecCCCCC
Q psy1680          84 --VRLDIADGKRN   94 (227)
Q Consensus        84 --l~v~~~~~~~~   94 (227)
                        |+|..+.++..
T Consensus        84 ~~i~v~~~~~~~~   96 (115)
T 3beg_B           84 AYIRVKVDGPRSP   96 (115)
T ss_dssp             CBCEEEECC----
T ss_pred             EEEEeccCCCCCC
Confidence              77777766544

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.69  E-value=4.7e-16  Score=117.30  Aligned_cols=72  Identities=21%  Similarity=0.157  Sum_probs=67.1

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .++.+|||+|||..+  ++++|+++|+.||.|..|.|+.++ ++.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        86 ~~~~~l~V~nLp~~~--te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr  157 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGV--SDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGR  157 (177)
T ss_dssp             TTCEEEEEECCCSCC--CHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSS
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCE
Confidence            457899999997655  799999999999999999999998 899999999999999999999999999999986

>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=99.69  E-value=1.4e-17  Score=120.51  Aligned_cols=70  Identities=19%  Similarity=0.135  Sum_probs=63.3

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ....+|||+|||+.+  ++++|+++|++|| |.+|+|++|++ ++++|||||+|.+.++|++|| .+|+..|+||
T Consensus        44 ~~~~~lfV~nLp~~~--te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR  113 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKA--TENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHR  113 (139)
T ss_dssp             -CCCCEECCSCCTTC--CHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSC
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCE
Confidence            356789999997655  8999999999999 77999999987 999999999999999999999 8899999987

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.69  E-value=3.2e-17  Score=116.59  Aligned_cols=70  Identities=16%  Similarity=0.258  Sum_probs=65.6

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..+|||+|||..+  ++++|+++|+.||.|.+|.|++++.++.++|||||+|.+.++|.+|+ .|||..|+|+
T Consensus        36 ~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  105 (124)
T 2jwn_A           36 KRSVYVGNVDYGS--TAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGR  105 (124)
T ss_dssp             HTEEEEEEECTTC--CHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTE
T ss_pred             CCEEEEeCCCCCC--CHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCe
Confidence            5789999997655  79999999999999999999999999999999999999999999999 8999999885

>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=99.69  E-value=2.5e-17  Score=129.28  Aligned_cols=72  Identities=11%  Similarity=0.109  Sum_probs=66.3

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhcccc--ceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVT--TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g--~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||..+  ++++|+++|+.||  .|++|+|++|+.|++++|||||+|.+.++|.+||+.|||..|+||
T Consensus        67 ~~~~lfVgnL~~~~--te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr  140 (229)
T 3q2s_C           67 KRIALYIGNLTWWT--TDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQ  140 (229)
T ss_dssp             --CEEEEESCCTTC--CHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTB
T ss_pred             CccEEEEeCCCCCC--CHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCE
Confidence            45689999996655  8999999999999  999999999999999999999999999999999999999999986

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=3.9e-17  Score=113.61  Aligned_cols=71  Identities=18%  Similarity=0.156  Sum_probs=64.8

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||...  ++++|+++|++||.|.+|+|++++  +.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        27 ~~~~~l~V~nLp~~~--te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~   97 (109)
T 2err_A           27 SQPKRLHVSNIPFRF--RDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGR   97 (109)
T ss_dssp             TCCCEEEEESCCTTC--CHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEECCCCcC--CHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            467899999997655  799999999999999999999985  45899999999999999999999999999985

>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=99.69  E-value=1.9e-16  Score=120.93  Aligned_cols=87  Identities=18%  Similarity=0.376  Sum_probs=75.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEe
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDI   88 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~   88 (227)
                      ..+.++|||+|||.++|+++|+++|++| .|..+.|+.++.++.++|||||+|.+.++|.+||..++ ..|+|+.|.|.+
T Consensus       101 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~~~-~~~~G~~i~v~~  179 (196)
T 1l3k_A          101 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY-HTVNGHNCEVRK  179 (196)
T ss_dssp             --CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSC-CEETTEECEEEE
T ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHhCC-cEECCEEEEEEe
Confidence            3456899999999999999999999999 99999999999899999999999999999999999788 999999999999


Q ss_pred             cCCCCCCCC
Q psy1680          89 ADGKRNDNK   97 (227)
Q Consensus        89 ~~~~~~~~~   97 (227)
                      +.++.....
T Consensus       180 a~~k~~~~~  188 (196)
T 1l3k_A          180 ALSKQEMAS  188 (196)
T ss_dssp             CC-------
T ss_pred             cCChhHhcc
Confidence            998876543

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=3.6e-16  Score=105.73  Aligned_cols=79  Identities=24%  Similarity=0.389  Sum_probs=70.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEe
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDI   88 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~   88 (227)
                      ....++|||+|||.++++++|+++|++| .|..|  +.++.+++   ||||+|.+.++|.+||++++ ..|+|+.|.|.+
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~l~g-~~~~g~~l~V~~   78 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLSQSQ-HSLGGHRLRVRP   78 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHTCSC-CEETTEECCCBC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHhcCC-eEECCEEEEEEE
Confidence            3456899999999999999999999999 99987  56666555   99999999999999999999 999999999998


Q ss_pred             cCCCCC
Q psy1680          89 ADGKRN   94 (227)
Q Consensus        89 ~~~~~~   94 (227)
                      +.++..
T Consensus        79 a~~~~~   84 (94)
T 2e5g_A           79 REQKEF   84 (94)
T ss_dssp             SCCSCC
T ss_pred             CCcCCC
Confidence            876554

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.69  E-value=5.6e-17  Score=106.60  Aligned_cols=65  Identities=11%  Similarity=0.024  Sum_probs=59.1

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +.-|||+||++..  ++++|+++|.+||.|.++++..      ++|||||+|.+.++|.+|++.|||..++||
T Consensus         7 ~~wL~VgNL~~~~--te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr   71 (89)
T 2wbr_A            7 SSWLLLKNLTAQI--DGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANT   71 (89)
T ss_dssp             CCEEEEECCCTTC--CCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             cceEEEeCCCccC--CHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCc
Confidence            5579999996555  7899999999999999999865      589999999999999999999999999986

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.1e-16  Score=109.77  Aligned_cols=70  Identities=23%  Similarity=0.243  Sum_probs=63.2

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.|   ..|.+++++.++.++|||||+|.+.++|.+||+.|||..|+|+
T Consensus        13 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   82 (102)
T 2fc8_A           13 QPSKTLFVKGLSEDT--TEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGN   82 (102)
T ss_dssp             CCCSSEEEECCCTTC--CHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEeCCCCcc--CHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            567899999997655  799999999977   3688889988999999999999999999999999999999885

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.68  E-value=8e-17  Score=114.80  Aligned_cols=70  Identities=11%  Similarity=0.104  Sum_probs=61.3

Q ss_pred             CCCCcceeccCCCCCCCChhhHH----hhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHG----LMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~----~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++..+|||+|||+.+  ++++|+    ++|++||.|.+|.+.+   +++++|||||+|.+.++|.+|++.|||..|.||
T Consensus        27 ~p~~~LfV~nL~~~~--~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr  100 (127)
T 2a3j_A           27 EPSQVVLITNINPEV--PKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGN  100 (127)
T ss_dssp             SCCSEEEEESCCTTS--CHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTS
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCC
Confidence            467899999997655  667654    7999999999998854   478999999999999999999999999999986

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=2.7e-17  Score=115.60  Aligned_cols=71  Identities=15%  Similarity=0.210  Sum_probs=65.9

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +..+|||+|||..+  ++++|+++|+.||.|..|.|++++.++.++|||||+|.+.++|.+||+. +|..|+||
T Consensus        26 ~~~~l~V~nLp~~~--te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~   96 (116)
T 1x4b_A           26 QFRKLFIGGLSFET--TEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGR   96 (116)
T ss_dssp             HHTEEEEECCTTCC--CHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTE
T ss_pred             CCCEEEEeCCCCCC--CHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCE
Confidence            35789999997655  7999999999999999999999999999999999999999999999999 99999885

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.68  E-value=8.3e-17  Score=110.31  Aligned_cols=76  Identities=18%  Similarity=0.368  Sum_probs=69.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ....++|||+|||.++++++|+++|++| .|..+.+++      ++|||||+|.+.++|.+|+. +++ ..++|+.|+|.
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g-~~~~g~~l~V~   96 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALAN-FPFQGRNLRTG   96 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTT-CEETTEECCCC
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCC-CeECCeEEEEE
Confidence            3456899999999999999999999999 999999973      37999999999999999998 999 99999999999


Q ss_pred             ecCCC
Q psy1680          88 IADGK   92 (227)
Q Consensus        88 ~~~~~   92 (227)
                      ++.++
T Consensus        97 ~a~~~  101 (101)
T 2la4_A           97 WGKER  101 (101)
T ss_dssp             BCCCC
T ss_pred             eccCC
Confidence            98764

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=9.3e-17  Score=110.06  Aligned_cols=69  Identities=17%  Similarity=0.320  Sum_probs=61.8

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|++||.|   +++++ .++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        13 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   81 (101)
T 2fc9_A           13 GESKTLVLSNLSYSA--TEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGR   81 (101)
T ss_dssp             CCCSEEEEESCCTTC--CHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCe
Confidence            467899999997665  899999999999977   66777 6799999999999999999999999999999885

>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=99.68  E-value=2.5e-16  Score=109.64  Aligned_cols=77  Identities=23%  Similarity=0.551  Sum_probs=70.0

Q ss_pred             CCCCCceEEEcCCCCC-CCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           9 PTEPPYTAFVGNLPNG-ITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~-~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      +....++|||+|||+. +++++|+++|++| .|..|.|        ++|||||+|.+.++|++||+ +++ ..|+|+.|.
T Consensus        23 ~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~l~   93 (110)
T 1wf1_A           23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENG-RVLAGQTLD   93 (110)
T ss_dssp             CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTT-CEETTEECC
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCC-CEECCeEEE
Confidence            3445589999999999 9999999999999 9999988        37899999999999999998 999 999999999


Q ss_pred             EEecCCCCC
Q psy1680          86 LDIADGKRN   94 (227)
Q Consensus        86 v~~~~~~~~   94 (227)
                      |.++.+++.
T Consensus        94 V~~a~~~~~  102 (110)
T 1wf1_A           94 INMAGEPKP  102 (110)
T ss_dssp             EEESCCCCS
T ss_pred             EEECCCCCC
Confidence            999986554

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.68  E-value=2.7e-16  Score=107.01  Aligned_cols=77  Identities=18%  Similarity=0.395  Sum_probs=69.9

Q ss_pred             CCCCCCceEEEcCCCC-CCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           8 LPTEPPYTAFVGNLPN-GITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~-~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      .+..+.++|||+|||. ++++++|+++|++| .|..+.|.        +|||||+|.+.++|.+|+. +++ ..++|+.|
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g-~~~~g~~l   87 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQ-EMNFGKKL   87 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTT-SEETTEEC
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCC-CEECCEEE
Confidence            3467789999999998 99999999999999 99999983        7899999999999999999 999 99999999


Q ss_pred             EEEecCCCC
Q psy1680          85 RLDIADGKR   93 (227)
Q Consensus        85 ~v~~~~~~~   93 (227)
                      .|.++.++.
T Consensus        88 ~V~~a~~~~   96 (97)
T 2xnq_A           88 ILEVSSSNA   96 (97)
T ss_dssp             EEEECCCCC
T ss_pred             EEEecCCCC
Confidence            999987643

>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=99.68  E-value=5.4e-17  Score=115.30  Aligned_cols=70  Identities=16%  Similarity=0.111  Sum_probs=62.3

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceE--EEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLV--SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~--~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ....+|||+|||+.+  ++++|+++|++| .|.  +|+|++|+. |+++|||||+|.+.++|.+||+. ++..|+||
T Consensus        40 ~~~~~lfVgnLp~~~--te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR  111 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGC--TKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKERIGHR  111 (126)
T ss_dssp             SSCCEEEEECCCTTC--CHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTB
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCE
Confidence            346789999997665  899999999999 576  999999987 99999999999999999999996 66899886

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=8.7e-16  Score=104.80  Aligned_cols=79  Identities=18%  Similarity=0.301  Sum_probs=69.9

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC---CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ---KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGL   82 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~---~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~   82 (227)
                      +....+.++|||+|||+.+++++|+++|++|   .|..+.++        +|||||+|.+.++|.+||. +++ ..|.|+
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g-~~~~g~   79 (99)
T 2cpd_A            9 EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNG-KVLDGS   79 (99)
T ss_dssp             CSCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSS-EEETTE
T ss_pred             ccccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCC-CEeCCc
Confidence            3445678999999999999999999999999   36666664        6799999999999999999 999 999999


Q ss_pred             EeEEEecCCCCC
Q psy1680          83 QVRLDIADGKRN   94 (227)
Q Consensus        83 ~l~v~~~~~~~~   94 (227)
                      .|.|.++.++..
T Consensus        80 ~l~v~~a~~~~~   91 (99)
T 2cpd_A           80 PIEVTLAKPVDK   91 (99)
T ss_dssp             EEEEECCCCCCC
T ss_pred             EEEEEECCCCCC
Confidence            999999987654

>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=99.68  E-value=1.1e-16  Score=112.20  Aligned_cols=70  Identities=11%  Similarity=0.073  Sum_probs=63.5

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +++++|||+|||..+  ++++|+++|++||.|.+|.|+++   +.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus         6 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   75 (115)
T 3lqv_A            6 EVNRILYIRNLPYKI--TAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNR   75 (115)
T ss_dssp             TCCSEEEEESCCTTC--CHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSC
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            457899999997655  79999999999999999999987   45699999999999999999999999999986

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.68  E-value=9.4e-17  Score=126.01  Aligned_cols=79  Identities=13%  Similarity=0.202  Sum_probs=73.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCCC---eEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQK---LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~~---i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ..++|||+|||+++|+++|+++|++|.   |..|.|++++.+++++|||||+|.+.++|.+||+ ||+ ..|.|+.|.|.
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng-~~~~Gr~l~V~  145 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPK-RELHGQNPVVT  145 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTT-SCBTTBCCEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCC-CeECCEEeEEE
Confidence            567899999999999999999999993   8999999999999999999999999999999999 999 99999999999


Q ss_pred             ecCC
Q psy1680          88 IADG   91 (227)
Q Consensus        88 ~~~~   91 (227)
                      ++.+
T Consensus       146 ~a~~  149 (229)
T 3q2s_C          146 PVNK  149 (229)
T ss_dssp             ECCH
T ss_pred             ECCC
Confidence            9864

>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=99.67  E-value=6.3e-17  Score=113.50  Aligned_cols=73  Identities=16%  Similarity=0.109  Sum_probs=62.6

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|..|.+..+..++.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        23 ~~~~~l~V~nLp~~~--t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~   95 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRV--TERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGK   95 (115)
T ss_dssp             SCCSEEEEECCCTTC--CHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSC
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            467899999997655  8999999999999995544443434789999999999999999999999999999886

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.67  E-value=1.2e-16  Score=108.51  Aligned_cols=77  Identities=19%  Similarity=0.439  Sum_probs=69.6

Q ss_pred             CCCCCceEEEcCCCC-CCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           9 PTEPPYTAFVGNLPN-GITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~-~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      ...+.++|||+|||+ .+++++|+++|++| .|..+.|.        +|||||+|.+.++|.+|++ +++ ..+.|+.|.
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~l~   76 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQ-EMNFGKKLI   76 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTC-SSCBTTTBC
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCC-CeeCCcEEE
Confidence            456789999999998 99999999999999 99999984        6899999999999999999 999 999999999


Q ss_pred             EEecCCCCC
Q psy1680          86 LDIADGKRN   94 (227)
Q Consensus        86 v~~~~~~~~   94 (227)
                      |.++.++..
T Consensus        77 V~~a~~~~~   85 (96)
T 2kvi_A           77 LEVSSSNAR   85 (96)
T ss_dssp             EEEEECCCC
T ss_pred             EEEcCcCCC
Confidence            999987654

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.67  E-value=1.5e-16  Score=120.05  Aligned_cols=82  Identities=22%  Similarity=0.355  Sum_probs=77.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ..+.++|||+|||+.+++++|+++|++| .|..|.|+.++ ++.++|||||+|.+.++|.+||+ +++ ..|+|+.|.|.
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng-~~l~Gr~l~V~  162 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKG-VPLDGRPMDIQ  162 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTT-CBCSSSBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCC-CEECCEEEEEE
Confidence            4567899999999999999999999999 99999999998 89999999999999999999999 999 99999999999


Q ss_pred             ecCCCC
Q psy1680          88 IADGKR   93 (227)
Q Consensus        88 ~~~~~~   93 (227)
                      ++....
T Consensus       163 ~a~~~~  168 (177)
T 2f3j_A          163 LVASQI  168 (177)
T ss_dssp             EESSGG
T ss_pred             EecCCC
Confidence            987654

>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=99.67  E-value=2.3e-16  Score=109.49  Aligned_cols=64  Identities=20%  Similarity=0.165  Sum_probs=59.5

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      ...+|||+|||..+  ++++|+++|++||.|..|.|+++       |||||+|.+.++|++||+.|||..|+|
T Consensus        14 ~~~~l~V~nLp~~~--t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g   77 (108)
T 1x4c_A           14 SENRVVVSGLPPSG--SWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRS   77 (108)
T ss_dssp             CCCEEEEESCCSSC--CHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEEC
T ss_pred             CCCEEEEeCCCCCC--CHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccC
Confidence            46789999997655  79999999999999999999887       899999999999999999999999988

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.67  E-value=2e-17  Score=113.43  Aligned_cols=71  Identities=27%  Similarity=0.285  Sum_probs=64.3

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|.. .++++..++.++|||||+|.+.++|.+|++ |||..|+||
T Consensus        15 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~   85 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNK--SVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGN   85 (101)
T ss_dssp             SCSEEEEEECCCTTS--CHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTB
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCc
Confidence            356789999997655  79999999999999988 778888889999999999999999999999 999999886

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=3.7e-17  Score=115.86  Aligned_cols=71  Identities=13%  Similarity=-0.017  Sum_probs=63.3

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccce----EEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTL----VSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i----~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ....+|||+|||+.+  ++++|+++|++||.|    ..|+|++| .+|+++|||||+|.+.++|.+||+. ++..|+||
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 ENQVIVRMRGLPFTA--TAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKR   95 (123)
T ss_dssp             CSCCEEEECSCCTTC--CHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSC
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCe
Confidence            345789999997655  899999999999875    69999999 4799999999999999999999997 88999886

>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=99.67  E-value=2.6e-16  Score=104.33  Aligned_cols=67  Identities=12%  Similarity=0.168  Sum_probs=60.9

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHc-CCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD-GRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l-~g~~i~gr  227 (227)
                      .+..+|||+|||...  ++++|+++|++||.|.+|.++++      +|||||+|.+.++|.+|++.| +|..|+|+
T Consensus        10 ~~~~~l~V~~l~~~~--t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~   77 (85)
T 2ytc_A           10 KTITTLYVGGLGDTI--TETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGR   77 (85)
T ss_dssp             SSCCCEEEECCTTTS--CHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTE
T ss_pred             CCccEEEEcCCCCCC--CHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCC
Confidence            466899999997655  79999999999999999999874      699999999999999999998 99999885

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=1.9e-16  Score=107.47  Aligned_cols=80  Identities=15%  Similarity=0.226  Sum_probs=72.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEE-EEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSV-RLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v-~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      .....++|||+|||+.+++++|+++|++| .|..+ .|+.++.++.    |||+|.+.++|.+|+. +++ ..++|+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~----afV~f~~~~~a~~Ai~~l~g-~~~~g~~l~   85 (96)
T 2e44_A           11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYSSKDQARQALDKLNG-FQLENFTLK   85 (96)
T ss_dssp             CCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEESSHHHHHHHHHHHTT-CBCSSCBCE
T ss_pred             CCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEECCHHHHHHHHHHhCC-CEECCcEEE
Confidence            34567999999999999999999999999 99999 5888766443    9999999999999999 999 999999999


Q ss_pred             EEecCCCC
Q psy1680          86 LDIADGKR   93 (227)
Q Consensus        86 v~~~~~~~   93 (227)
                      |.++.++.
T Consensus        86 V~~a~~~~   93 (96)
T 2e44_A           86 VAYIPDEM   93 (96)
T ss_dssp             EEECCCCC
T ss_pred             EEEcCccc
Confidence            99998874

>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=99.67  E-value=2e-16  Score=107.98  Aligned_cols=67  Identities=16%  Similarity=0.180  Sum_probs=61.2

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++..+|||+|||..+  ++++|+++|++||.|..|.|+++      +|||||+|.+.++|.+|++.|+|..|+|+
T Consensus        13 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~   79 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDI--TEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGK   79 (99)
T ss_dssp             CCTTEEEEESCCTTC--CHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTB
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            567899999997655  79999999999999999999865      69999999999999999999999999885

>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=99.67  E-value=1.9e-16  Score=116.33  Aligned_cols=80  Identities=31%  Similarity=0.480  Sum_probs=73.8

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      ....+.++|||+|||+.+|+++|+++|++| .|..|.|+++     ++|||||+|.+.++|.+||. +++ ..++|++|.
T Consensus        68 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~  141 (150)
T 2i2y_A           68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDG-RTLCGCRVR  141 (150)
T ss_dssp             SSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSS-SCSSSSCCE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCC-CEECCeEEE
Confidence            345677999999999999999999999999 9999999876     48999999999999999999 999 999999999


Q ss_pred             EEecCCCC
Q psy1680          86 LDIADGKR   93 (227)
Q Consensus        86 v~~~~~~~   93 (227)
                      |.++.+++
T Consensus       142 v~~a~~~~  149 (150)
T 2i2y_A          142 VELSNGEK  149 (150)
T ss_dssp             EEECCCCC
T ss_pred             EEEcCCCC
Confidence            99998764

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.66  E-value=1.7e-16  Score=110.36  Aligned_cols=79  Identities=23%  Similarity=0.288  Sum_probs=69.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC--CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~--~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      .....++|||+|||+++++++|+++|++|  .|..+.|+.+    +++|||||+|.+.++|++||+ +|+ ..|+|+.|.
T Consensus        24 ~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng-~~l~Gr~i~   98 (111)
T 2jvr_A           24 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNN-IEFRGSVIT   98 (111)
T ss_dssp             -CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTT-EEETTEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCC-CEECCeEEE
Confidence            44567899999999999999999999999  4888887532    468999999999999999998 999 999999999


Q ss_pred             EEecCCC
Q psy1680          86 LDIADGK   92 (227)
Q Consensus        86 v~~~~~~   92 (227)
                      |.++..+
T Consensus        99 V~~a~~~  105 (111)
T 2jvr_A           99 VERDDNP  105 (111)
T ss_dssp             EEESCC-
T ss_pred             EEECCCC
Confidence            9998754

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.47  E-value=6.7e-18  Score=118.80  Aligned_cols=73  Identities=19%  Similarity=0.227  Sum_probs=67.6

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEE--------EEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccc
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVS--------VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV  224 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~--------v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i  224 (227)
                      .+..+|||+|||..+  ++++|+++|++||.|..        |.|++++.++.++|||||+|.+.++|.+|++.|||..|
T Consensus         5 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   82 (116)
T 2lcw_A            5 SDNNTIFVQGLGENV--TIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   82 (116)
Confidence            456789999997655  78999999999999999        99999999999999999999999999999999999999


Q ss_pred             cCC
Q psy1680         225 DGL  227 (227)
Q Consensus       225 ~gr  227 (227)
                      +||
T Consensus        83 ~g~   85 (116)
T 2lcw_A           83 SGN   85 (116)
Confidence            886

>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=99.66  E-value=3e-16  Score=108.97  Aligned_cols=67  Identities=12%  Similarity=-0.031  Sum_probs=58.7

Q ss_pred             CCCCcceeccCCCC-CCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcC--CccccCC
Q psy1680         153 GEGPGGFRNNNGPN-RSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG--RITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~-~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~--g~~i~gr  227 (227)
                      .++.+|||+|||+. +  ++++|+++|++||.|.+|.|++.      +|||||+|++.++|.+|++.|+  +..|+||
T Consensus        23 ~p~~~l~V~NLp~~~~--te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr   92 (112)
T 1x4f_A           23 ELGRVIHLSNLPHSGY--SDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGR   92 (112)
T ss_dssp             CCCCEEEEESCCCSSC--CSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSS
T ss_pred             CCCCEEEEeCCCCccC--CHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCE
Confidence            56789999999765 5  78999999999999999999754      7999999999999999999885  4568876

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.66  E-value=4.9e-16  Score=103.75  Aligned_cols=76  Identities=16%  Similarity=0.206  Sum_probs=68.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      ...++|||+|||+.+++++|+++|++|.|..+.|.      +++|||||+|.+.++|.+|++ +++ ..+.|++|+|.++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g-~~~~g~~l~V~~a   75 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQ-YSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSCCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTT-EEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCC-CeECCcEEEEEEc
Confidence            35789999999999999999999999977777774      568999999999999999999 999 9999999999998


Q ss_pred             CCCC
Q psy1680          90 DGKR   93 (227)
Q Consensus        90 ~~~~   93 (227)
                      ....
T Consensus        76 ~~~~   79 (88)
T 1wg1_A           76 PTDA   79 (88)
T ss_dssp             CCCC
T ss_pred             CCCc
Confidence            6543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=3.4e-16  Score=106.45  Aligned_cols=68  Identities=12%  Similarity=0.085  Sum_probs=59.9

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +...+|||+|||..+  ++++|+++|+.||.|. +.++.+    .++|||||+|.+.++|.+|++.|||..|+||
T Consensus        17 ~~~~~l~V~nL~~~~--t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   84 (97)
T 2e5j_A           17 PLAADVYVGNLPRDA--RVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTD   84 (97)
T ss_dssp             CCCCEEEEECCCTTC--CHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSS
T ss_pred             CCCCEEEEeCCCCcC--cHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            456799999997655  7999999999999997 666654    6789999999999999999999999999986

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.65  E-value=1e-15  Score=118.66  Aligned_cols=83  Identities=18%  Similarity=0.337  Sum_probs=78.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      ...++|||+|||.++++++|+++|++| .|..+.|++++.+++++|||||+|.+.++|.+|++ +++ ..|+|+.|.|.+
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g-~~~~g~~i~V~~  201 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNL-FDLGGQYLRVGK  201 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT-CBCSSSBCEEEE
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccC-CEeCCcEEEEEE
Confidence            456899999999999999999999999 99999999999999999999999999999999999 999 999999999999


Q ss_pred             cCCCCC
Q psy1680          89 ADGKRN   94 (227)
Q Consensus        89 ~~~~~~   94 (227)
                      +.++..
T Consensus       202 a~~~~~  207 (216)
T 2qfj_A          202 AVTPPM  207 (216)
T ss_dssp             CSSCSS
T ss_pred             ecCCCC
Confidence            987654

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.65  E-value=8.3e-16  Score=114.95  Aligned_cols=80  Identities=26%  Similarity=0.450  Sum_probs=75.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ....++|||+|||..+++++|+++|++| .|..+.++.++.++.++|||||+|.+.++|.+|++ +++ ..++|+.|.|.
T Consensus        91 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~l~V~  169 (172)
T 2g4b_A           91 LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG-MQLGDKKLLVQ  169 (172)
T ss_dssp             CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTT-CEETTEECEEE
T ss_pred             CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCC-CEECCeEEEEE
Confidence            4557999999999999999999999999 99999999998899999999999999999999999 999 99999999999


Q ss_pred             ecC
Q psy1680          88 IAD   90 (227)
Q Consensus        88 ~~~   90 (227)
                      ++.
T Consensus       170 ~As  172 (172)
T 2g4b_A          170 RAS  172 (172)
T ss_dssp             ECC
T ss_pred             eCC
Confidence            873

>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=99.65  E-value=2.5e-16  Score=116.99  Aligned_cols=71  Identities=17%  Similarity=0.250  Sum_probs=66.6

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +++|||+|||+..  ++++|+++|+.||.|.+|.+++++.+|.++|||||+|.+.++|.+|++.|+|..|+|+
T Consensus         2 ~~~l~v~nlp~~~--~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~   72 (167)
T 1fxl_A            2 KTNLIVNYLPQNM--TQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTK   72 (167)
T ss_dssp             CSEEEEESCCTTC--CHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             cceEEEcCCCCCC--CHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCc
Confidence            5689999997665  7999999999999999999999998999999999999999999999999999999875

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.65  E-value=3e-16  Score=110.01  Aligned_cols=76  Identities=9%  Similarity=0.188  Sum_probs=68.7

Q ss_pred             ceEEEcCC----CCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCC----HHH----HHHHHH---hCCCc
Q psy1680          14 YTAFVGNL----PNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVD----VEN----LRQALL---KDGRI   77 (227)
Q Consensus        14 ~~l~V~nL----p~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~----~~~----a~~al~---~~~~~   77 (227)
                      .+|||+||    |+.+++.+|+++|++| +|.++.++.|+.||+++|||||+|.+    .++    |.+|+.   +++ .
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng-~   81 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSG-C   81 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTC-E
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcC-C
Confidence            78999999    9999999999999999 99999999999999999999999996    323    788876   699 9


Q ss_pred             eeCCeEeEEEecC
Q psy1680          78 TVDGLQVRLDIAD   90 (227)
Q Consensus        78 ~~~g~~l~v~~~~   90 (227)
                      .|+|++|+|.+-.
T Consensus        82 ~I~Gr~irV~ln~   94 (136)
T 2j8a_A           82 FIMGFKFEVILNK   94 (136)
T ss_dssp             EETTEEEEEEECC
T ss_pred             eecCcEEEEEECc
Confidence            9999999999864

>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=99.65  E-value=4.5e-16  Score=104.20  Aligned_cols=80  Identities=25%  Similarity=0.458  Sum_probs=62.1

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCC-ceeCCeEe
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR-ITVDGLQV   84 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~-~~~~g~~l   84 (227)
                      ..+..+.++|||+|||+++|+++|+++|++| .|.++.|+++     ++|||||+|.+.++|.+   +++. ..+.|+.|
T Consensus         5 ~~~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~---~~~~~~~~~g~~v   76 (89)
T 3d2w_A            5 HHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS---LCGEDLIIKGISV   76 (89)
T ss_dssp             ------CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH---HTTCEEEETTEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH---HcCCCcccCCEEE
Confidence            3466788999999999999999999999999 9999999874     68999999999999884   3440 45679999


Q ss_pred             EEEecCCCCC
Q psy1680          85 RLDIADGKRN   94 (227)
Q Consensus        85 ~v~~~~~~~~   94 (227)
                      .|.++.++..
T Consensus        77 ~v~~a~~k~~   86 (89)
T 3d2w_A           77 HISNAEPKHN   86 (89)
T ss_dssp             EEEECC----
T ss_pred             EEEEcCCCCc
Confidence            9999987654

>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=99.65  E-value=2.8e-16  Score=110.28  Aligned_cols=65  Identities=20%  Similarity=0.153  Sum_probs=58.7

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||..+  ++++|+++|++||.|..|.|+++       |||||+|.+.++|.+||+.|||.+|+|+
T Consensus        15 ~~~~l~V~nLp~~~--t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr   79 (115)
T 3beg_B           15 SENRVVVSGLPPSG--SWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSH   79 (115)
T ss_dssp             --CCEEEEECCSSC--CTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCT
T ss_pred             CCcEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            35789999997655  78999999999999999999876       8999999999999999999999999985

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.65  E-value=4.7e-17  Score=111.76  Aligned_cols=68  Identities=15%  Similarity=0.250  Sum_probs=61.1

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      ++.+|||+|||...  ++++|+++|+.||.|.+|+|++++ +|.++|||||+|.+.++|.+|++  +|..|+|
T Consensus         8 ~~~~l~V~nLp~~~--t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g   75 (102)
T 2xs2_A            8 MPNTVFVGGIDVRM--DETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHG   75 (102)
T ss_dssp             EEEEEEEECCCTTC--CHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETT
T ss_pred             CCCEEEEeCCCCCC--CHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECC
Confidence            46789999997655  799999999999999999999998 89999999999999999999999  5555555

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.65  E-value=7.7e-17  Score=112.98  Aligned_cols=70  Identities=6%  Similarity=-0.028  Sum_probs=62.1

Q ss_pred             CcceeccC----CCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcC----HHH----HHHHHH--HcCC
Q psy1680         156 PGGFRNNN----GPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVD----VEN----LRQALL--KDGR  221 (227)
Q Consensus       156 ~~l~v~nl----~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~----~~~----a~~Al~--~l~g  221 (227)
                      ..|||+||    |+..  ++++|+.+|+.||.|.+|.++.|+.||.++|||||+|.+    +++    |.+|++  .++|
T Consensus         3 ~kI~VgnL~~~~~~~t--te~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng   80 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNI--QDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSG   80 (136)
T ss_dssp             CEEEEEESSSSCCCCC--CHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTC
T ss_pred             cEEEEeCCCCCCCCCC--CHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcC
Confidence            57999999    7655  789999999999999999999999999999999999996    433    888988  8899


Q ss_pred             ccccCC
Q psy1680         222 ITVDGL  227 (227)
Q Consensus       222 ~~i~gr  227 (227)
                      ..|+||
T Consensus        81 ~~I~Gr   86 (136)
T 2j8a_A           81 CFIMGF   86 (136)
T ss_dssp             EEETTE
T ss_pred             CeecCc
Confidence            999986

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.65  E-value=1.2e-16  Score=111.17  Aligned_cols=68  Identities=21%  Similarity=0.085  Sum_probs=60.8

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhcccc-ceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVT-TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g-~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||+.+  ++++|+++|++|| .|..+.|..+    .++|||||+|.+.++|++|++.|||..|+||
T Consensus        27 ~~~~l~VgnLp~~~--te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr   95 (111)
T 2jvr_A           27 KRYRITMKNLPEGC--SWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGS   95 (111)
T ss_dssp             CCEEEEEECSSCCC--CHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTE
T ss_pred             CCCEEEEECCCCCC--CHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            45689999997655  7899999999999 8999988643    4789999999999999999999999999986

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=4.5e-16  Score=104.37  Aligned_cols=65  Identities=11%  Similarity=0.147  Sum_probs=59.4

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||...  ++++|+++|++||.|..|.|+        +|||||+|.+.++|.+|++.|||..|+|+
T Consensus         6 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~   70 (90)
T 2dnq_A            6 SGMVKLFIGNLPREA--TEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGV   70 (90)
T ss_dssp             SCCEEEEEESCCSSC--CHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSC
T ss_pred             CCCeEEEEeCCCCCC--CHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCc
Confidence            467899999997655  799999999999999999987        58999999999999999999999999886

>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=99.64  E-value=7.3e-17  Score=117.62  Aligned_cols=85  Identities=21%  Similarity=0.378  Sum_probs=72.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEE--E---eecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVR--L---VKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG   81 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~--i---~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g   81 (227)
                      +..++++|||+|||+.+|+++|+++|++| .|..+.  +   ++...+++++|||||+|.+.++|.+||. +|+ ..|.|
T Consensus        41 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng-~~~~g  119 (143)
T 3egn_A           41 PGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANG-YVLFG  119 (143)
T ss_dssp             CCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTT-BEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCC-CEeCC
Confidence            45678999999999999999999999999 876531  1   1112468889999999999999999999 999 99999


Q ss_pred             eEeEEEecCCCCC
Q psy1680          82 LQVRLDIADGKRN   94 (227)
Q Consensus        82 ~~l~v~~~~~~~~   94 (227)
                      +.|.|.++.+...
T Consensus       120 ~~l~V~~a~~~~~  132 (143)
T 3egn_A          120 KPMVVQFARSARP  132 (143)
T ss_dssp             EECEEEECCCSCC
T ss_pred             cEEEEEECCCCCC
Confidence            9999999976543

>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=99.64  E-value=1.6e-16  Score=108.03  Aligned_cols=70  Identities=11%  Similarity=0.157  Sum_probs=63.2

Q ss_pred             CCCCcceeccCCCCCCCChhhHH----hhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHG----LMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~----~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +++.+|||+|||...  ++++|+    ++|++||.|..|.+++   ++.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus         6 ~~~~~l~V~nLp~~~--~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   79 (97)
T 1nu4_A            6 RPNHTIYINNLNEKI--KKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK   79 (97)
T ss_dssp             CCCSEEEEESCCTTS--CHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCc
Confidence            567899999997655  789999    9999999999999874   478899999999999999999999999999885

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.64  E-value=1.3e-15  Score=116.51  Aligned_cols=83  Identities=25%  Similarity=0.443  Sum_probs=78.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      .+.++|||+|||..+++++|+++|++| .|..+.+++++.++.++|||||+|.+.++|.+|++ +++ ..++|+.|.|.+
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~v~~  190 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG-MQLGDKKLLVQR  190 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTT-CEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCC-CEECCEEEEEEE
Confidence            567999999999999999999999999 99999999998899999999999999999999999 999 999999999999


Q ss_pred             cCCCCC
Q psy1680          89 ADGKRN   94 (227)
Q Consensus        89 ~~~~~~   94 (227)
                      +.++..
T Consensus       191 a~~~~~  196 (198)
T 2yh0_A          191 ASVGAK  196 (198)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            987654

>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=99.64  E-value=2.3e-16  Score=117.48  Aligned_cols=80  Identities=19%  Similarity=0.403  Sum_probs=76.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEecC
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~~   90 (227)
                      +.++|||+|||..+++++|+++|++| .|..+.++.++.++.++|||||+|.+.++|.+|+++++ ..++|+.|.|.++.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~-~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKF-IDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHHCSE-ECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHhCCC-EEeCCeEEEEeecC
Confidence            46799999999999999999999999 99999999998899999999999999999999999999 99999999999998


Q ss_pred             CC
Q psy1680          91 GK   92 (227)
Q Consensus        91 ~~   92 (227)
                      ++
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            76

>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=99.64  E-value=3.9e-16  Score=108.83  Aligned_cols=75  Identities=20%  Similarity=0.167  Sum_probs=69.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      ...++|||+|||+.+++++|+++|++| .|..|.|+.      +++||||+|.+.++|.+||. ||+ ..|.|+.|.|.+
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g-~~~~g~~l~V~~   80 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAY-SKFHHVPLYLEW   80 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTT-CBSSSSBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCC-CEECCeEEEEEE
Confidence            346899999999999999999999999 999998874      37899999999999999999 999 999999999999


Q ss_pred             cCCC
Q psy1680          89 ADGK   92 (227)
Q Consensus        89 ~~~~   92 (227)
                      +...
T Consensus        81 a~~~   84 (111)
T 1whx_A           81 APIG   84 (111)
T ss_dssp             EETT
T ss_pred             CCCC
Confidence            8754

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=2.4e-16  Score=110.46  Aligned_cols=68  Identities=13%  Similarity=0.115  Sum_probs=60.7

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCC---CcccceEEEEEcCHHHHHHHHHHc---CCccc
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKET---DRFKGFCYVEFVDVENLRQALLKD---GRITV  224 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t---~~~~g~afV~F~~~~~a~~Al~~l---~g~~i  224 (227)
                      ...+|||+|||..+  ++++|+++|++||.|. +.++.+..+   |+++|||||+|.+.++|.+|++.|   +|..|
T Consensus         7 ~~~~lfVgnLp~~~--te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~~~G~~~   80 (114)
T 2dnl_A            7 GSRKVFVGGLPPDI--DEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLY   80 (114)
T ss_dssp             CCCCEEEECCCTTC--CHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEEETTEEE
T ss_pred             CCCEEEEcCCCCCC--CHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhhcCCcEE
Confidence            46789999997655  8999999999999999 999998888   799999999999999999999998   66533

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=4.8e-15  Score=100.72  Aligned_cols=77  Identities=17%  Similarity=0.269  Sum_probs=69.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ...+.++|||+||  ++++++|+++|++| .|..|.|.      +++|||||+|.+.++|.+||. +++ ..|.|+.|.|
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g-~~~~g~~l~v   81 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNG-TQVESVQLKV   81 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTT-EEETTEEEEE
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCC-CeECCeEEEE
Confidence            4457799999996  89999999999999 99999985      447899999999999999998 999 9999999999


Q ss_pred             EecCCCCC
Q psy1680          87 DIADGKRN   94 (227)
Q Consensus        87 ~~~~~~~~   94 (227)
                      .++.++..
T Consensus        82 ~~a~~~~~   89 (97)
T 1x5p_A           82 NIARKQPM   89 (97)
T ss_dssp             ECCSSCCC
T ss_pred             EECCCCCC
Confidence            99987654

>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=99.64  E-value=8.6e-16  Score=103.57  Aligned_cols=80  Identities=20%  Similarity=0.398  Sum_probs=69.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-C-eEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-K-LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~-i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      ...+.++|||+|||.++|+++|+++|++| . |..+.+.       ++|||||+|.+.++|.+|++ +|+...++|+.|.
T Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~   76 (93)
T 2cqh_A            4 GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIME   76 (93)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEE
Confidence            44667999999999999999999999999 8 5555552       37899999999999999999 8874589999999


Q ss_pred             EEecCCCCCC
Q psy1680          86 LDIADGKRND   95 (227)
Q Consensus        86 v~~~~~~~~~   95 (227)
                      |.++.++...
T Consensus        77 v~~a~~~~~~   86 (93)
T 2cqh_A           77 VDYSVSKKLR   86 (93)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEccCcccc
Confidence            9999876543

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=1.6e-15  Score=106.19  Aligned_cols=75  Identities=21%  Similarity=0.268  Sum_probs=63.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCC---CCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKET---DRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~---~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      ....++|||+|||+++++++|+++|++| .|. +.++.++.+   |+++|||||+|.+.++|++||+ ++   .++|+.+
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~---~~~G~~~   80 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL---EEDGKLY   80 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE---EETTEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh---hcCCcEE
Confidence            4567999999999999999999999999 998 888888777   7999999999999999999998 62   2445555


Q ss_pred             EEEe
Q psy1680          85 RLDI   88 (227)
Q Consensus        85 ~v~~   88 (227)
                      .+..
T Consensus        81 ~~~~   84 (114)
T 2dnl_A           81 LCVS   84 (114)
T ss_dssp             EEEC
T ss_pred             Eecc
Confidence            5443

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=1.2e-15  Score=103.50  Aligned_cols=68  Identities=18%  Similarity=0.117  Sum_probs=60.9

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEE-EEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSV-RLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v-~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||...  ++++|+++|++||.|.+| .|++++.++.    |||+|.+.++|.+|++.|||..|+||
T Consensus        14 ~~~~l~V~nlp~~~--t~~~l~~~F~~~G~v~~~~~i~~~~~~~~----afV~f~~~~~a~~Ai~~l~g~~~~g~   82 (96)
T 2e44_A           14 RIRKLQIRNIPPHL--QWEVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYSSKDQARQALDKLNGFQLENF   82 (96)
T ss_dssp             SCCCEEEEEECSSS--CHHHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEESSHHHHHHHHHHHTTCBCSSC
T ss_pred             CCCEEEEEcCCCCC--CHHHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEECCHHHHHHHHHHhCCCEECCc
Confidence            46789999997655  799999999999999999 5888876544    99999999999999999999999986

>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=99.63  E-value=5.7e-16  Score=107.63  Aligned_cols=67  Identities=13%  Similarity=0.238  Sum_probs=61.3

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +...+|||+|||..+  ++++|+++|++||.|..|.|+++      +|||||+|.+.++|.+|++.|+|..|+|+
T Consensus        23 ~~~~~l~V~nl~~~~--t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~   89 (109)
T 1x4g_A           23 PKNCTVYCGGIASGL--TDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGH   89 (109)
T ss_dssp             SSCCEEEEECCSSCC--CHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCcEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            456799999997655  79999999999999999999887      69999999999999999999999999885

>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=99.62  E-value=8.9e-16  Score=105.52  Aligned_cols=65  Identities=12%  Similarity=0.132  Sum_probs=58.7

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+.++|||+|||..+  ++++|+++|++||.|..|.|++        |||||+|.+.++|.+|++.|||..|+|+
T Consensus         9 ~~~~~l~V~nl~~~~--t~~~l~~~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~   73 (103)
T 2dgu_A            9 AKVKVLFVRNLANTV--TEEILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEEMNGKDLEGE   73 (103)
T ss_dssp             CCCCCEEEECCCTTC--CHHHHHHHHHHHSCEEEEEECS--------SCEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHHHHHHCCCccCCC
Confidence            456899999997655  7999999999999999999873        5999999999999999999999999885

>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=99.62  E-value=4.8e-16  Score=108.39  Aligned_cols=66  Identities=14%  Similarity=-0.012  Sum_probs=59.9

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..++|||+|||..+  ++++|+++|++||.|..|.|++      ++|||||+|.+.++|.+|++.|||..|+||
T Consensus         9 ~~~~l~V~nLp~~~--te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   74 (111)
T 1whx_A            9 SKTVILAKNLPAGT--LAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHV   74 (111)
T ss_dssp             EEEEEEEESCCTTC--CHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCEEEEeCCCCCC--CHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCe
Confidence            45789999997655  8999999999999999999875      468999999999999999999999999986

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.62  E-value=7.4e-16  Score=104.58  Aligned_cols=65  Identities=15%  Similarity=0.167  Sum_probs=58.8

Q ss_pred             CCCCcceeccCCC-CCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGP-NRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~-~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++..+|||+|||. .+  ++++|+++|++||.|.+|.|.        +|||||+|.+.++|.+|++.|||..|+|+
T Consensus         8 ~~~~~l~V~nlp~~~~--t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~   73 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNV--SKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGK   73 (96)
T ss_dssp             -CCEEEEEESSTTSCC--CHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTT
T ss_pred             CCCCEEEEeCCCcccC--CHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCc
Confidence            5678999999975 55  799999999999999999983        68999999999999999999999999886

>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=99.62  E-value=8.6e-16  Score=104.48  Aligned_cols=65  Identities=15%  Similarity=0.171  Sum_probs=59.1

Q ss_pred             CCCCcceeccCCC-CCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGP-NRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~-~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++..+|||+|||. ..  ++++|+++|+.||.|.+|+|.        +|||||+|.+.++|.+|++.|||..|+|+
T Consensus        20 ~~~~~l~V~nLp~~~~--t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   85 (97)
T 2xnq_A           20 HMKSRLFIGNLPLKNV--SKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGK   85 (97)
T ss_dssp             CTTCEEEEESCCSSCC--CHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTE
T ss_pred             CCCCEEEEeCCCcccC--CHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            5678999999975 55  799999999999999999983        68999999999999999999999999885

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.62  E-value=2.4e-16  Score=107.95  Aligned_cols=65  Identities=18%  Similarity=0.213  Sum_probs=59.9

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+|||+|||...  ++++|+++|++||.|.+|.|+++     ++|||||+|.+.++|.+|++.|+|..|+|+
T Consensus         1 ~~l~V~nLp~~~--t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   65 (101)
T 2hvz_A            1 MKVYVGNLGTGA--GKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGS   65 (101)
T ss_dssp             CEEEEECCCSSC--SHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSC
T ss_pred             CEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCc
Confidence            369999997655  89999999999999999999988     689999999999999999999999999886

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.62  E-value=6.5e-16  Score=105.79  Aligned_cols=66  Identities=11%  Similarity=0.152  Sum_probs=59.8

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||...  ++++|+++|+.||.|.+|+|++      ++|||||+|.+.++|.+|++.|||..|+||
T Consensus        26 ~~~~l~V~nlp~~~--~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   91 (101)
T 2la4_A           26 RVTTAYIGNIPHFA--TEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGR   91 (101)
T ss_dssp             SCCEEEEESCCTTC--CHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCEEEEcCCCccc--CHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            45789999997655  7999999999999999999973      479999999999999999999999999985

>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=99.62  E-value=9.8e-16  Score=102.23  Aligned_cols=78  Identities=23%  Similarity=0.459  Sum_probs=67.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEec
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA   89 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~   89 (227)
                      .++++|||+|||.++++++|+++|++| .|..+.|+.+     ++|||||+|.+.++|++++.. . ..+.++.|.|.++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~-~-~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE-D-LIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC-E-EEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC-C-ceeCCEEEEEEec
Confidence            467999999999999999999999999 9999999864     589999999999999765333 3 5679999999999


Q ss_pred             CCCCCC
Q psy1680          90 DGKRND   95 (227)
Q Consensus        90 ~~~~~~   95 (227)
                      .++...
T Consensus        76 ~~~~~~   81 (88)
T 1wf0_A           76 EPKHNS   81 (88)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            877653

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=1.1e-15  Score=106.31  Aligned_cols=79  Identities=14%  Similarity=0.285  Sum_probs=70.1

Q ss_pred             CCCCCceEEE--cCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCcee-----
Q psy1680           9 PTEPPYTAFV--GNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITV-----   79 (227)
Q Consensus         9 ~~~~~~~l~V--~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~-----   79 (227)
                      ...++++|||  +||++++++++|+++|++| .|..|.|+.+      +|||||+|.+.++|++|++ ||| ..+     
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG-~~~~~~lg   93 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNG-KEVVDDLG   93 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTT-CEEECTTS
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCC-CEEccccC
Confidence            4567899999  7799999999999999999 9999988643      7899999999999999999 999 988     


Q ss_pred             CCeEeEEEecCCCCC
Q psy1680          80 DGLQVRLDIADGKRN   94 (227)
Q Consensus        80 ~g~~l~v~~~~~~~~   94 (227)
                      .+++|.|.++.....
T Consensus        94 ~g~~l~v~~a~~~p~  108 (114)
T 2cq2_A           94 QKITLYLNFVEKVQW  108 (114)
T ss_dssp             CEEECEEEEESCCCC
T ss_pred             CCcEEEEEecccCcc
Confidence            688999999876544

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.62  E-value=6.8e-16  Score=107.07  Aligned_cols=65  Identities=14%  Similarity=0.174  Sum_probs=59.7

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||...  ++++|+++|++||.|..|.|+        +|||||+|.+.++|.+|++.|||..|+|+
T Consensus        29 ~~~~~l~V~nLp~~~--t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~   93 (108)
T 2jvo_A           29 LSNTRLFVRPFPLDV--QESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQ   93 (108)
T ss_dssp             CSCSEEEECSSCTTC--CHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEECCCCCC--CHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            567899999997655  799999999999999999987        68999999999999999999999999885

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.62  E-value=3.2e-15  Score=106.21  Aligned_cols=77  Identities=18%  Similarity=0.286  Sum_probs=68.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecE-EEEEeCCHHHHHHHHH-hCCCceeCC--eEeEE
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGF-CYVEFVDVENLRQALL-KDGRITVDG--LQVRL   86 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~-afv~f~~~~~a~~al~-~~~~~~~~g--~~l~v   86 (227)
                      +--.|||+||++.+|+++|+++|++| .|.+|.|+.+.     +|+ |||+|.+.++|..|++ ||| ..|.|  +.|+|
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG-~~i~g~~~~LrI  100 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDG-QNIYNACCTLRI  100 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTT-CEEETTEEEEEE
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCC-CeecCCCcEEEE
Confidence            33677899999999999999999999 99999887642     577 9999999999999999 999 99988  89999


Q ss_pred             EecCCCCC
Q psy1680          87 DIADGKRN   94 (227)
Q Consensus        87 ~~~~~~~~   94 (227)
                      .+++++.-
T Consensus       101 ~~ak~~~l  108 (130)
T 3zzy_A          101 DFSKLTSL  108 (130)
T ss_dssp             EECSCSSC
T ss_pred             EecCCCce
Confidence            99987654

>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=99.61  E-value=5.2e-16  Score=109.05  Aligned_cols=75  Identities=12%  Similarity=0.003  Sum_probs=65.8

Q ss_pred             CCCCcceeccCCCC---CCCChhhHHhhhccccceEEEEEeecCC----CCcccceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         153 GEGPGGFRNNNGPN---RSNSMNDHGLMVTEVTTLVSVRLVKDKE----TDRFKGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       153 ~~~~~l~v~nl~~~---~~~~~~~l~~~f~~~g~i~~v~i~~d~~----t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      +++++|++.|+-.+   .++.++||+++|++||.|.+|.|++++.    ++.++|++||+|.+.++|.+|++.|||+.++
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~   97 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA   97 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            46889999999432   2346799999999999999999999875    4578899999999999999999999999999


Q ss_pred             CC
Q psy1680         226 GL  227 (227)
Q Consensus       226 gr  227 (227)
                      ||
T Consensus        98 GR   99 (118)
T 3ue2_A           98 GR   99 (118)
T ss_dssp             TE
T ss_pred             Cc
Confidence            97

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=1.3e-15  Score=102.04  Aligned_cols=65  Identities=15%  Similarity=0.211  Sum_probs=59.0

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|++||.|..|.|+++        ||||+|.+.++|.+|++.|||..|+|+
T Consensus         7 ~~~~~l~V~nlp~~~--t~~~l~~~F~~~G~v~~~~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~   71 (90)
T 2dnp_A            7 GNTWKIFVGNVSAAC--TSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNGKEVKGK   71 (90)
T ss_dssp             CCSCCEEEESCCTTC--CHHHHHHHHHHHSCEEEEEECSS--------CEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHcCCCEEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            467899999997655  89999999999999999999743        999999999999999999999999885

>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=99.61  E-value=1.1e-16  Score=116.61  Aligned_cols=74  Identities=14%  Similarity=0.165  Sum_probs=62.1

Q ss_pred             CCCCCcceeccCCCCCCCChhhHHhhhccccceEEEE--E---eecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         152 GGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVR--L---VKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~--i---~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      ..++.+|||+|||+.+  ++++|+.+|+.||.|..|.  +   ++...++.++|||||+|.+.++|.+|++.|||..|+|
T Consensus        42 ~~~~~~l~V~nLp~~~--te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g  119 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHV--QEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFG  119 (143)
T ss_dssp             CSCCSEEEEEEECTTC--CHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETT
T ss_pred             CCCCCEEEEeCCCCCC--CHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCC
Confidence            3567899999997655  8999999999999887641  1   1123468999999999999999999999999999998


Q ss_pred             C
Q psy1680         227 L  227 (227)
Q Consensus       227 r  227 (227)
                      |
T Consensus       120 ~  120 (143)
T 3egn_A          120 K  120 (143)
T ss_dssp             E
T ss_pred             c
Confidence            5

>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=99.61  E-value=5.5e-16  Score=107.77  Aligned_cols=64  Identities=11%  Similarity=0.078  Sum_probs=56.6

Q ss_pred             CCCCccee--ccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccc
Q psy1680         153 GEGPGGFR--NNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV  224 (227)
Q Consensus       153 ~~~~~l~v--~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i  224 (227)
                      .+..+|||  +||+...  ++++|+++|++||.|.+|.|+.+      +|||||+|.+.++|.+|++.|||.+|
T Consensus        23 ~pt~~L~V~Ng~L~~~~--te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~   88 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGV--SRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   88 (114)
T ss_dssp             SCCSEEEEETCTGGGTC--CHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCEEEEECCCCCCCC--CHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEE
Confidence            46778999  6696544  89999999999999999988653      69999999999999999999999987

>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=99.61  E-value=4.5e-15  Score=110.41  Aligned_cols=80  Identities=23%  Similarity=0.429  Sum_probs=75.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC--eEe
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG--LQV   84 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g--~~l   84 (227)
                      ...+.++|||+|||..+++++|+++|++| .|..+.+++++.++.++|||||+|.+.++|.+|++ +++ ..+.|  ++|
T Consensus        85 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~~~l  163 (168)
T 1b7f_A           85 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNN-VIPEGGSQPL  163 (168)
T ss_dssp             STTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT-CCCTTCSSCC
T ss_pred             ccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcC-CEecCCCeEE
Confidence            34567999999999999999999999999 99999999998899999999999999999999999 999 99988  999


Q ss_pred             EEEec
Q psy1680          85 RLDIA   89 (227)
Q Consensus        85 ~v~~~   89 (227)
                      +|.+|
T Consensus       164 ~V~~A  168 (168)
T 1b7f_A          164 SVRLA  168 (168)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99875

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.61  E-value=3.7e-16  Score=105.97  Aligned_cols=68  Identities=16%  Similarity=0.218  Sum_probs=60.5

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||...  ++++|+++|+.||.|..+     ..++.++|||||+|.+.++|.+|++.|+|..|+||
T Consensus        14 ~~~~~l~V~nL~~~~--t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   81 (96)
T 1fjc_A           14 RAARTLLAKNLSFNI--TEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGR   81 (96)
T ss_dssp             TGGGEEEEESCCSSC--CHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCe
Confidence            457899999997655  799999999999988766     35689999999999999999999999999999885

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.61  E-value=3.3e-15  Score=112.08  Aligned_cols=80  Identities=25%  Similarity=0.395  Sum_probs=72.2

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      ....+.++|||+|||..+++++|+++|++| .|..+     ..++.++|||||+|.+.++|.+|+. +++ ..++|+.|.
T Consensus        94 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~i~  167 (175)
T 1fje_B           94 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQG-AEIDGRSVS  167 (175)
T ss_dssp             STTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTE-EEETTEEEE
T ss_pred             cccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCC-CEECCeEEE
Confidence            344567999999999999999999999999 87765     4678899999999999999999999 999 999999999


Q ss_pred             EEecCCCC
Q psy1680          86 LDIADGKR   93 (227)
Q Consensus        86 v~~~~~~~   93 (227)
                      |.++.++.
T Consensus       168 v~~a~~k~  175 (175)
T 1fje_B          168 LYYTGEKG  175 (175)
T ss_dssp             EEECSSCC
T ss_pred             EEecCCCC
Confidence            99998763

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.61  E-value=3.2e-15  Score=103.94  Aligned_cols=64  Identities=16%  Similarity=0.277  Sum_probs=58.5

Q ss_pred             CCCcceeccCCCC-CCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPN-RSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~-~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +..+|||+|||+. .  ++++|+++|++||.|..|.|        ++|||||+|.+.++|.+|++.|+|..|+|+
T Consensus        26 ~~~~l~V~nl~~~~~--t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   90 (110)
T 1wf1_A           26 INSRVFIGNLNTALV--KKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQ   90 (110)
T ss_dssp             CSSEEEECSCCCSSC--CHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTE
T ss_pred             CCcEEEEeCCCcccC--CHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            4579999999765 4  79999999999999999998        479999999999999999999999999885

>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=99.61  E-value=1.1e-15  Score=105.30  Aligned_cols=75  Identities=12%  Similarity=-0.064  Sum_probs=64.4

Q ss_pred             CCCCcceeccCCCC--CC------CChhhHHhhhccccceEEEEEeecCCC--CcccceEEEEEcCHHHHHHHHHHcCCc
Q psy1680         153 GEGPGGFRNNNGPN--RS------NSMNDHGLMVTEVTTLVSVRLVKDKET--DRFKGFCYVEFVDVENLRQALLKDGRI  222 (227)
Q Consensus       153 ~~~~~l~v~nl~~~--~~------~~~~~l~~~f~~~g~i~~v~i~~d~~t--~~~~g~afV~F~~~~~a~~Al~~l~g~  222 (227)
                      .|+++|.+.|+=.+  ..      ++++||+++|++||.|.+|.|++++.+  +.++|+|||+|.+.++|.+|++.|||+
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            57889999999322  21      134789999999999999999999865  368999999999999999999999999


Q ss_pred             cccCC
Q psy1680         223 TVDGL  227 (227)
Q Consensus       223 ~i~gr  227 (227)
                      .++||
T Consensus        83 ~f~GR   87 (105)
T 3v4m_A           83 KFANR   87 (105)
T ss_dssp             EETTE
T ss_pred             EeCCC
Confidence            99997

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.60  E-value=2.3e-15  Score=110.96  Aligned_cols=79  Identities=16%  Similarity=0.210  Sum_probs=70.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC--eEeEE
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG--LQVRL   86 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g--~~l~v   86 (227)
                      ....+|||+||++.+|+++|+++|++| .|..|.|+.+    .++|||||+|.+.++|+.|++ |+| ..|.|  +.|+|
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG-~~i~g~g~~L~V  118 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDG-QNIYNACCTLRI  118 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTT-BCSSSSCSCEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCC-CEecCCCcEEEE
Confidence            344778999999999999999999999 9999998654    247899999999999999999 999 99965  99999


Q ss_pred             EecCCCCC
Q psy1680          87 DIADGKRN   94 (227)
Q Consensus        87 ~~~~~~~~   94 (227)
                      .+++++..
T Consensus       119 ~~Ak~~~l  126 (164)
T 1sjr_A          119 DFSKLTSL  126 (164)
T ss_dssp             EECSSSSC
T ss_pred             EEecCCcc
Confidence            99987653

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.60  E-value=7.5e-15  Score=103.81  Aligned_cols=74  Identities=19%  Similarity=0.175  Sum_probs=65.9

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecE-EEEEeCCHHHHHHHHH-hCCCceeCC--eEeEEEe
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGF-CYVEFVDVENLRQALL-KDGRITVDG--LQVRLDI   88 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~-afv~f~~~~~a~~al~-~~~~~~~~g--~~l~v~~   88 (227)
                      ..|||+||++.+|+++|+++|++| .|..|.|+..      .|| |||+|.+.++|..|++ ||| ..|.|  +.|+|.+
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG-~~i~g~~~~l~V~~   98 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNG-ADIYAGCCTLKIEY   98 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTT-CCCBTTBSEEEEEC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCC-CEecCCCeEEEEEE
Confidence            346799999999999999999999 9999998652      275 9999999999999999 999 99987  6999999


Q ss_pred             cCCCCC
Q psy1680          89 ADGKRN   94 (227)
Q Consensus        89 ~~~~~~   94 (227)
                      ++++..
T Consensus        99 Ak~~~l  104 (124)
T 2e5i_A           99 ARPTRL  104 (124)
T ss_dssp             CSCSCC
T ss_pred             ecCCcc
Confidence            987654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=2.2e-15  Score=101.81  Aligned_cols=66  Identities=20%  Similarity=0.150  Sum_probs=58.4

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||..+  ++++|+++|+.||.|.+|  +.++.++.   ||||+|.+.++|.+|++ |||..|+||
T Consensus         7 ~~~~l~V~nl~~~~--t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~   72 (94)
T 2e5g_A            7 GLRSVFVSGFPRGV--DSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGH   72 (94)
T ss_dssp             TCCEEEEECCCTTC--CHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTE
T ss_pred             CCCEEEEECCCCCC--CHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCE
Confidence            45689999997655  899999999999999987  66666666   99999999999999999 999999985

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=1.7e-15  Score=101.97  Aligned_cols=65  Identities=15%  Similarity=0.199  Sum_probs=59.0

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|++||.|..|.|+++        ||||+|.+.++|.+|++.|||..|+|+
T Consensus         8 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~G~v~~v~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~   72 (92)
T 2dgt_A            8 KASTKLHVGNISPTC--TNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGLDNTEFQGK   72 (92)
T ss_dssp             CSSEEEEEESCCSSC--CHHHHHHHHHTTSCCCEEEECSS--------EEEEEESCHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcCCeEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCeeCCc
Confidence            467899999997655  79999999999999999999743        999999999999999999999999885

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=3.8e-15  Score=101.57  Aligned_cols=65  Identities=14%  Similarity=0.123  Sum_probs=58.4

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccc--cceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEV--TTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~--g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.|  |.|..|.+.        +|||||+|.+.++|.+|++.|||..|+||
T Consensus        13 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~   79 (99)
T 2cpd_A           13 SSVKILYVRNLMLST--SEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGS   79 (99)
T ss_dssp             SCCCEEEEESCCTTC--CHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTE
T ss_pred             CCcCEEEEeCCCCCC--CHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            467899999997665  799999999999  899999764        57999999999999999999999999885

>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=99.59  E-value=2.1e-15  Score=100.29  Aligned_cols=73  Identities=33%  Similarity=0.618  Sum_probs=65.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC------------CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCC
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ------------KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR   76 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~------------~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~   76 (227)
                      +..+.++|||+|||+++++++|+++|++|            .|..+.+.++      +|||||+|.+.++|.+|+.+++ 
T Consensus         2 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~~l~g-   74 (87)
T 2hzc_A            2 PLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAMAFDG-   74 (87)
T ss_dssp             CSGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHGGGTT-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHHhcCC-
Confidence            34567999999999999999999999987            5788888654      7999999999999999999999 


Q ss_pred             ceeCCeEeEEEe
Q psy1680          77 ITVDGLQVRLDI   88 (227)
Q Consensus        77 ~~~~g~~l~v~~   88 (227)
                      ..++|+.|+|..
T Consensus        75 ~~~~g~~l~V~r   86 (87)
T 2hzc_A           75 IIFQGQSLKIRR   86 (87)
T ss_dssp             CEETTEECEEEC
T ss_pred             CEECCeEEEEeC
Confidence            999999999974

>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=99.59  E-value=2.5e-15  Score=112.44  Aligned_cols=70  Identities=16%  Similarity=0.214  Sum_probs=64.1

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCC--cccceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETD--RFKGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~--~~~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      .+.+|||+|||+.+  ++++|+++|++||.|.+|+|++++.++  .++|||||+|.+.++|.+|++.|+|..+.
T Consensus         2 ~~~~l~V~nLp~~~--te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~   73 (175)
T 3nmr_A            2 DAIKMFVGQVPRTW--SEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVL   73 (175)
T ss_dssp             CCEEEEEESCCTTC--CHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCC
T ss_pred             CceEEEEeCCCCCC--CHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEc
Confidence            35689999997665  899999999999999999999999887  89999999999999999999999998764

>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=99.59  E-value=1.9e-15  Score=116.61  Aligned_cols=68  Identities=15%  Similarity=0.081  Sum_probs=61.7

Q ss_pred             CCCCcceeccCC-CCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNG-PNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~-~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +++.+|||+||| ..+  ++++|+++|++||.|.+|+|++++     +|||||+|.+.++|.+|++.|||..|.||
T Consensus         2 ~~~~~l~V~nL~~~~~--~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~~~g~   70 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKM--NCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQ   70 (205)
T ss_dssp             CCCSEEEEECCCTTTC--CHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEeCCCcccC--CHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            467899999997 444  789999999999999999998863     79999999999999999999999999885

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=4.9e-15  Score=98.29  Aligned_cols=74  Identities=19%  Similarity=0.246  Sum_probs=65.3

Q ss_pred             CCCCce-EEEcCCCCCCCHHH----HHhcccCC--CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC
Q psy1680          10 TEPPYT-AFVGNLPNGITQGD----VERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG   81 (227)
Q Consensus        10 ~~~~~~-l~V~nLp~~~t~~~----l~~~f~~~--~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g   81 (227)
                      .+++.+ |||+|||+.+++++    |+++|++|  +|.+|       ++   |+|||.|.+.++|.+|++ |+| ..+.|
T Consensus         5 ~~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G-~~l~g   73 (96)
T 2diu_A            5 SSGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMEN-EDVFG   73 (96)
T ss_dssp             CCCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTT-CCSSS
T ss_pred             CCCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcC-CccCC
Confidence            345666 99999999999987    55899999  68887       23   999999999999999999 999 99999


Q ss_pred             eEeEEEecCCCCC
Q psy1680          82 LQVRLDIADGKRN   94 (227)
Q Consensus        82 ~~l~v~~~~~~~~   94 (227)
                      ++|+|.++..++.
T Consensus        74 r~i~v~~A~~~sd   86 (96)
T 2diu_A           74 NRIIVSFTPKNRE   86 (96)
T ss_dssp             SCCEEESSCCSCC
T ss_pred             ceEEEEecCCCcc
Confidence            9999999987765

>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=99.58  E-value=1.9e-15  Score=100.91  Aligned_cols=65  Identities=14%  Similarity=0.131  Sum_probs=58.8

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||+..  ++++|+++|++| .|.+|+|.      +++|||||+|.+.++|.+|++.|||..|+||
T Consensus         4 ~~~~l~V~nLp~~~--t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~   68 (88)
T 1wg1_A            4 GSSGILVKNLPQDS--NCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGK   68 (88)
T ss_dssp             CCCCEEEESCCSSC--CHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTE
T ss_pred             CCCEEEEeCCCCCC--CHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCc
Confidence            45789999997655  799999999999 99999884      5789999999999999999999999999985

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=8.2e-15  Score=99.54  Aligned_cols=65  Identities=9%  Similarity=0.118  Sum_probs=58.3

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+||    +.++++|+++|++||.|.+|.|.      .++|||||+|.+.++|.+|++.|||..|+||
T Consensus        13 ~~~~~l~V~n~----~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~   77 (97)
T 1x5p_A           13 RKGNTLYVYGE----DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESV   77 (97)
T ss_dssp             CCCSEEEEECS----SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTE
T ss_pred             CCCCEEEEcCC----CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            45679999996    44899999999999999999984      4579999999999999999999999999885

>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=99.58  E-value=1.2e-14  Score=111.01  Aligned_cols=78  Identities=14%  Similarity=0.354  Sum_probs=72.1

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEecCC
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~~~   91 (227)
                      .++|||+|||+++|+++|+++|++| .|..|.|+++. +++++|||||+|.+.++|.+||...+ ..++|+.|.|.++..
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHH
Confidence            4899999999999999999999999 99999999985 48999999999999999999999667 799999999998765


Q ss_pred             C
Q psy1680          92 K   92 (227)
Q Consensus        92 ~   92 (227)
                      .
T Consensus       187 y  187 (193)
T 2voo_A          187 Y  187 (193)
T ss_dssp             C
T ss_pred             H
Confidence            4

>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=99.57  E-value=1.6e-15  Score=102.26  Aligned_cols=66  Identities=15%  Similarity=0.204  Sum_probs=57.4

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccc-eEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCC-ccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTT-LVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR-ITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~-i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g-~~i~gr  227 (227)
                      .+..+|||+|||...  ++++|+++|++||. |..+.+.       ++|||||+|.+.++|.+|++.||| ..|+|+
T Consensus         6 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~   73 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAV--TADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGK   73 (93)
T ss_dssp             CCCCCEEEECCCTTC--CHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTE
T ss_pred             CCCcEEEEeCCCCCC--CHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCE
Confidence            456799999997665  79999999999998 6666662       479999999999999999999999 999885

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.57  E-value=2.5e-15  Score=99.88  Aligned_cols=66  Identities=20%  Similarity=0.252  Sum_probs=59.4

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccc----c-------ceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEV----T-------TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR  221 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~----g-------~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g  221 (227)
                      .+..+|||+|||...  ++++|+++|+.|    |       .|.++.+.++      +|||||+|.+.++|.+|+ .|||
T Consensus         4 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g   74 (87)
T 2hzc_A            4 GSARRLYVGNIPFGI--TEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDG   74 (87)
T ss_dssp             GGGGEEEEESCCTTC--CHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTT
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCC
Confidence            356789999997655  789999999999    8       8999999766      699999999999999999 9999


Q ss_pred             ccccCC
Q psy1680         222 ITVDGL  227 (227)
Q Consensus       222 ~~i~gr  227 (227)
                      ..|+||
T Consensus        75 ~~~~g~   80 (87)
T 2hzc_A           75 IIFQGQ   80 (87)
T ss_dssp             CEETTE
T ss_pred             CEECCe
Confidence            999986

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=5e-15  Score=98.24  Aligned_cols=63  Identities=13%  Similarity=0.082  Sum_probs=54.3

Q ss_pred             CCCCc-ceeccCCCCCCCChhh----HHhhhcccc-ceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         153 GEGPG-GFRNNNGPNRSNSMND----HGLMVTEVT-TLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       153 ~~~~~-l~v~nl~~~~~~~~~~----l~~~f~~~g-~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      +|+.| |||+|||...  ++++    |+++|++|| .|.+|       |+   |+|||.|.+.++|.+|++.|||..|.|
T Consensus         6 ~p~~T~lYV~NL~~~~--~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~g   73 (96)
T 2diu_A            6 SGCHTLLYVYNLPANK--DGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFG   73 (96)
T ss_dssp             CCSSEEEEEESCCTTS--CHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSS
T ss_pred             CCcceEEEEeCCCCcC--CHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCC
Confidence            45666 9999997666  5565    668999995 99998       34   999999999999999999999999998


Q ss_pred             C
Q psy1680         227 L  227 (227)
Q Consensus       227 r  227 (227)
                      |
T Consensus        74 r   74 (96)
T 2diu_A           74 N   74 (96)
T ss_dssp             S
T ss_pred             c
Confidence            7

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.57  E-value=1.8e-14  Score=110.06  Aligned_cols=69  Identities=12%  Similarity=0.245  Sum_probs=62.0

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..+|||+|||...  ++++|+++|++||.|.+|+|+++.. +.++|||||+|.+.++|.+|++.++. .|+||
T Consensus       109 ~~~l~V~nLp~~~--t~~~L~~~F~~~G~v~~v~i~~~~~-~~~kG~aFVeF~~~e~A~~A~~~~~~-~~~Gr  177 (193)
T 2voo_A          109 NRSVYIKGFPTDA--TLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQ-KYKET  177 (193)
T ss_dssp             HTEEEEECCCTTC--CHHHHHHHHTTSCCEEEEEEEECTT-CCEEEEEEEEESSHHHHHHHHHCTTC-EETTE
T ss_pred             cCEEEecCCCCcC--CHHHHHHHHhcCCCEEEEEEEECCC-CCcccEEEEEECCHHHHHHHHHhCCC-eECCE
Confidence            4689999997655  7999999999999999999999964 99999999999999999999987764 88875

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.57  E-value=2.1e-14  Score=98.86  Aligned_cols=81  Identities=15%  Similarity=0.103  Sum_probs=72.0

Q ss_pred             CCCCceEEEcCCCC-----CCCHHHHHhcccCC-CeEEEEEeecCCC-CCeecEEEEEeCCHHHHHHHHH-hCCCceeCC
Q psy1680          10 TEPPYTAFVGNLPN-----GITQGDVERFFPEQ-KLVSVRLVKDKET-DRFKGFCYVEFVDVENLRQALL-KDGRITVDG   81 (227)
Q Consensus        10 ~~~~~~l~V~nLp~-----~~t~~~l~~~f~~~-~i~~v~i~~~~~~-~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g   81 (227)
                      ..+++.|+|+||..     +-++++|+++|++| .|.+|.|++++.+ ++++|+|||+|.+.++|.+|++ ||| ..++|
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG-~~~~G   83 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNG-RYFGG   83 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTT-CEETT
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCC-CEECC
Confidence            46789999999963     23789999999999 9999999998654 6889999999999999999999 999 99999


Q ss_pred             eEeEEEecCC
Q psy1680          82 LQVRLDIADG   91 (227)
Q Consensus        82 ~~l~v~~~~~   91 (227)
                      +.|.|.++.+
T Consensus        84 r~i~v~~a~~   93 (105)
T 2pe8_A           84 RVVKACFYNL   93 (105)
T ss_dssp             EECEEEECCH
T ss_pred             cEEEEEEcCH
Confidence            9999999864

>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=99.56  E-value=5.3e-15  Score=108.99  Aligned_cols=65  Identities=8%  Similarity=-0.029  Sum_probs=57.6

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      .+|||+||+++.  ++++|+++|++||.|++|+|..+.    ++|||||+|.+.++|.+|++.|||..|.|
T Consensus        47 l~l~VgNL~~~v--ted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g  111 (164)
T 1sjr_A           47 LRIIVENLFYPV--TLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYN  111 (164)
T ss_dssp             EEEEECSCCSCC--CHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSS
T ss_pred             EEEEEeCcCCCC--CHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecC
Confidence            458899996554  899999999999999999987542    57899999999999999999999999965

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.56  E-value=7e-15  Score=104.47  Aligned_cols=64  Identities=9%  Similarity=0.054  Sum_probs=56.9

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccce-EEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGF-CYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~-afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      -.|||+||+++.  ++++|+++|++||.|.+|+|+.+.     +|| |||+|.+.++|.+|++.|||..|.|
T Consensus        29 L~I~V~NL~~~v--te~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g   93 (130)
T 3zzy_A           29 LRIIVENLFYPV--TLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYN   93 (130)
T ss_dssp             EEEEEESCCSCC--CHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEET
T ss_pred             EEEEECCCCCCC--CHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecC
Confidence            357799997655  899999999999999999987653     577 9999999999999999999999976

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.56  E-value=3.6e-14  Score=100.32  Aligned_cols=65  Identities=14%  Similarity=0.008  Sum_probs=56.4

Q ss_pred             CCCc--ceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccce-EEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         154 EGPG--GFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGF-CYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       154 ~~~~--l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~-afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      ++.+  |||+||+...  ++++|+++|++||.|.+|+|+..      .|| |||+|.+.++|.+|++.|||..|.|
T Consensus        22 ps~vl~l~V~NL~~~v--t~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g   89 (124)
T 2e5i_A           22 GNKVLLLSIQNPLYPI--TVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYA   89 (124)
T ss_dssp             CCSEEEEEEESCCSCC--CHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBT
T ss_pred             CCcEEEEEEcCcCCCC--CHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecC
Confidence            4444  5799996555  89999999999999999998652      286 9999999999999999999999987

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.54  E-value=7.2e-15  Score=98.27  Aligned_cols=55  Identities=18%  Similarity=0.297  Sum_probs=48.4

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHH
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ  214 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~  214 (227)
                      ++..+|||+|||+++  ++++|+++|++||.|.+|+|+++     ++|||||+|.+.++|.+
T Consensus         9 ~~~~~l~V~~Lp~~~--te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~   63 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDM--TAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS   63 (89)
T ss_dssp             --CCEEEEESCCTTC--CHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH
Confidence            467899999997665  79999999999999999999885     68999999999999984

>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=99.53  E-value=2.4e-14  Score=99.91  Aligned_cols=72  Identities=14%  Similarity=0.009  Sum_probs=60.4

Q ss_pred             CCCCCcceeccCCCCCC---------CChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCc
Q psy1680         152 GGEGPGGFRNNNGPNRS---------NSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRI  222 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~---------~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~  222 (227)
                      ..++++|+|.||..+..         .++++|+++|++||.|.+|.| .++   .++|||||+|.+.++|.+|++.|||.
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~   87 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGR   87 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCC
Confidence            35788999999943321         135799999999999999966 553   37999999999999999999999999


Q ss_pred             cccCC
Q psy1680         223 TVDGL  227 (227)
Q Consensus       223 ~i~gr  227 (227)
                      .|+||
T Consensus        88 ~~~gr   92 (112)
T 2dit_A           88 WFGGR   92 (112)
T ss_dssp             EETTE
T ss_pred             EECCc
Confidence            99986

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=2.5e-13  Score=94.69  Aligned_cols=85  Identities=18%  Similarity=0.193  Sum_probs=71.4

Q ss_pred             CCCCCCCCCceEEEcCCCCCCC-----------HHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH
Q psy1680           5 QKTLPTEPPYTAFVGNLPNGIT-----------QGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL   72 (227)
Q Consensus         5 ~~~~~~~~~~~l~V~nLp~~~t-----------~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~   72 (227)
                      ..+....++++|+|+||....+           +++|+++|++| .|..|.| .++   .++|||||+|.+.++|.+|+.
T Consensus         7 ~~~~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~   82 (112)
T 2dit_A            7 GGPSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQ   82 (112)
T ss_dssp             SCCCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHH
T ss_pred             CCCCCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHH
Confidence            3444567789999999954432           57999999999 9999966 443   368999999999999999998


Q ss_pred             -hCCCceeCCeEeEEEecCCCCC
Q psy1680          73 -KDGRITVDGLQVRLDIADGKRN   94 (227)
Q Consensus        73 -~~~~~~~~g~~l~v~~~~~~~~   94 (227)
                       +|+ ..|+|+.|.|.++.++..
T Consensus        83 ~lng-~~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           83 TLDG-RWFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             HSTT-CEETTEECEEEECCSCCC
T ss_pred             HcCC-CEECCcEEEEEEeCCCCC
Confidence             999 999999999999987654

>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=99.50  E-value=3.4e-14  Score=111.43  Aligned_cols=68  Identities=13%  Similarity=0.097  Sum_probs=62.5

Q ss_pred             CCCCcceeccCCC-CCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGP-NRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~-~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +++.+|||+|||+ ..  ++++|+++|++||.|.+|+|++++     +|||||+|.+.++|.+|++.|+|..|+||
T Consensus        32 ~~~~~l~V~nLp~~~~--te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~  100 (229)
T 2adc_A           32 AGNSVLLVSNLNPERV--TPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGK  100 (229)
T ss_dssp             CCCSEEEEESCCTTTC--CHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSS
T ss_pred             CCCCEEEEeCCCcccC--CHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            5678999999976 55  789999999999999999999985     79999999999999999999999999886

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.49  E-value=4.3e-14  Score=110.73  Aligned_cols=78  Identities=18%  Similarity=0.279  Sum_probs=69.0

Q ss_pred             CCCCceEEEcCCCCCC---------CHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCce
Q psy1680          10 TEPPYTAFVGNLPNGI---------TQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRIT   78 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~---------t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~   78 (227)
                      ....++|||+||+..+         ++++|+++|++| .|..|.|+..      +|||||+|.+.++|+.|++ |++ ..
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g-~~  203 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSN-QT  203 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTT-CC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCC-CE
Confidence            4567999999999998         799999999999 9999999854      8999999999999999999 999 99


Q ss_pred             e------------CCeEeEEEecCCCCC
Q psy1680          79 V------------DGLQVRLDIADGKRN   94 (227)
Q Consensus        79 ~------------~g~~l~v~~~~~~~~   94 (227)
                      |            .|+.|.|.++.....
T Consensus       204 l~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          204 LLLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             EeccccccccccCCCCEEEEEEccCCCC
Confidence            9            899999999986543

>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=99.47  E-value=6.7e-14  Score=115.25  Aligned_cols=67  Identities=12%  Similarity=0.060  Sum_probs=59.8

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      .|+++|||+|++.....++++|+++|++||.|.+|.+.+      +||||||+|.+.++|++|++.|||.++-
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~   82 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVV   82 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccc
Confidence            678899999976566679999999999999999988754      4799999999999999999999999873

>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=99.47  E-value=6.2e-14  Score=96.39  Aligned_cols=55  Identities=15%  Similarity=0.205  Sum_probs=50.1

Q ss_pred             hhHHhhh-ccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         172 NDHGLMV-TEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       172 ~~l~~~f-~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++|+++| ++||.|.+|.|+++.. +.++|||||+|.+.++|.+|++.|||..++||
T Consensus        41 edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr   96 (104)
T 1jmt_A           41 EEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ   96 (104)
T ss_dssp             HHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             HHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCE
Confidence            5556666 9999999999999865 78999999999999999999999999999996

>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=99.46  E-value=2.5e-13  Score=109.55  Aligned_cols=75  Identities=21%  Similarity=0.332  Sum_probs=69.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeC-CeEeEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVD-GLQVRL   86 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~-g~~l~v   86 (227)
                      ..+.++|||+|||..+++++|+++|++| .|..|.|+.++     +|||||+|.+.++|.+|++ +|+ ..+. |+.|+|
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g-~~~~~g~~l~v  277 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQG-FKITQNNAMKI  277 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCC-cEeCCCCEEEE
Confidence            3467899999999999999999999999 99999998653     5899999999999999999 999 9999 999999


Q ss_pred             EecC
Q psy1680          87 DIAD   90 (227)
Q Consensus        87 ~~~~   90 (227)
                      .+++
T Consensus       278 ~~ak  281 (282)
T 3pgw_A          278 SFAK  281 (282)
T ss_pred             EEec
Confidence            9985

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.46  E-value=4.8e-14  Score=110.51  Aligned_cols=66  Identities=12%  Similarity=0.077  Sum_probs=58.9

Q ss_pred             CCCCcceeccCCCCCC-------CChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccc
Q psy1680         153 GEGPGGFRNNNGPNRS-------NSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV  224 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~-------~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i  224 (227)
                      ....+|||+||+...+       .++++|+.+|++||.|++|+|+.+      +|||||+|.+.++|+.|+++|+|..|
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            4578999999976541       268999999999999999999864      79999999999999999999999999

>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=99.46  E-value=1.7e-14  Score=96.14  Aligned_cols=55  Identities=16%  Similarity=0.288  Sum_probs=49.1

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHH
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA  215 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A  215 (227)
                      ++++|||+|||..+  ++++|+++|++||.|.+|+|+++     ++|||||+|.+.++|++|
T Consensus         4 ~~~~l~V~nLp~~~--te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~   58 (88)
T 1wf0_A            4 GSSGVFVGRCTGDM--TEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSL   58 (88)
T ss_dssp             CCCEEEEESCCSSS--CHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHT
T ss_pred             CCcEEEEeCCCCCC--CHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHH
Confidence            56799999997655  79999999999999999999876     589999999999999864

>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=99.46  E-value=3.1e-14  Score=99.30  Aligned_cols=71  Identities=11%  Similarity=-0.059  Sum_probs=59.6

Q ss_pred             CCCCcceeccCCCCC--------CCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccc
Q psy1680         153 GEGPGGFRNNNGPNR--------SNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV  224 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~--------~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i  224 (227)
                      .++++|.+.|+=.+.        .+.++||+++|++||.|.+|.|.++.    ++|+|||+|.+.++|.+|++.|||+.+
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            357789999983221        23457889999999999999997763    489999999999999999999999999


Q ss_pred             cCC
Q psy1680         225 DGL  227 (227)
Q Consensus       225 ~gr  227 (227)
                      +||
T Consensus        81 ~GR   83 (114)
T 3s6e_A           81 AGK   83 (114)
T ss_dssp             TTE
T ss_pred             CCE
Confidence            997

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.43  E-value=7.7e-14  Score=106.73  Aligned_cols=66  Identities=14%  Similarity=0.102  Sum_probs=60.8

Q ss_pred             CCcceeccCCC-CCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGP-NRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~-~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +++|||+|||+ ..  ++++|+++|+.||.|.+|+|++++     +|||||+|.+.++|.+|++.|+|..|+|+
T Consensus         3 ~~~l~v~nlp~~~~--~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~   69 (198)
T 1qm9_A            3 NSVLLVSNLNPERV--TPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGK   69 (198)
T ss_dssp             CCEEEEECCCSSSC--CHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSC
T ss_pred             CcEEEEeCCCcccC--CHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCe
Confidence            56899999976 55  789999999999999999999885     78999999999999999999999999886

>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=99.42  E-value=4.2e-13  Score=92.33  Aligned_cols=80  Identities=19%  Similarity=0.186  Sum_probs=69.4

Q ss_pred             CCCceEEEcCC--CCCCC--------HHHHHhcccCC-CeEEEEEeecCCC--CCeecEEEEEeCCHHHHHHHHH-hCCC
Q psy1680          11 EPPYTAFVGNL--PNGIT--------QGDVERFFPEQ-KLVSVRLVKDKET--DRFKGFCYVEFVDVENLRQALL-KDGR   76 (227)
Q Consensus        11 ~~~~~l~V~nL--p~~~t--------~~~l~~~f~~~-~i~~v~i~~~~~~--~~~~g~afv~f~~~~~a~~al~-~~~~   76 (227)
                      .+++.|.+.|+  |..+.        +++|++.|++| .|.+|.|++++.+  ++++|+|||+|.+.++|.+|+. ||| 
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG-   81 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG-   81 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTT-
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCC-
Confidence            46889999998  33333        36899999999 9999999988754  4678999999999999999999 999 


Q ss_pred             ceeCCeEeEEEecCC
Q psy1680          77 ITVDGLQVRLDIADG   91 (227)
Q Consensus        77 ~~~~g~~l~v~~~~~   91 (227)
                      ..++|+.|.|.++..
T Consensus        82 ~~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           82 RKFANRVVVTKYCDP   96 (105)
T ss_dssp             CEETTEECEEEEECH
T ss_pred             CEeCCCEEEEEEeCH
Confidence            999999999999764

>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=99.41  E-value=7.6e-13  Score=105.71  Aligned_cols=82  Identities=22%  Similarity=0.199  Sum_probs=73.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-h-CCCceeC---CeEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-K-DGRITVD---GLQV   84 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~-~~~~~~~---g~~l   84 (227)
                      .+..+|||+|||..+|+++|+++|+.| .|..|.|+.+ .+++++|||||+|.+.++|.+||. + ++ ..+.   +++|
T Consensus        94 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~-~~~~~~~~r~i  171 (261)
T 3sde_A           94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDG-AFLLTTTPRPV  171 (261)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHS-CEESSSSCCBC
T ss_pred             ccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCC-eEEecCCCceE
Confidence            456899999999999999999999999 9999999999 579999999999999999999999 7 55 5555   8999


Q ss_pred             EEEecCCCCC
Q psy1680          85 RLDIADGKRN   94 (227)
Q Consensus        85 ~v~~~~~~~~   94 (227)
                      .|.++.+...
T Consensus       172 ~v~~~~~~~~  181 (261)
T 3sde_A          172 IVEPMEQFDD  181 (261)
T ss_dssp             EEEECCCEES
T ss_pred             EEeeccccCc
Confidence            9999886543

>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=99.40  E-value=1.4e-12  Score=91.49  Aligned_cols=80  Identities=18%  Similarity=0.221  Sum_probs=70.0

Q ss_pred             CCCceEEEcCCCC--CC---CHHHHHhcccCC-CeEEEEEeecCC----CCCeecEEEEEeCCHHHHHHHHH-hCCCcee
Q psy1680          11 EPPYTAFVGNLPN--GI---TQGDVERFFPEQ-KLVSVRLVKDKE----TDRFKGFCYVEFVDVENLRQALL-KDGRITV   79 (227)
Q Consensus        11 ~~~~~l~V~nLp~--~~---t~~~l~~~f~~~-~i~~v~i~~~~~----~~~~~g~afv~f~~~~~a~~al~-~~~~~~~   79 (227)
                      ++++.|++.|+-.  ++   .+++|++.|++| .|.+|.|++++.    +++++|++||+|.+.++|.+|+. ||| ..+
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnG-r~f   96 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNG-RWF   96 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTT-CEE
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCC-CEE
Confidence            4789999999942  22   357899999999 999999999864    46788999999999999999999 999 999


Q ss_pred             CCeEeEEEecCC
Q psy1680          80 DGLQVRLDIADG   91 (227)
Q Consensus        80 ~g~~l~v~~~~~   91 (227)
                      +|+.|.|.++..
T Consensus        97 ~GR~i~v~~~~~  108 (118)
T 3ue2_A           97 AGRKVVAEVYDQ  108 (118)
T ss_dssp             TTEECEEEEECH
T ss_pred             CCcEEEEEEcCh
Confidence            999999999754

>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=99.38  E-value=1.2e-13  Score=94.87  Aligned_cols=70  Identities=13%  Similarity=0.340  Sum_probs=61.3

Q ss_pred             EcCCCCCCCHHHHHhcc------------cCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeE
Q psy1680          18 VGNLPNGITQGDVERFF------------PEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQ   83 (227)
Q Consensus        18 V~nLp~~~t~~~l~~~f------------~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~   83 (227)
                      +.|||..+++++|+++|            ++| .|..|.|++++. ++++|||||+|.+.++|.+|+. +|| ..++|+.
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng-~~~~Gr~   97 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNN-RWFNGQP   97 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTT-CEETTEE
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCC-CEECCEE
Confidence            55677777777777666            999 999999998854 7899999999999999999999 999 9999999


Q ss_pred             eEEEec
Q psy1680          84 VRLDIA   89 (227)
Q Consensus        84 l~v~~~   89 (227)
                      |.|.++
T Consensus        98 i~v~~s  103 (104)
T 1jmt_A           98 IHAELS  103 (104)
T ss_dssp             CCEEEC
T ss_pred             EEEEEc
Confidence            999886

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.26  E-value=4.7e-11  Score=81.11  Aligned_cols=75  Identities=13%  Similarity=0.186  Sum_probs=62.0

Q ss_pred             CceEEEcCCC-------CCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEe
Q psy1680          13 PYTAFVGNLP-------NGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQV   84 (227)
Q Consensus        13 ~~~l~V~nLp-------~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l   84 (227)
                      .++|-|.-..       ..+++++|+++|++| .|..|.|+     ++++|||||+|.+.++|..||+. . ..+.+++|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~-~-~~~~g~~l   82 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQN-E-VGLVDNPL   82 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHT-C-CBCSSSBC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHh-c-CCCCCCeE
Confidence            5667666443       458999999999999 99999997     36689999999999999999983 2 34579999


Q ss_pred             EEEecCCCCC
Q psy1680          85 RLDIADGKRN   94 (227)
Q Consensus        85 ~v~~~~~~~~   94 (227)
                      .|.++.++..
T Consensus        83 ~V~~a~~~~~   92 (100)
T 2d9o_A           83 KISWLEGQPQ   92 (100)
T ss_dssp             EEECSSCCCC
T ss_pred             EEEEccCCCC
Confidence            9999887654

>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=99.26  E-value=1.1e-11  Score=102.19  Aligned_cols=76  Identities=16%  Similarity=0.275  Sum_probs=64.8

Q ss_pred             CCCCCCceEEEcC--CCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeC---
Q psy1680           8 LPTEPPYTAFVGN--LPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVD---   80 (227)
Q Consensus         8 ~~~~~~~~l~V~n--Lp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~---   80 (227)
                      ....++.+|||+|  |+..+|+++|+++|++| .|..|.+..      +||||||+|.+.++|++||+ ||| ..+.   
T Consensus        13 ~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG-~~~~~~~   85 (345)
T 3tht_A           13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNG-KEVVDDL   85 (345)
T ss_dssp             CCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTT-CEEECTT
T ss_pred             ecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCC-Ccccccc
Confidence            3568889999999  57899999999999999 999887753      37999999999999999999 999 8773   


Q ss_pred             Ce--EeEEEecC
Q psy1680          81 GL--QVRLDIAD   90 (227)
Q Consensus        81 g~--~l~v~~~~   90 (227)
                      |+  .|.|.++.
T Consensus        86 g~~~~ly~~~~~   97 (345)
T 3tht_A           86 GQKITLYLNFVE   97 (345)
T ss_dssp             SCEEECEEEECS
T ss_pred             CCceEEEEEEee
Confidence            34  57777764

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.26  E-value=2.6e-11  Score=82.41  Aligned_cols=49  Identities=16%  Similarity=0.154  Sum_probs=44.4

Q ss_pred             CCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCC
Q psy1680         168 SNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR  221 (227)
Q Consensus       168 ~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g  221 (227)
                      ..++++|+++|++||.|.+|.|+     ++++|||||+|.+.++|.+|++.+++
T Consensus        28 ~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~   76 (100)
T 2d9o_A           28 GYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG   76 (100)
T ss_dssp             SCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC
Confidence            45899999999999999999997     35789999999999999999998765

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.19  E-value=1.2e-10  Score=80.97  Aligned_cols=77  Identities=16%  Similarity=0.102  Sum_probs=64.9

Q ss_pred             CCCCceEEEcCCCCCCC----------HHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCc
Q psy1680          10 TEPPYTAFVGNLPNGIT----------QGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRI   77 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t----------~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~   77 (227)
                      ..+++.|.+.|+-....          +++|++.|++| .|.+|.|.++.    ++|++||+|.+.++|.+|+. ||| .
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG-~   78 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHG-R   78 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTT-C
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCC-C
Confidence            34678899999843322          24789999999 99999997653    48999999999999999999 999 9


Q ss_pred             eeCCeEeEEEecCC
Q psy1680          78 TVDGLQVRLDIADG   91 (227)
Q Consensus        78 ~~~g~~l~v~~~~~   91 (227)
                      .++|+.|.|.++..
T Consensus        79 ~f~GR~i~v~~~~~   92 (114)
T 3s6e_A           79 WFAGKMITAAYVPL   92 (114)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EECCEEEEEEEEcH
Confidence            99999999999864

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.11  E-value=9.2e-11  Score=77.06  Aligned_cols=67  Identities=13%  Similarity=0.131  Sum_probs=56.2

Q ss_pred             CCCCCcceeccCCC--CCCCCh----hhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         152 GGEGPGGFRNNNGP--NRSNSM----NDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       152 ~~~~~~l~v~nl~~--~~~~~~----~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      +||..||+|...+.  ..++..    .+|.+.|+.||.|..+++..|+        +||+|.+.++|.+|++ |||..|+
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~   74 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELL   74 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEET
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeC
Confidence            47788999999862  122222    6789999999999999999874        8999999999999998 9999999


Q ss_pred             CC
Q psy1680         226 GL  227 (227)
Q Consensus       226 gr  227 (227)
                      ||
T Consensus        75 Gr   76 (91)
T 2dnr_A           75 NR   76 (91)
T ss_dssp             TE
T ss_pred             Ce
Confidence            86

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.09  E-value=2.4e-10  Score=79.86  Aligned_cols=67  Identities=7%  Similarity=0.051  Sum_probs=58.0

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcC-HHHHHHHHHHc--CCccccC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVD-VENLRQALLKD--GRITVDG  226 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~-~~~a~~Al~~l--~g~~i~g  226 (227)
                      +++..|+|+||+... +++++|+++|+.||.|..|.+.++..      .|||+|.+ .++|..|++++  ++.+|+|
T Consensus        16 ~~G~il~v~~l~~~~-~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g   85 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQ-TCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRN   85 (121)
T ss_dssp             CCCCEEEEEESCCSS-CCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTS
T ss_pred             cCCeEEEEecCCCCc-CCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeC
Confidence            567889999997651 37999999999999999999999865      59999999 89999999999  4777765

>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=99.07  E-value=1.9e-10  Score=89.56  Aligned_cols=59  Identities=12%  Similarity=0.052  Sum_probs=53.5

Q ss_pred             CChhhHHhhhccccceEEEEEeecCC----CCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         169 NSMNDHGLMVTEVTTLVSVRLVKDKE----TDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       169 ~~~~~l~~~f~~~g~i~~v~i~~d~~----t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +.+++|++.|++||.|.++.|+++..    ++.++|++||+|.+.++|.+|++.|||+.++||
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr  203 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR  203 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCe
Confidence            45689999999999999999996544    448999999999999999999999999999998

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.01  E-value=1.7e-09  Score=75.51  Aligned_cols=76  Identities=8%  Similarity=0.122  Sum_probs=67.1

Q ss_pred             CCCCCCceEEEcCCCCC-CCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCC-HHHHHHHHH-h--CCCceeCC
Q psy1680           8 LPTEPPYTAFVGNLPNG-ITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVD-VENLRQALL-K--DGRITVDG   81 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~-~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~-~~~a~~al~-~--~~~~~~~g   81 (227)
                      .+-++.+.|||+||+.. +++++|+++|++| +|..|.++++..      .|||.|.+ ..+|..|+. +  .+ ..|.+
T Consensus        13 ~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~-~~i~g   85 (121)
T 1owx_A           13 LEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGN-LQLRN   85 (121)
T ss_dssp             CSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSC-BCTTS
T ss_pred             ccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCC-cEEeC
Confidence            45678899999999999 9999999999999 999999988754      59999999 899999998 6  46 88999


Q ss_pred             eEeEEEecC
Q psy1680          82 LQVRLDIAD   90 (227)
Q Consensus        82 ~~l~v~~~~   90 (227)
                      ..+.+....
T Consensus        86 ~~~~~evL~   94 (121)
T 1owx_A           86 KEVTWEVLE   94 (121)
T ss_dssp             SSEEEEECC
T ss_pred             cEEEEEECC
Confidence            988887765

>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=99.00  E-value=1.5e-10  Score=76.45  Aligned_cols=68  Identities=19%  Similarity=0.193  Sum_probs=56.7

Q ss_pred             CCCCCCcceeccCCCC---CCCC----hhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcc
Q psy1680         151 RGGEGPGGFRNNNGPN---RSNS----MNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRIT  223 (227)
Q Consensus       151 ~~~~~~~l~v~nl~~~---~~~~----~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~  223 (227)
                      -+||..||+|..++..   ..+-    ..+|.+.|+.||.|..+++..|+        +||+|.+.++|.+||+ |+|..
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~   81 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMK   81 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCee
Confidence            3478889999998632   1111    25688999999999999999984        9999999999999999 99999


Q ss_pred             ccCC
Q psy1680         224 VDGL  227 (227)
Q Consensus       224 i~gr  227 (227)
                      |+||
T Consensus        82 v~Gr   85 (95)
T 1ufw_A           82 VKGR   85 (95)
T ss_dssp             ETTE
T ss_pred             eCCe
Confidence            9986

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.99  E-value=1.6e-09  Score=71.20  Aligned_cols=73  Identities=16%  Similarity=0.257  Sum_probs=62.0

Q ss_pred             CCCCceEEEcCCC----CCCCH----HHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeC
Q psy1680          10 TEPPYTAFVGNLP----NGITQ----GDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVD   80 (227)
Q Consensus        10 ~~~~~~l~V~nLp----~~~t~----~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~   80 (227)
                      -++..+|+|.-.+    .++-.    .+|.+.|++| .|..++++.++        +||+|.+.++|.+||++|| ..++
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~mnG-~~v~   74 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLSLNG-KELL   74 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGGGTT-CEET
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHhcCC-eEeC
Confidence            3567788887665    23433    5788999999 99999999763        8999999999999999999 9999


Q ss_pred             CeEeEEEecCC
Q psy1680          81 GLQVRLDIADG   91 (227)
Q Consensus        81 g~~l~v~~~~~   91 (227)
                      |+.|+|+++++
T Consensus        75 Gr~LkV~lkt~   85 (91)
T 2dnr_A           75 NRTITIALKSP   85 (91)
T ss_dssp             TEEEEEEECCC
T ss_pred             CeEEEEEeCCC
Confidence            99999999875

>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=98.72  E-value=7.1e-09  Score=68.41  Aligned_cols=74  Identities=19%  Similarity=0.189  Sum_probs=62.0

Q ss_pred             CCCCCceEEEcCCCCC-----CCH----HHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCce
Q psy1680           9 PTEPPYTAFVGNLPNG-----ITQ----GDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRIT   78 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~-----~t~----~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~   78 (227)
                      .-++..+|+|.-++..     +-.    .+|.+.|++| .|..++++.++        +||+|.+.++|.+||+++| ..
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~ldG-~~   81 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLDVDG-MK   81 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHHGGG-SE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHhcCC-ee
Confidence            3467789999877643     322    4588899999 99999999773        9999999999999999999 99


Q ss_pred             eCCeEeEEEecCC
Q psy1680          79 VDGLQVRLDIADG   91 (227)
Q Consensus        79 ~~g~~l~v~~~~~   91 (227)
                      ++|+.|+|.+..+
T Consensus        82 v~Gr~L~V~~k~~   94 (95)
T 1ufw_A           82 VKGRAVKISGPSS   94 (95)
T ss_dssp             ETTEEEEEECCCC
T ss_pred             eCCeEEEEeccCC
Confidence            9999999998653

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.71  E-value=3.4e-08  Score=76.70  Aligned_cols=65  Identities=20%  Similarity=0.211  Sum_probs=58.1

Q ss_pred             CCHHHHHhcccCC-CeEEEEEeecC----CCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecC
Q psy1680          25 ITQGDVERFFPEQ-KLVSVRLVKDK----ETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        25 ~t~~~l~~~f~~~-~i~~v~i~~~~----~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~   90 (227)
                      -.+++|++.|++| .|..+.|+++.    .+++++|++||+|.+.++|.+|+. ||| ..++|+.|.+.++.
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~g-r~~~gr~i~~~~~~  211 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNG-RWFAGRKVVAEVYD  211 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTT-CBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcC-ceECCeEEEEEEcC
Confidence            3457899999999 99999998654    445899999999999999999999 999 99999999999975

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.57  E-value=1.2e-07  Score=63.91  Aligned_cols=66  Identities=14%  Similarity=-0.058  Sum_probs=59.8

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccc-----cceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEV-----TTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~-----g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..++|-+-+||+.+  +...|+.+.+++     |.|+.|.|..|.      +-|+|+|.+...|-+|..+|+|.+|+||
T Consensus        20 ~~rtiaL~~ipDtv--ndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr   90 (117)
T 2l9w_A           20 LETLICLFPLSDKV--SPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGK   90 (117)
T ss_dssp             TTSCEEEECCCTTC--CHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTE
T ss_pred             CCcEEEEecCCCCC--CHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCe
Confidence            36789999998776  678899999999     999999999996      5799999999999999999999999986

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.88  E-value=5.3e-05  Score=51.03  Aligned_cols=73  Identities=18%  Similarity=0.213  Sum_probs=62.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC------CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCe
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ------KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGL   82 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~------~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~   82 (227)
                      .+..++|-+-|||..+++..|+.+.+++      .+..+.+..|      -+-|+|+|.+...|-+|.- ++| .+|.|+
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD------H~GAivef~d~~~AgKasLaL~G-~ef~gr   90 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD------FNGAIIIFRDSKFAAKMLMILNG-SQFQGK   90 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT------TTEEEEECSCHHHHHHHHHHHSS-EEETTE
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC------CCceEEEEccchhhHHHHhhcCC-eeecCe
Confidence            3457888889999999999999888765      3677888776      4689999999999999986 999 999999


Q ss_pred             EeEEEec
Q psy1680          83 QVRLDIA   89 (227)
Q Consensus        83 ~l~v~~~   89 (227)
                      .|++.-.
T Consensus        91 ~Lr~gTv   97 (117)
T 2l9w_A           91 VIRSGTI   97 (117)
T ss_dssp             EEEEECH
T ss_pred             EEEecCH
Confidence            9998653

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.80  E-value=0.0003  Score=46.92  Aligned_cols=75  Identities=15%  Similarity=0.162  Sum_probs=61.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccC----C--CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPE----Q--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQV   84 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~----~--~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l   84 (227)
                      ....+|.|.|||+.+.++.|+-+|+.    -  +|..+....        +-|+|+|.+.+.|++.|+... +.|++.+|
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~-H~L~~~~L   76 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQAD-HELHGAQL   76 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSC-CBSSSSBC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCc-ceecCeEE
Confidence            34689999999999999999999976    2  566666542        579999999999999999766 89999999


Q ss_pred             EEEecCCCCC
Q psy1680          85 RLDIADGKRN   94 (227)
Q Consensus        85 ~v~~~~~~~~   94 (227)
                      .|....++..
T Consensus        77 sV~P~~~~~~   86 (104)
T 2dhx_A           77 SLRPAPPRAP   86 (104)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEcCCCCCc
Confidence            9988665543

>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=97.55  E-value=0.00029  Score=46.43  Aligned_cols=53  Identities=9%  Similarity=0.072  Sum_probs=42.5

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHc
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD  219 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l  219 (227)
                      ..+++ .+|...  -..||.++|++||.|. |+++-|-       .|||.|.+++.|..||..+
T Consensus        17 HVf~l-~FP~ew--Kt~DI~~lFs~fggv~-I~WidDT-------sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           17 HVLHV-TFPKEW--KTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             SEEEE-ECCTTC--CHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             eEEEE-eCChhh--hhHHHHHHhhccCCEE-EEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            44555 776544  6789999999999555 7887773       6999999999999999876

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.42  E-value=0.00074  Score=44.33  Aligned_cols=67  Identities=12%  Similarity=0.171  Sum_probs=52.8

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCC--CeecEEEEEeCCHHHHHHHHH-hCCCceeCC
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETD--RFKGFCYVEFVDVENLRQALL-KDGRITVDG   81 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~--~~~g~afv~f~~~~~a~~al~-~~~~~~~~g   81 (227)
                      ++|.|++||+.+|++++.+.++.+ .+.....+..+.+.  ..-+-|+|.|.+.+++....+ ++| ..+.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g-~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDG-YVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTT-CEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCC-cEEEc
Confidence            578999999999999999999998 77666555443332  233679999999999999998 999 66543

>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=97.37  E-value=0.00022  Score=47.75  Aligned_cols=67  Identities=10%  Similarity=0.043  Sum_probs=55.1

Q ss_pred             CCcceeccCCCCC---CCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNR---SNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~---~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +++|+|.||+..+   +...+.++++|..|+.+.....++...      -..|.|.++++|.+|...|++..++|+
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR------Rirv~F~~~~~A~~AR~~Lh~~~f~g~   74 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK------RVRINFSNPLSAADARLRLHKTEFLGK   74 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT------EEEEECSSTTHHHHHHHTSTTSEETTE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce------EEEEEeCChHHHHHHHHHhccceecCc
Confidence            5689999997533   222367899999999999898888753      478999999999999999999999874

>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=97.35  E-value=0.00057  Score=45.04  Aligned_cols=56  Identities=14%  Similarity=0.262  Sum_probs=46.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-h
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-K   73 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~   73 (227)
                      ....+.++| ++|+.+.-.||.++|+.|.-..|.++-|.       .|||.|.+.+.|..||. +
T Consensus        13 p~r~HVf~l-~FP~ewKt~DI~~lFs~fggv~I~WidDT-------sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           13 PKRDHVLHV-TFPKEWKTSDLYQLFSAFGNIQISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCCCSEEEE-ECCTTCCHHHHHHHHTTTCSCCCEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             CCCCeEEEE-eCChhhhhHHHHHHhhccCCEEEEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            345577777 99999999999999999944456666553       69999999999999998 5

>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=97.17  E-value=0.00047  Score=45.55  Aligned_cols=53  Identities=9%  Similarity=0.079  Sum_probs=42.4

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcC
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG  220 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~  220 (227)
                      .+++ .+|+..  -..||.++|++||.|. |+++-|-       .|||.|.+++.|..||..+.
T Consensus         8 V~~l-~FP~ew--Kt~Di~~lFs~fggv~-I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEW--KTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTC--CHHHHHHHTTTSEEEE-EEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhh--hhHHHHHHHhccCCEE-EEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            4445 775544  6789999999999554 8888873       69999999999999999764

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.00  E-value=0.003  Score=41.40  Aligned_cols=67  Identities=6%  Similarity=-0.041  Sum_probs=55.4

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCc--ccceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDR--FKGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~--~~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      +|.|++||+.+  |++++.+..++...+.....+....+.+  .-.-|+|.|.+.+++..-.+.++|+.+-
T Consensus         3 KvVIRrLPP~L--teeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            3 KVVIRRLPPTL--TKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             EEEEEEECTTC--CHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             EEEEeCCCCCC--CHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            68899999888  7899999999988887777776654443  2356999999999999999999998773

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.95  E-value=0.0016  Score=44.81  Aligned_cols=61  Identities=10%  Similarity=-0.035  Sum_probs=46.3

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      .-|.|...|  .. ..+.+...|+.||.|.+.....      ...+-.|.|.+..+|++||.+ ||..|+|
T Consensus        25 ~wVtVFGFp--~~-~~~~VL~~F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~k-NG~ii~g   85 (119)
T 1wwh_A           25 TWVTVFGFP--QA-SASYILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALSK-DGRIFGE   85 (119)
T ss_dssp             GEEEEECCC--GG-GHHHHHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHTT-TTCEETT
T ss_pred             CEEEEECCC--HH-HHHHHHHHHHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHHHh-CCeEecC
Confidence            345566654  33 3577899999999999887622      246899999999999999988 6777764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.93  E-value=0.0022  Score=42.42  Aligned_cols=69  Identities=13%  Similarity=0.143  Sum_probs=50.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCC--CeecEEEEEeCCHHHHHHHHH-hCCCceeCC
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETD--RFKGFCYVEFVDVENLRQALL-KDGRITVDG   81 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~--~~~g~afv~f~~~~~a~~al~-~~~~~~~~g   81 (227)
                      -+-+|.|+.||+.+||+++.+.++.+ .+.....+..+.+.  ..-.-|+|.|.+.+++....+ .+| ..+.+
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g-~~F~D   80 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDG-YIFLD   80 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTT-EEEEC
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCC-cEEEe
Confidence            35789999999999999999999888 75333222222221  122579999999999999998 999 66643

>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=96.90  E-value=0.002  Score=43.04  Aligned_cols=74  Identities=14%  Similarity=0.104  Sum_probs=59.5

Q ss_pred             CCceEEEcCCCCCC-CH----HHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680          12 PPYTAFVGNLPNGI-TQ----GDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus        12 ~~~~l~V~nLp~~~-t~----~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      -.++|+|.||+..+ +.    +.++.+|..| ++......+.      -.=..|.|.+.++|.+|-. +++ ..+.|+.|
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS------FRRirv~F~~~~~A~~AR~~Lh~-~~f~g~~~   76 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHK-TEFLGKEM   76 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTT-SEETTEEC
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc------ceEEEEEeCChHHHHHHHHHhcc-ceecCcee
Confidence            35789999998754 22    4678999999 8877766643      2246899999999999998 999 99999999


Q ss_pred             EEEecCCC
Q psy1680          85 RLDIADGK   92 (227)
Q Consensus        85 ~v~~~~~~   92 (227)
                      +|.++.+.
T Consensus        77 r~YFgq~~   84 (104)
T 1wey_A           77 KLYFAQTL   84 (104)
T ss_dssp             EEECCCCS
T ss_pred             EEEecCCC
Confidence            99998743

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.90  E-value=0.001  Score=43.96  Aligned_cols=54  Identities=15%  Similarity=0.280  Sum_probs=45.4

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hC
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KD   74 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~   74 (227)
                      .+.++| ++|+++.-.||.++|+.|.-..|.++-|.       .|||.|.+.+.|..||. +.
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fggv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSEEEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccCCEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            466777 89999999999999999955567776653       69999999999999998 54

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.65  E-value=0.0056  Score=40.79  Aligned_cols=55  Identities=11%  Similarity=-0.020  Sum_probs=44.4

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhcc-----ccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHH
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTE-----VTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK  218 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~-----~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~  218 (227)
                      ...+|.|.|||+..  .++.|.-+|+.     -|.|.++....        +-|+|+|.+.+.|++.|+.
T Consensus         7 ~~~~I~V~~lPp~~--~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k   66 (104)
T 2dhx_A            7 GGVAVEVRGLPPAV--PDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ   66 (104)
T ss_dssp             CCCEEEEESCCTTS--CHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC
T ss_pred             CccEEEEECCCCCC--ChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC
Confidence            35689999998766  46788888987     24888887644        3699999999999999987

>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=96.00  E-value=0.031  Score=38.36  Aligned_cols=73  Identities=12%  Similarity=0.099  Sum_probs=58.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCC-eEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG-LQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g-~~l~v~   87 (227)
                      ....+-|.|-+.|+.. -..|...|++| .|.+....      ....+-.|.|.+..+|++||..|| ..+++ ..|-|.
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~------~~~NWihI~Y~s~~~A~rAL~kNG-~ii~g~~mIGV~   92 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSKDG-RIFGESIMIGVK   92 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHTTTT-CEETTTEECEEE
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC------CCCCeEEEEeCCHHHHHHHHHhCC-eEecCCEEEEEE
Confidence            3446888899999885 46677889999 99887762      124699999999999999999999 99985 677777


Q ss_pred             ecC
Q psy1680          88 IAD   90 (227)
Q Consensus        88 ~~~   90 (227)
                      ...
T Consensus        93 p~~   95 (119)
T 1wwh_A           93 PCI   95 (119)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            754

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.71  E-value=0.023  Score=37.51  Aligned_cols=69  Identities=4%  Similarity=-0.085  Sum_probs=51.5

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCc--ccceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDR--FKGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~--~~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      +-+|.|+.||+.+  |++++.+.+++.-.+.....+....+.+  .-.-|+|.|.+.++...-.+..+|..+-
T Consensus         9 ~~KvVIRrLPP~L--tee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~   79 (97)
T 2l08_A            9 SHMVVIRRLPPGL--TKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFL   79 (97)
T ss_dssp             CCCEEEECCCSCS--CHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEE
T ss_pred             ceeEEEeCCCCCC--CHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            4579999999888  7899988888766654444444333222  1246899999999999999999998774

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=94.47  E-value=0.017  Score=49.17  Aligned_cols=56  Identities=11%  Similarity=-0.008  Sum_probs=40.3

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHH
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK  218 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~  218 (227)
                      .+.|+|. .|...  ++.+|.+.|+.||.|.++.+-++.     .-||.|+|.+.+++.+++..
T Consensus        53 ~rsv~v~-~~~~~--~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKI--SENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC-----CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCC--CHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHhc
Confidence            3678997 55444  678899999999999999886654     26999999999988877644

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=94.20  E-value=0.055  Score=37.65  Aligned_cols=78  Identities=13%  Similarity=0.270  Sum_probs=54.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEE-EEEeec--------CCCC-----CeecEEEEEeCCHHHHHHHHHhCCC
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVS-VRLVKD--------KETD-----RFKGFCYVEFVDVENLRQALLKDGR   76 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~-v~i~~~--------~~~~-----~~~g~afv~f~~~~~a~~al~~~~~   76 (227)
                      ...-|.|-+.|+..+ ..+-+.|++| .|.+ ..+.+.        +.+.     ....+-.|+|.+..+|.+||..|| 
T Consensus         6 ~e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG-   83 (132)
T 3p3d_A            6 GELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENG-   83 (132)
T ss_dssp             --CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTT-
T ss_pred             CceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCC-
Confidence            345677888987765 4566788888 7765 222110        0000     124688999999999999999999 


Q ss_pred             ceeCCeEeEEEecCC
Q psy1680          77 ITVDGLQVRLDIADG   91 (227)
Q Consensus        77 ~~~~g~~l~v~~~~~   91 (227)
                      ..|+|..|-|.+..+
T Consensus        84 ~ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           84 AVFNGVLLGVIPYTK   98 (132)
T ss_dssp             CEETTEECEEEECCH
T ss_pred             eEeCcEEEEEEECCH
Confidence            999999888888753

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=93.88  E-value=0.031  Score=38.91  Aligned_cols=66  Identities=11%  Similarity=0.138  Sum_probs=42.6

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEE-EEEeecC--------CCC-----cccceEEEEEcCHHHHHHHHHHcCCc
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVS-VRLVKDK--------ETD-----RFKGFCYVEFVDVENLRQALLKDGRI  222 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~-v~i~~d~--------~t~-----~~~g~afV~F~~~~~a~~Al~~l~g~  222 (227)
                      -|.|...|+.   ....+-+.|++||.|.+ ....++.        .+.     ...++--|+|++..+|.+||... |.
T Consensus         9 ~VtVFGFp~~---~~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~N-G~   84 (132)
T 3p3d_A            9 AILVFGYPET---MANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLEN-GA   84 (132)
T ss_dssp             EEEEECCCGG---GHHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTT-TC
T ss_pred             EEEEEecCHH---HHHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhC-Ce
Confidence            3566666533   35778899999998876 2222100        000     12467899999999999999764 45


Q ss_pred             cccC
Q psy1680         223 TVDG  226 (227)
Q Consensus       223 ~i~g  226 (227)
                      .|+|
T Consensus        85 ii~G   88 (132)
T 3p3d_A           85 VFNG   88 (132)
T ss_dssp             EETT
T ss_pred             EeCc
Confidence            5655

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=93.66  E-value=0.027  Score=47.99  Aligned_cols=57  Identities=12%  Similarity=0.179  Sum_probs=42.3

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCC
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG   75 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~   75 (227)
                      .+.|+|. .|..+++.+|.++|++| +|..+..-+++     .-||.|+|.+.+++..++....
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~~~~  110 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQNGTH  110 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHSSCC
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHhccC
Confidence            4789997 79999999999999999 99998887542     2599999999999998876434

>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=81.78  E-value=3.9  Score=35.25  Aligned_cols=56  Identities=14%  Similarity=0.217  Sum_probs=44.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCC
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDG   75 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~   75 (227)
                      .++.++|+ +|..|...+|.++|+.|.-..|.++-+       ..|||.|.+.+.|..++. +..
T Consensus       439 R~~vl~v~-f~~~~~~~~i~~~fs~fg~v~V~widd-------t~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          439 RDHVLHVT-FPKEWKTSDLYQLFSAFGNIQISWIDD-------TSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGGEEEEE-CCTTCCHHHHHHHGGGGCCCEEEECSS-------SEEEEECSCHHHHHHHHHHHTT
T ss_pred             cCcEEEEe-CCCCCCHHHHHHHHHhcCCEEEEEEcC-------CeEEEEECCHHHHHHHHHHHHh
Confidence            45677776 999999999999999993345556543       369999999999999998 543

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=80.99  E-value=2.8  Score=36.19  Aligned_cols=54  Identities=9%  Similarity=0.050  Sum_probs=41.2

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG  220 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~  220 (227)
                      ..++|+ +|.  .+...+|.+.|+.||.| +|+++-|       ..|||.|.+.+.|..++..+.
T Consensus       441 ~vl~v~-f~~--~~~~~~i~~~fs~fg~v-~V~widd-------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          441 HVLHVT-FPK--EWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GEEEEE-CCT--TCCHHHHHHHGGGGCCC-EEEECSS-------SEEEEECSCHHHHHHHHHHHT
T ss_pred             cEEEEe-CCC--CCCHHHHHHHHHhcCCE-EEEEEcC-------CeEEEEECCHHHHHHHHHHHH
Confidence            345554 644  44678999999999954 5776665       369999999999999999884

---

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	227
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-12
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	9e-12
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-10
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-10
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-09
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	6e-09
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	9e-09
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-08
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-08
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	4e-08
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	7e-08
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-07
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-07
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-07
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-07
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-07
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-07
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-07
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-07
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-07
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-07
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-07
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-07
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-07
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	6e-07
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	7e-07
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-07
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	8e-07
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	9e-07
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-06
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-06
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	3e-06
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-06
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	3e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	5e-06
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-06
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	6e-06
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	8e-06
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	9e-06
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-05
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-05
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-05
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-05
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	5e-05
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-05
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	5e-05
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	6e-05
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-04
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	1e-04
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-04
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-04
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	4e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	4e-04
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	4e-04
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	8e-04
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	0.001
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	0.002
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.002
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	0.002

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.1 bits (145), Expect = 1e-12
 Identities = 32/99 (32%), Positives = 53/99 (53%), Gaps = 2/99 (2%)

Query: 2   GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVE 60
           G +   LP  PPYTAF+GNLP  +T+  ++ FF            +    +R KGF Y E
Sbjct: 4   GSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAE 63

Query: 61  FVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGG 99
           F D+++L  AL  +   ++   ++R+D+AD  ++ + G 
Sbjct: 64  FEDLDSLLSALSLNEE-SLGNKRIRVDVADQAQDKDSGP 101

>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 = 57.3 bits (138), Expect = 9e-12
 Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 2/81 (2%)

Query: 15 TAFVGNLPNGITQGDVERFFPEQKLV-SVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
          T F   L   I   D+E FF     V  VR++ D+ + R KG  YVEF +++++  A+  
Sbjct: 20 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGL 79

Query: 74 DGRITVDGLQVRLDIADGKRN 94
           G+  + G+ + +  +  ++N
Sbjct: 80 TGQ-RLLGVPIIVQASQAEKN 99

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.9 bits (129), Expect = 3e-10
 Identities = 21/99 (21%), Positives = 38/99 (38%), Gaps = 2/99 (2%)

Query: 8   LPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENL 67
           LP E     ++ NLP  IT  ++   F   K   +R ++   T   +G  YV + D+ + 
Sbjct: 2   LPPEVNRILYIRNLPYKITAEEMYDIF--GKYGPIRQIRVGNTPETRGTAYVVYEDIFDA 59

Query: 68  RQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNR 106
           + A        V    + +   +  R   K     K+ +
Sbjct: 60  KNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQ 98

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.1 bits (127), Expect = 3e-10
 Identities = 20/88 (22%), Positives = 41/88 (46%), Gaps = 3/88 (3%)

Query: 10 TEPPYTAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLR 68
           +      V  LP   T+ D++ +F    +++ V++ KD +T   KGF +V F + E   
Sbjct: 5  VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV 64

Query: 69 QALLKDGRITVDGLQVRLDIADGKRNDN 96
          + +    R  +DG      + + K++ +
Sbjct: 65 KVM--SQRHMIDGRWCDCKLPNSKQSQD 90

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.6 bits (123), Expect = 1e-09
 Identities = 14/79 (17%), Positives = 29/79 (36%), Gaps = 1/79 (1%)

Query: 12 PPYTAFVGNLPNGITQGDVERFFPEQK-LVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 70
           P    V N+P  ++  ++  FF   + +     +K  E     G   V F   +    A
Sbjct: 8  GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 67

Query: 71 LLKDGRITVDGLQVRLDIA 89
          ++      +   +V+L + 
Sbjct: 68 VIDLNDRPIGSRKVKLVLG 86

>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 = 50.3 bits (120), Expect = 3e-09
 Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 5/86 (5%)

Query: 11 EPPYTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKE-TDRFKGFCYVEFVDVENLR 68
          +      V N+P    Q ++   F    +L +VRL K    T   +GF +V+F+  ++ +
Sbjct: 6  QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 65

Query: 69 QAL--LKDGRITVDGLQVRLDIADGK 92
          +A   L      + G ++ L+ AD +
Sbjct: 66 KAFNALCHSTH-LYGRRLVLEWADSE 90

>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 = 6e-09
 Identities = 17/84 (20%), Positives = 37/84 (44%), Gaps = 4/84 (4%)

Query: 17 FVGNLPNGITQGDVERFFPEQKLV--SVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 74
          F+GNL   I +  +   F    ++  + ++++D +T   KG+ ++ F   +    A+   
Sbjct: 2  FIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAM 61

Query: 75 GRITVDGLQVRLDIADGKRNDNKG 98
              +    + +  A  K  D+KG
Sbjct: 62 NGQYLCNRPITVSYAFKK--DSKG 83

>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 = 48.8 bits (116), Expect = 9e-09
 Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 3/79 (3%)

Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          +VG+L   +T+  +   F P   ++S+R+ +D  T R  G+ YV F    +  +AL    
Sbjct: 4  YVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMN 63

Query: 76 RITVDGLQVRLDIADGKRN 94
             + G  VR+  +  +R+
Sbjct: 64 FDVIKGKPVRIMWS--QRD 80

>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 = 48.0 bits (114), Expect = 2e-08
 Identities = 19/80 (23%), Positives = 32/80 (40%), Gaps = 1/80 (1%)

Query: 15 TAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
          T +VGNL    T+  +   F     +  + +  DK      GFC+VE+    +   A+  
Sbjct: 9  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 74 DGRITVDGLQVRLDIADGKR 93
               +D   +R D   G +
Sbjct: 69 INGTRLDDRIIRTDWDAGFK 88

>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 = 47.7 bits (113), Expect = 3e-08
 Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 1/80 (1%)

Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          F+G LPN +    V+        L +  LVKD  T   KG+ + E+VD+    QA+    
Sbjct: 5  FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 64

Query: 76 RITVDGLQVRLDIADGKRND 95
           + +   ++ +  A     +
Sbjct: 65 GMQLGDKKLLVQRASVGAKN 84

>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 = 47.3 bits (112), Expect = 4e-08
 Identities = 21/80 (26%), Positives = 31/80 (38%), Gaps = 2/80 (2%)

Query: 11 EPPYTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 69
          E     F+G L    T   +   F     L    +++D  T R +GF +V +  VE +  
Sbjct: 4  EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 70 ALLKDGRITVDGLQVRLDIA 89
          A+       VDG  V    A
Sbjct: 64 AMNARPH-KVDGRVVEPKRA 82

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.1 bits (111), Expect = 7e-08
 Identities = 18/86 (20%), Positives = 34/86 (39%), Gaps = 1/86 (1%)

Query: 9  PTEPPYTAFVGNLPNGITQGDVERFFPEQKLV-SVRLVKDKETDRFKGFCYVEFVDVENL 67
          P EP    ++ NL   +T+ D+   F   +      +     T R +G  ++ F + E  
Sbjct: 14 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIA 73

Query: 68 RQALLKDGRITVDGLQVRLDIADGKR 93
           QAL       + G  + ++    K+
Sbjct: 74 WQALHLVNGYKLYGKILVIEFGKNKK 99

>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 = 46.3 bits (109), Expect = 1e-07
 Identities = 28/82 (34%), Positives = 49/82 (59%), Gaps = 2/82 (2%)

Query: 17 FVGNLPNGITQGDVERFFPEQKLVSV-RLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          FVG L     +  +E+ F +   +S   +VKD+ET R +GF +V F ++++ + A++   
Sbjct: 9  FVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMN 68

Query: 76 RITVDGLQVRLDIADGKRNDNK 97
            +VDG Q+R+D A  K +DN+
Sbjct: 69 GKSVDGRQIRVDQAG-KSSDNR 89

>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 = 45.7 bits (108), Expect = 1e-07
 Identities = 15/74 (20%), Positives = 30/74 (40%)

Query: 17 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 76
           V NL  G++  D++  F E   +    V    + R  G   V F    +  +A+ +   
Sbjct: 4  LVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNG 63

Query: 77 ITVDGLQVRLDIAD 90
          + +DG  + + +  
Sbjct: 64 VPLDGRPMNIQLVT 77

>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 = 45.0 bits (106), Expect = 2e-07
 Identities = 17/74 (22%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          FVG L     +  +  +F    ++ S+ L  D +T++ +GFC++ F + E +++ + K  
Sbjct: 3  FVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKY 62

Query: 76 RITVDGLQVRLDIA 89
             V   +  + +A
Sbjct: 63 H-NVGLSKCEIKVA 75

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.0 bits (106), Expect = 2e-07
 Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 2/74 (2%)

Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          F+G L    TQ  +  +F    ++    +++D  T R +GF +V F+D   + + L +  
Sbjct: 4  FIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR 63

Query: 76 RITVDGLQVRLDIA 89
             +D   +   +A
Sbjct: 64 H-ELDSKTIDPKVA 76

>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 = 45.5 bits (107), Expect = 2e-07
 Identities = 17/83 (20%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 17 FVGNLPNGITQGDVERFFPE--QKLVSVRLVKDKE-TDRFKGFCYVEFVDVENLRQAL-- 71
          F+G +P    + ++     +  + ++ V +        + +GF +VE+        A   
Sbjct: 5  FIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRK 64

Query: 72 LKDGRITVDGLQVRLDIADGKRN 94
          L  GRI + G Q+ +D A+ + +
Sbjct: 65 LMPGRIQLWGHQIAVDWAEPEID 87

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 2e-07
 Identities = 16/79 (20%), Positives = 37/79 (46%), Gaps = 6/79 (7%)

Query: 17 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-DG 75
          ++GNL   +T  D+ + F ++K     L    +     G+ +V++ D     +A+    G
Sbjct: 5  YIGNLSPAVTADDLRQLFGDRK-----LPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSG 59

Query: 76 RITVDGLQVRLDIADGKRN 94
          ++ + G  + +D +  K+ 
Sbjct: 60 KVELHGKIMEVDYSVSKKL 78

>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 = 44.9 bits (105), Expect = 3e-07
 Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 11 EPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 70
            P+  F+GNL    +  +++    E    +   V D  T   + F YV+F   E+L +A
Sbjct: 11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKA 70

Query: 71 LLKDGRITVDGLQVRLDIADGK 92
          L   G   V G +++L+   G+
Sbjct: 71 LELTGL-KVFGNEIKLEKPKGR 91

>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 = 45.4 bits (107), Expect = 3e-07
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 2/83 (2%)

Query: 11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 69
          E     F+G L    T+  +  ++ +  KL    +++D  + R +GF +V F  +  +  
Sbjct: 18 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDA 77

Query: 70 ALLKDGRITVDGLQVRLDIADGK 92
          A+      ++DG  V    A  +
Sbjct: 78 AMAARPH-SIDGRVVEPKRAVAR 99

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.6 bits (105), Expect = 3e-07
 Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          F+G L    T+ D++ +F    ++V   L  D  T R +GF +V F + E++ + + +  
Sbjct: 3  FIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKE 62

Query: 76 RITVDGLQVR 85
             ++G  + 
Sbjct: 63 H-KLNGKVID 71

>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 = 44.6 bits (105), Expect = 3e-07
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 4/81 (4%)

Query: 17 FVGNLPNGITQGDVERFF----PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 72
          F+ NL    T+  ++  F      +     +           GF +VE+   E  ++AL 
Sbjct: 2  FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 73 KDGRITVDGLQVRLDIADGKR 93
          +    TVDG ++ + I++   
Sbjct: 62 QLQGHTVDGHKLEVRISERAT 82

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.7 bits (105), Expect = 3e-07
 Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 1/81 (1%)

Query: 15 TAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
            +VG L   +    +   F P   +  +++  D ET++ +GF +VEF   E+   A+  
Sbjct: 7  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 74 DGRITVDGLQVRLDIADGKRN 94
               + G  +R+++A   R 
Sbjct: 67 MNESELFGRTIRVNLAKPMRI 87

>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 = 44.6 bits (105), Expect = 5e-07
 Identities = 17/85 (20%), Positives = 30/85 (35%), Gaps = 4/85 (4%)

Query: 10 TEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 69
               T    NL   IT+ +++  F +       +    +  + KG  Y+EF    +  +
Sbjct: 13 VRAARTLLAKNLSFNITEDELKEVFEDAL----EIRLVSQDGKSKGIAYIEFKSEADAEK 68

Query: 70 ALLKDGRITVDGLQVRLDIADGKRN 94
           L +     +DG  V L     K  
Sbjct: 69 NLEEKQGAEIDGRSVSLYYTGEKGG 93

>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 = 44.6 bits (105), Expect = 5e-07
 Identities = 19/87 (21%), Positives = 40/87 (45%), Gaps = 1/87 (1%)

Query: 10 TEPPYTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLR 68
               T +VG L   +++  +   F     +V+  + KD+ T + +G+ +VEF+  E+  
Sbjct: 6  RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 65

Query: 69 QALLKDGRITVDGLQVRLDIADGKRND 95
           A+     I + G  +R++ A     +
Sbjct: 66 YAIKIMDMIKLYGKPIRVNKASAHNKN 92

>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 = 44.3 bits (104), Expect = 6e-07
 Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 1/85 (1%)

Query: 11 EPPYTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 69
          +   T  V NL     + D++  F P   +  + L KDK T + KGF ++ F   E+  +
Sbjct: 6  DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 65

Query: 70 ALLKDGRITVDGLQVRLDIADGKRN 94
          A+        D L + ++ A    N
Sbjct: 66 AIAGVSGFGYDHLILNVEWAKPSTN 90

>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 = 43.9 bits (103), Expect = 7e-07
 Identities = 17/86 (19%), Positives = 34/86 (39%), Gaps = 1/86 (1%)

Query: 11 EPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 70
            P    V N+P      D+ + F +   + + +         KGF +V F +  +  +A
Sbjct: 9  STPKRLHVSNIPFRFRDPDLRQMFGQFGKI-LDVEIIFNERGSKGFGFVTFENSADADRA 67

Query: 71 LLKDGRITVDGLQVRLDIADGKRNDN 96
            K     V+G ++ ++ A  +   N
Sbjct: 68 REKLHGTVVEGRKIEVNNATARVMTN 93

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.9 bits (103), Expect = 7e-07
 Identities = 20/91 (21%), Positives = 38/91 (41%), Gaps = 1/91 (1%)

Query: 10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLR 68
          +      FV NL    ++ D+E+ F     L  +    D  T + KGF +V F+  E+  
Sbjct: 5  SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV 64

Query: 69 QALLKDGRITVDGLQVRLDIADGKRNDNKGG 99
          +A  +       G  + +  +  K+  ++ G
Sbjct: 65 KAYAEVDGQVFQGRMLHVLPSTIKKEASQSG 95

>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 = 44.0 bits (103), Expect = 8e-07
 Identities = 22/94 (23%), Positives = 43/94 (45%), Gaps = 9/94 (9%)

Query: 8  LPTEPP--YTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDV 64
          LP++     T F+ NL     +  +         L  VR+V   +T+  KG  + +F+  
Sbjct: 1  LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 60

Query: 65 ENLRQAL------LKDGRITVDGLQVRLDIADGK 92
          E  ++ L       + G + +DG Q+++D+A  +
Sbjct: 61 EAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTR 94

>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 = 43.5 bits (102), Expect = 9e-07
 Identities = 13/82 (15%), Positives = 33/82 (40%), Gaps = 5/82 (6%)

Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 74
            +V NL    ++  +E+ F        +    +   + + + +V F + E+  +A+   
Sbjct: 10 ILYVRNLMLSTSEEMIEKEFNNI-----KPGAVERVKKIRDYAFVHFSNREDAVEAMKAL 64

Query: 75 GRITVDGLQVRLDIADGKRNDN 96
              +DG  + + +A     D+
Sbjct: 65 NGKVLDGSPIEVTLAKPVDKDS 86

>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 = 43.2 bits (101), Expect = 1e-06
 Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 2/74 (2%)

Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          FVG L    T  DV+ +F +  K+    L+ DK T+R +GF +V F   + + +      
Sbjct: 3  FVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHF 62

Query: 76 RITVDGLQVRLDIA 89
             ++   V    A
Sbjct: 63 H-EINNKMVECKKA 75

>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 = 43.5 bits (102), Expect = 1e-06
 Identities = 22/84 (26%), Positives = 34/84 (40%), Gaps = 2/84 (2%)

Query: 11 EPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 70
                +VGNLP  I   D+E  F   K  ++R +  K       F +VEF D  +   A
Sbjct: 12 NNDCRIYVGNLPPDIRTKDIEDVF--YKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDA 69

Query: 71 LLKDGRITVDGLQVRLDIADGKRN 94
          +        DG ++R++     R 
Sbjct: 70 VYGRDGYDYDGYRLRVEFPRSGRG 93

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.1 bits (101), Expect = 1e-06
 Identities = 13/85 (15%), Positives = 33/85 (38%), Gaps = 2/85 (2%)

Query: 12 PPYTAFVGNLPNGITQGDVERFFPE--QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 69
          P +T ++ NL   I + ++++       +   +  +    + + +G  +V F +V +   
Sbjct: 2  PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 70 ALLKDGRITVDGLQVRLDIADGKRN 94
          AL            +R+  A    +
Sbjct: 62 ALRSMQGFPFYDKPMRIQYAKTDSD 86

>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 = 42.7 bits (100), Expect = 2e-06
 Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 6/83 (7%)

Query: 17 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 76
          FVG     +T+ ++  FF +       ++       F+ F +V F D +  +    +D  
Sbjct: 9  FVGRCTGDMTEDELREFFSQYG----DVMDVFIPKPFRAFAFVTFADDQIAQSLCGED-- 62

Query: 77 ITVDGLQVRLDIADGKRNDNKGG 99
          + + G+ V +  A+ K N N G 
Sbjct: 63 LIIKGISVHISNAEPKHNSNSGP 85

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 42.0 bits (98), Expect = 3e-06
 Identities = 12/79 (15%), Positives = 28/79 (35%), Gaps = 4/79 (5%)

Query: 17 FVGNLPNGITQGDVERFFPEQ---KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
           + NL   +   ++ R   E              KE        ++ F + ++  +AL  
Sbjct: 8  MIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQM 67

Query: 74 DGRITVDGLQVRLDIADGK 92
          +    +   ++ + +AD K
Sbjct: 68 NRS-LLGNREISVSLADKK 85

>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 = 41.6 bits (97), Expect = 3e-06
 Identities = 15/74 (20%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          FVG +     +  +  +F +  K+  + ++ D+ + + +GF +V F D +++ + +++  
Sbjct: 6  FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY 65

Query: 76 RITVDGLQVRLDIA 89
            TV+G    +  A
Sbjct: 66 -HTVNGHNCEVRKA 78

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.1 bits (98), Expect = 3e-06
 Identities = 16/101 (15%), Positives = 37/101 (36%), Gaps = 2/101 (1%)

Query: 9   PTEPPYTAFVGNLPNGITQGDVERFFPEQKLV-SVRLVKDKETDRFKGFCYVEFVDVENL 67
                  A + N+P  IT+ DV +F     +  +   V      +  G   V+F + ++ 
Sbjct: 4   VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 63

Query: 68  RQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGG 108
           R++     +  ++G +  + +   +           Q + G
Sbjct: 64  RKSERLHRK-KLNGREAFVHVVTLEDMREIEKNPPAQGKSG 103

>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 = 41.7 bits (97), Expect = 5e-06
 Identities = 28/97 (28%), Positives = 48/97 (49%), Gaps = 6/97 (6%)

Query: 15  TAFVGNLPNGITQGDV-ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
           + FVGN+P   T+  + + F     +VS RLV D+ET + KG+ + E+ D E    A+  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 74  DGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGS 110
                  G  +R+D A  ++N  +      ++ G G+
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEE-----LKSLGTGA 101

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.4 bits (97), Expect = 6e-06
 Identities = 23/98 (23%), Positives = 42/98 (42%), Gaps = 8/98 (8%)

Query: 2  GRNQKTLPTEPPYTAFVGNL-PNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVE 60
          G + KT P       F+GNL    + + DVE  F +   +             KGF +V+
Sbjct: 4  GSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKI-------VGCSVHKGFAFVQ 56

Query: 61 FVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKG 98
          +V+  N R A+  +    + G  + +++A   + +  G
Sbjct: 57 YVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVNRSG 94

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.8 bits (95), Expect = 6e-06
 Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 11 EPPYTAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 69
          +P     V  L    T+ D+   F +   +  V +V D+++ R +GF +V F +V++ ++
Sbjct: 7  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 66

Query: 70 ALLKDGRITVDGLQVR 85
          A  +   + +DG ++R
Sbjct: 67 AKERANGMELDGRRIR 82

>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 = 40.8 bits (95), Expect = 8e-06
 Identities = 14/73 (19%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          +V  LP  +TQ ++E+ F    ++++ R++ D+ T   +G  ++ F       +A+    
Sbjct: 10 YVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN 69

Query: 76 RITVDGLQVRLDI 88
               G    + +
Sbjct: 70 GQKPSGATEPITV 82

>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 = 41.3 bits (96), Expect = 9e-06
 Identities = 20/98 (20%), Positives = 42/98 (42%), Gaps = 9/98 (9%)

Query: 17  FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
           FVG LP   T   + ++F     +    ++ D++T + +G+ +V   D     +A  KD 
Sbjct: 14  FVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA-CKDP 72

Query: 76  RITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGM 113
              +DG +  +++A             +  + G + G+
Sbjct: 73  NPIIDGRKANVNLAYLGAKP-------RSLQTGFAIGV 103

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.4 bits (94), Expect = 1e-05
 Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 1/84 (1%)

Query: 11 EPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 70
            P T +VGNL   +T+  +      Q           E      +C+VEF +  +   A
Sbjct: 6  GQPRTLYVGNLSRDVTEVLI-LQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAA 64

Query: 71 LLKDGRITVDGLQVRLDIADGKRN 94
          L       + G +V+++ A    +
Sbjct: 65 LAAMNGRKILGKEVKVNWATTPSS 88

>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 = 40.9 bits (95), Expect = 1e-05
 Identities = 20/98 (20%), Positives = 34/98 (34%), Gaps = 2/98 (2%)

Query: 2  GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEF 61
          G +  +  +   +   +  LP   T+ D+  FF     + V +    +  R  G   VEF
Sbjct: 4  GSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDG-RVTGEADVEF 62

Query: 62 VDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGG 99
             E+   A+ KD    +    V L +         G 
Sbjct: 63 ATHEDAVAAMAKDKA-NMQHRYVELFLNSTAGTSGSGP 99

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 1e-05
 Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 7/75 (9%)

Query: 17 FVGNLPNGITQGDVERFFPEQ------KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 70
          +VGN+P GIT+  +  FF  Q             V   + ++ K F ++EF  V+   QA
Sbjct: 5  YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 64

Query: 71 LLKDGRITVDGLQVR 85
          +  DG I   G  ++
Sbjct: 65 MAFDG-IIFQGQSLK 78

>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 = 39.3 bits (91), Expect = 3e-05
 Identities = 14/80 (17%), Positives = 34/80 (42%), Gaps = 1/80 (1%)

Query: 14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 72
          +  FV ++     + +++  F +  ++ ++ L  D+ T   KG+  VE+   +    A  
Sbjct: 8  WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 73 KDGRITVDGLQVRLDIADGK 92
                + G  +++D    K
Sbjct: 68 ALNGAEIMGQTIQVDWCFVK 87

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.1 bits (95), Expect = 3e-05
 Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 69
          E     F+G L    T   +   F +   L    +++D  T R +GF +V +  VE +  
Sbjct: 4  EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 70 AL 71
          A+
Sbjct: 64 AM 65

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 4e-05
 Identities = 14/78 (17%), Positives = 33/78 (42%), Gaps = 3/78 (3%)

Query: 17 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          F+ NL   I    +   F     ++S ++V D+   +   + +V F   E   +A+ K  
Sbjct: 12 FIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG--YGFVHFETQEAAERAIEKMN 69

Query: 76 RITVDGLQVRLDIADGKR 93
           + ++  +V +     ++
Sbjct: 70 GMLLNDRKVFVGRFKSRK 87

>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 = 38.8 bits (90), Expect = 5e-05
 Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
          +V NLP  IT   ++  F +   +V   +++DK T R +G  +V +   E  ++A+    
Sbjct: 10 YVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 69

Query: 76 RITVDGLQVRLDI 88
           +  +G    L +
Sbjct: 70 NVIPEGGSQPLSV 82

>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 = 38.4 bits (89), Expect = 5e-05
 Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 17 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
           V  LP  +T  ++   F     + + R+++D +T    G+ +V+F    + ++A+    
Sbjct: 6  IVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLN 65

Query: 76 RITVDGLQVRLDIA 89
           ITV   ++++  A
Sbjct: 66 GITVRNKRLKVSYA 79

>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 = 39.0 bits (90), Expect = 5e-05
 Identities = 19/95 (20%), Positives = 34/95 (35%), Gaps = 9/95 (9%)

Query: 11  EPPYTAFVGNLPNGITQGDVERFF---------PEQKLVSVRLVKDKETDRFKGFCYVEF 61
                 +V  L + +T  D+  FF                + +  DKET + KG   V +
Sbjct: 6   SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSY 65

Query: 62  VDVENLRQALLKDGRITVDGLQVRLDIADGKRNDN 96
            D    + A+         G ++++ +A  K   N
Sbjct: 66  EDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 100

>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 = 38.5 bits (89), Expect = 6e-05
 Identities = 17/74 (22%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 17 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 75
           V  LP  +TQ +    F    ++ S +LV+DK T +  G+ +V ++D ++  +A+    
Sbjct: 6  IVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLN 65

Query: 76 RITVDGLQVRLDIA 89
           + +    +++  A
Sbjct: 66 GLRLQTKTIKVSYA 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 = 38.0 bits (88), Expect = 1e-04
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 7/81 (8%)

Query: 15 TAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 73
          T + G + +G+T   + + F P  +++ +R+         KG+ +V F   E+   A++ 
Sbjct: 20 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVRFSTHESAAHAIVS 73

Query: 74 DGRITVDGLQVRLDIADGKRN 94
              T++G  V+        +
Sbjct: 74 VNGTTIEGHVVKCYWGKESPD 94

>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 = 37.6 bits (87), Expect = 1e-04
 Identities = 17/78 (21%), Positives = 33/78 (42%), Gaps = 5/78 (6%)

Query: 17 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 76
          FVGNLP  IT+ ++ + F +          +    + KGF ++          A ++   
Sbjct: 12 FVGNLPPDITEEEMRKLFEK-----YGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDN 66

Query: 77 ITVDGLQVRLDIADGKRN 94
          + + G Q+R+  A    +
Sbjct: 67 MPLRGKQLRVRFACHSAS 84

>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 = 37.4 bits (86), Expect = 1e-04
 Identities = 12/76 (15%), Positives = 30/76 (39%), Gaps = 1/76 (1%)

Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 74
          + ++   P   T  D++ +  ++  V    ++      FKG  +V F  +E+ ++ +   
Sbjct: 8  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 67

Query: 75 GRITVDGLQVRLDIAD 90
          G        + +   D
Sbjct: 68 G-QKYKETDLLILFKD 82

>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 = 38.3 bits (88), Expect = 1e-04
 Identities = 18/102 (17%), Positives = 43/102 (42%), Gaps = 5/102 (4%)

Query: 11  EPPYTAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 69
           +      V  +P  + +  + + F     + SV++V D+ET + +G+ +V+F    + +Q
Sbjct: 40  DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99

Query: 70  ALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSG 111
           A+       +   ++++ +A                 G G+G
Sbjct: 100 AIAGLNGFNILNKRLKVALAASGHQRPGIA----GAVGDGNG 137

>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 = 37.1 bits (85), Expect = 2e-04
 Identities = 11/78 (14%), Positives = 31/78 (39%), Gaps = 1/78 (1%)

Query: 14 YTAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 72
           T ++ N P   TQ ++     +   +     +     +  + F Y++    E+ R  + 
Sbjct: 2  CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 73 KDGRITVDGLQVRLDIAD 90
          K   + ++G  +   +++
Sbjct: 62 KLNGLKIEGYTLVTKVSN 79

>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 = 37.8 bits (87), Expect = 2e-04
 Identities = 18/87 (20%), Positives = 41/87 (47%), Gaps = 2/87 (2%)

Query: 12  PPYTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 70
                F+ +LP      D+ + F P   +VS ++  DK+T+  K F +V + +  + + A
Sbjct: 17  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 76

Query: 71  LLKDGRITVDGLQVRLDIADGKRNDNK 97
           +       +   ++++ +    +ND+K
Sbjct: 77  IQSMNGFQIGMKRLKVQLKR-SKNDSK 102

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.4 bits (84), Expect = 4e-04
 Identities = 11/58 (18%), Positives = 16/58 (27%), Gaps = 1/58 (1%)

Query: 37 QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRN 94
           K   +R +         G   V F D E     +         G Q+     DG  +
Sbjct: 41 SKFGQIRKLLLF-DRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTD 97

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 36.0 bits (82), Expect = 4e-04
 Identities = 15/73 (20%), Positives = 26/73 (35%), Gaps = 2/73 (2%)

Query: 15 TAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 74
          T  V NLP    Q  V ++F     +    V      +   F  +EF   +    A+ K 
Sbjct: 2  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA-DSLKKNFRFARIEFARYDGALAAITKT 60

Query: 75 GRITVDGLQVRLD 87
           +  V   ++ + 
Sbjct: 61 HK-VVGQNEIIVS 72

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.1 bits (83), Expect = 4e-04
 Identities = 11/69 (15%), Positives = 24/69 (34%), Gaps = 6/69 (8%)

Query: 17 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 76
           V   P       + +F     ++   +           + ++ +      R+AL KDGR
Sbjct: 8  TVFGFPQASASYILLQFAQYGNILKHVMSNTG------NWMHIRYQSKLQARKALSKDGR 61

Query: 77 ITVDGLQVR 85
          I  + + + 
Sbjct: 62 IFGESIMIG 70

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.5 bits (81), Expect = 8e-04
 Identities = 13/90 (14%), Positives = 24/90 (26%), Gaps = 6/90 (6%)

Query: 9  PTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLR 68
               +   V  LP   +  D++    E               +  G   VE++  E++ 
Sbjct: 11 TRRSDFRVLVSGLPPSGSWQDLKDHMREAG------DVCYADVQKDGMGMVEYLRKEDME 64

Query: 69 QALLKDGRITVDGLQVRLDIADGKRNDNKG 98
           AL K         +            + G
Sbjct: 65 YALRKLDDTKFRSHEGETSYIRVYPERSSG 94

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.8 bits (79), Expect = 0.001
 Identities = 8/88 (9%), Positives = 23/88 (26%)

Query: 10 TEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 69
          +            + +      R   E    +       +  +      + F +  +   
Sbjct: 2  SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAAD 61

Query: 70 ALLKDGRITVDGLQVRLDIADGKRNDNK 97
          A L+  +    G +++L  A      + 
Sbjct: 62 ARLRLHKTEFLGKEMKLYFAQTLHIGSS 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 = 34.3 bits (78), Expect = 0.002
 Identities = 14/79 (17%), Positives = 30/79 (37%), Gaps = 4/79 (5%)

Query: 12 PPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 71
          P  T  + N+P  +++ D++  F     V   +   K   + +    ++   VE   QAL
Sbjct: 9  PSATLHLSNIPPSVSEEDLKVLFSSNGGV---VKGFKFFQKDRKMALIQMGSVEEAVQAL 65

Query: 72 -LKDGRITVDGLQVRLDIA 89
                   +   +R+  +
Sbjct: 66 IDLHNHDLGENHHLRVSFS 84

>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 = 34.4 bits (78), Expect = 0.002
 Identities = 16/101 (15%), Positives = 34/101 (33%), Gaps = 9/101 (8%)

Query: 9   PTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLR 68
                    V  L   + + D+     +        +       FK    VEF ++++ +
Sbjct: 11  KVSVSPVVHVRGLCESVVEADLVEALEKF-----GTICYVMMMPFKRQALVEFENIDSAK 65

Query: 69  QAL--LKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRG 107
           + +    D  + + G Q   + +  KR    G  N+  + G
Sbjct: 66  ECVTFAADVPVYIAGQQAFFNYSTSKRITRPG--NSGPSSG 104

>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 = 33.6 bits (76), Expect = 0.002
 Identities = 14/71 (19%), Positives = 30/71 (42%), Gaps = 3/71 (4%)

Query: 17 FVGNLPNGITQGDVERFFPEQKLV-SVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-D 74
          ++  L  G T  D+ +       + S + + DK T++ KG+ +V+F      ++A+    
Sbjct: 2  YIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALK 61

Query: 75 GRITVDGLQVR 85
              V     +
Sbjct: 62 AS-GVQAQMAK 71

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	227
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	100.0
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.86
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.86
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.86
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.86
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.85
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.85
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.85
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.85
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.85
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.84
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.84
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.84
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.84
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.84
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.84
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.83
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.83
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.83
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.83
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.83
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.82
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.82
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.82
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.82
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.82
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.82
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.82
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.82
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.82
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.82
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.82
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.82
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.82
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.82
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.82
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.81
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.81
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.81
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.81
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.81
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.81
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.81
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.81
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.81
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.8
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.8
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.8
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.8
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.8
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.8
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.79
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.79
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.79
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.79
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.79
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.79
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.79
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.79
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.79
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.78
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.78
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.78
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.78
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.78
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.78
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.77
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.77
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.77
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.77
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.77
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.77
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.77
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.76
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.76
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.76
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.75
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.75
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.75
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.75
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.75
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.75
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.75
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.74
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.74
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.74
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.74
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.74
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.74
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.74
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.74
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.74
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.73
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.73
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.73
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.73
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.73
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.73
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.73
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.72
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.72
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.72
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.72
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.72
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.72
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.72
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.72
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.71
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.71
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.71
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.71
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.71
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.71
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.71
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.71
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.7
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.7
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.7
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.7
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.7
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.7
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.69
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.69
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.69
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.69
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.68
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.68
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.68
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.67
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.67
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.66
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.66
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.66
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.66
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.65
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.65
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.65
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.65
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.64
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.63
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.63
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.63
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.63
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.61
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.61
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.61
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.6
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.59
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.58
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.58
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.58
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.57
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.56
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.54
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.53
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.53
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.46
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.45
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	99.45
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.41
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.4
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.4
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.39
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.39
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.24
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.26
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.07
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.95
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.94
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.93
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.75
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	95.29
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.02

>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=100.00  E-value=2.3e-32  Score=206.54  Aligned_cols=160  Identities=19%  Similarity=0.294  Sum_probs=140.0

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEecCC
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~~~   91 (227)
                      .++|||+|||+++|+++|+++|++| .|..+.+++++.++.++|||||+|.+.++|..|+.+++ ..+..+.+.+....+
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~-~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP-HKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCS-CEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcC-Ccccccchhhhhhhh
Confidence            3799999999999999999999999 99999999999999999999999999999999999777 789999998888655


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeccCCCCCCCCh
Q psy1680          92 KRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQGGSFNRDNMRNNSRGGGASSGGGFNDFSRGGEGPGGFRNNNGPNRSNSM  171 (227)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~  171 (227)
                      +......                                                   .......+|||+|||..+  ++
T Consensus        85 ~~~~~~~---------------------------------------------------~~~~~~~~i~V~~lp~~~--te  111 (183)
T d1u1qa_          85 REDSQRP---------------------------------------------------GAHLTVKKIFVGGIKEDT--EE  111 (183)
T ss_dssp             TTGGGST---------------------------------------------------TTTCCCSEEEEECCCTTC--CH
T ss_pred             ccccccc---------------------------------------------------ccccccceeEEccCCCcC--CH
Confidence            4432110                                                   001245689999997655  78


Q ss_pred             hhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         172 NDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       172 ~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++|+++|+.||.|..+.|++|..++.++|||||+|.+.++|.+||+ +++..|+|+
T Consensus       112 ~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~  166 (183)
T d1u1qa_         112 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGH  166 (183)
T ss_dssp             HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTE
T ss_pred             HHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCE
Confidence            9999999999999999999999999999999999999999999997 677888875

>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=99.86  E-value=2.2e-21  Score=128.91  Aligned_cols=84  Identities=25%  Similarity=0.378  Sum_probs=79.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ...+.++|||+|||.++++++|+++|++| .|..+.|+.++.++.++|||||+|.+.++|.+||+ +++ ..++|+.|+|
T Consensus         4 ~~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g-~~~~g~~i~v   82 (90)
T d2cq0a1           4 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG-FGYDHLILNV   82 (90)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTT-CEETTEECEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCC-CEECCEEEEE
Confidence            34567899999999999999999999999 99999999999999999999999999999999999 999 9999999999


Q ss_pred             EecCCCC
Q psy1680          87 DIADGKR   93 (227)
Q Consensus        87 ~~~~~~~   93 (227)
                      .+++|+.
T Consensus        83 ~~akp~~   89 (90)
T d2cq0a1          83 EWAKPST   89 (90)
T ss_dssp             EESSCCC
T ss_pred             EeeeCCC
Confidence            9998765

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.2e-21  Score=131.01  Aligned_cols=84  Identities=24%  Similarity=0.413  Sum_probs=79.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ..+.++|||+|||..+|+++|+++|++| .|..+.|++++.++.++|||||+|.+.++|++||+ +++ ..|+|+.|+|+
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g-~~~~g~~l~V~   84 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDM-IKLYGKPIRVN   84 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSS-CBCSSCBCEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCC-CEECCEEEEEE
Confidence            3456899999999999999999999999 99999999999999999999999999999999998 999 99999999999


Q ss_pred             ecCCCCC
Q psy1680          88 IADGKRN   94 (227)
Q Consensus        88 ~~~~~~~   94 (227)
                      ++.++..
T Consensus        85 ~A~~~~~   91 (93)
T d1x5ua1          85 KASAHNK   91 (93)
T ss_dssp             ETTTTSC
T ss_pred             EcCCCCC
Confidence            9987654

>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=99.86  E-value=2.9e-21  Score=129.05  Aligned_cols=84  Identities=24%  Similarity=0.406  Sum_probs=78.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ...+++|||+|||+++|+++|+++|++| +|..|.+++++.++.++|||||+|.+.++|..||+ +|+ ..++|++|+|.
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g-~~~~gr~i~V~   82 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYING-TRLDDRIIRTD   82 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTT-SEETTEECEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCC-CEECCEEEEEE
Confidence            4578899999999999999999999999 99999999999999999999999999999999998 999 99999999999


Q ss_pred             ecCCCCC
Q psy1680          88 IADGKRN   94 (227)
Q Consensus        88 ~~~~~~~   94 (227)
                      ++...+.
T Consensus        83 ~a~~~~~   89 (93)
T d1h2vz_          83 WDAGFKE   89 (93)
T ss_dssp             EESCCCT
T ss_pred             EcCCCCC
Confidence            9875443

>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=99.86  E-value=1.7e-21  Score=128.81  Aligned_cols=83  Identities=18%  Similarity=0.274  Sum_probs=77.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ...+.++|||+|||.++|+++|+++|++| .|..+.+++++.+++++|||||+|.+.++|++|+. +|+ ..+.|+.|+|
T Consensus         3 ~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng-~~l~g~~l~V   81 (88)
T d1rk8a_           3 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNG-AEIMGQTIQV   81 (88)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTT-CEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCC-CEECCEEEEE
Confidence            34567899999999999999999999999 99999999999999999999999999999999998 999 9999999999


Q ss_pred             EecCCC
Q psy1680          87 DIADGK   92 (227)
Q Consensus        87 ~~~~~~   92 (227)
                      .++.++
T Consensus        82 ~~a~~k   87 (88)
T d1rk8a_          82 DWCFVK   87 (88)
T ss_dssp             EESEEC
T ss_pred             EEecCC
Confidence            998764

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=1.1e-21  Score=130.09  Aligned_cols=83  Identities=22%  Similarity=0.361  Sum_probs=78.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      ...++|||+|||+++|+++|+++|++| +|..+.|++++.+++++|||||+|.+.++|.+||. +|+ ..++|+.|.|.+
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~-~~i~g~~l~v~~   81 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE-SELFGRTIRVNL   81 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTT-EEETTEEEEEEE
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCC-CEECCEEEEEEE
Confidence            457899999999999999999999999 99999999999999999999999999999999998 999 999999999999


Q ss_pred             cCCCCC
Q psy1680          89 ADGKRN   94 (227)
Q Consensus        89 ~~~~~~   94 (227)
                      +.+++.
T Consensus        82 a~p~~~   87 (89)
T d2cqba1          82 AKPMRI   87 (89)
T ss_dssp             CCCCCC
T ss_pred             eCCCCC
Confidence            987654

>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=99.85  E-value=1.6e-21  Score=127.44  Aligned_cols=78  Identities=22%  Similarity=0.401  Sum_probs=75.3

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecC
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~   90 (227)
                      .++|||+|||+++|+++|+++|++| .|..+.|++++.+++++|||||+|.+.++|++||+ +|+ ..+.|+.|+|.+++
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng-~~~~g~~l~v~~a~   80 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNG-ITVRNKRLKVSYAR   80 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTT-CEETTEECEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCC-CEECCEEEEEEEcC
Confidence            5789999999999999999999999 99999999999999999999999999999999998 999 99999999999997


Q ss_pred             C
Q psy1680          91 G   91 (227)
Q Consensus        91 ~   91 (227)
                      |
T Consensus        81 p   81 (82)
T d1b7fa1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=2.8e-21  Score=131.34  Aligned_cols=86  Identities=19%  Similarity=0.325  Sum_probs=80.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ..+++++|||+|||+++++++|+++|++| .+..+.++.++.++.++|||||+|.+.++|..||+ +|+ ..|.|+.|+|
T Consensus        14 ~~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng-~~~~g~~i~V   92 (102)
T d2cpza1          14 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNG-FQIGMKRLKV   92 (102)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTT-CEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCC-CEECCEEEEE
Confidence            34567899999999999999999999999 99999999999999999999999999999999998 999 9999999999


Q ss_pred             EecCCCCCC
Q psy1680          87 DIADGKRND   95 (227)
Q Consensus        87 ~~~~~~~~~   95 (227)
                      .++.++...
T Consensus        93 ~~a~~k~~~  101 (102)
T d2cpza1          93 QLKRSKNDS  101 (102)
T ss_dssp             ECCCCSCCC
T ss_pred             EEeCCCCCC
Confidence            999887653

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=1.4e-21  Score=128.44  Aligned_cols=81  Identities=26%  Similarity=0.441  Sum_probs=76.9

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecC
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~   90 (227)
                      .++|||+|||.++|+++|+++|++| +|..+.|++|+.+|+++|||||+|.+.++|..|++ +++ ..|+|++|.|.++.
T Consensus         1 a~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~-~~l~g~~l~V~~A~   79 (85)
T d2u2fa_           1 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG-MQLGDKKLLVQRAS   79 (85)
T ss_dssp             CCCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSS-CCCSSSCCEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCC-CEECCEEEEEEECC
Confidence            3689999999999999999999999 99999999999999999999999999999999999 999 99999999999998


Q ss_pred             CCCC
Q psy1680          91 GKRN   94 (227)
Q Consensus        91 ~~~~   94 (227)
                      +...
T Consensus        80 ~~~~   83 (85)
T d2u2fa_          80 VGAK   83 (85)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=99.85  E-value=3.4e-21  Score=130.27  Aligned_cols=84  Identities=25%  Similarity=0.326  Sum_probs=79.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      ...+++|||+|||+++++++|+++|++| .|..+.|++++.+++++|||||+|.+.++|+.||+ ||+ ..|+|+.|+|.
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g-~~~~gr~i~V~   83 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDG-QVFQGRMLHVL   83 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTT-EESSSCEEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCC-CEECCEEEEEE
Confidence            4557899999999999999999999999 99999999999999999999999999999999998 999 99999999999


Q ss_pred             ecCCCCC
Q psy1680          88 IADGKRN   94 (227)
Q Consensus        88 ~~~~~~~   94 (227)
                      ++.++..
T Consensus        84 ~a~~~~~   90 (99)
T d1whwa_          84 PSTIKKE   90 (99)
T ss_dssp             ECCCCST
T ss_pred             ECCCCCc
Confidence            9987664

>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=99.85  E-value=7.4e-21  Score=126.05  Aligned_cols=84  Identities=23%  Similarity=0.373  Sum_probs=77.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLD   87 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~   87 (227)
                      .....++|||+|||+++|+++|+++|++| .|..+.|++|+.+++++|||||+|.+.++|.+||+ +. ..|+|+.|.|+
T Consensus         4 ~~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~-~~-~~l~Gr~i~v~   81 (90)
T d2cqga1           4 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QR-HMIDGRWCDCK   81 (90)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SC-EEETTEEEEEE
T ss_pred             CCcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh-cC-CccCCEEeEEE
Confidence            44567899999999999999999999999 99999999999999999999999999999999998 45 67999999999


Q ss_pred             ecCCCCC
Q psy1680          88 IADGKRN   94 (227)
Q Consensus        88 ~~~~~~~   94 (227)
                      ++.+++.
T Consensus        82 ~a~~k~~   88 (90)
T d2cqga1          82 LPNSKQS   88 (90)
T ss_dssp             CCCTTCC
T ss_pred             eCCCCCC
Confidence            9988764

>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=99.84  E-value=4.4e-21  Score=124.59  Aligned_cols=75  Identities=25%  Similarity=0.403  Sum_probs=73.0

Q ss_pred             eEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecC
Q psy1680          15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        15 ~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~   90 (227)
                      .|||+|||+.+|+++|+++|++| +|..++|++++.+++++|||||+|.+.++|..||+ ++| ..+.|++|+|.++.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g-~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNF-DVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTT-CEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCC-CEECCEEEEEEEeC
Confidence            69999999999999999999999 99999999999999999999999999999999998 999 99999999999984

>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=99.84  E-value=2e-21  Score=127.13  Aligned_cols=73  Identities=18%  Similarity=0.234  Sum_probs=68.3

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .++.+|||+|||..+  ++++|+++|++||.|.+|.|++|+.++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus         7 ~~~~~l~V~nL~~~~--te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr   79 (83)
T d2cqca1           7 DPNCCLGVFGLSLYT--TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR   79 (83)
T ss_dssp             CGGGCEEEESCCSSC--CHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCE
Confidence            456799999996555  8999999999999999999999999999999999999999999999999999999986

>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=6.4e-21  Score=124.87  Aligned_cols=78  Identities=26%  Similarity=0.368  Sum_probs=74.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEecC
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~~   90 (227)
                      ..++|||+|||+++|+++|+++|++| .|..+.|++|+.+++++|||||+|.+.++|++||++++ ..|+|+.|+|+.|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~-~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP-HKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCS-CEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCC-CEECCEEEEEEeee
Confidence            45799999999999999999999999 99999999999999999999999999999999999999 99999999998874

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=9.1e-21  Score=123.72  Aligned_cols=78  Identities=23%  Similarity=0.442  Sum_probs=74.8

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecC
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~   90 (227)
                      .++|||+|||.++++++|+++|++| .|..+.+++++.+++++|||||+|.+.++|+.|++ +++ ..+.|+.|+|.+++
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g-~~~~g~~l~v~~Ak   80 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNG-LRLQTKTIKVSYAR   80 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT-CEETTEECEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCC-CEECCEEEEEEEee
Confidence            3579999999999999999999999 99999999999999999999999999999999998 999 99999999999987


Q ss_pred             C
Q psy1680          91 G   91 (227)
Q Consensus        91 ~   91 (227)
                      |
T Consensus        81 P   81 (82)
T d1fxla1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.84  E-value=1.2e-21  Score=126.15  Aligned_cols=75  Identities=23%  Similarity=0.420  Sum_probs=72.6

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEec
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA   89 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~   89 (227)
                      ++|||+|||+++|+++|+++|++| .|..+.|++|+.+++++|||||+|.+.++|++||++++ ..++|+.|.|+.|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~~~~-~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCC-CEECCeEEEEEEC
Confidence            689999999999999999999999 99999999999999999999999999999999999999 9999999999876

>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=99.84  E-value=3.1e-20  Score=126.29  Aligned_cols=85  Identities=19%  Similarity=0.350  Sum_probs=76.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLD   87 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~   87 (227)
                      .....++|||+|||+.+++++|+++|++| .|..+.|++++.+++++|||||+|.+.++|++||+..+ ..|+|+.|.|.
T Consensus         6 ~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~l~Gr~l~V~   84 (103)
T d2cqda1           6 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN-PIIDGRKANVN   84 (103)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSS-CEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCC-CcCCCEEEEEE
Confidence            34455789999999999999999999999 99999999999999999999999999999999999334 46999999999


Q ss_pred             ecCCCCC
Q psy1680          88 IADGKRN   94 (227)
Q Consensus        88 ~~~~~~~   94 (227)
                      ++..+..
T Consensus        85 ~a~~~~~   91 (103)
T d2cqda1          85 LAYLGAK   91 (103)
T ss_dssp             ESTTTCC
T ss_pred             EcCCCCC
Confidence            9876543

>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=99.83  E-value=1e-20  Score=128.45  Aligned_cols=81  Identities=21%  Similarity=0.386  Sum_probs=77.4

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEecCC
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~~~   91 (227)
                      .++|||+|||+++|+++|+++|++| .|..+.|++++.++.++|||||+|.+.++|.+||++++ ..|+|+.|.|.++.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~-~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARP-HSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCS-EEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCC-CeECCEEEEEEECcc
Confidence            3799999999999999999999999 99999999999999999999999999999999999999 999999999999988


Q ss_pred             CCC
Q psy1680          92 KRN   94 (227)
Q Consensus        92 ~~~   94 (227)
                      +..
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            765

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=5.2e-21  Score=127.11  Aligned_cols=85  Identities=31%  Similarity=0.575  Sum_probs=79.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLD   87 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~   87 (227)
                      .....+|||+|||+++++++|+++|++| .|..+.+++++.++.++|||||+|.++++|++||. +++ ..|+|++|.|.
T Consensus         2 ~~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~-~~~~g~~l~V~   80 (90)
T d1x5sa1           2 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNG-KSVDGRQIRVD   80 (90)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTT-CCTTSCCCEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCC-CEECCEEEEEE
Confidence            3567889999999999999999999999 99999999999999999999999999999999998 999 99999999999


Q ss_pred             ecCCCCCC
Q psy1680          88 IADGKRND   95 (227)
Q Consensus        88 ~~~~~~~~   95 (227)
                      ++.++...
T Consensus        81 ~a~~~~~~   88 (90)
T d1x5sa1          81 QAGKSSDN   88 (90)
T ss_dssp             EEECCCCC
T ss_pred             EcCCCCCC
Confidence            99877653

>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=99.83  E-value=2.5e-20  Score=133.73  Aligned_cols=83  Identities=19%  Similarity=0.397  Sum_probs=78.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      ...++|||+|||+++|+++|+++|++| .|..|.|++++.+++++|||||+|.+.++|..||+ +|+ ..|+|+.|+|.+
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng-~~~~gr~l~V~~  118 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG-FNILNKRLKVAL  118 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTT-EECSSCEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCC-CEECCEEEEEEE
Confidence            344789999999999999999999999 99999999999999999999999999999999998 999 999999999999


Q ss_pred             cCCCCC
Q psy1680          89 ADGKRN   94 (227)
Q Consensus        89 ~~~~~~   94 (227)
                      +.++..
T Consensus       119 a~~~~~  124 (139)
T d1u6fa1         119 AASGHQ  124 (139)
T ss_dssp             SSCCCC
T ss_pred             cCCCCC
Confidence            986654

>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=99.83  E-value=1.9e-20  Score=122.48  Aligned_cols=75  Identities=27%  Similarity=0.480  Sum_probs=72.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      .++++|||+|||+.+|+++|+++|++| .|..+.|++++.+++++|||||+|.+.++|.+||. +++ ..|+|++|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g-~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG-MELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTT-EEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCC-CEECCEEeEC
Confidence            457899999999999999999999999 99999999999999999999999999999999998 999 9999999987

>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=99.83  E-value=8.6e-21  Score=125.41  Aligned_cols=72  Identities=17%  Similarity=0.106  Sum_probs=67.1

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+.+|||+|||..+  ++++|+++|+.||.|.+|+|++|+.+|.++|||||+|.+.++|++|++.|||..|+||
T Consensus         6 ~~~~l~V~nL~~~~--t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~   77 (88)
T d1rk8a_           6 EGWILFVTSIHEEA--QEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQ   77 (88)
T ss_dssp             -CEEEEEESCCTTC--CHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCEEEEeCCCCCC--CHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCE
Confidence            46789999997655  7899999999999999999999999999999999999999999999999999999985

>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=99.82  E-value=2.9e-20  Score=122.09  Aligned_cols=78  Identities=23%  Similarity=0.436  Sum_probs=73.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC--eEeEE
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG--LQVRL   86 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g--~~l~v   86 (227)
                      ...++|||+|||.++++++|+++|++| +|..++|++++.+++++|||||+|.+.++|.+||+ +|+ ..+.|  ++|.|
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g-~~~~g~~~~l~V   82 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNN-VIPEGGSQPLSV   82 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT-CCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCC-CEeCCCCeEEEE
Confidence            456789999999999999999999999 99999999999999999999999999999999999 999 88876  88999


Q ss_pred             Eec
Q psy1680          87 DIA   89 (227)
Q Consensus        87 ~~~   89 (227)
                      ++|
T Consensus        83 ~~A   85 (85)
T d1b7fa2          83 RLA   85 (85)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            886

>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=8.5e-21  Score=121.61  Aligned_cols=74  Identities=24%  Similarity=0.413  Sum_probs=70.8

Q ss_pred             eEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEec
Q psy1680          15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA   89 (227)
Q Consensus        15 ~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~   89 (227)
                      +|||+|||+++|+++|+++|++| +|..+.|++++.+++++|||||+|.+.++|++||++++ ..|+|+.|.|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~-~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKE-HKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCC-CCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCC-CEECCCEEEeeEC
Confidence            59999999999999999999999 99999999999999999999999999999999999988 8999999998754

>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=99.82  E-value=1.4e-20  Score=125.60  Aligned_cols=72  Identities=18%  Similarity=0.204  Sum_probs=67.7

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||..+  ++++|+++|++||.|.+|+|++|+.||.++|||||+|.+.++|.+|++.|||..|+||
T Consensus         8 ~~~tlfV~nLp~~~--t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~   79 (93)
T d1x5ua1           8 QDATVYVGGLDEKV--SEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGK   79 (93)
T ss_dssp             TTTEEEEECCCTTC--CHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSC
T ss_pred             CCCEEEEeCCCCcC--CHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCE
Confidence            45689999997665  7899999999999999999999999999999999999999999999999999999986

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=5.9e-21  Score=123.98  Aligned_cols=69  Identities=19%  Similarity=0.224  Sum_probs=65.6

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .|||+|||+.+  ++++|+++|++||.|.+|+|++|+.||.++|||||+|.++++|.+|++.|||..|+||
T Consensus         2 slfV~nL~~~~--te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr   70 (80)
T d1cvja1           2 SLYVGDLHPDV--TEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGK   70 (80)
T ss_dssp             EEEEESCCTTC--CHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTE
T ss_pred             EEEEeCCCCcC--CHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCE
Confidence            58999997655  8999999999999999999999999999999999999999999999999999999986

>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=99.82  E-value=1e-20  Score=126.33  Aligned_cols=73  Identities=14%  Similarity=0.136  Sum_probs=68.4

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .++.+|||+|||+.+  ++++|+++|++||.|.+|.|++++.++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus         5 ~~s~tlfV~nlp~~~--te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr   77 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYT--TEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDR   77 (93)
T ss_dssp             TTCCEEEEESCCTTC--CHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            357799999997655  7999999999999999999999999999999999999999999999999999999986

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.82  E-value=7.4e-21  Score=124.15  Aligned_cols=71  Identities=15%  Similarity=0.195  Sum_probs=66.6

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .++|||+|||+.+  ++++|+++|++||.|.+|+|++++.+|.++|||||+|.+.++|++|++.|||..|+||
T Consensus         2 ~t~l~V~nLp~~~--t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~   72 (82)
T d1b7fa1           2 NTNLIVNYLPQDM--TDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNK   72 (82)
T ss_dssp             CSEEEEECCCTTC--CHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCEEEEeCCCCCC--CHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCE
Confidence            4579999997665  7899999999999999999999999999999999999999999999999999999885

>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=99.82  E-value=3e-20  Score=124.28  Aligned_cols=84  Identities=24%  Similarity=0.414  Sum_probs=77.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecC-CCCCeecEEEEEeCCHHHHHHHHH-h-CCCceeCCeEeE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDK-ETDRFKGFCYVEFVDVENLRQALL-K-DGRITVDGLQVR   85 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~-~~~~~~g~afv~f~~~~~a~~al~-~-~~~~~~~g~~l~   85 (227)
                      ..++.+|||+|||+++++++|+++|++| .|..+.|++++ .+|+++|||||+|.+.++|.+||. | ++ ..++|++|.
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~-~~~~Gr~l~   83 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHS-THLYGRRLV   83 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTC-CBSSSCBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCC-cEECCEEEE
Confidence            4567899999999999999999999999 99999999875 478999999999999999999998 7 89 999999999


Q ss_pred             EEecCCCCC
Q psy1680          86 LDIADGKRN   94 (227)
Q Consensus        86 v~~~~~~~~   94 (227)
                      |.++.+...
T Consensus        84 V~~A~~~~~   92 (94)
T d2cpha1          84 LEWADSEVT   92 (94)
T ss_dssp             EEECCCCCC
T ss_pred             EEEcCCCCC
Confidence            999987543

>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=99.82  E-value=1.5e-20  Score=123.48  Aligned_cols=71  Identities=10%  Similarity=0.149  Sum_probs=66.6

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..+|||+|||+.+  ++++|+++|++||.|.+|+|++|+.+|.++|||||+|.+.++|.+|++.|||..++|+
T Consensus         6 ~~~lfV~nLp~~~--te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~   76 (85)
T d1fxla2           6 DANLYVSGLPKTM--TQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA   76 (85)
T ss_dssp             TCEEEEESCCTTC--CHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             CCEEEEeCCCCCC--CHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCC
Confidence            4579999997665  7999999999999999999999999999999999999999999999999999999985

>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=99.82  E-value=5.3e-20  Score=119.14  Aligned_cols=76  Identities=20%  Similarity=0.449  Sum_probs=73.1

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEec
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA   89 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~   89 (227)
                      .++|||+|||+++|+++|+++|++| .+..+.++.++.++.++|||||+|.+.+++.+|+++++ ..|+|+.|+|+.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~-~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY-HTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSC-CEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCC-CEECCEEEEEEEC
Confidence            4799999999999999999999999 99999999999999999999999999999999999999 9999999999876

>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=99.82  E-value=3.9e-21  Score=130.18  Aligned_cols=79  Identities=28%  Similarity=0.503  Sum_probs=75.5

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEecCC
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~~~   91 (227)
                      .++|||+|||+++++++|+++|+.| .|..|.|++++.+|+++|||||+|.+.++|.+|+++++ ..|+|+.|.|.++.+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g-~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTG-QRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTT-EEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCC-CEECCEEEEEEECCC
Confidence            4789999999999999999999999 99999999999999999999999999999999999999 999999999999865


Q ss_pred             C
Q psy1680          92 K   92 (227)
Q Consensus        92 ~   92 (227)
                      +
T Consensus        97 ~   97 (101)
T d2cq4a1          97 E   97 (101)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=99.82  E-value=1.8e-20  Score=124.37  Aligned_cols=73  Identities=21%  Similarity=0.251  Sum_probs=68.0

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||...  ++++|+++|+.||.|.+|.|++|+.+|.++|||||+|.+.++|.+|++.|||..|+||
T Consensus         6 ~~~~~i~V~nLp~~~--t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~   78 (90)
T d2cq0a1           6 DDNATIRVTNLSEDT--RETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHL   78 (90)
T ss_dssp             SSSEEEEEESCCTTC--CHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTE
T ss_pred             CCCCEEEEECCCCCC--CHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCE
Confidence            356789999997665  7999999999999999999999999999999999999999999999999999999985

>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=99.82  E-value=3.5e-20  Score=121.63  Aligned_cols=77  Identities=21%  Similarity=0.421  Sum_probs=72.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC--eEeEEE
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG--LQVRLD   87 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g--~~l~v~   87 (227)
                      ..++|||+|||+.+|+++|+++|++| +|.++.|++++.+++++|||||+|.+.++|.+|++ ||+ ..+.|  ++|.|.
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng-~~~~G~~~~i~V~   83 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG-QKPSGATEPITVK   83 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT-CCCTTCSSCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCC-CEeCCCCEEEEEE
Confidence            45789999999999999999999999 99999999999999999999999999999999998 999 99987  468888


Q ss_pred             ec
Q psy1680          88 IA   89 (227)
Q Consensus        88 ~~   89 (227)
                      +|
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=2.1e-20  Score=126.94  Aligned_cols=73  Identities=19%  Similarity=0.160  Sum_probs=68.6

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +++.+|||+|||+.+  ++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|.+||+.|||..|+||
T Consensus        16 p~~~~l~V~nLp~~~--te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~   88 (102)
T d2cpza1          16 PEGANLFIYHLPQEF--GDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMK   88 (102)
T ss_dssp             STTCCEEEESCCSSC--CHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCE
Confidence            567789999997666  7899999999999999999999999999999999999999999999999999999985

>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=99.82  E-value=2.4e-20  Score=121.97  Aligned_cols=78  Identities=19%  Similarity=0.355  Sum_probs=73.0

Q ss_pred             EEEcCCCCCCCHHHHHhcccCC-CeEEE-EEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecCCC
Q psy1680          16 AFVGNLPNGITQGDVERFFPEQ-KLVSV-RLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIADGK   92 (227)
Q Consensus        16 l~V~nLp~~~t~~~l~~~f~~~-~i~~v-~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~~~   92 (227)
                      |||+|||+++|+++|+++|++| .|..+ .|++++.+++++|||||+|.+.++|.+||+ +++ ..++|++|+|.++.++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g-~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNG-QYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTT-CEETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCC-cEECCEEEEEEEecCC
Confidence            7999999999999999999999 88664 789999999999999999999999999998 999 9999999999999876


Q ss_pred             CC
Q psy1680          93 RN   94 (227)
Q Consensus        93 ~~   94 (227)
                      ..
T Consensus        80 ~~   81 (83)
T d1x5ta1          80 DS   81 (83)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>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=99.82  E-value=1.8e-20  Score=122.04  Aligned_cols=78  Identities=14%  Similarity=0.322  Sum_probs=67.9

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecC
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~   90 (227)
                      .++|||+|||+++|+++|+++|++| .|..+.++.+..+++++|||||+|.+.++|.+|++ +|+ ..++|++|.|+++.
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g-~~~~g~~i~V~~a~   79 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNG-LKIEGYTLVTKVSN   79 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTT-CEETTEECEEEECC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCC-CEECCEEEEEEEcc
Confidence            3799999999999999999999999 99888888888889999999999999999999998 999 99999999999997


Q ss_pred             C
Q psy1680          91 G   91 (227)
Q Consensus        91 ~   91 (227)
                      |
T Consensus        80 P   80 (81)
T d2ghpa1          80 P   80 (81)
T ss_dssp             C
T ss_pred             C
Confidence            6

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=6.2e-20  Score=121.75  Aligned_cols=83  Identities=23%  Similarity=0.460  Sum_probs=75.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      +..+.++|||+|||.++|+++|+++|++| +|..+.|+.++.++  ++||||+|.+.++|..|+. +++ ..|.|+.|+|
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~-~~~~g~~i~v   80 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNG-RKILGKEVKV   80 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTT-EEETTEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCC-CEECCEEEEE
Confidence            34567899999999999999999999999 99999999987654  7899999999999999999 999 9999999999


Q ss_pred             EecCCCCC
Q psy1680          87 DIADGKRN   94 (227)
Q Consensus        87 ~~~~~~~~   94 (227)
                      .++.++..
T Consensus        81 ~~a~~~~~   88 (90)
T d2cqia1          81 NWATTPSS   88 (90)
T ss_dssp             EECCCTTC
T ss_pred             EEcCCCCC
Confidence            99987654

>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=99.81  E-value=8.8e-21  Score=129.39  Aligned_cols=82  Identities=33%  Similarity=0.534  Sum_probs=77.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      .+.++|||+|||+++++++|+++|++| .|..|.|++++.+++++|||||+|.+.++|.+||+ +++ ..|.|+.|.|.+
T Consensus         6 ~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~-~~~~g~~i~V~~   84 (104)
T d1p1ta_           6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNG-REFSGRALRVDN   84 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSS-BSCSSSCBEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCC-CEECCEEEEEEE
Confidence            345789999999999999999999999 99999999999999999999999999999999998 999 999999999999


Q ss_pred             cCCCC
Q psy1680          89 ADGKR   93 (227)
Q Consensus        89 ~~~~~   93 (227)
                      +.++.
T Consensus        85 a~~~~   89 (104)
T d1p1ta_          85 AASEK   89 (104)
T ss_dssp             TTCTT
T ss_pred             CCCCC
Confidence            87654

>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=99.81  E-value=7.3e-21  Score=126.07  Aligned_cols=72  Identities=15%  Similarity=0.152  Sum_probs=67.7

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..++|||+|||..+  ++++|+++|++||.|.+|.|++|+.+|.++|||||+|.+.++|.+|++.|||..|+||
T Consensus         4 ~~~tlfV~nLp~~~--te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~   75 (89)
T d2cqba1           4 TKRVLYVGGLAEEV--DDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGR   75 (89)
T ss_dssp             CCSCEEEESCCSSC--CHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTE
T ss_pred             CCcEEEEeCCCCcC--CHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCE
Confidence            46799999997665  7999999999999999999999999999999999999999999999999999999985

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=2e-20  Score=122.82  Aligned_cols=70  Identities=21%  Similarity=0.235  Sum_probs=66.1

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+|||+|||..+  ++++|+++|++||.|.+|+|++|+.||.++|||||+|.++++|.+|++.|||..|+||
T Consensus         2 ~rlfV~nlp~~~--te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~   71 (85)
T d2u2fa_           2 HKLFIGGLPNYL--NDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK   71 (85)
T ss_dssp             CCEEEETCCSSC--CSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSS
T ss_pred             CEEEEECCCCCC--CHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            369999997666  7899999999999999999999999999999999999999999999999999999986

>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=99.81  E-value=8.1e-20  Score=123.19  Aligned_cols=87  Identities=23%  Similarity=0.381  Sum_probs=79.0

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hC------CCce
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KD------GRIT   78 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~------~~~~   78 (227)
                      |....+.++|||+|||+++|+++|+++|++| .+..+.++.++.++.++|||||+|.+.++|.+||+ ++      + ..
T Consensus         2 P~~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g-~~   80 (98)
T d1x4ha1           2 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGG-LK   80 (98)
T ss_dssp             CCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCC-EE
T ss_pred             ccCCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCC-cE
Confidence            3345667899999999999999999999999 99999999999999999999999999999999998 75      6 78


Q ss_pred             eCCeEeEEEecCCCCC
Q psy1680          79 VDGLQVRLDIADGKRN   94 (227)
Q Consensus        79 ~~g~~l~v~~~~~~~~   94 (227)
                      ++|+.|+|.++.++..
T Consensus        81 ~~gr~l~v~~a~~k~~   96 (98)
T d1x4ha1          81 LDGRQLKVDLAVTRDE   96 (98)
T ss_dssp             SSSCEEEEECCCCCCC
T ss_pred             ECCEEEEEEECCCCCc
Confidence            9999999999987654

>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=99.81  E-value=2.2e-19  Score=122.34  Aligned_cols=88  Identities=38%  Similarity=0.744  Sum_probs=77.2

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeec-CCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeE
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKD-KETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVR   85 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~-~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~   85 (227)
                      ..+..+.++|||+|||+++|+++|+++|++|.+..+.++.+ ..+++++|||||+|.+.++|++|+++|+ ..|+|+.|+
T Consensus         9 ~~p~~p~~~v~V~nLp~~~te~~l~~~f~~~g~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~-~~~~gr~l~   87 (104)
T d1wi8a_           9 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNE-ESLGNKRIR   87 (104)
T ss_dssp             CCCSSSCEEEEEESCCSSCCHHHHHHHTTTSCEEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGT-CEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCcCCHHHHHHHHHHhccccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCC-CEECCEEEE
Confidence            34566789999999999999999999999997667777665 4578999999999999999998888999 999999999


Q ss_pred             EEecCCCCCC
Q psy1680          86 LDIADGKRND   95 (227)
Q Consensus        86 v~~~~~~~~~   95 (227)
                      |.++.++...
T Consensus        88 V~~a~~~~~~   97 (104)
T d1wi8a_          88 VDVADQAQDK   97 (104)
T ss_dssp             EEECCCCCCC
T ss_pred             EEECCCCCCC
Confidence            9999876654

>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=7.5e-21  Score=121.64  Aligned_cols=74  Identities=23%  Similarity=0.480  Sum_probs=70.6

Q ss_pred             eEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEec
Q psy1680          15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA   89 (227)
Q Consensus        15 ~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~   89 (227)
                      +|||+|||+++|+++|+++|++| +|..+.|++++.+++++|||||+|.+.++|++||+.++ ..++|+.|.|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~-~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKY-HNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSS-CCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCC-CEECCEEeEEEEC
Confidence            69999999999999999999999 99999999999999999999999999999999999887 8899999999864

>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=99.81  E-value=3.1e-20  Score=121.17  Aligned_cols=70  Identities=17%  Similarity=0.259  Sum_probs=65.9

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+|||+|||..+  ++++|+++|++||.|.+|+|++|+.++.++|||||+|.+.++|++|++.|||..|+||
T Consensus         3 t~l~V~nLp~~~--te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~   72 (82)
T d1fxla1           3 TNLIVNYLPQNM--TQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTK   72 (82)
T ss_dssp             SEEEEESCCTTC--CHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CEEEEECCCCCC--CHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            469999997665  7899999999999999999999999999999999999999999999999999999985

>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=99.81  E-value=5.4e-20  Score=118.73  Aligned_cols=74  Identities=23%  Similarity=0.413  Sum_probs=70.9

Q ss_pred             eEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecC
Q psy1680          15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        15 ~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~   90 (227)
                      +|||+|||+++++++|+++|++| .|..+.|+.++ +++++|||||+|.+.++|.+|++ +|+ ..++|++|+|+++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g-~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNG-VPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTT-CEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCC-CEECCEEEEEEEee
Confidence            69999999999999999999999 99999999985 68999999999999999999998 999 99999999999975

>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=99.81  E-value=3.3e-20  Score=118.80  Aligned_cols=68  Identities=19%  Similarity=0.232  Sum_probs=63.4

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +|||+|||+..  ++++|+++|++||.|.+|.|++|+.|++++|||||+|.+.++|++||+ +++..|+||
T Consensus         1 klfV~nl~~~~--te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr   68 (75)
T d1hd0a_           1 KMFIGGLSWDT--TKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGK   68 (75)
T ss_dssp             CEEEECCCTTC--CHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTB
T ss_pred             CEEEeCCCCcC--CHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCC
Confidence            48999997655  899999999999999999999999999999999999999999999997 688899986

>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=99.81  E-value=5e-20  Score=123.14  Aligned_cols=73  Identities=18%  Similarity=0.210  Sum_probs=66.6

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCC-CCcccceEEEEEcCHHHHHHHHHHc-CCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKE-TDRFKGFCYVEFVDVENLRQALLKD-GRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~-t~~~~g~afV~F~~~~~a~~Al~~l-~g~~i~gr  227 (227)
                      .++.+|||+|||..+  ++++|+++|+.||.|.+|+|++++. +|.++|||||+|.+.++|.+|++.| ||..|+||
T Consensus         6 ~~~~~l~V~nLp~~~--~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr   80 (94)
T d2cpha1           6 QTTSKILVRNIPFQA--NQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGR   80 (94)
T ss_dssp             SCCCCEEEESCCTTC--CHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSC
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCE
Confidence            456789999997655  7999999999999999999998854 7899999999999999999999998 99999986

>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=99.81  E-value=3.4e-20  Score=125.26  Aligned_cols=72  Identities=21%  Similarity=0.180  Sum_probs=67.4

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+.+|||+|||+.+  ++++|+++|++||.|.+|+|++|+.++.++|||||+|.+.++|.+||+.|||..|+||
T Consensus         7 ~~~~lfV~nL~~~~--t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr   78 (99)
T d1whwa_           7 GSGRLFVRNLSYTS--SEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGR   78 (99)
T ss_dssp             SCEEEEEECCCTTC--CHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSC
T ss_pred             CCCEEEEECCCCcC--CHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCE
Confidence            45679999997655  7999999999999999999999999999999999999999999999999999999986

>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=99.80  E-value=1.4e-20  Score=121.11  Aligned_cols=68  Identities=18%  Similarity=0.240  Sum_probs=63.9

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +|||+|||++.  ++++|+++|++||.|.+|+|++|+.||+++|||||+|.+.++|.+||+ +++..|+||
T Consensus         2 klfV~nLp~~~--te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr   69 (77)
T d1uawa_           2 KMFIGGLSWQT--TQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSK   69 (77)
T ss_dssp             CEEEESCCSSC--CSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSC
T ss_pred             EEEEeCCCCcC--CHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCe
Confidence            69999997665  789999999999999999999999999999999999999999999997 699999997

>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=99.80  E-value=1e-19  Score=119.39  Aligned_cols=76  Identities=28%  Similarity=0.422  Sum_probs=70.7

Q ss_pred             EEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCC---CeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecC
Q psy1680          16 AFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETD---RFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        16 l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~---~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~   90 (227)
                      |||+|||+++|+++|+++|++| +|..+.|++++.++   +++|||||+|.+.++|.+||+ +|+ ..++|+.|.|+++.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~-~~~~g~~i~V~~a~   79 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQG-HTVDGHKLEVRISE   79 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTT-CEETTEECEEECSS
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCC-CEECCEEEEEEECC
Confidence            7999999999999999999999 99999999887665   578999999999999999998 999 99999999999986


Q ss_pred             CC
Q psy1680          91 GK   92 (227)
Q Consensus        91 ~~   92 (227)
                      .+
T Consensus        80 ~~   81 (85)
T d2cpfa1          80 RA   81 (85)
T ss_dssp             CS
T ss_pred             CC
Confidence            43

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.80  E-value=7.1e-20  Score=120.18  Aligned_cols=71  Identities=15%  Similarity=0.259  Sum_probs=66.1

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      ...+|||+|||..+  ++++|+++|++||.|.+|+|++|+.+|.++|||||+|.+.++|.+|++.|||..++|
T Consensus         5 ~~t~lfV~nlp~~~--te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   75 (85)
T d1b7fa2           5 KDTNLYVTNLPRTI--TDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEG   75 (85)
T ss_dssp             TTCEEEEESCCTTC--CHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTT
T ss_pred             CCCEEEEeCCCCCC--CHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCC
Confidence            35579999997655  899999999999999999999999999999999999999999999999999999876

>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=99.80  E-value=2.9e-19  Score=128.12  Aligned_cols=72  Identities=17%  Similarity=0.138  Sum_probs=67.6

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..++|||+|||+++  ++++|+++|+.||.|.+|.|++|+.||.++|||||+|.+.++|.+||+.|||..|+||
T Consensus        41 ~~~~l~V~nLp~~~--te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr  112 (139)
T d1u6fa1          41 VLRNLMVNYIPTTV--DEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNK  112 (139)
T ss_dssp             TTSEEEEESCSTTC--CHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSC
T ss_pred             CCCEEEEeCCCCCC--CHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCE
Confidence            34679999997665  7899999999999999999999999999999999999999999999999999999997

>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=99.80  E-value=3.6e-19  Score=118.71  Aligned_cols=83  Identities=22%  Similarity=0.401  Sum_probs=75.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      .....++|||+|||+++++++|+++|++| +|..|.++.++.  .++|||||+|.+.++|.+||+ +|+ ..|+|+.|.|
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~-~~~~g~~l~V   83 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHG-TVVEGRKIEV   83 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTT-CEETTEECEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCC-CEECCEEEEE
Confidence            45567899999999999999999999999 999999998864  368999999999999999998 999 9999999999


Q ss_pred             EecCCCCC
Q psy1680          87 DIADGKRN   94 (227)
Q Consensus        87 ~~~~~~~~   94 (227)
                      .++.++..
T Consensus        84 ~~A~~r~~   91 (93)
T d2cq3a1          84 NNATARVM   91 (93)
T ss_dssp             EECCSSCC
T ss_pred             EecCcCCC
Confidence            99987653

>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=99.80  E-value=1.9e-20  Score=127.65  Aligned_cols=71  Identities=27%  Similarity=0.280  Sum_probs=67.0

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .++|||+|||..+  ++++|+++|++||.|.+|+|++++.||+++|||||+|.+.++|.+|++.|||..|+||
T Consensus         8 ~rtl~V~nLp~~~--te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~   78 (104)
T d1p1ta_           8 LRSVFVGNIPYEA--TEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGR   78 (104)
T ss_dssp             HSCEEEESCCTTS--CHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSS
T ss_pred             CCEEEEECCCCcC--CHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCE
Confidence            4689999997655  7999999999999999999999999999999999999999999999999999999986

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=8.5e-20  Score=120.86  Aligned_cols=71  Identities=18%  Similarity=0.200  Sum_probs=63.4

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ....+|||+|||+++  ++++|+++|+.||.|.+|+|++|+.||.++|||||+|.+.++|.+||+.+  ..|+||
T Consensus         6 ~~~~~lfV~nLp~~~--te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~--~~l~Gr   76 (90)
T d2cqga1           6 QKTSDLIVLGLPWKT--TEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMIDGR   76 (90)
T ss_dssp             CCCCCEEEESCCSSC--CHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEETTE
T ss_pred             cCCCeEEEECCCCCC--CHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--CccCCE
Confidence            346789999997655  79999999999999999999999999999999999999999999999853  467764

>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=99.79  E-value=2.7e-19  Score=121.25  Aligned_cols=86  Identities=23%  Similarity=0.323  Sum_probs=77.6

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-Ce--------EEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCc
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KL--------VSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRI   77 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i--------~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~   77 (227)
                      .......+|||+|||..+|+++|+++|++| .|        ..+.+..++.+++++|||||+|.+.++|..||+ +++ .
T Consensus         3 ~~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g-~   81 (101)
T d2cpea1           3 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDG-K   81 (101)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTT-C
T ss_pred             CCCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCC-C
Confidence            345677999999999999999999999998 76        356778888899999999999999999999999 999 9


Q ss_pred             eeCCeEeEEEecCCCCC
Q psy1680          78 TVDGLQVRLDIADGKRN   94 (227)
Q Consensus        78 ~~~g~~l~v~~~~~~~~   94 (227)
                      .|+|+.|+|.++.++..
T Consensus        82 ~~~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          82 DFQGSKLKVSLARKKPP   98 (101)
T ss_dssp             EETTEECEEECSSCCCC
T ss_pred             EECCEEEEEEEcCCCCC
Confidence            99999999999987654

>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=99.79  E-value=1.6e-19  Score=119.50  Aligned_cols=80  Identities=20%  Similarity=0.328  Sum_probs=73.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      ...+|||+|||+++++++|+++|++| .|..+.|+.++.  .++|||||+|.+.++|++||+ +|+ ..|+|+.|.|.++
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g-~~~~g~~i~V~~a   83 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNG-MLLNDRKVFVGRF   83 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSE-EEETTEEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCC-CEECCEEEEEEEC
Confidence            34689999999999999999999999 999999998864  468999999999999999998 999 9999999999999


Q ss_pred             CCCCC
Q psy1680          90 DGKRN   94 (227)
Q Consensus        90 ~~~~~   94 (227)
                      .+++.
T Consensus        84 ~~~~~   88 (89)
T d1cvja2          84 KSRKE   88 (89)
T ss_dssp             CCTTT
T ss_pred             CCCCC
Confidence            87654

>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=3.9e-20  Score=117.62  Aligned_cols=68  Identities=19%  Similarity=0.250  Sum_probs=64.5

Q ss_pred             ceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         158 GFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       158 l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      |||+|||...  ++++|+++|++||.|..+++.+++.++.++|+|||+|.+.++|.+|++.|||..|+||
T Consensus         1 lyV~nLp~~~--te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr   68 (72)
T d1x4ea1           1 LYIRGLQPGT--TDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQ   68 (72)
T ss_dssp             EEEESCCTTC--CHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEE
T ss_pred             CEEeCCCCcC--CHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCE
Confidence            7999996655  7999999999999999999999999999999999999999999999999999999986

>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=99.79  E-value=6.9e-20  Score=117.40  Aligned_cols=74  Identities=27%  Similarity=0.372  Sum_probs=71.3

Q ss_pred             eEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEec
Q psy1680          15 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA   89 (227)
Q Consensus        15 ~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~   89 (227)
                      +|||+|||+++|+++|+++|++| .+..+.++.++.++.+++||||+|.+.++|++||++++ ..|+|+.|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~-~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHF-HEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSS-CCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHhcCC-CEECCeEEEEEEC
Confidence            59999999999999999999999 99999999999999999999999999999999999999 9999999999875

>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=99.79  E-value=7.8e-20  Score=119.59  Aligned_cols=70  Identities=21%  Similarity=0.235  Sum_probs=64.7

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .++|||+|||.++  ++++|+++|+.||.|.+|+|++|+.||.++|||||+|.+.++|.+|++. ++..|+||
T Consensus         6 ~~~lfV~nlp~~~--te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~-~~~~i~Gr   75 (84)
T d1l3ka1           6 LRKLFIGGLSFET--TDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGR   75 (84)
T ss_dssp             GGEEEEESCCTTC--CHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTE
T ss_pred             CcEEEEECCCCCC--CHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHh-CCCEECCE
Confidence            4689999997666  7999999999999999999999999999999999999999999999975 78889886

>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=99.79  E-value=5.2e-20  Score=124.57  Aligned_cols=70  Identities=21%  Similarity=0.292  Sum_probs=65.2

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .++|||+|||..+  ++++|+++|+.||.|.+|+|++|+.+|.++|||||+|.+.++|.+|++ |||..|+||
T Consensus        18 ~~tifV~nL~~~~--te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~   87 (101)
T d2cq4a1          18 ARTVFCMQLAARI--RPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGV   87 (101)
T ss_dssp             HTEEEEESCCTTC--CHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTE
T ss_pred             CCEEEEECCCCCC--CHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCE
Confidence            4689999996655  899999999999999999999999999999999999999999999995 999999985

>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=99.79  E-value=1.1e-19  Score=123.60  Aligned_cols=71  Identities=13%  Similarity=0.148  Sum_probs=64.9

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||..+  ++++|+++|++||.|.+|+|++|+.||.++|||||+|.+.++|.+|++.+|+ .|+||
T Consensus         9 ~~~~lfV~nLp~~~--te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr   79 (103)
T d2cqda1           9 TFTKIFVGGLPYHT--TDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGR   79 (103)
T ss_dssp             SSSEEEEECCCSSC--CHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTE
T ss_pred             CCcEEEEeCCCCcC--cHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCE
Confidence            34569999997655  8999999999999999999999999999999999999999999999999986 68885

>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=99.79  E-value=3.2e-20  Score=118.67  Aligned_cols=68  Identities=19%  Similarity=0.299  Sum_probs=62.0

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +|||+|||++.  ++++|+++|++||.|.+|+|++|+.|++++|||||+|.+.++|++||+. ++.+|+|+
T Consensus         1 klfVgnLp~~~--te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~-~~~~i~g~   68 (75)
T d1x0fa1           1 KIFVGGLSPDT--PEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLS   68 (75)
T ss_dssp             EEEEESCCSSC--CHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTB
T ss_pred             CEEEcCCCCCC--CHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECCE
Confidence            48999997655  8999999999999999999999999999999999999999999999975 66778875

>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=99.79  E-value=8.6e-20  Score=117.75  Aligned_cols=68  Identities=21%  Similarity=0.150  Sum_probs=63.8

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +|||+|||+.+  ++++|+++|++||.|.+|+|++++ +|+++|||||+|.+.++|.+|++.|||..|+||
T Consensus         2 rl~V~nLp~~~--~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~   69 (78)
T d1no8a_           2 KLLVSNLDFGV--SDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGR   69 (78)
T ss_dssp             EEEEESCCTTC--CHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             EEEEECCCCCC--CHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            58999997665  799999999999999999999995 699999999999999999999999999999986

>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=99.79  E-value=1.2e-19  Score=119.20  Aligned_cols=80  Identities=14%  Similarity=0.206  Sum_probs=70.6

Q ss_pred             CCceEEEcCCCCCCC-HHHHHhcccCC-CeEEEEEeec-CCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEe
Q psy1680          12 PPYTAFVGNLPNGIT-QGDVERFFPEQ-KLVSVRLVKD-KETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDI   88 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t-~~~l~~~f~~~-~i~~v~i~~~-~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~   88 (227)
                      ..++|||+|||++++ +++|+++|++| .|..+.|+.+ +.+++++|||||+|.+.++|.+||++|+ ..|+|+.|+|.+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~-~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNR-SLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTT-EEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCC-CEECCEEEEEEE
Confidence            468999999999976 56699999999 9999998764 6789999999999999999999999999 999999999999


Q ss_pred             cCCC
Q psy1680          89 ADGK   92 (227)
Q Consensus        89 ~~~~   92 (227)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9865

>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=99.78  E-value=1.1e-18  Score=118.70  Aligned_cols=87  Identities=16%  Similarity=0.141  Sum_probs=77.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLD   87 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~   87 (227)
                      .......|||+|||+++|+++|+++|..+ .+..+.++.+..+++++|||||+|.+.++|++||++++ ..|+|+.|+|.
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~-~~i~gR~i~V~   89 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHK-ERIGHRYIEIF   89 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTT-CCSSSSCCEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCC-CEEcceEEEEE
Confidence            44566789999999999999999999999 88777677777789999999999999999999999999 99999999999


Q ss_pred             ecCCCCCCC
Q psy1680          88 IADGKRNDN   96 (227)
Q Consensus        88 ~~~~~~~~~   96 (227)
                      ++.+++...
T Consensus        90 ~~~~~~~~~   98 (104)
T d1wg5a_          90 KSSRAEVRT   98 (104)
T ss_dssp             EECTTTSCC
T ss_pred             ECCHHHhcc
Confidence            998776543

>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=99.78  E-value=4.3e-20  Score=125.48  Aligned_cols=85  Identities=22%  Similarity=0.356  Sum_probs=79.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      +..++++|||+|||.++++++|+++|++| .|..+.++.+..+++++|||||+|.+.++|..||+ +|+ ..|.|++|.|
T Consensus        14 ~~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g-~~~~g~~l~V   92 (102)
T d2cpxa1          14 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNG-YKLYGKILVI   92 (102)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTT-CBCSSCBCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCC-CEECCEEEEE
Confidence            45678999999999999999999999999 99988888888889999999999999999999998 999 9999999999


Q ss_pred             EecCCCCC
Q psy1680          87 DIADGKRN   94 (227)
Q Consensus        87 ~~~~~~~~   94 (227)
                      .++.+++.
T Consensus        93 ~~ak~k~~  100 (102)
T d2cpxa1          93 EFGKNKKQ  100 (102)
T ss_dssp             EECCCCSC
T ss_pred             EeCCCccc
Confidence            99988664

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=7.7e-19  Score=119.08  Aligned_cols=86  Identities=21%  Similarity=0.255  Sum_probs=75.8

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLD   87 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~   87 (227)
                      ......++|||+|||+++|+++|+++|..+.+..+.++.+. ++.++|||||+|.+.++|++||++|+ ..|+|+.|+|.
T Consensus        10 ~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~~~~-~~i~gR~I~V~   87 (102)
T d1weza_          10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDK-ANMQHRYVELF   87 (102)
T ss_dssp             CCCSSSCEEEEESCCTTCCHHHHHHSSCSCCCSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSS-CCSSSSCCEEE
T ss_pred             CcCCCCCEEEEeCCCCcCCHHHHHHHHhccCcceeeeEEec-CCcceEEEEEEECCHHHHHHHHHcCC-CEECCEEEEEE
Confidence            35566789999999999999999999999955577777774 48899999999999999999999999 99999999999


Q ss_pred             ecCCCCCC
Q psy1680          88 IADGKRND   95 (227)
Q Consensus        88 ~~~~~~~~   95 (227)
                      ++.++...
T Consensus        88 ~s~~~~~~   95 (102)
T d1weza_          88 LNSTAGTS   95 (102)
T ss_dssp             EECCCCCC
T ss_pred             EcCCCCCC
Confidence            98876543

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=1.6e-19  Score=119.84  Aligned_cols=72  Identities=22%  Similarity=0.365  Sum_probs=67.3

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||+.+  ++++|+++|++||.|..|.++++..++.++|||||+|.+.++|++|++.|||..|+||
T Consensus         4 ~~~kifV~nLp~~~--t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~   75 (90)
T d1x5sa1           4 DEGKLFVGGLSFDT--NEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGR   75 (90)
T ss_dssp             CCSEEEEESCCTTC--CHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSC
T ss_pred             CCCEEEEECCCCcC--CHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            45679999997665  7899999999999999999999999999999999999999999999999999999986

>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=99.78  E-value=1.6e-19  Score=118.52  Aligned_cols=68  Identities=25%  Similarity=0.248  Sum_probs=62.7

Q ss_pred             ceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCC---cccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         158 GFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETD---RFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       158 l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~---~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      |||+|||..+  ++++|+++|++||.|.+|+|++++.++   .++|||||+|.+.++|.+|++.|||..|+||
T Consensus         1 LfV~nLp~~~--t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~   71 (85)
T d2cpfa1           1 LFIKNLNFST--TEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGH   71 (85)
T ss_dssp             EEEESCCTTC--CHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTE
T ss_pred             CEEcCCCCCC--CHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            7999997655  899999999999999999999988776   4799999999999999999999999999986

>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=99.78  E-value=1e-18  Score=114.45  Aligned_cols=77  Identities=14%  Similarity=0.365  Sum_probs=72.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEecC
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~~   90 (227)
                      ..++|||+|||.++|+++|+++|+.| .|..+.|+.++ +++++|||||+|.+.++|.+||++++ ..+.|+.|.|.+..
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~~~~-~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHTCCC-CEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHHHCC-CEECCEEEEEEEcC
Confidence            35799999999999999999999999 99999998874 78999999999999999999999999 99999999999864

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=1.3e-18  Score=116.38  Aligned_cols=80  Identities=26%  Similarity=0.470  Sum_probs=72.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ...+.++|||+|||+++|+++|+++|++| .|..+.+..+   ..+++||||+|.+.++|..||+ ||+ ..|.|++|+|
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g-~~~~g~~l~V   85 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDG-YDYDGYRLRV   85 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTT-CEETTEECEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCC-CEECCEEEEE
Confidence            45677899999999999999999999999 9999888654   4568999999999999999998 999 9999999999


Q ss_pred             EecCCC
Q psy1680          87 DIADGK   92 (227)
Q Consensus        87 ~~~~~~   92 (227)
                      .++++.
T Consensus        86 ~~a~~~   91 (95)
T d1x4aa1          86 EFPRSG   91 (95)
T ss_dssp             ECCCCC
T ss_pred             EeccCC
Confidence            998753

>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=99.77  E-value=4.4e-20  Score=122.63  Aligned_cols=84  Identities=25%  Similarity=0.434  Sum_probs=75.5

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeE
Q psy1680           7 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVR   85 (227)
Q Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~   85 (227)
                      ..+....++|||+|||+++|+++|+++|++| .|..+.|+.+ .+++++|||||+|.+.++|++||++++ ..++|+.|+
T Consensus         7 ~~~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~~~g-~~~~g~~i~   84 (91)
T d1fjeb1           7 GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALELTG-LKVFGNEIK   84 (91)
T ss_dssp             SSSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHHGGG-EEETTEEEE
T ss_pred             CCCCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHhcCC-cEECCEEEE
Confidence            3445667899999999999999999999999 8888887654 678999999999999999999999999 999999999


Q ss_pred             EEecCCC
Q psy1680          86 LDIADGK   92 (227)
Q Consensus        86 v~~~~~~   92 (227)
                      |.++..+
T Consensus        85 V~~ak~k   91 (91)
T d1fjeb1          85 LEKPKGR   91 (91)
T ss_dssp             EECCCCS
T ss_pred             EEecCCC
Confidence            9998764

>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=99.77  E-value=1.2e-19  Score=118.59  Aligned_cols=68  Identities=13%  Similarity=0.187  Sum_probs=62.9

Q ss_pred             ceeccCCCCCCCChhhHHhhhccccceEEE-EEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         158 GFRNNNGPNRSNSMNDHGLMVTEVTTLVSV-RLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       158 l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v-~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      |||+|||+.+  ++++|+++|++||.|..+ +|++|+.||+++|||||+|.+.++|.+|++.|+|..|+||
T Consensus         1 lfV~nLp~~~--te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr   69 (83)
T d1x5ta1           1 IFIGNLDPEI--DEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNR   69 (83)
T ss_dssp             EEEECCCTTC--CHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTE
T ss_pred             CEEcCCCCcC--cHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCE
Confidence            7999997655  799999999999998654 7999999999999999999999999999999999999986

>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=99.77  E-value=2.6e-19  Score=118.35  Aligned_cols=73  Identities=12%  Similarity=0.060  Sum_probs=65.0

Q ss_pred             CCCCcceeccCCCCCCCChhhH---HhhhccccceEEEEEeecCCCCcc---cceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDH---GLMVTEVTTLVSVRLVKDKETDRF---KGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l---~~~f~~~g~i~~v~i~~d~~t~~~---~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      ...++|||+|||+..  ++++|   .++|++||.|.+|.|++++.++.+   +|||||+|.+.++|.+|++.|||..|+|
T Consensus         6 iq~n~vyV~nLp~~~--t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~g   83 (89)
T d2cpia1           6 VQKNLVFVVGLSQRL--ADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG   83 (89)
T ss_dssp             CCSSCEEEEEECTTT--CCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             EecCEEEEECCCCcc--CHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECC
Confidence            346789999997766  67889   778999999999999999887765   4899999999999999999999999998


Q ss_pred             C
Q psy1680         227 L  227 (227)
Q Consensus       227 r  227 (227)
                      |
T Consensus        84 r   84 (89)
T d2cpia1          84 R   84 (89)
T ss_dssp             E
T ss_pred             E
Confidence            6

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=8.1e-19  Score=118.76  Aligned_cols=82  Identities=13%  Similarity=0.280  Sum_probs=74.1

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      ......++|||+|||+++++++|+++|++| .|..+.++.+ .++.++|||||+|.+.++|.+||+ +|| ..|.|+++.
T Consensus        13 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng-~~i~gr~~~   90 (101)
T d1x5oa1          13 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNG-KFIKTPPGV   90 (101)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBT-CCCCCCTTS
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCC-CEECCcCCc
Confidence            345667899999999999999999999999 9999998887 468999999999999999999998 999 999999988


Q ss_pred             EEecCC
Q psy1680          86 LDIADG   91 (227)
Q Consensus        86 v~~~~~   91 (227)
                      |.++.|
T Consensus        91 v~~~~P   96 (101)
T d1x5oa1          91 SAPTEP   96 (101)
T ss_dssp             CCCSSC
T ss_pred             cCCCCC
Confidence            877654

>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=99.77  E-value=4.5e-19  Score=114.69  Aligned_cols=69  Identities=14%  Similarity=0.272  Sum_probs=64.0

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++|||+|||+..  |+++|+++|+.||.|..+.++.++.++.++|||||+|.++++|.+|++ ++|..|+||
T Consensus         3 r~lfV~nLp~~~--te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr   71 (79)
T d1l3ka2           3 KKIFVGGIKEDT--EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGH   71 (79)
T ss_dssp             SEEEEECCTTTC--CHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTE
T ss_pred             CEEEECCCCCcC--CHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCE
Confidence            579999997655  899999999999999999999999999999999999999999999985 799999986

>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=99.77  E-value=1.4e-18  Score=120.18  Aligned_cols=80  Identities=20%  Similarity=0.291  Sum_probs=72.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      |.+.+++|||+|||..+++++|+++|++| .|..|.+..+   +.++|||||+|.+.++|..||+ ||| ..|.|+.|.|
T Consensus         3 pp~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g-~~~~gr~l~V   78 (114)
T d2f9da1           3 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSG-FNVCNRYLVV   78 (114)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTT-CEETTEECEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCC-CEECCEEEEE
Confidence            44567899999999999999999999999 9999999754   5668999999999999999998 999 9999999999


Q ss_pred             EecCCC
Q psy1680          87 DIADGK   92 (227)
Q Consensus        87 ~~~~~~   92 (227)
                      .++.+.
T Consensus        79 ~~a~~~   84 (114)
T d2f9da1          79 LYYNAN   84 (114)
T ss_dssp             EECCHH
T ss_pred             EEcCCC
Confidence            998653

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.6e-18  Score=117.33  Aligned_cols=71  Identities=10%  Similarity=0.127  Sum_probs=65.4

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||+++  ++++|+++|+.||.|..+.+..+ .++.++|||||+|.+.++|.+|++.|||..|.||
T Consensus        17 ~~~~lfV~nLp~~~--te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr   87 (101)
T d1x5oa1          17 DPTNLYISNLPLSM--DEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTP   87 (101)
T ss_dssp             CTTEEEEESCCTTC--CHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCC
T ss_pred             CCCEEEEeCCCCCC--CHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCc
Confidence            45689999997665  79999999999999999999998 4689999999999999999999999999999986

>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=99.76  E-value=2e-19  Score=116.97  Aligned_cols=70  Identities=11%  Similarity=0.193  Sum_probs=58.9

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+|||+|||+..  ++++|+++|++||.|..+.++++..+|.++|||||+|.+.++|.+|++.|||..|+||
T Consensus         2 ~tl~v~nLp~~~--t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~   71 (81)
T d2ghpa1           2 CTLWMTNFPPSY--TQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGY   71 (81)
T ss_dssp             CEEEEECCCTTC--CHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             cEEEEECCCCcC--CHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCE
Confidence            479999997666  7899999999999999999988888899999999999999999999999999999986

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=3.8e-19  Score=113.85  Aligned_cols=68  Identities=18%  Similarity=0.196  Sum_probs=63.7

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +|||+|||+++  ++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|++ +||..|+||
T Consensus         1 rlfV~nLp~~~--te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr   68 (75)
T d2msta_           1 KIFVGGLSVNT--TVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNK   68 (75)
T ss_dssp             CEEEECCCSSC--CHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTB
T ss_pred             CEEEeCCCCCC--CHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCe
Confidence            48999997655  899999999999999999999999999999999999999999999996 999999996

>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=99.76  E-value=1.8e-18  Score=115.28  Aligned_cols=71  Identities=18%  Similarity=0.148  Sum_probs=64.1

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ....+|||+|||+.+  ++++|+++|++||.|.+|.|+.++  +.++|||||+|.+.++|.+|++.|||..|+||
T Consensus         9 ~~~~~l~v~nLp~~~--t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~   79 (93)
T d2cq3a1           9 STPKRLHVSNIPFRF--RDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGR   79 (93)
T ss_dssp             CCCCEEEEESCCTTC--CHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEECCCCCC--CHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCE
Confidence            346689999997655  789999999999999999999986  44799999999999999999999999999986

>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=99.75  E-value=1.8e-18  Score=116.46  Aligned_cols=73  Identities=23%  Similarity=0.343  Sum_probs=65.7

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcC------CccccC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG------RITVDG  226 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~------g~~i~g  226 (227)
                      ....+|||+|||+.+  ++++|+++|++||.|.++.++.+..++.++|||||+|.+.++|.+|++.||      |..|+|
T Consensus         6 ~~~~tlfV~nLp~~~--te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDS--EEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCCCEEEESCCTTC--CHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCCEEEEcCCCCcC--CHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC
Confidence            456789999996655  899999999999999999999999999999999999999999999999987      566776


Q ss_pred             C
Q psy1680         227 L  227 (227)
Q Consensus       227 r  227 (227)
                      |
T Consensus        84 r   84 (98)
T d1x4ha1          84 R   84 (98)
T ss_dssp             C
T ss_pred             E
Confidence            5

>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=99.75  E-value=1.1e-18  Score=115.52  Aligned_cols=71  Identities=14%  Similarity=0.234  Sum_probs=64.0

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+.++|||+|||..+  ++++|+++|+.||.|.+|+|++|+.++  +|||||+|.+.++|.+|++.|+|..|+||
T Consensus         6 ~~~~tl~V~nLp~~~--te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~   76 (90)
T d2cqia1           6 GQPRTLYVGNLSRDV--TEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGK   76 (90)
T ss_dssp             CCCCEEEEESCCTTC--CHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCEEEEECCCCCC--CHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCE
Confidence            456799999997655  799999999999999999999987654  79999999999999999999999999885

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=5e-19  Score=120.01  Aligned_cols=70  Identities=16%  Similarity=0.205  Sum_probs=64.4

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..+|||+|||+.+  ++++|+++|++||.|..+.|++|+.++.++|||||+|.+.++|.+||+ ++|..|+||
T Consensus        20 ~~~lfVgnLp~~~--te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~   89 (103)
T d1x4ba1          20 FRKLFIGGLSFET--TEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGR   89 (103)
T ss_dssp             HTEEEEECCTTCC--CHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTE
T ss_pred             CCEEEEeCCCCcC--CHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCE
Confidence            3689999997666  799999999999999999999999999999999999999999999996 688889885

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.9e-19  Score=121.30  Aligned_cols=74  Identities=18%  Similarity=0.137  Sum_probs=68.7

Q ss_pred             CCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         152 GGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +.|+++|||+|||..+  ++++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        15 ~~ps~tl~V~nLp~~~--t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~   88 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRV--TERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGK   88 (102)
T ss_dssp             CSCCSEEEEECCCTTC--CHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSC
T ss_pred             CCCCCEEEEeCCCCCC--CHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCE
Confidence            3567899999997655  7899999999999999999999988999999999999999999999999999999986

>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=99.75  E-value=1.4e-18  Score=114.22  Aligned_cols=78  Identities=18%  Similarity=0.224  Sum_probs=68.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      +..+.|||+|||+++++++|+++|+.| .+....++.+..+++++|+|||+|.+.++|.+||+ +|+ ..++|++|+|.+
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~-~~l~gr~i~v~l   85 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLND-RPIGSRKVKLVL   85 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTT-CEETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCC-CEECCEEEEEEE
Confidence            446789999999999999999999999 77654444445779999999999999999999998 999 999999999987


Q ss_pred             c
Q psy1680          89 A   89 (227)
Q Consensus        89 ~   89 (227)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            4

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.75  E-value=2.8e-18  Score=115.01  Aligned_cols=81  Identities=25%  Similarity=0.399  Sum_probs=72.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEE
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRL   86 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v   86 (227)
                      ...+.++|||+|||+++|+++|+++|++| .|..+.     .++++++||||+|.+.++|..|++ +|+ ..|+|++|+|
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~-~~~~gr~i~V   85 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQG-AEIDGRSVSL   85 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTE-EEETTEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCC-CEECCEEEEE
Confidence            34567999999999999999999999999 776553     347889999999999999999998 999 9999999999


Q ss_pred             EecCCCCCC
Q psy1680          87 DIADGKRND   95 (227)
Q Consensus        87 ~~~~~~~~~   95 (227)
                      .++.++...
T Consensus        86 ~~a~~k~~~   94 (96)
T d1fjca_          86 YYTGEKGGT   94 (96)
T ss_dssp             EECSSSCCC
T ss_pred             EEeCCCCCC
Confidence            999987653

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1.3e-18  Score=120.47  Aligned_cols=69  Identities=12%  Similarity=0.044  Sum_probs=62.7

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+++|||+|||..+  ++++|+++|+.||.|.+|++..+   +.++|||||+|.+.++|..|++.|||..|+||
T Consensus         6 ~~r~l~V~nLp~~~--te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr   74 (114)
T d2f9da1           6 VNRILYIRNLPYKI--TAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNR   74 (114)
T ss_dssp             CCSEEEEESCCTTC--CHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCEEEEECCCCCC--CHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            45789999997655  79999999999999999999875   56799999999999999999999999999986

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=3.1e-18  Score=114.68  Aligned_cols=76  Identities=21%  Similarity=0.456  Sum_probs=70.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      +..++|||+|||..+++++|+++|++| .|..|+|+++      +|||||+|.+.++|..|+. +++ ..|.|+.|+|.|
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~-~~i~g~~l~v~~   88 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNG-TTIEGHVVKCYW   88 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTT-CEETTEECEEEC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCC-CEECCEEEEEEE
Confidence            456799999999999999999999999 9999999876      7899999999999999998 999 999999999999


Q ss_pred             cCCCC
Q psy1680          89 ADGKR   93 (227)
Q Consensus        89 ~~~~~   93 (227)
                      ++++.
T Consensus        89 ak~~p   93 (96)
T d1x4ga1          89 GKESP   93 (96)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            87643

>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=99.74  E-value=1e-17  Score=112.47  Aligned_cols=78  Identities=29%  Similarity=0.523  Sum_probs=69.4

Q ss_pred             CCCCCCceEEEcCCC-CCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEe
Q psy1680           8 LPTEPPYTAFVGNLP-NGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQV   84 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp-~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l   84 (227)
                      .+....++|||+||| ..+++++|+++|++| .|..+.|.        +|||||+|.+.++|.+||+ +|+ ..|.|+.|
T Consensus        10 ~~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng-~~~~g~~l   80 (98)
T d1wf2a_          10 DPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDG-RMIAGQVL   80 (98)
T ss_dssp             CCSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTT-CEETTEEC
T ss_pred             CCCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCC-CEECCEEE
Confidence            345666889999997 568889999999999 99999983        6899999999999999999 999 99999999


Q ss_pred             EEEecCCCCC
Q psy1680          85 RLDIADGKRN   94 (227)
Q Consensus        85 ~v~~~~~~~~   94 (227)
                      +|.++.+++.
T Consensus        81 ~V~~a~~~~~   90 (98)
T d1wf2a_          81 DINLAAEPKV   90 (98)
T ss_dssp             EEEETTSCCC
T ss_pred             EEEECCCCCC
Confidence            9999976544

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.74  E-value=7.3e-19  Score=115.48  Aligned_cols=72  Identities=14%  Similarity=0.073  Sum_probs=60.3

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeec-CCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKD-KETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d-~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+++|||+|||++.. .+++|+++|++||.|++|+|+++ ..++.++|||||+|.+.++|.+|++ |||..|+||
T Consensus         3 e~~~l~V~nLp~~~t-~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr   75 (86)
T d2ghpa3           3 EGREIMIRNLSTELL-DENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNR   75 (86)
T ss_dssp             TTTEEEEEEECTTTC-CHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTE
T ss_pred             CCCEEEEECCCCCcc-cHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCE
Confidence            357899999976653 35669999999999999998764 5678999999999999999999995 999999986

>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=99.74  E-value=2e-18  Score=115.75  Aligned_cols=83  Identities=18%  Similarity=0.275  Sum_probs=72.9

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-C-eEEEEEeecC-CCCCeecEEEEEeCCHHHHHHHHH-hCC-CceeCCeEeEEE
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-K-LVSVRLVKDK-ETDRFKGFCYVEFVDVENLRQALL-KDG-RITVDGLQVRLD   87 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~-i~~v~i~~~~-~~~~~~g~afv~f~~~~~a~~al~-~~~-~~~~~g~~l~v~   87 (227)
                      .++|||+|||.++++++|+++|++| + |..+.++++. .+++++|||||+|.+.++|..||+ +++ ...++|+.|.|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            4789999999999999999999999 6 8899999874 568999999999999999999998 753 156789999999


Q ss_pred             ecCCCCCC
Q psy1680          88 IADGKRND   95 (227)
Q Consensus        88 ~~~~~~~~   95 (227)
                      ++.++...
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99876653

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=1.2e-18  Score=110.54  Aligned_cols=69  Identities=23%  Similarity=0.411  Sum_probs=66.1

Q ss_pred             EEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680          16 AFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus        16 l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      |||+|||.++|+++|+++|++| .|..+.+++++.++.++|||||+|.+.++|++|++ +|| ..++|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng-~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA-SGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHH-HTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCC-CEECCEECc
Confidence            7999999999999999999999 99999999999999999999999999999999998 999 999998763

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.74  E-value=6e-18  Score=110.28  Aligned_cols=77  Identities=21%  Similarity=0.328  Sum_probs=69.3

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCcee-CCeEe
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITV-DGLQV   84 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~-~g~~l   84 (227)
                      .+.+|+++|||+|||.++|+++|+++|++| +|..+.+++++     +|||||+|.+.++|..|+. |+| ..+ +|++|
T Consensus         3 ~~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g-~~~~~~~~i   76 (83)
T d2b0ga1           3 TEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQG-FKITPTHAM   76 (83)
T ss_dssp             CCCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTT-CBSSTTCBC
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCC-cEeCCCcEE
Confidence            345678999999999999999999999999 99999998652     6899999999999999999 999 888 56899


Q ss_pred             EEEecC
Q psy1680          85 RLDIAD   90 (227)
Q Consensus        85 ~v~~~~   90 (227)
                      +|.+++
T Consensus        77 ~v~~ak   82 (83)
T d2b0ga1          77 KITFAK   82 (83)
T ss_dssp             EEEECC
T ss_pred             EEEEec
Confidence            999985

>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=99.74  E-value=1.3e-18  Score=112.63  Aligned_cols=75  Identities=19%  Similarity=0.431  Sum_probs=66.7

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecCC
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~~   91 (227)
                      ++|||+|||.++|+++|+++|++| .+..+.++..      +|||||+|.+.++|.+||+ +||...++|++|.|.++.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            479999999999999999999999 8877666543      7899999999999999998 9982369999999999998


Q ss_pred             CCC
Q psy1680          92 KRN   94 (227)
Q Consensus        92 ~~~   94 (227)
                      ++.
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            764

>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=99.74  E-value=5.6e-18  Score=111.10  Aligned_cols=75  Identities=29%  Similarity=0.429  Sum_probs=69.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          12 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      ..++|||+|||.++++++|+++|++| .|..+.++++      ++||||+|.+.++|.+|++ +|+ ..|+|+.|+|.++
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g-~~i~g~~l~V~~A   79 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDN-MPLRGKQLRVRFA   79 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTT-CCBTTBCCEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCC-CEECCEEEEEEEC
Confidence            35689999999999999999999999 9999999865      6899999999999999999 999 9999999999999


Q ss_pred             CCCC
Q psy1680          90 DGKR   93 (227)
Q Consensus        90 ~~~~   93 (227)
                      .++.
T Consensus        80 ~~~~   83 (86)
T d2cpja1          80 CHSA   83 (86)
T ss_dssp             SCCS
T ss_pred             CCcC
Confidence            8754

>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=99.74  E-value=8.6e-19  Score=115.89  Aligned_cols=69  Identities=17%  Similarity=0.173  Sum_probs=62.8

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..+|||+|||+.+  ++++|+++|+.||.|.+|+|+.+.  +.++|||||+|.+.++|.+|++.|||..|+||
T Consensus         8 ~~~l~V~nLp~~~--t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~   76 (89)
T d1cvja2           8 VGNIFIKNLDKSI--DNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDR   76 (89)
T ss_dssp             TTEEEEESCCSSC--CHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTE
T ss_pred             CCEEEEeCCCCCC--CHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCE
Confidence            3579999997665  789999999999999999999986  45789999999999999999999999999985

>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=99.73  E-value=2.1e-18  Score=116.78  Aligned_cols=74  Identities=15%  Similarity=0.154  Sum_probs=66.4

Q ss_pred             CCCCCcceeccCCCCCCCChhhHHhhhccccce--------EEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcc
Q psy1680         152 GGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTL--------VSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRIT  223 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i--------~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~  223 (227)
                      .....+|||+|||..+  ++++|+++|+.||.|        ..+.+.+|+.+|.++|||||+|.+.++|.+|++.|||..
T Consensus         5 ~~~~~~i~V~nLp~~~--te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~   82 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSV--TLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   82 (101)
T ss_dssp             CCCCCEEEEECCCTTC--CHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             CCCCCEEEEECCCCcC--CHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCE
Confidence            3456799999997655  899999999999987        467788899999999999999999999999999999999


Q ss_pred             ccCC
Q psy1680         224 VDGL  227 (227)
Q Consensus       224 i~gr  227 (227)
                      |+||
T Consensus        83 ~~gr   86 (101)
T d2cpea1          83 FQGS   86 (101)
T ss_dssp             ETTE
T ss_pred             ECCE
Confidence            9986

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=3.1e-18  Score=112.11  Aligned_cols=69  Identities=10%  Similarity=0.184  Sum_probs=62.5

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .++|||+|||..+  ++++|+++|+.||.|.+|+|+++. +|.++|||||+|.+.++|.+||+ ++|..++||
T Consensus         6 ~rtvfV~nlp~~~--te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~   74 (85)
T d1zh5a2           6 NRSVYIKGFPTDA--TLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKET   74 (85)
T ss_dssp             TTEEEEECCCTTC--CHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTE
T ss_pred             cCEEEEECCCCCC--CHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCE
Confidence            4689999997665  799999999999999999998885 79999999999999999999996 699999885

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=5.3e-18  Score=111.93  Aligned_cols=75  Identities=19%  Similarity=0.321  Sum_probs=68.2

Q ss_pred             CCceEEEcCCCCCCCHHHH---HhcccCC-CeEEEEEeecCCCCCe---ecEEEEEeCCHHHHHHHHH-hCCCceeCCeE
Q psy1680          12 PPYTAFVGNLPNGITQGDV---ERFFPEQ-KLVSVRLVKDKETDRF---KGFCYVEFVDVENLRQALL-KDGRITVDGLQ   83 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l---~~~f~~~-~i~~v~i~~~~~~~~~---~g~afv~f~~~~~a~~al~-~~~~~~~~g~~   83 (227)
                      ..++|||+|||+++++++|   +++|++| .|..|.|++++.++.+   +|||||+|.+.++|.+||+ +|| ..++|+.
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng-~~~~gr~   85 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNN-VVVDGRT   85 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTT-EEETTEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCC-CEECCEE
Confidence            4578999999999999999   7899999 9999999999776654   4899999999999999998 999 9999999


Q ss_pred             eEEE
Q psy1680          84 VRLD   87 (227)
Q Consensus        84 l~v~   87 (227)
                      |+|.
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9873

>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=99.73  E-value=1.3e-17  Score=109.39  Aligned_cols=77  Identities=19%  Similarity=0.306  Sum_probs=69.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      ...++|||+|||+++++++|+++|++| .+..+.+.+      ++|||||+|.+.++|..||. +|+ ..|+|+.|.|.+
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~-~~i~g~~i~V~~   78 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNG-KVLDGSPIEVTL   78 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSS-EEETTEEEEEEC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCC-CEECCEEEEEEe
Confidence            345899999999999999999999999 887776643      47899999999999999999 999 999999999999


Q ss_pred             cCCCCC
Q psy1680          89 ADGKRN   94 (227)
Q Consensus        89 ~~~~~~   94 (227)
                      +.|+..
T Consensus        79 akP~~~   84 (86)
T d2cpda1          79 AKPVDK   84 (86)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            987654

>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=99.73  E-value=5.2e-18  Score=111.81  Aligned_cols=78  Identities=23%  Similarity=0.465  Sum_probs=69.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEec
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA   89 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~   89 (227)
                      ..+++|||+|||+++|+++|+++|++| .|..+.++.     .+++||||+|.+.++|++||. ++ ..|+|+.|.|.++
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~-~~-~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG-ED-LIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT-CE-EEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh-CC-CEECCEEeEEEeC
Confidence            457899999999999999999999999 999987753     357899999999999999986 77 8999999999999


Q ss_pred             CCCCCC
Q psy1680          90 DGKRND   95 (227)
Q Consensus        90 ~~~~~~   95 (227)
                      .++...
T Consensus        76 ~~k~~~   81 (88)
T d1wf0a_          76 EPKHNS   81 (88)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            877653

>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=99.73  E-value=6.1e-19  Score=119.86  Aligned_cols=81  Identities=17%  Similarity=0.171  Sum_probs=71.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEec
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA   89 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~   89 (227)
                      ....+|||+|||+++|+++|+++|..| .+..+.++....+|+++|||||+|.+.++|++||++++ ..|+|+.|.|.++
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~-~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHR-KKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCS-EEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCC-CeECCcEEEEEEC
Confidence            345679999999999999999999999 77765555555789999999999999999999999999 9999999999987


Q ss_pred             CCC
Q psy1680          90 DGK   92 (227)
Q Consensus        90 ~~~   92 (227)
                      ..+
T Consensus        85 ~~~   87 (103)
T d2cpya1          85 TLE   87 (103)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            643

>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=99.73  E-value=9.9e-18  Score=114.95  Aligned_cols=75  Identities=19%  Similarity=0.278  Sum_probs=68.6

Q ss_pred             CceEEEcCCCC-CCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          13 PYTAFVGNLPN-GITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        13 ~~~l~V~nLp~-~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      +++|||+|||+ .+|+++|+++|+.| .|..|.|++++     +|||||+|.+.++|.+||+ +++ ..|.|+.|+|.++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng-~~l~g~~l~v~~s   75 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNG-HKLHGKPIRITLS   75 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTT-CBCSSSBCEEECC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCC-CEECCEEEEEEEC
Confidence            57899999965 59999999999999 99999998874     6899999999999999999 999 9999999999998


Q ss_pred             CCCC
Q psy1680          90 DGKR   93 (227)
Q Consensus        90 ~~~~   93 (227)
                      ..+.
T Consensus        76 ~~~~   79 (109)
T d2adca1          76 KHQN   79 (109)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7554

>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=99.72  E-value=1.1e-17  Score=111.87  Aligned_cols=70  Identities=17%  Similarity=0.192  Sum_probs=62.0

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||+.+  ++++|+++|+.||.|..+.+..+   +.++|||||+|.+.++|++|++.|||..|+||
T Consensus        12 ~~~~~l~V~nLp~~~--t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~   81 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDI--RTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGY   81 (95)
T ss_dssp             CCSSEEEEESCCTTC--CHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEECCCCCC--CHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            345689999997665  78999999999999999988665   45789999999999999999999999999885

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.1e-17  Score=110.24  Aligned_cols=76  Identities=17%  Similarity=0.316  Sum_probs=68.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCcee-CCeEeEEE
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITV-DGLQVRLD   87 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~-~g~~l~v~   87 (227)
                      +++++|||+|||.++++++|+++|++| .+..+.++..    ++++||||+|.+.++|.+|+. |++ ..+ +|+.|+|.
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~-~~i~~g~~l~v~   82 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHN-HDLGENHHLRVS   82 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTT-CBSSSSCBCEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccC-CEecCCCEEEEE
Confidence            568899999999999999999999999 9988877543    347899999999999999998 999 887 58999999


Q ss_pred             ecCC
Q psy1680          88 IADG   91 (227)
Q Consensus        88 ~~~~   91 (227)
                      ++++
T Consensus        83 ~sk~   86 (88)
T d2adca2          83 FSKS   86 (88)
T ss_dssp             ECSS
T ss_pred             eCCC
Confidence            9875

>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=99.72  E-value=2.1e-18  Score=113.29  Aligned_cols=73  Identities=11%  Similarity=-0.056  Sum_probs=63.0

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +...+|||+|||..+  +++||+++|+.||.|....++.+..++.++|+|||+|.+.++|++|++.|||..|+||
T Consensus         7 p~~~~l~v~nLp~~~--~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr   79 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTV--SIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSR   79 (86)
T ss_dssp             CSSEEEEEESCCTTC--CHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTE
T ss_pred             CCCCEEEEECCCCCC--CHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCE
Confidence            345579999997655  8999999999999887654444447799999999999999999999999999999986

>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=99.72  E-value=4.7e-18  Score=117.10  Aligned_cols=85  Identities=15%  Similarity=0.230  Sum_probs=75.0

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEe
Q psy1680           6 KTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQV   84 (227)
Q Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l   84 (227)
                      ...+....++|||+|||+++|+++|+++|+.+ .+..+.++.+..+|.++|||||+|.+.++|++||++|+ ..|+|+.|
T Consensus        11 ~~~~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~-~~i~gR~i   89 (112)
T d1wela1          11 SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHK-QYMGNRFI   89 (112)
T ss_dssp             CSSCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCS-BCSTTSCB
T ss_pred             CCCCCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCC-CcCCCEEE
Confidence            33456677899999999999999999999999 77666566666789999999999999999999999999 99999999


Q ss_pred             EEEecCC
Q psy1680          85 RLDIADG   91 (227)
Q Consensus        85 ~v~~~~~   91 (227)
                      .|..+.+
T Consensus        90 ~V~~~~~   96 (112)
T d1wela1          90 QVHPITK   96 (112)
T ss_dssp             EEEEECH
T ss_pred             EEEEcCh
Confidence            9998764

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=5.9e-18  Score=112.25  Aligned_cols=79  Identities=19%  Similarity=0.421  Sum_probs=70.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHh----cccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeE
Q psy1680          12 PPYTAFVGNLPNGITQGDVER----FFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVR   85 (227)
Q Consensus        12 ~~~~l~V~nLp~~~t~~~l~~----~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~   85 (227)
                      |+++|||+|||+.+++++|++    +|++| +|..|.+..   +++++|||||+|.+.++|.+|++ +|+ ..++|+.|.
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~-~~~~g~~l~   77 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQG-FPFYDKPMR   77 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTT-CEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCC-CEECCEEEE
Confidence            578999999999999998864    68999 999988764   46778999999999999999998 999 999999999


Q ss_pred             EEecCCCCC
Q psy1680          86 LDIADGKRN   94 (227)
Q Consensus        86 v~~~~~~~~   94 (227)
                      |.++.++..
T Consensus        78 v~~ak~~~~   86 (91)
T d1nu4a_          78 IQYAKTDSD   86 (91)
T ss_dssp             EEECSSCCT
T ss_pred             EEEeCCCch
Confidence            999987643

>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=99.72  E-value=1e-17  Score=109.16  Aligned_cols=67  Identities=15%  Similarity=0.117  Sum_probs=60.6

Q ss_pred             CCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         152 GGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      .+|+++|||+|||..+  ++++|+++|+.||.|.+|++++++     +|||||+|.+.++|.+|++.|+|..|.
T Consensus         5 ~pP~~tl~V~nLp~~~--t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~   71 (83)
T d2b0ga1           5 QPPNQILFLTNLPEET--NEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKIT   71 (83)
T ss_dssp             CSCCSEEEEESCCTTC--CHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEECCCCCC--CHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeC
Confidence            3678899999997655  789999999999999999998763     689999999999999999999999985

>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=99.72  E-value=2.1e-17  Score=110.87  Aligned_cols=68  Identities=16%  Similarity=0.272  Sum_probs=61.7

Q ss_pred             CCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         152 GGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+|+++|||+|||+++  ++++|+++|++||.|..|++.++      ++||||+|.+.++|.+|++.|||..|+|+
T Consensus        14 ~~Ps~tl~V~nLp~~~--t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~   81 (97)
T d1whya_          14 ANPTTRLWVGGLGPNT--SLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGP   81 (97)
T ss_dssp             CCCCSCEEEECCCSSC--CHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSS
T ss_pred             CCCCCEEEEcCCCCCC--CHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCC
Confidence            3578899999998765  78999999999999999999776      58999999999999999999999999873

>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=99.72  E-value=1.8e-17  Score=112.57  Aligned_cols=71  Identities=11%  Similarity=-0.034  Sum_probs=63.4

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||+.+  +++||+++|+.+|.|..+.++.+..++.++|||||+|.+.++|++|++ +++..|+||
T Consensus        14 ~~~~v~v~nLP~~~--te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR   84 (104)
T d1wg5a_          14 NDGFVRLRGLPFGC--SKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHR   84 (104)
T ss_dssp             CCCEEEEESCCTTC--CHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSS
T ss_pred             CCcEEEEeCCCCCC--CHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcce
Confidence            45579999997666  799999999999999887777777889999999999999999999996 889999987

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.71  E-value=1.7e-17  Score=105.83  Aligned_cols=73  Identities=21%  Similarity=0.312  Sum_probs=67.4

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEEEec
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA   89 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v~~~   89 (227)
                      .+|||+|||+++++++|+++|+.| .|..+.++.++..+  ++||||+|.+.++|.+||.+++ ..|+|++|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~--~~~afV~F~~~~~a~~Al~~~~-~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN--FRFARIEFARYDGALAAITKTH-KVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS--SEEEEEEESSHHHHHHHHTTTT-CEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc--ceEEEEEEcchHHhHHHHHhcC-cEECCEEEEEEEC
Confidence            479999999999999999999999 99999999886543  5799999999999999999999 9999999999875

>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=99.71  E-value=6.4e-19  Score=116.89  Aligned_cols=70  Identities=26%  Similarity=0.307  Sum_probs=62.8

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||+.+  ++++|+++|+.||.|.++.|+.+ .+|+++|||||+|.+.++|.+||+ |||..|+||
T Consensus        12 ~~~~ifV~nL~~~~--te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~   81 (91)
T d1fjeb1          12 TPFNLFIGNLNPNK--SVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGN   81 (91)
T ss_dssp             SSEEEEEECCCTTS--CHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTE
T ss_pred             CCcEEEEeCccCcc--hHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCE
Confidence            45689999996655  89999999999999999988755 679999999999999999999996 999999986

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=2.8e-17  Score=108.13  Aligned_cols=77  Identities=17%  Similarity=0.223  Sum_probs=66.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCCCeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      ..+.+|||+|||+++++++|+++|++|.+..+.+      ++.++||||+|.+.++|++||+ ||+ ..|+|++|.|+++
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~-~~~~G~~l~V~~a   75 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQ-YSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSCCCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTT-EEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcCceeeee------eccCCceEEEECCHHHHHHHHHHhCC-CEECCEEEEEEEc
Confidence            3467899999999999999999999994333444      3448999999999999999998 999 9999999999998


Q ss_pred             CCCCC
Q psy1680          90 DGKRN   94 (227)
Q Consensus        90 ~~~~~   94 (227)
                      ..+..
T Consensus        76 ~~~~~   80 (88)
T d1wg1a_          76 PTDAL   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            66543

>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=99.71  E-value=9.4e-18  Score=110.29  Aligned_cols=63  Identities=21%  Similarity=0.161  Sum_probs=57.9

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++|||+|||+.+  ++++|+++|+.||.|.+|.|.+|       |||||+|.+.++|.+||+.|||..|+||
T Consensus         1 nrvfV~nlp~~~--~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~   63 (87)
T d3begb1           1 NRVVVSGLPPSG--SWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSH   63 (87)
T ss_dssp             CCEEEEECCSSC--CTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCT
T ss_pred             CeEEEECCCCcC--CHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCc
Confidence            469999997665  78999999999999999998765       8999999999999999999999999986

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=9.6e-17  Score=108.93  Aligned_cols=81  Identities=15%  Similarity=0.197  Sum_probs=71.9

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-h--CCCceeCCeE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-K--DGRITVDGLQ   83 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~--~~~~~~~g~~   83 (227)
                      ....++.+|||+|||..+|+++|.++|++| .|..+.+.++      +++|||+|.+.++|+.||. +  ++ ..+.|++
T Consensus        10 ~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~-~~~~g~~   82 (104)
T d1wexa_          10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVP-VYIAGQQ   82 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSC-CBSSSSB
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCC-cEEeeEE
Confidence            455788999999999999999999999999 9999999754      6899999999999999998 5  56 7889999


Q ss_pred             eEEEecCCCCCC
Q psy1680          84 VRLDIADGKRND   95 (227)
Q Consensus        84 l~v~~~~~~~~~   95 (227)
                      |+|.+++.++..
T Consensus        83 l~v~~s~~~~~~   94 (104)
T d1wexa_          83 AFFNYSTSKRIT   94 (104)
T ss_dssp             CEEEECSSSSCC
T ss_pred             EEEEEcCCCccC
Confidence            999999776543

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.71  E-value=8e-18  Score=107.41  Aligned_cols=67  Identities=12%  Similarity=0.075  Sum_probs=59.5

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+|||+|||+..  ++++|+++|+.||.|..|+|++++.  ..++||||+|.+.++|.+||. +++..|+||
T Consensus         1 Ttv~V~nlp~~~--t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~   67 (75)
T d2ghpa2           1 TTVLVKNLPKSY--NQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT-KTHKVVGQN   67 (75)
T ss_dssp             CEEEEEEECTTC--CHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTTCEETTE
T ss_pred             CEEEEECCCCCC--CHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHH-hcCcEECCE
Confidence            379999997665  7999999999999999999999875  345799999999999999985 799999985

>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=99.71  E-value=2.2e-17  Score=110.79  Aligned_cols=81  Identities=16%  Similarity=0.202  Sum_probs=72.6

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeE
Q psy1680           6 KTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQ   83 (227)
Q Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~   83 (227)
                      .+....+.++|||+|||+.+++++|+++|++| .|..+.|.+       +|||||+|.+.++|++||+ ||+ ..|.|+.
T Consensus         8 gp~~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng-~~~~g~~   79 (98)
T d1wg4a_           8 GPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDD-TKFRSHE   79 (98)
T ss_dssp             CCCCCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSS-EEEECTT
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCC-CEeCCeE
Confidence            34455677899999999999999999999999 999999864       4899999999999999998 999 9999999


Q ss_pred             eEEEecCCCCC
Q psy1680          84 VRLDIADGKRN   94 (227)
Q Consensus        84 l~v~~~~~~~~   94 (227)
                      |+|.+++.+..
T Consensus        80 i~v~~~~~~~~   90 (98)
T d1wg4a_          80 GETSYIRVYPE   90 (98)
T ss_dssp             SCEEEEEEECC
T ss_pred             EEEEEEecCCC
Confidence            99999876554

>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=99.71  E-value=7.6e-17  Score=106.13  Aligned_cols=78  Identities=14%  Similarity=0.187  Sum_probs=70.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-h--CCCceeCCeEe
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-K--DGRITVDGLQV   84 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~--~~~~~~~g~~l   84 (227)
                      ..+++++|||+|||..+++++|+++|++| .|..+.+.++      +++|||+|.+.++|..|++ +  ++ ..+.|++|
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~-~~~~g~~l   76 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVT-PHLRNQPI   76 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSC-CEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCC-CccCCCEE
Confidence            46789999999999999999999999999 9999998765      5799999999999999997 4  67 89999999


Q ss_pred             EEEecCCCC
Q psy1680          85 RLDIADGKR   93 (227)
Q Consensus        85 ~v~~~~~~~   93 (227)
                      .|.++..+.
T Consensus        77 ~v~~sk~~~   85 (88)
T d2cq1a1          77 YIQYSNHKE   85 (88)
T ss_dssp             EEEECSCSS
T ss_pred             EEEECCCCC
Confidence            999997654

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=2.2e-17  Score=106.51  Aligned_cols=74  Identities=18%  Similarity=0.300  Sum_probs=67.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      ...++|||+||+  +|+++|+++|++| .|.++.+.++      ++||||+|.+.++|..|++ +|+ ..++|++|+|.+
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng-~~~~g~~l~V~~   73 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNG-TQVESVQLKVNI   73 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTT-CBCSSCBCEEEE
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCC-CEECCEEEEEEE
Confidence            457899999996  8999999999999 9999999754      6799999999999999998 999 999999999999


Q ss_pred             cCCCC
Q psy1680          89 ADGKR   93 (227)
Q Consensus        89 ~~~~~   93 (227)
                      ++++.
T Consensus        74 a~~~P   78 (79)
T d2bz2a1          74 ARKQP   78 (79)
T ss_dssp             CCSSC
T ss_pred             ecCCC
Confidence            97653

>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=99.70  E-value=1.1e-17  Score=111.97  Aligned_cols=67  Identities=13%  Similarity=0.238  Sum_probs=60.9

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++..+|||+|||...  ++++|+++|++||.|.+|+|+++      +|||||+|.+.++|.+|++.|||..|+||
T Consensus        16 ~~~~~l~v~nL~~~~--te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~   82 (96)
T d1x4ga1          16 PKNCTVYCGGIASGL--TDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGH   82 (96)
T ss_dssp             SSCCEEEEECCSSCC--CHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEcCCCCCC--CHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            345689999997665  79999999999999999999987      68999999999999999999999999985

>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=99.70  E-value=2.2e-17  Score=108.73  Aligned_cols=69  Identities=14%  Similarity=0.075  Sum_probs=60.5

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccc-cCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV-DGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i-~gr  227 (227)
                      +|+++|||+|||.++  ++++|+++|++||.|..+.+..+    +++|||||+|.+.++|.+|+..|+|..| +||
T Consensus         8 pPs~tL~V~NLp~~~--te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~   77 (88)
T d2adca2           8 PPSATLHLSNIPPSV--SEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENH   77 (88)
T ss_dssp             CSCSEEEEECCCTTC--CHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CCCCEEEEECCCCCC--CHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCC
Confidence            578899999997665  79999999999999988877554    3478999999999999999999999988 565

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=3.8e-18  Score=112.19  Aligned_cols=72  Identities=21%  Similarity=0.217  Sum_probs=65.9

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecCC
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIADG   91 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~~   91 (227)
                      ++|||+|||+++++++|+++|++| .|..+.|+++       |||||+|.+.++|++||+ |++ ..|.|+.|.|.++.+
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g-~~~~g~~i~v~~~~~   72 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDN-TKFRSHEGETAYIRV   72 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTT-CBCCCTTSCCCBCEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCC-CEECCcEeEEeEEec
Confidence            479999999999999999999999 9999998754       799999999999999998 999 999999999888765


Q ss_pred             CC
Q psy1680          92 KR   93 (227)
Q Consensus        92 ~~   93 (227)
                      +.
T Consensus        73 ~~   74 (87)
T d3begb1          73 KV   74 (87)
T ss_dssp             EE
T ss_pred             Cc
Confidence            43

>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=99.70  E-value=2.3e-17  Score=112.15  Aligned_cols=70  Identities=23%  Similarity=0.324  Sum_probs=60.2

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecC-CCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDK-ETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~-~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +..+|||+|||+.+  ++++|+++|+.|| |..++++++. .++.++|||||+|.+.++|++|+ .||+..|+||
T Consensus        14 p~~~v~V~nLp~~~--te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr   84 (104)
T d1wi8a_          14 PPYTAFLGNLPYDV--TEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNK   84 (104)
T ss_dssp             SCEEEEEESCCSSC--CHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTE
T ss_pred             CCCEEEEeCCCCcC--CHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCE
Confidence            56799999997655  8999999999999 7778777665 47889999999999999998776 5999999986

>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=99.70  E-value=4.3e-17  Score=109.29  Aligned_cols=78  Identities=21%  Similarity=0.408  Sum_probs=69.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCC--eEe
Q psy1680           9 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDG--LQV   84 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g--~~l   84 (227)
                      ...++++|||+|||+++++++|+++|++| .|..+.+.++      ++||||+|.+.++|..|++ |++ ..|.|  ++|
T Consensus        13 ~~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~-~~i~g~~~~l   85 (97)
T d1whya_          13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRG-FPLGGPDRRL   85 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTT-CBCSSSSCBC
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCC-CEeCCCceEE
Confidence            34668999999999999999999999999 9999999765      6799999999999999999 999 99976  489


Q ss_pred             EEEecCCCC
Q psy1680          85 RLDIADGKR   93 (227)
Q Consensus        85 ~v~~~~~~~   93 (227)
                      +|.++++.+
T Consensus        86 ~v~~ak~~~   94 (97)
T d1whya_          86 RVDFAKSGP   94 (97)
T ss_dssp             EEEECCCCC
T ss_pred             EEEeCCCCC
Confidence            999987644

>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=99.69  E-value=2.9e-17  Score=110.26  Aligned_cols=66  Identities=20%  Similarity=0.294  Sum_probs=57.3

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ....+|||+|||+.. +++++|+++|++||.|.+|.|        ++|||||+|++.++|.+|++.|||..|+||
T Consensus        13 ~~~~~lfV~nL~~~~-~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~   78 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLV-VKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQ   78 (98)
T ss_dssp             SCCCCEEEEEECTTT-CCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTE
T ss_pred             CCCcEEEEeCCCccc-CCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            345689999996332 357889999999999999988        368999999999999999999999999985

>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=99.69  E-value=2.6e-17  Score=113.22  Aligned_cols=76  Identities=20%  Similarity=0.156  Sum_probs=68.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEe
Q psy1680          11 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDI   88 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~   88 (227)
                      ...++|||+|||+.+++++|+++|++| .|..|.|..      .++||||+|.+.++|.+||+ ||+ ..|.|++|.|.+
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng-~~~~gr~l~v~~   80 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAY-SKFHHVPLYLEW   80 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTT-CBSSSSBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcC-CccCCCeEEEEE
Confidence            345799999999999999999999999 999998853      37899999999999999998 999 999999999999


Q ss_pred             cCCCC
Q psy1680          89 ADGKR   93 (227)
Q Consensus        89 ~~~~~   93 (227)
                      +....
T Consensus        81 a~~~~   85 (111)
T d1whxa_          81 APIGV   85 (111)
T ss_dssp             EETTT
T ss_pred             CCCCc
Confidence            86543

>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=99.69  E-value=1.9e-17  Score=113.55  Aligned_cols=67  Identities=15%  Similarity=0.126  Sum_probs=60.7

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +.+|||+||++.. .++++|+++|+.||.|..|.|++++     +|||||+|.+.++|.+|++.|||..|+||
T Consensus         2 ~~~l~V~nL~p~~-~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~   68 (109)
T d2adca1           2 NSVLLVSNLNPER-VTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGK   68 (109)
T ss_dssp             CSEEEEESCCTTT-CCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSS
T ss_pred             CCEEEEeCCCccc-CCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            4689999996542 4789999999999999999999884     69999999999999999999999999986

>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=99.69  E-value=3e-17  Score=111.08  Aligned_cols=70  Identities=16%  Similarity=0.115  Sum_probs=61.7

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ....+|||+|||+++  |++||+++|+.|+ +..|.++++.. +.++|||||+|.+.++|++||+ +|+..|+||
T Consensus        13 ~~~~~v~v~nLp~~~--te~dl~~~F~~~~-~~~v~~~~~~~-g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR   82 (102)
T d1weza_          13 TTGHCVHMRGLPYRA--TENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEFATHEDAVAAMA-KDKANMQHR   82 (102)
T ss_dssp             SSSCEEEEESCCTTC--CHHHHHHSSCSCC-CSEEEEEESSS-SCEEEEEEEECSSSHHHHHHHT-TSSCCSSSS
T ss_pred             CCCCEEEEeCCCCcC--CHHHHHHHHhccC-cceeeeEEecC-CcceEEEEEEECCHHHHHHHHH-cCCCEECCE
Confidence            356789999997666  8999999999997 55788888854 8999999999999999999986 899999997

>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=99.68  E-value=2.1e-17  Score=108.31  Aligned_cols=65  Identities=17%  Similarity=0.182  Sum_probs=59.6

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..+|||+|||...  ++++|+++|++||.|.+|++.++      +|||||+|.+.++|.+|++.|||..|+||
T Consensus         8 ~~~l~V~nLp~~~--~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~   72 (86)
T d2cpja1           8 RSRLFVGNLPPDI--TEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGK   72 (86)
T ss_dssp             TTEEEEESCCTTC--CHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTB
T ss_pred             CCEEEEECCCCCC--CHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            4579999997655  78999999999999999999876      58999999999999999999999999986

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.68  E-value=7e-17  Score=108.34  Aligned_cols=65  Identities=18%  Similarity=0.149  Sum_probs=58.9

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||..+  ++++|+++|+.||.|+.|.|.+       +|||||+|.+.++|++||+.|||..|+||
T Consensus        14 ~~~~i~V~Nlp~~~--~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~   78 (98)
T d1wg4a_          14 SDFRVLVSGLPPSG--SWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSH   78 (98)
T ss_dssp             CSCEEEEECCCSSC--CHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECT
T ss_pred             CCCEEEEECCCCCC--CHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCe
Confidence            45679999997665  7899999999999999999864       48999999999999999999999999986

>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=99.68  E-value=1.3e-16  Score=101.73  Aligned_cols=70  Identities=14%  Similarity=0.299  Sum_probs=62.8

Q ss_pred             EEEcCCCCCCCHHHHHhcccCCCeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecCCC
Q psy1680          16 AFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIADGK   92 (227)
Q Consensus        16 l~V~nLp~~~t~~~l~~~f~~~~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~~~   92 (227)
                      |||+|||+++++++|+++|++|.+..+.+.      +++|||||.|.+.++|.+|+. +|+ ..+.|++|.|+++...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g~~~~~~~------~~~g~afv~f~~~~~A~~Ai~~ln~-~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYELKYCFVD------KYKGTAFVTLLNGEQAEAAINTFHQ-SRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHHTT-EESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhcccccceeec------ccceeEEEEECCHHHHHHHHHHhCC-ccCCCCEEEEEEeCCC
Confidence            799999999999999999999975555553      458999999999999999998 999 9999999999998654

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=8.4e-17  Score=110.01  Aligned_cols=80  Identities=16%  Similarity=0.210  Sum_probs=70.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCcee--CCeEeE
Q psy1680          10 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITV--DGLQVR   85 (227)
Q Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~--~g~~l~   85 (227)
                      ..+..+|||+|||+.+|+++|+++|++| .|..+.|+.++    .+|||||+|.+.++|+.||. +++ ..|  .++.|+
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~-~~l~~~~~~l~   78 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDG-QNIYNACCTLR   78 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHS-CCSSTTCCCCE
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCC-CEeccCCcEEE
Confidence            3556889999999999999999999999 99999998764    38999999999999999999 999 887  578899


Q ss_pred             EEecCCCCC
Q psy1680          86 LDIADGKRN   94 (227)
Q Consensus        86 v~~~~~~~~   94 (227)
                      |.++.++..
T Consensus        79 v~~s~~~~~   87 (108)
T d2adba1          79 IDFSKLTSL   87 (108)
T ss_dssp             EEECSSCSC
T ss_pred             EEecCCccc
Confidence            999876554

>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=99.67  E-value=2.5e-17  Score=109.20  Aligned_cols=69  Identities=12%  Similarity=0.164  Sum_probs=60.1

Q ss_pred             CCCcceeccCCCCCCCChhhHH----hhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHG----LMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~----~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      |+++|||+|||+..  +++||+    .+|++||.|.+|++.+   ++.++|||||+|.+.++|.+|++.+||..|+|+
T Consensus         2 P~~tl~V~nLp~~~--t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~   74 (91)
T d1nu4a_           2 PNHTIYINNLNEKI--KKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK   74 (91)
T ss_dssp             CCSEEEEESCCTTS--CHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCEEEEeCCCCCC--CHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCE
Confidence            56899999997666  677775    5689999999998865   377899999999999999999999999999885

>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=99.66  E-value=4.7e-17  Score=111.88  Aligned_cols=66  Identities=14%  Similarity=-0.012  Sum_probs=59.4

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..++|||+|||+.+  ++++|+++|+.||.|..|.|.+      ++|||||+|.+.++|.+|++.|||..|.||
T Consensus         9 ~~~~l~V~nLp~~~--t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr   74 (111)
T d1whxa_           9 SKTVILAKNLPAGT--LAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHV   74 (111)
T ss_dssp             EEEEEEEESCCTTC--CHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCEEEEECCCCCC--CHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCC
Confidence            35689999997655  7899999999999999998854      469999999999999999999999999986

>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=99.66  E-value=2.1e-16  Score=106.13  Aligned_cols=78  Identities=18%  Similarity=0.261  Sum_probs=69.6

Q ss_pred             CCCCCceEEEcCCCCC-CCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH---hCCCceeCCeE
Q psy1680           9 PTEPPYTAFVGNLPNG-ITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL---KDGRITVDGLQ   83 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~-~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~---~~~~~~~~g~~   83 (227)
                      ...++++|||+|||.+ +|+++|.++|++| .|..+.++++      +++|||+|.+.++|.+|++   +++ ..++|+.
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~-~~~~gr~   86 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKA-LWFQGRC   86 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSC-CCSSSSC
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCC-ceECCEE
Confidence            3456789999999985 8999999999999 9999999865      6899999999999999996   678 8999999


Q ss_pred             eEEEecCCCC
Q psy1680          84 VRLDIADGKR   93 (227)
Q Consensus        84 l~v~~~~~~~   93 (227)
                      |.|.++..++
T Consensus        87 l~V~~s~~~~   96 (99)
T d1x4fa1          87 VKVDLSEKYK   96 (99)
T ss_dssp             CEEEEECSCS
T ss_pred             EEEEEcCCcc
Confidence            9999997654

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.7e-17  Score=112.53  Aligned_cols=71  Identities=13%  Similarity=0.006  Sum_probs=62.3

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+|||+.+  ++++|+++|+.||.|..+.++.+..+|.++|+|||+|.+.++|.+||+ +||..|+||
T Consensus         7 ~~~~v~v~nLp~~~--t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr   77 (103)
T d2cpya1           7 AKVCAHITNIPFSI--TKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGR   77 (103)
T ss_dssp             CCCEEEEESCCTTS--CHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTE
T ss_pred             CceEEEEeCCCCCC--CHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCc
Confidence            45679999997666  799999999999988876666666789999999999999999999996 899999986

>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=99.66  E-value=6.2e-17  Score=110.68  Aligned_cols=67  Identities=7%  Similarity=-0.047  Sum_probs=60.0

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      +..+|||+|||..+  |+++|+++|++||.|.+|.|++++    ++|+|||+|.+.++|.+|++.|||..|.+
T Consensus         6 ~~~~v~V~NL~~~v--te~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~   72 (108)
T d2adba1           6 PVLRIIVENLFYPV--TLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYN   72 (108)
T ss_dssp             CEEEEESCSCCSTT--HHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSST
T ss_pred             CeEEEEEeCcCCCC--CHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEecc
Confidence            55679999997655  899999999999999999998874    48999999999999999999999999853

>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=99.65  E-value=5.1e-17  Score=111.77  Aligned_cols=71  Identities=10%  Similarity=0.038  Sum_probs=63.1

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      +..+|||+|||+.+  +++||.++|+.||.+..+.++.+..+|.++|+|||+|.+.++|++||+ +||..|+||
T Consensus        17 ~~~~i~v~nLp~~~--t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR   87 (112)
T d1wela1          17 AGFCVYLKGLPFEA--ENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNR   87 (112)
T ss_dssp             CCCEEEEECCCTTC--CHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTS
T ss_pred             CCeEEEEecCCCcC--cHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCE
Confidence            45689999997666  789999999999988877666666789999999999999999999996 899999997

>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=99.65  E-value=3.1e-16  Score=106.34  Aligned_cols=70  Identities=13%  Similarity=0.081  Sum_probs=60.1

Q ss_pred             CCCCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHc--CCccccCC
Q psy1680         150 SRGGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD--GRITVDGL  227 (227)
Q Consensus       150 ~~~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l--~g~~i~gr  227 (227)
                      ...+++++|||+|||+..  ++++|.++|++||.|..|++.++      +|+|||+|.+.++|++|++.+  ++..++|+
T Consensus        10 ~~~~ps~~l~v~nlp~~~--te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~   81 (104)
T d1wexa_          10 HKVSVSPVVHVRGLCESV--VEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQ   81 (104)
T ss_dssp             CCCCCCSEEEEESCCSSC--CHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSS
T ss_pred             CcCCCCCEEEEeCCCCCC--CHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeE
Confidence            344678899999997655  89999999999999999999765      689999999999999999977  55667664

>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=4.1e-16  Score=116.32  Aligned_cols=86  Identities=19%  Similarity=0.377  Sum_probs=79.5

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEE
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRL   86 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v   86 (227)
                      ......++|||+|||..+|+++|+++|+.| .|..+.|+.++.++.++|||||+|.+.++|.+||++++ ..++|+.|+|
T Consensus        92 ~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~~-~~~~G~~i~V  170 (183)
T d1u1qa_          92 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY-HTVNGHNCEV  170 (183)
T ss_dssp             TTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSSC-EEETTEEEEE
T ss_pred             ccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHHhCC-CeECCEEEEE
Confidence            345667899999999999999999999999 99999999999999999999999999999999999888 8999999999


Q ss_pred             EecCCCCC
Q psy1680          87 DIADGKRN   94 (227)
Q Consensus        87 ~~~~~~~~   94 (227)
                      .++.+++.
T Consensus       171 ~~A~~k~e  178 (183)
T d1u1qa_         171 RKALSKQE  178 (183)
T ss_dssp             EECCCHHH
T ss_pred             EecCCccc
Confidence            99987643

>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=99.65  E-value=2.4e-16  Score=103.63  Aligned_cols=68  Identities=7%  Similarity=-0.037  Sum_probs=59.6

Q ss_pred             CCCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHc--CCccccCC
Q psy1680         152 GGEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD--GRITVDGL  227 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l--~g~~i~gr  227 (227)
                      ++|+++|||+|||..+  ++++|+++|++||.|.++++.++      +|+|||+|.+.++|.+|++.+  ++..|+||
T Consensus         5 ~~Ps~~l~V~nLp~~~--t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~   74 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEV--TETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQ   74 (88)
T ss_dssp             SSCCSEEEEESCCTTC--CHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTE
T ss_pred             CCCCCEEEEeCCCCCC--CHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCC
Confidence            4688999999997655  89999999999999999998866      489999999999999999865  56778775

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=1.3e-16  Score=102.82  Aligned_cols=64  Identities=9%  Similarity=0.154  Sum_probs=58.3

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+++|||+|+  +.  |+++|+++|++||.|.+|.+.++      +|||||+|.+.++|.+|++.|||..|+|+
T Consensus         4 ~~~ti~V~~~--~~--te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~   67 (79)
T d2bz2a1           4 KGNTLYVYGE--DM--TPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESV   67 (79)
T ss_dssp             CCCEEEEECS--SC--CHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSC
T ss_pred             CCCEEEEECC--CC--CHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCE
Confidence            4679999998  34  79999999999999999999765      58999999999999999999999999986

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.63  E-value=1.2e-16  Score=106.96  Aligned_cols=68  Identities=16%  Similarity=0.217  Sum_probs=60.0

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+..+|||+|||..+  ++++|+++|+.||.|..++     .++.++|||||+|.+.++|.+|++.|||..|+||
T Consensus        14 ~~~~~l~V~nL~~~~--te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr   81 (96)
T d1fjca_          14 RAARTLLAKNLSFNI--TEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGR   81 (96)
T ss_dssp             TGGGEEEEESCCSSC--CHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTE
T ss_pred             CCCCEEEEeCCCCCC--CHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCE
Confidence            356899999997665  7999999999999876654     3588999999999999999999999999999986

>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=99.63  E-value=1.1e-15  Score=100.61  Aligned_cols=78  Identities=12%  Similarity=0.143  Sum_probs=69.6

Q ss_pred             CCCCCceEEEcCCCCC-CCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-h--CCCceeCCeE
Q psy1680           9 PTEPPYTAFVGNLPNG-ITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-K--DGRITVDGLQ   83 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~-~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~--~~~~~~~g~~   83 (227)
                      ..++++.|||+|||.. +|++||.++|++| .|..+.++.+      +++|||+|.+.++|..|++ +  ++ ..+.|++
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~-~~~~gr~   76 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTP-ALVFGKP   76 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSC-CEETTEE
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCC-CccCCce
Confidence            4577899999999986 8899999999999 9999999865      5699999999999999998 5  67 8999999


Q ss_pred             eEEEecCCCC
Q psy1680          84 VRLDIADGKR   93 (227)
Q Consensus        84 l~v~~~~~~~   93 (227)
                      |+|.++...+
T Consensus        77 l~V~~s~~~~   86 (89)
T d1x4da1          77 VRVHLSQKYK   86 (89)
T ss_dssp             CEEEEECCCT
T ss_pred             EEEEECCCcc
Confidence            9999997544

>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=99.63  E-value=1.9e-16  Score=105.91  Aligned_cols=69  Identities=17%  Similarity=0.136  Sum_probs=59.4

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccc-eEEEEEeecC-CCCcccceEEEEEcCHHHHHHHHHHcCC--ccccCC
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTT-LVSVRLVKDK-ETDRFKGFCYVEFVDVENLRQALLKDGR--ITVDGL  227 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~-i~~v~i~~d~-~t~~~~g~afV~F~~~~~a~~Al~~l~g--~~i~gr  227 (227)
                      +|||+|||..+  ++++|+++|+.||. |.++.|++|+ .+++++|||||+|.+.++|.+|++.|++  ..++||
T Consensus         3 rLyV~nLp~~~--te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~   75 (96)
T d2disa1           3 RLFIGGIPKMK--KREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGH   75 (96)
T ss_dssp             EEEEECCCTTS--CHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTB
T ss_pred             EEEEcCCCCcC--CHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCE
Confidence            69999997655  78999999999994 9999999985 4688999999999999999999999864  444553

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=6.3e-17  Score=104.54  Aligned_cols=64  Identities=13%  Similarity=0.190  Sum_probs=56.2

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCc-cccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRI-TVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~-~i~gr  227 (227)
                      ++|||+|||.+.  ++++|+++|++||.|.++.+.+.      +|||||+|.+.++|.+|++.|||. .|+|+
T Consensus         2 n~l~V~nLp~~~--te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~   66 (80)
T d2cqha1           2 NKLYIGNLSPAV--TADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGK   66 (80)
T ss_dssp             CCEEEECCCTTC--CHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTE
T ss_pred             CEEEEECCCCCC--CHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCE
Confidence            369999997666  79999999999999887776654      699999999999999999999996 58885

>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=99.61  E-value=3.9e-16  Score=102.20  Aligned_cols=66  Identities=14%  Similarity=0.095  Sum_probs=58.3

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..++|||+|||...  ++++|+++|+.||.|..+.+.      .++|||||+|.+.++|.+|+..|||..|+||
T Consensus         7 ~~k~l~V~nLp~~~--te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~   72 (86)
T d2cpda1           7 SVKILYVRNLMLST--SEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGS   72 (86)
T ss_dssp             CCCEEEEESCCTTC--CHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTE
T ss_pred             CCCEEEEcCCCCCC--CHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCE
Confidence            35689999997655  799999999999998887764      3479999999999999999999999999985

>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=99.61  E-value=5.5e-18  Score=112.19  Aligned_cols=77  Identities=29%  Similarity=0.496  Sum_probs=66.3

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEe-----ecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCeEeEE
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLV-----KDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRL   86 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~-----~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~~l~v   86 (227)
                      .++|||+|||..+|+++|+++|++| .+..+.+.     .+..+++++|||||+|.+.++|+.|+++|+ ..+.|+.|+|
T Consensus         1 aRrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g-~~~~Gr~l~V   79 (90)
T d1u2fa_           1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDG-IIFQGQSLKI   79 (90)
T ss_dssp             CCEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSS-CCSSSSCCCC
T ss_pred             CCEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCC-cEECCEEEEE
Confidence            3689999999999999999999988 76555443     345667889999999999999999999999 9999999999


Q ss_pred             EecC
Q psy1680          87 DIAD   90 (227)
Q Consensus        87 ~~~~   90 (227)
                      ..++
T Consensus        80 ~r~k   83 (90)
T d1u2fa_          80 RRPH   83 (90)
T ss_dssp             BCTT
T ss_pred             CCCC
Confidence            7543

>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=99.61  E-value=3.2e-16  Score=102.95  Aligned_cols=65  Identities=15%  Similarity=0.170  Sum_probs=55.4

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+.+|||+|||+.+  +++||+++|++|| +..+.+      +.++|||||+|.+.++|.+|++.|||..|+||
T Consensus         4 ~s~~i~V~nLp~~~--t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~   68 (88)
T d1wg1a_           4 GSSGILVKNLPQDS--NCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGK   68 (88)
T ss_dssp             CCCCEEEESCCSSC--CHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTE
T ss_pred             CCCEEEEeCCCCcc--ChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCE
Confidence            35689999997655  7999999999999 333433      45689999999999999999999999999986

>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=99.60  E-value=1.2e-15  Score=97.14  Aligned_cols=61  Identities=11%  Similarity=0.117  Sum_probs=53.6

Q ss_pred             ceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         158 GFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       158 l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      |||+|||++.  ++++|+++|++|| +..+.+      ++++|||||+|.+.++|.+|++.|||..|+||
T Consensus         1 i~V~nLp~~~--t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~   61 (75)
T d1wi6a1           1 ILIRGLPGDV--TNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRER   61 (75)
T ss_dssp             EEEECCCTTC--CHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSC
T ss_pred             CEEeCCCCcC--CHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCC
Confidence            6999997665  7899999999999 555554      44689999999999999999999999999996

>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=99.59  E-value=2e-16  Score=104.02  Aligned_cols=65  Identities=15%  Similarity=0.286  Sum_probs=56.6

Q ss_pred             CCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      .+++|||+|||+.+  ++++|+++|++||.|.+|+++.+     ++|||||+|.+.++|++|+.  ++..|+||
T Consensus         4 ~s~~lfV~nLp~~~--te~~L~~~F~~~G~v~~v~~~~~-----~~gfafV~f~~~~~a~~a~~--~~~~i~g~   68 (88)
T d1wf0a_           4 GSSGVFVGRCTGDM--TEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGI   68 (88)
T ss_dssp             CCCEEEEESCCSSS--CHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTE
T ss_pred             CCCEEEEeCCCCCC--CHHHHHHHHHHcCCceEEEEeec-----cCceEEEEECCHHHHHHHHh--CCCEECCE
Confidence            46789999997665  89999999999999999987544     57999999999999999985  77888875

>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=99.58  E-value=2.8e-15  Score=100.57  Aligned_cols=68  Identities=12%  Similarity=-0.012  Sum_probs=59.4

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHH--HcCCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL--KDGRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~--~l~g~~i~gr  227 (227)
                      .++++|||+|||.+. .|+++|..+|++||.|.+|.++++      +|+|||+|.+.++|.+|++  .+++..|+||
T Consensus        16 ~~~~~l~v~nLp~~~-~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr   85 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSG-YSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGR   85 (99)
T ss_dssp             CCCCEEEEESCCCSS-CCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSS
T ss_pred             CCCCEEEEeCCcCCc-cCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCE
Confidence            456789999997542 378999999999999999999876      5899999999999999998  5788888886

>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=99.58  E-value=2.3e-15  Score=101.81  Aligned_cols=77  Identities=13%  Similarity=0.092  Sum_probs=67.8

Q ss_pred             CCCceEEEcCCCCCC-CH----HHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeE
Q psy1680          11 EPPYTAFVGNLPNGI-TQ----GDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQ   83 (227)
Q Consensus        11 ~~~~~l~V~nLp~~~-t~----~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~   83 (227)
                      ..+.+|||+||+..+ ++    ++|+++|+.| .|.++.+++.      ++||||+|.+.++|.+|+. ||| ..|+|+.
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng-~~~~g~~   75 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHK-TEFLGKE   75 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTT-SEETTEE
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcc-cccCCCE
Confidence            457899999999875 33    5699999999 9999999754      7899999999999999999 999 9999999


Q ss_pred             eEEEecCCCCC
Q psy1680          84 VRLDIADGKRN   94 (227)
Q Consensus        84 l~v~~~~~~~~   94 (227)
                      |+|.++.++..
T Consensus        76 l~v~~a~~~~~   86 (104)
T d1weya_          76 MKLYFAQTLHI   86 (104)
T ss_dssp             CEEECCCCSSC
T ss_pred             eEEeecccCCC
Confidence            99999976654

>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=99.58  E-value=1.8e-15  Score=99.45  Aligned_cols=68  Identities=10%  Similarity=-0.031  Sum_probs=58.9

Q ss_pred             CCCCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHc--CCccccCC
Q psy1680         153 GEGPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD--GRITVDGL  227 (227)
Q Consensus       153 ~~~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l--~g~~i~gr  227 (227)
                      .++++|||+|||.. ..|++||.++|++||.|.+|.++++      +++|||+|++.++|.+|++.+  ++..++||
T Consensus         6 ~~sr~v~v~nl~~~-~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr   75 (89)
T d1x4da1           6 ETRRVVHIMDFQRG-KNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGK   75 (89)
T ss_dssp             CCCCEEEEESCCCS-SSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTE
T ss_pred             CCCcEEEEECCCCC-cCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCc
Confidence            56889999999733 2479999999999999999999877      469999999999999999965  67788875

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=3.9e-17  Score=108.03  Aligned_cols=69  Identities=16%  Similarity=0.112  Sum_probs=59.7

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEe-----ecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLV-----KDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~-----~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ++|||+|||..+  ++++|+++|+.||.|..+.+.     .+..++.++|||||+|.+.++|++|++ |||..++||
T Consensus         2 RrlyVgNLp~~~--te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr   75 (90)
T d1u2fa_           2 RRLYVGNIPFGI--TEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQ   75 (90)
T ss_dssp             CEEEECSCCTTC--CTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSS
T ss_pred             CEEEEcCCCCcc--chHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCE
Confidence            479999997665  789999999999988766654     455778899999999999999999985 999999996

>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=99.56  E-value=2.8e-16  Score=106.37  Aligned_cols=69  Identities=13%  Similarity=0.084  Sum_probs=61.8

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..++|.+++.+.  ++++|+++|++||.|.+|+|+++ .++.++|+|||+|.+.++|.+|++.|||+.++||
T Consensus        28 ~~~~v~~~~~~~--~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr   96 (104)
T d1jmta_          28 SDVEMQEHYDEF--FEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ   96 (104)
T ss_dssp             HHHHHHHHHHHH--HHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             chHHhhhhhhhh--hHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCE
Confidence            357888885444  68899999999999999999888 5799999999999999999999999999999996

>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=99.54  E-value=2.8e-15  Score=100.83  Aligned_cols=64  Identities=13%  Similarity=0.092  Sum_probs=56.8

Q ss_pred             CCCCcceecc--CCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccc
Q psy1680         153 GEGPGGFRNN--NGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV  224 (227)
Q Consensus       153 ~~~~~l~v~n--l~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i  224 (227)
                      .|..+|+|.|  ||...  |+++|+++|++||.|+.|+++++      +|||||+|.+.++|.+|++.|||..|
T Consensus        16 ~pt~~l~V~ng~L~~~v--te~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGV--SRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTC--CHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCC--CHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            4567889966  86555  89999999999999999998876      57999999999999999999999987

>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=99.53  E-value=1.9e-15  Score=102.22  Aligned_cols=68  Identities=9%  Similarity=0.003  Sum_probs=58.8

Q ss_pred             CCCcceeccCCCCCC---CChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         154 EGPGGFRNNNGPNRS---NSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       154 ~~~~l~v~nl~~~~~---~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ...+|||+||+..+.   +++++|+++|+.||.|.++++++.      +++|||+|.+.++|.+|++.|||..|+|+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~   74 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGK   74 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCC
Confidence            456899999986542   334679999999999999999864      68999999999999999999999999985

>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=99.53  E-value=2.1e-15  Score=102.08  Aligned_cols=75  Identities=12%  Similarity=-0.035  Sum_probs=63.4

Q ss_pred             CCCCcceeccC--CCCCC------CChhhHHhhhccccceEEEEEeecCCCCc--ccceEEEEEcCHHHHHHHHHHcCCc
Q psy1680         153 GEGPGGFRNNN--GPNRS------NSMNDHGLMVTEVTTLVSVRLVKDKETDR--FKGFCYVEFVDVENLRQALLKDGRI  222 (227)
Q Consensus       153 ~~~~~l~v~nl--~~~~~------~~~~~l~~~f~~~g~i~~v~i~~d~~t~~--~~g~afV~F~~~~~a~~Al~~l~g~  222 (227)
                      +|+++|.+.|+  |....      +..+||+..|++||.|++|.|++++.+..  ..|++||+|.+.++|.+|+..|||+
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            67889999999  33322      23468999999999999999998776543  4689999999999999999999999


Q ss_pred             cccCC
Q psy1680         223 TVDGL  227 (227)
Q Consensus       223 ~i~gr  227 (227)
                      .++||
T Consensus        82 ~f~gR   86 (104)
T d1o0pa_          82 KFANR   86 (104)
T ss_dssp             CSSSS
T ss_pred             EECCe
Confidence            99998

>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=99.46  E-value=2e-14  Score=96.23  Aligned_cols=71  Identities=13%  Similarity=0.028  Sum_probs=59.9

Q ss_pred             CCCCcceeccC--CCCC-------CCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCcc
Q psy1680         153 GEGPGGFRNNN--GPNR-------SNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRIT  223 (227)
Q Consensus       153 ~~~~~l~v~nl--~~~~-------~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~  223 (227)
                      ..+++|+|.||  |.+.       .+.++||+..|++||.|..|.+..+.    ++|+|||+|.+.++|.+|+..|||+.
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~----~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC----TTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC----CccEEEEEECCHHHHHHHHHHhCCcE
Confidence            56789999999  4321       12347899999999999999987653    57999999999999999999999999


Q ss_pred             ccCC
Q psy1680         224 VDGL  227 (227)
Q Consensus       224 i~gr  227 (227)
                      |+||
T Consensus        82 ~~gr   85 (99)
T d2dita1          82 FGGR   85 (99)
T ss_dssp             ETTE
T ss_pred             ECCE
Confidence            9997

>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=99.45  E-value=5.5e-14  Score=96.40  Aligned_cols=63  Identities=6%  Similarity=0.006  Sum_probs=55.3

Q ss_pred             cceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCH-HHHHHHHHHcCCccccCC
Q psy1680         157 GGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDV-ENLRQALLKDGRITVDGL  227 (227)
Q Consensus       157 ~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~-~~a~~Al~~l~g~~i~gr  227 (227)
                      .+||+|||+..  |+++|+++|++||.|.+|.|+++      +|||||.|.+. ++|.+|+..+++..|.++
T Consensus        13 ~~fvgnL~~~~--tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~   76 (113)
T d1owxa_          13 LKFSGDLDDQT--CREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLR   76 (113)
T ss_dssp             EEEEESCCSSC--CHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTT
T ss_pred             EEEECCCCCCC--CHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecC
Confidence            45999997655  89999999999999999999876      68999999985 789999999999888654

>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=99.45  E-value=4.5e-15  Score=100.33  Aligned_cols=74  Identities=11%  Similarity=0.175  Sum_probs=68.1

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEec
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIA   89 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~   89 (227)
                      ..++|++++..+++++|+++|++| .|.+|.|+++ .+++++|+|||+|.+.++|.+|+. +|| ..++|++|.|.++
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng-~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNN-RWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTT-CEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCC-CEECCEEEEEEEC
Confidence            357788888889999999999999 9999999877 578999999999999999999999 999 9999999999875

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.41  E-value=1.5e-13  Score=92.22  Aligned_cols=65  Identities=14%  Similarity=0.269  Sum_probs=58.0

Q ss_pred             CCCCCCceEEEc--CCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCcee
Q psy1680           8 LPTEPPYTAFVG--NLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITV   79 (227)
Q Consensus         8 ~~~~~~~~l~V~--nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~   79 (227)
                      ....++.+|||.  |||..+|+++|+++|++| .|..+.++.+      ++||||+|.+.++|.+|+. ||| ..+
T Consensus        13 ~~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng-~~i   81 (101)
T d2cq2a1          13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNG-KEV   81 (101)
T ss_dssp             CCSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTT-CEE
T ss_pred             cCCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCC-CCC
Confidence            345678899995  599999999999999999 9999988765      6799999999999999999 999 776

>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=99.40  E-value=2.2e-13  Score=87.41  Aligned_cols=72  Identities=14%  Similarity=0.110  Sum_probs=61.9

Q ss_pred             CceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCceeCCe-EeEEEecC
Q psy1680          13 PYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL-QVRLDIAD   90 (227)
Q Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~~~g~-~l~v~~~~   90 (227)
                      .+.|+|.|+|++++++.| ++|++| .|.++.+.++      ++||||+|.+.++|++||.+|| ..|+|+ .|.|....
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~------~~~~fV~f~~~~~A~~Al~~nG-~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALSKDG-RIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHTTTT-CEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC------CCEEEEEEcccHHHHHHHhcCC-CeECCcEEEEEEeCC
Confidence            467999999999987655 579999 9999988543      7899999999999999999999 999997 56788876


Q ss_pred             CC
Q psy1680          91 GK   92 (227)
Q Consensus        91 ~~   92 (227)
                      .+
T Consensus        76 ~k   77 (81)
T d1wwha1          76 DK   77 (81)
T ss_dssp             CH
T ss_pred             Ch
Confidence            54

>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=99.40  E-value=5.5e-13  Score=91.30  Aligned_cols=70  Identities=10%  Similarity=0.128  Sum_probs=60.1

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCH-HHHHHHHH-hCCCceeCCeEeEEEecC
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDV-ENLRQALL-KDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~-~~a~~al~-~~~~~~~~g~~l~v~~~~   90 (227)
                      ..+||+|||..+|+++|+++|++| +|..|.|+++      ++||||.|.+. ++|..|+. +++ ..+.++.+.|.+..
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~-~~l~~~~~~v~~~~   84 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANN-GNLQLRNKEVTWEV   84 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTT-SCBCTTSSSEEEEE
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcC-CceecCceEEEEee
Confidence            455999999999999999999999 9999999865      78999999985 77888998 998 88877766666654

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=6.5e-13  Score=88.71  Aligned_cols=82  Identities=18%  Similarity=0.225  Sum_probs=68.8

Q ss_pred             CCCCCCceEEEcCC--CCCCC---------HHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hC
Q psy1680           8 LPTEPPYTAFVGNL--PNGIT---------QGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KD   74 (227)
Q Consensus         8 ~~~~~~~~l~V~nL--p~~~t---------~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~   74 (227)
                      .....+++|+|.||  |.++.         +++|++.|++| .|..+.+..+    ..+|+|||+|.+.++|.+|+. +|
T Consensus         3 ~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~ln   78 (99)
T d2dita1           3 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLD   78 (99)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhC
Confidence            34567899999999  54322         25789999999 9999988765    347999999999999999999 99


Q ss_pred             CCceeCCeEeEEEecCCCCC
Q psy1680          75 GRITVDGLQVRLDIADGKRN   94 (227)
Q Consensus        75 ~~~~~~g~~l~v~~~~~~~~   94 (227)
                      | ..++|++|.|.++.++..
T Consensus        79 g-~~~~gr~i~v~~~~g~~~   97 (99)
T d2dita1          79 G-RWFGGRQITAQAWDGTTD   97 (99)
T ss_dssp             T-CEETTEECEEEECCSCCC
T ss_pred             C-cEECCEEEEEEEeCCcCC
Confidence            9 999999999999877653

>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=99.39  E-value=1.9e-13  Score=87.68  Aligned_cols=62  Identities=6%  Similarity=-0.068  Sum_probs=52.5

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccCC
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL  227 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~gr  227 (227)
                      ..|+|.++|+..  + +++.++|++||.|.++++.++      +|||||+|.+.++|.+||+ +||..|+||
T Consensus         5 ~wV~V~G~p~~~--~-~~il~~F~~~G~I~~~~~~~~------~~~~fV~f~~~~~A~~Al~-~nG~~~~g~   66 (81)
T d1wwha1           5 TWVTVFGFPQAS--A-SYILLQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALS-KDGRIFGES   66 (81)
T ss_dssp             GEEEEECCCGGG--H-HHHHHHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHT-TTTCEETTT
T ss_pred             cEEEEECCChHH--H-HHHHHHHHhhhhhheEEecCC------CCEEEEEEcccHHHHHHHh-cCCCeECCc
Confidence            458999997644  4 556678999999999987544      6899999999999999995 899999986

>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=99.24  E-value=3.9e-12  Score=85.63  Aligned_cols=80  Identities=19%  Similarity=0.186  Sum_probs=67.6

Q ss_pred             CCCceEEEcCC--CCCCC--------HHHHHhcccCC-CeEEEEEeecCCCC--CeecEEEEEeCCHHHHHHHHH-hCCC
Q psy1680          11 EPPYTAFVGNL--PNGIT--------QGDVERFFPEQ-KLVSVRLVKDKETD--RFKGFCYVEFVDVENLRQALL-KDGR   76 (227)
Q Consensus        11 ~~~~~l~V~nL--p~~~t--------~~~l~~~f~~~-~i~~v~i~~~~~~~--~~~g~afv~f~~~~~a~~al~-~~~~   76 (227)
                      +|++.|.|.||  |..+.        .+||++.|++| .|.+|.|++++.+.  ...|++||+|.+.++|.+|+. |+| 
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 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG-   80 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSS-
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCC-
Confidence            56889999999  44432        34689999999 99999998865443  446899999999999999999 999 


Q ss_pred             ceeCCeEeEEEecCC
Q psy1680          77 ITVDGLQVRLDIADG   91 (227)
Q Consensus        77 ~~~~g~~l~v~~~~~   91 (227)
                      ..++|+.|.+.++.+
T Consensus        81 r~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          81 RKFANRVVVTKYCDP   95 (104)
T ss_dssp             CCSSSSCCEEEEECH
T ss_pred             CEECCeEEEEEEcCH
Confidence            999999999999763

>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=97.26  E-value=0.00067  Score=42.82  Aligned_cols=66  Identities=12%  Similarity=0.161  Sum_probs=52.8

Q ss_pred             ceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCC--eecEEEEEeCCHHHHHHHHH-hCCCceeC
Q psy1680          14 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDR--FKGFCYVEFVDVENLRQALL-KDGRITVD   80 (227)
Q Consensus        14 ~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~--~~g~afv~f~~~~~a~~al~-~~~~~~~~   80 (227)
                      ++|.|+.||+.+|++++.+.+... .+....-...+.+.+  .-.-|+|.|.+.+++....+ .+| ..+.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g-~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDG-YVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTT-CEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCC-cEEE
Confidence            578999999999999999999988 777665555433322  22589999999999999998 999 6653

>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=97.07  E-value=0.00052  Score=42.83  Aligned_cols=73  Identities=19%  Similarity=0.215  Sum_probs=56.9

Q ss_pred             CCCCCceEEEcCCCCCCCH---------HHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHHhCCCce
Q psy1680           9 PTEPPYTAFVGNLPNGITQ---------GDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRIT   78 (227)
Q Consensus         9 ~~~~~~~l~V~nLp~~~t~---------~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~~~~~~~   78 (227)
                      .-++.-+|.|.=...+..+         .+|.+.|..| +|.-++++.+        -.+|+|.+-++|.+|+.+++ .+
T Consensus        11 qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l~g-~~   81 (95)
T d1ufwa_          11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDVDG-MK   81 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHGGG-SE
T ss_pred             cCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhccCC-eE
Confidence            3456677777533333222         2577788889 9999999855        68999999999999999999 99


Q ss_pred             eCCeEeEEEecC
Q psy1680          79 VDGLQVRLDIAD   90 (227)
Q Consensus        79 ~~g~~l~v~~~~   90 (227)
                      +.|+.|.|....
T Consensus        82 v~G~~l~It~~~   93 (95)
T d1ufwa_          82 VKGRAVKISGPS   93 (95)
T ss_dssp             ETTEEEEEECCC
T ss_pred             EcceEEEEecCC
Confidence            999999998654

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.95  E-value=0.0014  Score=38.82  Aligned_cols=63  Identities=13%  Similarity=0.237  Sum_probs=50.9

Q ss_pred             CCCHHHH----HhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH-hCCCceeCCeEeEEEecC
Q psy1680          24 GITQGDV----ERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL-KDGRITVDGLQVRLDIAD   90 (227)
Q Consensus        24 ~~t~~~l----~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~-~~~~~~~~g~~l~v~~~~   90 (227)
                      .+.+.+|    .+.|.++ .|..+.+....   ...-.|-|...+.++|.-|+. |+. .++++++|.|.++.
T Consensus         3 ~L~~kelqq~L~~~f~~h~~V~sv~l~~~~---dg~~~A~V~v~~~q~A~~~v~~LhR-~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1           3 RLSRKELQQLLQEAFARHGKVKSVELSPHT---DYQLKAVVQMENLQDAIGAVNSLHR-YKIGSKKILVSLAT   71 (73)
T ss_dssp             TSCHHHHHHHHHHHHHHHSCEEEEEECSCC---STTCCEEEEESSHHHHHHHHHHHTT-EEETTEEEEEEECC
T ss_pred             cCCHHHHHHHHHHHHHhheeEEEEEEEecc---CCcEEEEEEcCCHHHHHHHHHHHHH-HhcCCeEEEEEEec
Confidence            3455554    4568888 99999886542   224589999999999999999 999 99999999999875

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.94  E-value=0.0002  Score=44.78  Aligned_cols=66  Identities=20%  Similarity=0.157  Sum_probs=48.4

Q ss_pred             CCCCCcceeccCCCCCCC-------ChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccc
Q psy1680         152 GGEGPGGFRNNNGPNRSN-------SMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITV  224 (227)
Q Consensus       152 ~~~~~~l~v~nl~~~~~~-------~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i  224 (227)
                      +||..||.|.-..+..++       -.++|.+.|+.||.|.-|+++.|        ...|+|.+-..|-+|+. ++|.++
T Consensus        12 GPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v   82 (95)
T d1ufwa_          12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEE
T ss_pred             CCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEE
Confidence            467778888666422211       13678888999999999999887        48999999999999876 444555


Q ss_pred             cC
Q psy1680         225 DG  226 (227)
Q Consensus       225 ~g  226 (227)
                      .|
T Consensus        83 ~G   84 (95)
T d1ufwa_          83 KG   84 (95)
T ss_dssp             TT
T ss_pred             cc
Confidence            54

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.93  E-value=0.0018  Score=40.78  Aligned_cols=68  Identities=6%  Similarity=-0.065  Sum_probs=56.7

Q ss_pred             CcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcc--cceEEEEEcCHHHHHHHHHHcCCcccc
Q psy1680         156 PGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRF--KGFCYVEFVDVENLRQALLKDGRITVD  225 (227)
Q Consensus       156 ~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~--~g~afV~F~~~~~a~~Al~~l~g~~i~  225 (227)
                      .+|.|+.||+.+  |++++.+.+++.+.+..........+.+.  -.-|+|.|.+.++...-.+..+|+.+-
T Consensus         2 tKvVvRrLPP~L--te~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTL--TKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTC--CHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCC--CHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            368999999888  78999999999999988888776555442  246899999999999999999998763

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.75  E-value=0.0024  Score=40.46  Aligned_cols=55  Identities=9%  Similarity=0.106  Sum_probs=41.2

Q ss_pred             CCcceeccCCCCCCCChhhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHc
Q psy1680         155 GPGGFRNNNGPNRSNSMNDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD  219 (227)
Q Consensus       155 ~~~l~v~nl~~~~~~~~~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l  219 (227)
                      ..-+|.-..  +..+...||.++|++||.|. |.++-|-       -|||...+.++|+.++..+
T Consensus        15 RdHVf~~tF--P~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~~~~v~~~~   69 (100)
T d1whva_          15 RDHVLHVTF--PKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCSEEEEEC--CTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             cceeEEEeC--CcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHHHHHHHHHh
Confidence            344555555  55667899999999999776 5555442       6999999999988887654

>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=95.29  E-value=0.021  Score=33.57  Aligned_cols=52  Identities=12%  Similarity=0.057  Sum_probs=43.5

Q ss_pred             hhHHhhhccccceEEEEEeecCCCCcccceEEEEEcCHHHHHHHHHHcCCccccC
Q psy1680         172 NDHGLMVTEVTTLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDG  226 (227)
Q Consensus       172 ~~l~~~f~~~g~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~Al~~l~g~~i~g  226 (227)
                      +-|...|.+++.|.++.|..-.+ +..  .|-|...+..+|.-|+..|+-+.|++
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~d-g~~--~A~V~v~~~q~A~~~v~~LhR~KiG~   62 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTD-YQL--KAVVQMENLQDAIGAVNSLHRYKIGS   62 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCS-TTC--CEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             HHHHHHHHhheeEEEEEEEeccC-CcE--EEEEEcCCHHHHHHHHHHHHHHhcCC
Confidence            45677899999999999977643 444  69999999999999999999988875

>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=95.02  E-value=0.039  Score=34.66  Aligned_cols=57  Identities=12%  Similarity=0.144  Sum_probs=44.5

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHhcccCC-CeEEEEEeecCCCCCeecEEEEEeCCHHHHHHHHH
Q psy1680           8 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL   72 (227)
Q Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~-~i~~v~i~~~~~~~~~~g~afv~f~~~~~a~~al~   72 (227)
                      .+.+...-||.-.+|..|...||.++|+.| .|.-.+| -+       --|||.....++|..++.
T Consensus        10 d~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-dd-------TSa~V~L~~~e~~~~v~~   67 (100)
T d1whva_          10 DLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DD-------TSAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCCCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ET-------TEEEEECSCHHHHHHHHH
T ss_pred             CCCCCcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cC-------ceEEEEecCHHHHHHHHH
Confidence            344555667777899999999999999999 5544444 33       269999999999999886