Citrus Sinensis ID: 009860

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520---
Protein Sequence
MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLEFLKVIAKPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAAESGAQESLAVGRVGRRSRAASASKTSSTTTKRGSEKKKYILKDSAKNARRKDKSTFTVVAKREDQPASSSGKETSASETICGVEGSVGIPLTSDTGKKKILLLKGKEREIPHVPDALLDKQRESSPVKNSASPTVPKQIQRREAGGRLIRKILLNNETRQTQSVTGVQPQQKMQNLNQENGKPLPGPTSSPNGHVTNNDSPIFSFDGNTKRSSDDRFARKVLHGSGAVSEKQEKRTRNKDRPDRVVWTPRRSDVSQANGERLSSSQPTQLLSDSVEVTRGEMKDDMSYGSKTVDIAAPTSGGSHRHNGRRAATNITKDDGCINMIEGKSSKRRGAAGSGGNEKQVWIQKSSSGH
Secondary Structure (PSIPRED)
ccccccccEEEEEcccccccHHHHHHHHcccccccccEEEEEccccccccccccEEEEEcccHHHHHHHHHHHcccEEEEccccccccEEEEcccccccccccccccccccccccHHHHHHHHHHcccccccccHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHccccHHHHHHccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccc
Secondary Structure Prediction (SSPRO)
ccccccccEEEEEcccccccHHHHHHHHcccccccccEEEEEccccccccccccEEEEEEccHHHHHHHHHHcccEEEEccccccccEEEEEcccccccccccccccccccccccHHHHHHHHHHccccccccccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHccccccccHHcccccccEEEcccccccccccccccEccccccccccccccccccccccHHccccccccccEccccccEEEEEcccccccccccccccHcccccccccccccccccHHcccccccccEEEEEEccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccccHHcccccccccccccHHHHHccccccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccEEcccccccccccccccccccEEEEEEEccccc
Coil and Loop (DISEMBL)
MKEPLQRTKVVirhlppslsqnDLLALFRDHFndrynwfcfrpgkssykhqrySRAYVELKKPAGVFEFAELlnghvfvnekGAQFKAIVeyapsqrvpkpfsrkdsregtifkdpdYLEFLKVIAkpaenlpsaEIQLERKEaelsgapketlvvTPLMEYVRQKRAAESGAQESLAVgrvgrrsraasasktsstttkrgsekkKYILKDSaknarrkdkstFTVVAkredqpasssgketsaseticgvegsvgipltsdtgKKKILLLKgkereiphvpdalldkqresspvknsasptvpkqiQRREAGGRLIRKILLNnetrqtqsvtgvqpqqkmqnlnqengkplpgptsspnghvtnndspifsfdgntkrssddrFARKVlhgsgavsekqekrtrnkdrpdrvvwtprrsdvsqangerlsssqptqllsdsvevtrgemkddmsygsktvdiaaptsggshrhngrraatnitkddgcinmiegksskrrgaagsggneKQVWIQKSSSGH
Flexible Loop (DISEMBL)
mkeplqrtkvvirhlppslsqnDLLALFRDHFNDRYNWFCfrpgkssykhQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVeyapsqrvpkpfsrkdsregtifkdpdYLEFLKVIAKPAENLPSAEIQLERkeaelsgapketlvvtPLMEYVRQKraaesgaqeslavgrvgrrsraasasktsstttkrgsekkkyilkdsaknarrkdkstftvvakredqpasssgketsaseticgvegsvgipltsdtgKKKILLlkgkereiphvpdalldkqresspvknsasptvpkqiqrreaGGRLIRKILlnnetrqtqsvtgvqpqqkMQNLNQENGKPLPGPTSSPNGHVTNNDSPIFSFDGNTKRSSDDRFARKvlhgsgavsekqekrtrnkdrpdrvvwtprrsdvsqangerlsssqptqllsdSVEVTRGEMKDDMSYGSKTVDiaaptsggshrhngrraatnitkddgciNMIEGKSSkrrgaagsggnekqvwiqksssgh
Low Complexity Region (SEG)
MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLEFLKVIAKPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAAESGAQESLavgrvgrrsraasasktsstttkrgsekkkYILKDSAKNARRKDKSTFTVVAKREDQPASSSGKETSASETICGVEGSVGIPLTSDTgkkkilllkgkEREIPHVPDALLDKQRESSPVKNSASPTVPKQIQRREAGGRLIRKILLNNETRQTQSVTGVQPQQKMQNLNQENGKPLPGPTSSPNGHVTNNDSPIFSFDGNTKRSSDDRFARKVLHGSGAVSEKQEKRTRNKDRPDRVVWTPRRSDVSQANGERLSSSQPTQLLSDSVEVTRGEMKDDMSYGSKTVDIAAPTSGGSHRHNGRRAATNITKDDGCINMIEgksskrrgaagsggNEKQVWIQKSSSGH
Disordered region (IsUnstruct)
*********VVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYA*****************TIFKDPDYLEFLKVIAK***************************VVTPLM****************************************************************************************ICGVEGSVGIPLT*****KKILLL*********************************************IRKIL*********************************************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
*****QR*KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQR****************KDPDYLEFLKVIA******************************TPL*********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************Q******
Disordered Region (DISEMBL)
MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLEFLKVIAKPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQK***************************************KKYILKDSAKNARRKDKSTFTVVA******************TICGVEGSVGIPLTSDTGKKKILLLKGKEREIPHVPDALLDK*****************QIQRREAGGRLIRKILLNNETR**********QQKMQNLNQENGKPLPGPTSSPNGHVTNNDSPIFSFDGNTKRSSDDRFARKVLHG*****************PDRVVWTP********************LLSDSVEVTRGEMKDDMSYGSKTVDIAAP**********RRAATNITKDDGCINMIEGKS*************************
Disordered Region (DISPRO)
*****QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPF*****REGTIFKDPDYLEFLKVIAKP***LPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAAE***********************************************************************************************KKKIL**KG*****************************************RLIR**LLN*********************************************************************************RNKDRPDRVVWTPR***************************************************************************************SGGNEKQVWIQKS****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLEFLKVIAKPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAAESGAQESLAVGRVGRRSRAASASKTSSTTTKRGSEKKKYILKDSAKNARRKDKSTFTVVAKREDQPASSSGKETSASETICGVEGSVGIPLTSDTGKKKILLLKGKEREIPHVPDALLDKQRESSPVKNSASPTVPKQIQRREAGGRLIRKILLNNETRQTQSVTGVQPQQKMQNLNQENGKPLPGPTSSPNGHVTNNDSPIFSFDGNTKRSSDDRFARKVLHGSGAVSEKQEKRTRNKDRPDRVVWTPRRSDVSQANGERLSSSQPTQLLSDSVEVTRGEMKDDMSYGSKTVDIAAPTSGGSHRHNGRRAATNITKDDGCINMIEGKSSKRRGAAGSGGNEKQVWIQKSSSGH
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	523	2.2.26 [Sep-21-2011]
B0S733	452	Regulator of nonsense tra	no	no	0.290	0.336	0.343	3e-16
Q9BZI7	483	Regulator of nonsense tra	yes	no	0.290	0.314	0.325	8e-14
Q9H1J1	476	Regulator of nonsense tra	no	no	0.294	0.323	0.329	4e-13
Q10267	278	Nonsense-mediated mRNA de	yes	no	0.282	0.532	0.288	1e-11

>sp|B0S733|REN3A_DANRE Regulator of nonsense transcripts 3A OS=Danio rerio GN=upf3a PE=2 SV=2

 Score = 87.4 bits (215), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 57/166 (34%), Positives = 95/166 (57%), Gaps = 14/166 (8%)

Query: 8   TKVVIRHLPPSLSQNDLLALFRDHFND--RYNWFCFRPGKSSYKHQRYSRAYVELKKPAG 65
           +KVVIR LPPSLS++ L    ++H +    +++F F P   S     +SRAY+  K P  
Sbjct: 43  SKVVIRRLPPSLSKDQL----QEHLSPLPSFDYFEFFPADQSLYPHLFSRAYINFKNPED 98

Query: 66  VFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSRE-GTIFKDPDYLEFLKV 124
           +  F +  +G+VF++ KG ++ A+VE+AP Q+V K   +K   + GTI +DP+Y  FL+ 
Sbjct: 99  IIIFRDRFDGYVFIDNKGQEYPAVVEFAPFQKVSKKKLKKKDAKAGTIEEDPEYRRFLEN 158

Query: 125 IAKPAE-NLPSAEIQLERKEAELSGAPKETLV--VTPLMEYVRQKR 167
            +   E ++ + E  L     E+    +E +    TPL+EY++ K+
Sbjct: 159 YSCDEEKSMANPETLL----GEIEAKTRELIAKRTTPLLEYIKNKK 200

Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC) and serving as link between the EJC core and NMD machinery. Recruits UPF2 at the cytoplasmic side of the nuclear envelope and the subsequent formation of an UPF1-UPF2-UPF3 surveillance complex (including UPF1 bound to release factors at the stalled ribosome) is believed to activate NMD. Binds spliced mRNA upstream of exon-exon junctions.
Danio rerio (taxid: 7955)

>sp|Q9BZI7|REN3B_HUMAN Regulator of nonsense transcripts 3B OS=Homo sapiens GN=UPF3B PE=1 SV=1

 Score = 79.0 bits (193), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 54/166 (32%), Positives = 91/166 (54%), Gaps = 14/166 (8%)

Query: 8   TKVVIRHLPPSLSQNDLLALFRDHFND--RYNWFCFRPGKSSYKHQRYSRAYVELKKPAG 65
           +KVVIR LPP+L++  L    ++H      +++F F    +S     Y+RAY+  K    
Sbjct: 51  SKVVIRRLPPTLTKEQL----QEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQED 106

Query: 66  VFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSRE-GTIFKDPDYLEFLKV 124
           +  F +  +G+VF++ KG ++ AIVE+AP Q+  K  ++K   + GTI  DP+Y +FL+ 
Sbjct: 107 IILFRDRFDGYVFLDNKGQEYPAIVEFAPFQKAAKKKTKKRDTKVGTIDDDPEYRKFLES 166

Query: 125 IAKPAENLPSA-EIQLERKEAELSGAPKETLV--VTPLMEYVRQKR 167
            A   E + S  E  LE    E+    +E +    TPL+ +++ K+
Sbjct: 167 YATDNEKMTSTPETLLE----EIEAKNRELIAKKTTPLLSFLKNKQ 208

Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC) and serving as link between the EJC core and NMD machinery. Recruits UPF2 at the cytoplasmic side of the nuclear envelope and the subsequent formation of an UPF1-UPF2-UPF3 surveillance complex (including UPF1 bound to release factors at the stalled ribosome) is believed to activate NMD. In cooperation with UPF2 stimulates both ATPase and RNA helicase activities of UPF1. Binds spliced mRNA upstream of exon-exon junctions. In vitro, stimulates translation; the function is indepenedent of association with UPF2 and components of the EJC core.

Homo sapiens (taxid: 9606)

>sp|Q9H1J1|REN3A_HUMAN Regulator of nonsense transcripts 3A OS=Homo sapiens GN=UPF3A PE=1 SV=1

 Score = 76.6 bits (187), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 54/164 (32%), Positives = 86/164 (52%), Gaps = 10/164 (6%)

Query: 8   TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVF 67
           +KVVIR LPP L++  L    R      Y  F F    S Y H  YSRAY+  + P  + 
Sbjct: 68  SKVVIRRLPPGLTKEQLEEQLRPLPAHDYFEF-FAADLSLYPHL-YSRAYINFRNPDDIL 125

Query: 68  EFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSRE-GTIFKDPDYLEFLKVIA 126
            F +  +G++F++ KG ++ A+VE+AP Q++ K   RK   + G+I  DP+Y +FL+   
Sbjct: 126 LFRDRFDGYIFLDSKGLEYPAVVEFAPFQKIAKKKLRKKDAKTGSIEDDPEYKKFLETYC 185

Query: 127 KPAENLPS-AEIQLERKEAELSGAPKETLV--VTPLMEYVRQKR 167
              E   +  E  L     E+    +E +    TPL+EY++ ++
Sbjct: 186 VEEEKTSANPETLL----GEMEAKTRELIARRTTPLLEYIKNRK 225

Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC) and serving as link between the EJC core and NMD machinery. Recruits UPF2 at the cytoplasmic side of the nuclear envelope and the subsequent formation of an UPF1-UPF2-UPF3 surveillance complex (including UPF1 bound to release factors at the stalled ribosome) is believed to activate NMD. However, UPF3A is shown to be only marginally active in NMD as compared to UPF3B. Binds spliced mRNA upstream of exon-exon junctions. In vitro, weakly stimulates translation.

Homo sapiens (taxid: 9606)

>sp|Q10267|UPF3_SCHPO Nonsense-mediated mRNA decay protein 3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=upf3 PE=3 SV=1

 Score = 71.6 bits (174), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 47/163 (28%), Positives = 83/163 (50%), Gaps = 15/163 (9%)

Query: 9   KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSY--KHQRYSRAYVELKKPAGV 66
           KV++ +LPP+L +   L    + F     W  F  GK++   + +  S AY++ +    V
Sbjct: 13  KVLVFNLPPTLPEQVFLQSI-NSFLPHVEWHRFSKGKATVGTRSELLSFAYLKFQSATAV 71

Query: 67  FEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLEFLKVIA 126
            EF  +  GH F+++K   ++AIV  AP Q++P    + DS EG++ +DP + EF KV  
Sbjct: 72  QEFFRVYQGHTFIDKKNNTYRAIVTIAPYQKIPPSKVKADSLEGSLEQDPKFQEF-KVQR 130

Query: 127 KPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAA 169
           +      S +  +E+ +             TPL++Y+ +K+ A
Sbjct: 131 ESYSQTASNDDVIEKLQTS-----------TPLLQYLAEKKNA 162

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

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	523
449447609	506	PREDICTED: uncharacterized protein LOC10	0.946	0.978	0.575	1e-146
356507710	535	PREDICTED: uncharacterized protein LOC10	0.969	0.947	0.560	1e-141
356517820	529	PREDICTED: uncharacterized protein LOC10	0.950	0.939	0.560	1e-139
357455505	1203	B3 domain-containing protein [Medicago t	0.956	0.415	0.530	1e-126
30692963	482	Smg-4/UPF3-like protein [Arabidopsis tha	0.906	0.983	0.500	1e-117
297739512	519	unnamed protein product [Vitis vinifera]	0.959	0.967	0.507	1e-116
297846376	486	ATUPF3/UPF3 [Arabidopsis lyrata subsp. l	0.913	0.983	0.506	1e-115
186488168	484	Smg-4/UPF3-like protein [Arabidopsis tha	0.906	0.979	0.497	1e-115
224146308	527	predicted protein [Populus trichocarpa]	0.965	0.958	0.494	1e-111
10086477	525	Unknown protein [Arabidopsis thaliana]	0.850	0.847	0.496	1e-108

>gi|449447609|ref|XP_004141560.1| PREDICTED: uncharacterized protein LOC101208317 [Cucumis sativus] gi|449517953|ref|XP_004166008.1| PREDICTED: uncharacterized LOC101208317 [Cucumis sativus]

 Score =  526 bits (1354), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 306/532 (57%), Positives = 375/532 (70%), Gaps = 37/532 (6%)

Query: 1   MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVEL 60
           MK+PL+RTKVVIRHLPPSLS +DL     D F  R+NW  +RPGK+S K QRY+RAY++ 
Sbjct: 1   MKDPLERTKVVIRHLPPSLSHSDLFHHIHDRFAGRFNWSYYRPGKTSQKDQRYARAYIDF 60

Query: 61  KKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLE 120
            +P  VFEFAE  +GHVFVNEKGAQ+KA+VEYAPSQRVP+  ++KD REGTI+KDPDYLE
Sbjct: 61  TRPEDVFEFAEFFDGHVFVNEKGAQYKAVVEYAPSQRVPRSSTKKDGREGTIYKDPDYLE 120

Query: 121 FLKVIAKPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAAESGAQESLAVG 180
           FLK+IAKPAE+LPSAEIQLERKEAE SGA KET +VTPLME+VRQKRA ESG Q S +V 
Sbjct: 121 FLKLIAKPAEHLPSAEIQLERKEAEQSGAAKETPIVTPLMEFVRQKRAVESGTQGS-SVP 179

Query: 181 RVGRRSRAASASKTSSTTTKRGSEKKKYILKDSAKNARRKDKSTFTVVAKREDQPASSSG 240
           R  +R  AAS+ K  S + KRG EKKKYILKDS KN  R+DKS F +V +REDQ A+SS 
Sbjct: 180 RKVKRGGAASSRKPESNSMKRGMEKKKYILKDSVKNTNRRDKSNFILVPRREDQSATSSA 239

Query: 241 KETSASETICGVEGSVGIPLTSDTGKKKILLLKGKEREIPHVPDALLDKQRESSPVKNSA 300
                     G+   VG   T+D GKKKILLLKGKER+I H+         +S+    ++
Sbjct: 240 ---------IGIS-DVG---TADFGKKKILLLKGKERDISHL---------QSATSSGNS 277

Query: 301 SPTVPKQIQRREAGGRLIRKILLNNETRQTQSVTGVQPQQKMQNLNQENGKPLPGPTSSP 360
             +  K   RREAGG +IR ILLNNE R  QS +  Q  QK+Q LN +NGK  P PT++ 
Sbjct: 278 PASASKHNHRREAGGGVIRSILLNNEARHGQSSSVAQSHQKIQILNSDNGKRPPRPTNAR 337

Query: 361 NG--HVTNNDSPIFSFDGNTKRSSDDRFARKVLHGSGAVSEKQEKRTRNKDRPDRVVWTP 418
           +G   +++N+      +G+ KR+SD++F++K LHG G+ SEKQEKR RNKDRPDR VW P
Sbjct: 338 SGSNDISSNEPNPSGSEGDGKRASDNKFSKKELHGLGSASEKQEKRIRNKDRPDRGVWAP 397

Query: 419 R-RSDVSQANGERLSSSQPTQLLSDSVEVTRGEMKDDMSYGSKTVDIAAPTSG------- 470
           R RSD S +  E  S  Q + LLSDSVE  RGEMK+D+ +GS+T D+    SG       
Sbjct: 398 RSRSDASVSQLEESSVPQSSHLLSDSVEAFRGEMKEDI-HGSRTGDVTTIVSGRNSSVEN 456

Query: 471 GSHRHNGRRAATNITKDDGCINMIEGKSSKRRGAAGSGGNEKQVWIQKSSSG 522
           GS RH GRR A ++ KDDG +N  EGK SK RG A  GG+EKQVW+QKSSSG
Sbjct: 457 GSVRHVGRRGAGHVMKDDGSLNPNEGKPSK-RGVA--GGHEKQVWVQKSSSG 505

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356507710|ref|XP_003522607.1| PREDICTED: uncharacterized protein LOC100801152 [Glycine max]

 Score =  507 bits (1305), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 301/537 (56%), Positives = 376/537 (70%), Gaps = 30/537 (5%)

Query: 6   QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAG 65
           ++TKVVIRHLPPSL+Q+DL      HF  RYNWF FRPG +S+K QR+SRAY++ K P  
Sbjct: 8   EKTKVVIRHLPPSLTQSDLFQHIDSHFASRYNWFSFRPGNNSHKRQRHSRAYIDFKCPDD 67

Query: 66  VFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLEFLKVI 125
           VFEFAE  +GHVFVNE+GAQ K IVEYAPSQRVPKP ++KD REGTIFKDPDYLEFLK+I
Sbjct: 68  VFEFAEFFDGHVFVNERGAQHKVIVEYAPSQRVPKPSAKKDGREGTIFKDPDYLEFLKLI 127

Query: 126 AKPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAAESGAQESLAVGRVGRR 185
           AKP E+LPSAEIQLERKE+E  GA KET +VTPLMEY+RQKRA +SG Q S AV +V RR
Sbjct: 128 AKPQEHLPSAEIQLERKESEQVGASKETPIVTPLMEYIRQKRAVDSGMQASSAVAKVCRR 187

Query: 186 SRAASASKTSSTTTKRGSEKKKYILKDSAKNARRKDK---STFTVVAKREDQPASSSGKE 242
           SRAA   K  S   KRGSEKKKY+ KD+AK+A RK+    S F VV +R+DQ A SS K 
Sbjct: 188 SRAALPGKPGSGNIKRGSEKKKYVQKDNAKSATRKESKNMSAFIVVPRRDDQFAESSIKG 247

Query: 243 TSASETICGVEGSV-GIPLTSDTGKKKILLLKGKEREIPHVPDALLDKQRESSPVKNSAS 301
            S  +T+ GVEGS+ GIPLTS++GKKK LLLKGK+++IP   +A + +Q   S   NS  
Sbjct: 248 ISDIKTLHGVEGSISGIPLTSESGKKKFLLLKGKQQDIPSATEATVKQQNVQS--GNSPI 305

Query: 302 PTVPKQIQRREAGGRLIRKILLNNETRQTQSVTGVQPQQKMQNLNQENGKPLP---GPTS 358
            T  KQ QRREA GRLIR ILLNNE RQ+QS TG   Q K+Q L+ ENG+      G  S
Sbjct: 306 STPAKQNQRREASGRLIRSILLNNEARQSQSTTGT--QHKIQILSSENGQRPSRRFGSRS 363

Query: 359 SPNGHVTNNDSPIFSFDGNTKRSSDDRFARKVLHGSGAVSEKQEKRTRNKDRPDRVVWTP 418
             N  V+N+D+   + +G+++R+ D++F ++ LHG G+ S K EKRTRNKDRPDR VWTP
Sbjct: 364 GLNNQVSNHDAAQINSEGDSRRALDEKFIKRDLHGLGS-SAKTEKRTRNKDRPDRGVWTP 422

Query: 419 -RRSDVSQANGERLSSS--QPTQLLSDSVEVTRGEMKDDMSYGSKTVDIAAPTSG----- 470
            RRSDVS A  +  SSS  QPTQ   +S E   GE+K+++  G++  + +A   G     
Sbjct: 423 LRRSDVSHAGNDYSSSSLAQPTQSNPESAE---GEVKENVPSGNRGGEFSASAGGHGGNP 479

Query: 471 ----GSHRHNGRRAATNITKDDGCINMI-EGKSSKRRGAAGSGGNEKQVWIQKSSSG 522
               GS R+     A+ + KDDG ++ I +GK SK+  + G   +EKQVW+ KSSSG
Sbjct: 480 SIENGSQRNFIHHGASYVVKDDGAVSSISKGKPSKK--SVGHSAHEKQVWVHKSSSG 534

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356517820|ref|XP_003527584.1| PREDICTED: uncharacterized protein LOC100795376 [Glycine max]

 Score =  503 bits (1294), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 300/535 (56%), Positives = 369/535 (68%), Gaps = 38/535 (7%)

Query: 6   QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAG 65
           ++TKVVIRHLPPSLSQ+DL      HF  RYNWF FRPG +S+  QR+SRAY++ K P  
Sbjct: 14  EKTKVVIRHLPPSLSQSDLSQHIDSHFASRYNWFSFRPGNNSHTRQRHSRAYIDFKCPDD 73

Query: 66  VFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLEFLKVI 125
           VFEFAE  +GHVFVNE+GAQ K IVEYAPSQRVPKP ++KD REGTI+KDPDYLEFLK+I
Sbjct: 74  VFEFAEFFDGHVFVNERGAQHKVIVEYAPSQRVPKPSAKKDGREGTIYKDPDYLEFLKLI 133

Query: 126 AKPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAAESGAQESLAVGRVGRR 185
           AKP E+LPSAE+QLERKEAE +GA KET +VTPLME+VRQ+RA +SG Q S AV +V RR
Sbjct: 134 AKPQEHLPSAEVQLERKEAEQAGANKETRIVTPLMEFVRQRRAVDSGMQASSAVAKVSRR 193

Query: 186 SRAASASKTSSTTTKRGSEKKKYILKDSAKNARR---KDKSTFTVVAKREDQPASSSGKE 242
           SRAA   K  S  TKRGSEKKKY+ KD+AK   R   KDKS F VV +R++Q A      
Sbjct: 194 SRAALPGKPGSGNTKRGSEKKKYVQKDNAKGVARKESKDKSAFVVVPRRDNQSA------ 247

Query: 243 TSASETICGVEGSV-GIPLTSDTGKKKILLLKGKEREIPHVPDALLDKQRESSPVKNSAS 301
               E++ G+EG   GI LTSD+GKKKILLLKGK+REIP   +  + +Q   S   NS  
Sbjct: 248 ----ESMHGIEGPFSGISLTSDSGKKKILLLKGKQREIPSAIEGTVKQQNIQS--GNSPI 301

Query: 302 PTVPKQIQRREAGGRLIRKILLNNETRQTQSVTGVQPQQKMQNLNQENGKPLP---GPTS 358
               KQ QRREA GRLIR ILLNNE+RQ+ S TG   Q K+Q L+ ENGK  P   G  S
Sbjct: 302 SAPAKQNQRREASGRLIRSILLNNESRQSLSTTGA--QHKIQILSSENGKRPPRTFGSRS 359

Query: 359 SPNGHVTNNDSPIFSFDGNTKRSSDDRFARKVLHGSGAVSEKQEKRTRNKDRPDRVVWTP 418
             N  V+NND+   + +G++K + D +F ++ LHG G+  EK EKRTRNKDRPDR VWTP
Sbjct: 360 GLNDQVSNNDAAQVNSEGDSKMALDKKFVKRDLHGLGS-GEKTEKRTRNKDRPDRGVWTP 418

Query: 419 -RRSDVSQANGERLSSS--QPTQLLSDSVEVTRGEMKDDMSYGSKTVDIAAPTSG----- 470
            RRSDVS A  +  SSS  QPTQ   +S E   GE+K+++  G++  + +A   G     
Sbjct: 419 LRRSDVSNAGNDHSSSSLAQPTQSNPESAE---GEVKENVPSGNRGGEFSASAGGRGNPS 475

Query: 471 ---GSHRHNGRRAATNITKDDGCINMIEGKSSKRRGAAGSGGNEKQVWIQKSSSG 522
               S R+  RR A+ I KDDG +++ EGK SK+  + G   +EKQVW+QKSSSG
Sbjct: 476 IENDSQRNFTRRGASYIVKDDGAVSISEGKPSKK--SVGHSAHEKQVWVQKSSSG 528

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357455505|ref|XP_003598033.1| B3 domain-containing protein [Medicago truncatula] gi|355487081|gb|AES68284.1| B3 domain-containing protein [Medicago truncatula]

 Score =  458 bits (1178), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 283/533 (53%), Positives = 359/533 (67%), Gaps = 33/533 (6%)

Query: 7   RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGV 66
           RTKVVIRHLPPSL+++DL+    + F+ RY+WF FR G +SY++Q+Y+RAY++   P  V
Sbjct: 9   RTKVVIRHLPPSLTESDLIQHIDNRFSSRYHWFVFRSGNTSYRNQKYARAYLDFNSPDDV 68

Query: 67  FEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLEFLKVIA 126
           FEFAE  NGHVFVNEKG Q KA+VEYAPSQRVPK  ++KD REGTI+KDPDYLEFLK+I+
Sbjct: 69  FEFAEFFNGHVFVNEKGVQHKAVVEYAPSQRVPKLSTKKDGREGTIYKDPDYLEFLKLIS 128

Query: 127 KPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAAESGAQESLAVGRVGRRS 186
           KP E+LPSAEIQLERKEAE +GA KE  +VTPLM Y+RQKRA +SG   S A  RVGRR+
Sbjct: 129 KPQEHLPSAEIQLERKEAEQAGASKEAPIVTPLMAYIRQKRAVDSGPLVSSAATRVGRRA 188

Query: 187 RAASASKTSSTTTKRGSEKKKYILKDSAKNARR---KDKSTFTVVAKREDQPASSSGK-- 241
           RA    K   + T+RGSEKKKY+ KD+ KNA R   KDKS FTVV +RED  + SS K  
Sbjct: 189 RAMQG-KPGPSNTRRGSEKKKYVQKDNVKNANRKDSKDKSAFTVVPRREDHSSESSIKGV 247

Query: 242 -ETSASETI-----CGVEGSV-GIPLTSDTGKKKILLLKGKEREIPHVPDALLDKQRESS 294
            E  +S  I      G+EGS+ GIPLTSD+GKKKILLLKGK+REIP   + ++ +Q   S
Sbjct: 248 YEIDSSHVIDEFAVHGIEGSISGIPLTSDSGKKKILLLKGKQREIPKATEGMVKQQNAQS 307

Query: 295 PVKNSASPTVPKQIQRREAGGRLIRKILLNNETRQTQSVTGVQPQQKMQNLNQENGKPLP 354
              N   PT  KQ QRREAGGRLIR ILLNNE+RQ+QS +    Q K+Q L  ENG+  P
Sbjct: 308 --ANLPIPTTAKQNQRREAGGRLIRSILLNNESRQSQSTSTA--QHKIQILTSENGRRPP 363

Query: 355 GPTSSPNG---HVTNNDSPIFSFDGNTKRSSDDRFARKVLHGSGAVSEKQEKRTRNKDRP 411
            P  S +G    V+++D+   + +G +KR  D++F R+  HGSG + +K E+RTRNKDRP
Sbjct: 364 RPFGSRSGLSDQVSSHDAGHVNSEGESKRDLDEKFVRRDFHGSG-IGDKTERRTRNKDRP 422

Query: 412 DRVVWTP-RRSDVSQANGERLSSSQPTQLLSDSVEVTRGEMKDDMSYGSKTVDIAAPTSG 470
           DR VW P RRSD S ++ E  SSS      S+  E   GE+K++   G+++ + +A   G
Sbjct: 423 DRGVWAPLRRSDSSHSSNELSSSSLAQSAPSNP-ESVEGEVKENAYSGNRSGEFSASAGG 481

Query: 471 --------GSHRHNGRRAATNITKDDGCINMIEGKSSKRRGAAGSGGNEKQVW 515
                   GS R   RR A  I KDDG ++  EGK SK+    G+  +E   W
Sbjct: 482 RSSPSVENGSQRIFTRRGAPYIVKDDGAVSSSEGKLSKK--GVGNSTHEFAYW 532

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30692963|ref|NP_174660.2| Smg-4/UPF3-like protein [Arabidopsis thaliana] gi|10092444|gb|AAG12847.1|AC079286_4 unknown protein; 6107-8789 [Arabidopsis thaliana] gi|22136008|gb|AAM91586.1| unknown protein [Arabidopsis thaliana] gi|23197808|gb|AAN15431.1| unknown protein [Arabidopsis thaliana] gi|332193532|gb|AEE31653.1| Smg-4/UPF3-like protein [Arabidopsis thaliana]

 Score =  427 bits (1098), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 265/529 (50%), Positives = 336/529 (63%), Gaps = 55/529 (10%)

Query: 1   MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVEL 60
           MKEPLQ+ KVV+RHLPPSLSQ+DLL+     F DRYNW  FRPGKSSYK+Q+YSRAYV  
Sbjct: 1   MKEPLQKKKVVVRHLPPSLSQSDLLSQIDPRFADRYNWVSFRPGKSSYKNQKYSRAYVSF 60

Query: 61  KKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLE 120
           K P  V+EFA   NGHVFVNEKGAQFKAIVEYAPSQRVPKP  +KD REG+I KDPDYLE
Sbjct: 61  KAPEDVYEFAAFFNGHVFVNEKGAQFKAIVEYAPSQRVPKPSDKKDPREGSISKDPDYLE 120

Query: 121 FLKVIAKPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAAESGAQESLAVG 180
           FLKVIA+P ENLPSAEIQLER+EAE SGA K   +VTPLME++RQKRA   G Q    + 
Sbjct: 121 FLKVIAQPVENLPSAEIQLERREAEQSGASKAAPIVTPLMEFIRQKRATVMGPQGLSDIR 180

Query: 181 RVGRRSRAASASKTSSTTTKRGSEKKKYILKDSAKNARRKDKSTFTVVAKRED-QPASSS 239
           R GRR+R  SA+K S   +KR SEKKKY+ K+S+KN  R  K+T  V + + D + ++SS
Sbjct: 181 RGGRRTRVVSANKPSPRPSKRNSEKKKYVEKESSKNVPR--KTTADVSSSKPDYRQSNSS 238

Query: 240 GKETSASETICGVEGS-VGIPLTSDTGKKKILLLKGKEREIPHVPDALLDKQRESSPVKN 298
           GKE   +ET   ++ S  GI LT D+GKKKILLL+ K+R+ P  P    ++  +++  +N
Sbjct: 239 GKELPGNETAAIIDSSPPGIALTMDSGKKKILLLRSKDRDNPDNPPPQPEQHIDTNLSRN 298

Query: 299 SASPTVPKQIQRREAGGRLIRKILLNNETRQTQSVTGVQPQQKMQNLNQENGKPLPGPTS 358
           S   T  +Q Q+ + GGRLI+ ILL N++R +QS T VQ +Q+++    EN K    P  
Sbjct: 299 S---TDSRQNQKSDVGGRLIKGILLRNDSRPSQSSTFVQSEQRVEPSEAENYKRPSRP-- 353

Query: 359 SPNGHVTNNDSPIFSFDGNTKRSSDDRFARKVLHGSGAVSEKQEKRTRNKDRPDRVVWTP 418
                             NT+       A K  H SG +SEKQE+RTRNKDRPDRV+W P
Sbjct: 354 -----------------ANTR-------AGKDYHTSGTISEKQERRTRNKDRPDRVMWAP 389

Query: 419 RRSDVSQANGERLSSSQPTQLLSDSVEVTRGEMKDDMSYGSKTVDIAAPTSG-----GSH 473
           RR           S  QP     ++     GE+KD M +  ++ ++   + G     GS 
Sbjct: 390 RRDG---------SEDQPLSSAGNN-----GEVKDRM-FSQRSGEVVNSSGGHTLENGSA 434

Query: 474 RHNGRRAATNITKDDGCINMIEGKSSKRRGAAGSGGNEKQVWIQKSSSG 522
           RH+ RR      K++  I   EGK+S+R    G   +EKQ+WIQK SSG
Sbjct: 435 RHSSRRVGGRNRKEEVVIG--EGKTSRRGSGGGPSSHEKQMWIQKPSSG 481

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297739512|emb|CBI29694.3| unnamed protein product [Vitis vinifera]

 Score =  426 bits (1096), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 273/538 (50%), Positives = 350/538 (65%), Gaps = 36/538 (6%)

Query: 1   MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVEL 60
           MK PL RTKVV+RHLPP++S+   L      F  RY    FRPGK+S K Q YSRAY++ 
Sbjct: 1   MKGPLDRTKVVVRHLPPTISEAAFLEQIDTVFKGRYTLVKFRPGKNSQKRQSYSRAYLDF 60

Query: 61  KKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLE 120
           K+P  V EFAE  +GHVFVNEKG QFK IVEYAPSQR+PK + +KD REGTIFKDP+Y+E
Sbjct: 61  KRPEDVIEFAEFFDGHVFVNEKGTQFKTIVEYAPSQRIPKHWPKKDGREGTIFKDPEYME 120

Query: 121 FLKVIAKPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAAESGAQESLAVG 180
           F++++AKP ENLPSAEIQLER+EAE +GA K+T +VTPLM++VRQKRAA+  ++ SL+ G
Sbjct: 121 FVELLAKPVENLPSAEIQLERREAERAGAVKDTPIVTPLMDFVRQKRAAKGVSRRSLSNG 180

Query: 181 RVGRRSRAASASKTSSTTTKRGSEKKK-----YILKDSAKNARRKDKSTFTVVAKREDQP 235
           ++ RR+  +S+   S  ++KRGSEK++     Y+L+D+AK+   KDKSTF +V KR+DQ 
Sbjct: 181 KLSRRASGSSSGNPSLGSSKRGSEKRRLSTTMYVLRDTAKSTSAKDKSTFILVPKRDDQL 240

Query: 236 ASSSGKETSASETICGVEGSVGIPLTSDTGKKKILLLKGKEREIPHVPDALLDKQRESSP 295
            S      +A      +E   G+    D GKKK+LLLKGKEREI H     L +Q  +SP
Sbjct: 241 LSDKSVNLAAGGGAEALEEESGVSGAVDAGKKKVLLLKGKEREISH----HLLQQNVTSP 296

Query: 296 VKNSASPTVPKQIQRREAGGRLIRKILLNNETRQTQSVTGVQPQQKMQNLNQENGKPLPG 355
           VKN      PKQ QRRE  GR+IR ILLN + RQ+QS +  Q +Q+ Q  N E  K  P 
Sbjct: 297 VKNILGANAPKQNQRREGSGRIIRSILLNKDARQSQS-SMFQTEQQSQASNLEKEKRPPR 355

Query: 356 PTSSPNGHVTNNDSPIFSFDGNTKRSSDDRFARKVLHGSGAVSEKQEKRTRNKDRPDRVV 415
           P   P+  + + +         T  + DD+     +H    VSEKQ+KRTRNKDRPDR V
Sbjct: 356 P---PHIQLASKE---------TNGAQDDKVVGNDVH--SFVSEKQDKRTRNKDRPDRGV 401

Query: 416 WTP-RRSDVSQANGERLSSSQPTQLLSDSVEVTRGEMKDDMSYGSKTVDIAAPTSG---- 470
           WTP RRSD S A+ E LSSS      SD  E + GEM+ DMS  +++ ++ A  SG    
Sbjct: 402 WTPLRRSDGSHASDESLSSSASQPTSSDFPEGSHGEMRSDMS-NARSGEVKALGSGRGGH 460

Query: 471 -----GSHRHNGRRAATNITKD-DGCINMIEGKSSKRRGAAGSGGNEKQVWIQKSSSG 522
                GSH+H+GRR  T+  KD DG   + EGK SKR  A G G +EKQVW+QKSSSG
Sbjct: 461 SALDNGSHKHSGRRGPTHSVKDADGSSIVSEGKHSKRGSAPGYGSHEKQVWVQKSSSG 518

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297846376|ref|XP_002891069.1| ATUPF3/UPF3 [Arabidopsis lyrata subsp. lyrata] gi|297336911|gb|EFH67328.1| ATUPF3/UPF3 [Arabidopsis lyrata subsp. lyrata]

 Score =  421 bits (1082), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 268/529 (50%), Positives = 337/529 (63%), Gaps = 51/529 (9%)

Query: 1   MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVEL 60
           MKEPLQ+ KVV+RHLPPSLSQ+DLL+     F DRYNW  FRPGKSSYK+Q+YSRAYV  
Sbjct: 1   MKEPLQKKKVVVRHLPPSLSQSDLLSQIDPRFADRYNWVSFRPGKSSYKNQKYSRAYVSF 60

Query: 61  KKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLE 120
           K P  V+EFA   NGHVFVNEKGAQFKA+VEYAPSQRVPKP  +KD REG+I KDPDYLE
Sbjct: 61  KAPEDVYEFAAFFNGHVFVNEKGAQFKAVVEYAPSQRVPKPCDKKDPREGSISKDPDYLE 120

Query: 121 FLKVIAKPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAAESGAQESLAVG 180
           FLKVIA+P ENLPSAEIQLER+EAE SGA K   +VTPLME++RQKRA   G+Q    V 
Sbjct: 121 FLKVIAQPVENLPSAEIQLERREAEQSGASKAAPIVTPLMEFIRQKRATVMGSQGLSDVR 180

Query: 181 RVGRRSRAASASKTSSTTTKRGSEKKKYILKDSAKNARRKDKSTFTVVAKRED-QPASSS 239
           R GRR+R  SA+K SS  +KR SEKKKY+ KDS+KN  R  K+T  V + + D + ++SS
Sbjct: 181 RGGRRARVVSANKPSSRPSKRNSEKKKYVEKDSSKNVPR--KTTADVSSSKPDYRQSNSS 238

Query: 240 GKETSASETICGVEGSV-GIPLTSDTGKKKILLLKGKEREIPHVPDALLDKQRESSPVKN 298
           G ET    T   ++ S+ GI LT D+GKKKILLLK K+R+    P    ++  E+    N
Sbjct: 239 GNETGNKSTAPVIDSSLPGIALTMDSGKKKILLLKSKDRDNSDNPPPQPEQHIETILSGN 298

Query: 299 SASPTVPKQIQRREAGGRLIRKILLNNETRQTQSVTGVQPQQKMQNLNQENGKPLPGPTS 358
           S   T  +Q Q+ + GGRLI+ IL+ +++R +QS T VQP+Q+++    EN K  P P  
Sbjct: 299 S---TASRQNQKSDVGGRLIKGILMKSDSRPSQSSTFVQPEQRVEPSEAENYKRPPRP-- 353

Query: 359 SPNGHVTNNDSPIFSFDGNTKRSSDDRFARKVLHGSGAVSEKQEKRTRNKDRPDRVVWTP 418
                             NT+       A K  H SG +SEKQE+RTRNKDRPDRVVW P
Sbjct: 354 -----------------ANTR-------AGKDYHASGTISEKQERRTRNKDRPDRVVWAP 389

Query: 419 RRSDVSQANGERLSSSQPTQLLSDSVEVTRGEMKDDMSYGSKTVDIAAPTSG-----GSH 473
            R D     G  +S  QP     ++     GE+KD M +  ++ ++   + G     GS 
Sbjct: 390 LRRD-----GSNISEDQPLSSAGNN-----GEVKDRM-FSQRSGEVVNSSGGHTLENGSA 438

Query: 474 RHNGRRAATNITKDDGCINMIEGKSSKRRGAAGSGGNEKQVWIQKSSSG 522
           RH+ RR      K++  +   EGK+S+R G  G    EKQ+WIQK S G
Sbjct: 439 RHSSRRVGGRNRKEE--LMTGEGKTSRRGGGGGPNSQEKQMWIQKPSLG 485

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|186488168|ref|NP_001117406.1| Smg-4/UPF3-like protein [Arabidopsis thaliana] gi|332193533|gb|AEE31654.1| Smg-4/UPF3-like protein [Arabidopsis thaliana]

 Score =  421 bits (1081), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 264/531 (49%), Positives = 335/531 (63%), Gaps = 57/531 (10%)

Query: 1   MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKS--SYKHQRYSRAYV 58
           MKEPLQ+ KVV+RHLPPSLSQ+DLL+     F DRYNW  FRPGKS   YK+Q+YSRAYV
Sbjct: 1   MKEPLQKKKVVVRHLPPSLSQSDLLSQIDPRFADRYNWVSFRPGKSRLGYKNQKYSRAYV 60

Query: 59  ELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDY 118
             K P  V+EFA   NGHVFVNEKGAQFKAIVEYAPSQRVPKP  +KD REG+I KDPDY
Sbjct: 61  SFKAPEDVYEFAAFFNGHVFVNEKGAQFKAIVEYAPSQRVPKPSDKKDPREGSISKDPDY 120

Query: 119 LEFLKVIAKPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAAESGAQESLA 178
           LEFLKVIA+P ENLPSAEIQLER+EAE SGA K   +VTPLME++RQKRA   G Q    
Sbjct: 121 LEFLKVIAQPVENLPSAEIQLERREAEQSGASKAAPIVTPLMEFIRQKRATVMGPQGLSD 180

Query: 179 VGRVGRRSRAASASKTSSTTTKRGSEKKKYILKDSAKNARRKDKSTFTVVAKRED-QPAS 237
           + R GRR+R  SA+K S   +KR SEKKKY+ K+S+KN  R  K+T  V + + D + ++
Sbjct: 181 IRRGGRRTRVVSANKPSPRPSKRNSEKKKYVEKESSKNVPR--KTTADVSSSKPDYRQSN 238

Query: 238 SSGKETSASETICGVEGS-VGIPLTSDTGKKKILLLKGKEREIPHVPDALLDKQRESSPV 296
           SSGKE   +ET   ++ S  GI LT D+GKKKILLL+ K+R+ P  P    ++  +++  
Sbjct: 239 SSGKELPGNETAAIIDSSPPGIALTMDSGKKKILLLRSKDRDNPDNPPPQPEQHIDTNLS 298

Query: 297 KNSASPTVPKQIQRREAGGRLIRKILLNNETRQTQSVTGVQPQQKMQNLNQENGKPLPGP 356
           +NS   T  +Q Q+ + GGRLI+ ILL N++R +QS T VQ +Q+++    EN K    P
Sbjct: 299 RNS---TDSRQNQKSDVGGRLIKGILLRNDSRPSQSSTFVQSEQRVEPSEAENYKRPSRP 355

Query: 357 TSSPNGHVTNNDSPIFSFDGNTKRSSDDRFARKVLHGSGAVSEKQEKRTRNKDRPDRVVW 416
                               NT+       A K  H SG +SEKQE+RTRNKDRPDRV+W
Sbjct: 356 -------------------ANTR-------AGKDYHTSGTISEKQERRTRNKDRPDRVMW 389

Query: 417 TPRRSDVSQANGERLSSSQPTQLLSDSVEVTRGEMKDDMSYGSKTVDIAAPTSG-----G 471
            PRR           S  QP     ++     GE+KD M +  ++ ++   + G     G
Sbjct: 390 APRRDG---------SEDQPLSSAGNN-----GEVKDRM-FSQRSGEVVNSSGGHTLENG 434

Query: 472 SHRHNGRRAATNITKDDGCINMIEGKSSKRRGAAGSGGNEKQVWIQKSSSG 522
           S RH+ RR      K++  I   EGK+S+R    G   +EKQ+WIQK SSG
Sbjct: 435 SARHSSRRVGGRNRKEEVVIG--EGKTSRRGSGGGPSSHEKQMWIQKPSSG 483

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224146308|ref|XP_002325958.1| predicted protein [Populus trichocarpa] gi|222862833|gb|EEF00340.1| predicted protein [Populus trichocarpa]

 Score =  410 bits (1053), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 265/536 (49%), Positives = 328/536 (61%), Gaps = 31/536 (5%)

Query: 2   KEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELK 61
           KEPL RTKVVIRHLPPSLSQ++L + F   F  RYNWF FRPG SS+K QRYSRAY++ K
Sbjct: 5   KEPLGRTKVVIRHLPPSLSQSNLFSQFDHLFCHRYNWFRFRPGNSSHKSQRYSRAYIDFK 64

Query: 62  KPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLEF 121
            P  V EFA   +GHVFVNEKG+QFKAIVEYAP Q VPK    KDSREGTI+ DPDYLEF
Sbjct: 65  NPEDVLEFAGFFHGHVFVNEKGSQFKAIVEYAPCQHVPKSCPHKDSREGTIYTDPDYLEF 124

Query: 122 LKVIAKPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAAESGAQESLAVGR 181
           LK+IAKPA N PSAEI+LERKEAE S A K   + TPLME+VR+KR A+ G Q S AV +
Sbjct: 125 LKLIAKPARNPPSAEIKLERKEAEESEAVKGAPISTPLMEFVRKKR-ADKGVQGS-AVVK 182

Query: 182 VGRRSRAASASKTSSTTTKRGSEKKKYILKDSAKNARRKDKSTFTVVAKREDQPASSSGK 241
             +R+ +AS + + S+  K+GS KK+YILKDS KN+  K KS   +  K+E  P +S  K
Sbjct: 183 NRKRAGSASLTNSGSSNAKQGSGKKRYILKDSTKNSNWKGKSIIIMARKQEGLPTTSGRK 242

Query: 242 ETSASETICGVEGSVG-IPLTSDTGKKKILLLKGKEREIPHVPDALLDKQRESSPVKNSA 300
           E S  E+I GVEGS   I L +++G+K  LLL GK+REI    +  L +   +S   +S 
Sbjct: 243 EISEVESISGVEGSASKISLDAESGRKINLLLDGKKREISLESEGPLHQLGLTSNFGSSV 302

Query: 301 SPTVPKQIQRREAGGRLIRKILLNNETRQTQSVTGVQPQQKMQNLNQENGKPLPGPTSSP 360
           S T  KQ QR EA  RLI+ IL +              ++K QNL  EN K    P ++ 
Sbjct: 303 S-TAAKQYQRHEASERLIKSILPSK---------AASAKKKFQNLEVENDKQPIQPKTTQ 352

Query: 361 ---NGHVTNNDSPIFSF-DGNTKRSSDDRFARKVLHGSGAVSEKQEKR---TRNKDRPDR 413
              +GHV   + P+ S  D + K SS D+  +K  H  G+  EKQ+KR   TRNKDRP R
Sbjct: 353 VGLSGHVPYKE-PLASMSDNDVKSSSYDKLVKKDQHDPGSHFEKQQKREKHTRNKDRPCR 411

Query: 414 VVWTPRRSDVS-QANGERLSSS-QPTQLLSDSVEVTRGEMKDDMSY-----GSKTVDIAA 466
            VWTP R+  S  AN E L+SS   +++ SDSV  T GE+KD   Y     GS      +
Sbjct: 412 GVWTPVRNCPSKHANAEHLTSSILQSEVHSDSVRETHGEVKDGTQYRDHNQGSAGSPSGS 471

Query: 467 PTSGG---SHRHNGRRAATNITKDDGCINMIEGKSSKRRGAAGSGGNEKQVWIQKS 519
             S     S R  GRR   +    D   +   GK SK+ G AG    EKQVW+QKS
Sbjct: 472 NNSSAENVSRRDFGRRVTAHNIMLDSSPSATGGKFSKKGGHAGYTAQEKQVWVQKS 527

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|10086477|gb|AAG12537.1|AC015446_18 Unknown protein [Arabidopsis thaliana]

 Score =  397 bits (1021), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 248/500 (49%), Positives = 316/500 (63%), Gaps = 55/500 (11%)

Query: 1   MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVEL 60
           MKEPLQ+ KVV+RHLPPSLSQ+DLL+     F DRYNW  FRPGKSSYK+Q+YSRAYV  
Sbjct: 1   MKEPLQKKKVVVRHLPPSLSQSDLLSQIDPRFADRYNWVSFRPGKSSYKNQKYSRAYVSF 60

Query: 61  KKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLE 120
           K P  V+EFA   NGHVFVNEKGAQFKAIVEYAPSQRVPKP  +KD REG+I KDPDYLE
Sbjct: 61  KAPEDVYEFAAFFNGHVFVNEKGAQFKAIVEYAPSQRVPKPSDKKDPREGSISKDPDYLE 120

Query: 121 FLKVIAKPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAAESGAQES--LA 178
           FLKVIA+P ENLPSAEIQLER+EAE SGA K   +VTPLME++RQKRA   G Q+     
Sbjct: 121 FLKVIAQPVENLPSAEIQLERREAEQSGASKAAPIVTPLMEFIRQKRATVMGPQQQGLSD 180

Query: 179 VGRVGRRSRAASASKTSSTTTKRGSEKKKYILKDSAKNARRKDKSTFTVVAKRED-QPAS 237
           + R GRR+R  SA+K S   +KR SEKKKY+ K+S+KN  R  K+T  V + + D + ++
Sbjct: 181 IRRGGRRTRVVSANKPSPRPSKRNSEKKKYVEKESSKNVPR--KTTADVSSSKPDYRQSN 238

Query: 238 SSGKETSASETICGVEGS-VGIPLTSDTGKKKILLLKGKEREIPHVPDALLDKQRESSPV 296
           SSGKE   +ET   ++ S  GI LT D+GKKKILLL+ K+R+ P  P    ++  +++  
Sbjct: 239 SSGKELPGNETAAIIDSSPPGIALTMDSGKKKILLLRSKDRDNPDNPPPQPEQHIDTNLS 298

Query: 297 KNSASPTVPKQIQRREAGGRLIRKILLNNETRQTQSVTGVQPQQKMQNLNQENGKPLPGP 356
           +NS   T  +Q Q+ + GGRLI+ ILL N++R +QS T VQ +Q+++    EN K    P
Sbjct: 299 RNS---TDSRQNQKSDVGGRLIKGILLRNDSRPSQSSTFVQSEQRVEPSEAENYKRPSRP 355

Query: 357 TSSPNGHVTNNDSPIFSFDGNTKRSSDDRFARKVLHGSGAVSEKQEKRTRNKDRPDRVVW 416
                               NT+   D        H SG +SEKQE+RTRNKDRPDRV+W
Sbjct: 356 -------------------ANTRAGKD-------YHTSGTISEKQERRTRNKDRPDRVMW 389

Query: 417 TPRRSDVSQANGERLSSSQPTQLLSDSVEVTRGEMKDDMSYGSKTVDIAAPTSG-----G 471
            PRR           S  QP     ++     GE+KD M +  ++ ++   + G     G
Sbjct: 390 APRRDG---------SEDQPLSSAGNN-----GEVKDRM-FSQRSGEVVNSSGGHTLENG 434

Query: 472 SHRHNGRRAATNITKDDGCI 491
           S RH+ RR      K++  I
Sbjct: 435 SARHSSRRVGGRNRKEEVVI 454

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	523
TAIR|locus:2009026	484	UPF3 [Arabidopsis thaliana (ta	0.804	0.869	0.442	6.6e-81
ZFIN|ZDB-GENE-060721-2	452	upf3a "UPF3 regulator of nonse	0.302	0.349	0.363	2.4e-20
UNIPROTKB|Q2T9M5	307	UPF3B "UPF3 regulator of nonse	0.313	0.534	0.359	1.5e-18
UNIPROTKB|E1BZ48	478	UPF3B "Uncharacterized protein	0.311	0.341	0.373	2.3e-18
UNIPROTKB|F1NQA5	478	UPF3B "Uncharacterized protein	0.311	0.341	0.373	4.1e-18
UNIPROTKB|J9NUU8	457	UPF3B "Uncharacterized protein	0.313	0.358	0.359	9.2e-18
UNIPROTKB|F1PPT4	481	UPF3B "Uncharacterized protein	0.313	0.340	0.359	1.4e-17
UNIPROTKB|E2R5F4	463	UPF3A "Uncharacterized protein	0.317	0.358	0.333	2.4e-17
UNIPROTKB|F1RUA3	470	LOC414433 "Uncharacterized pro	0.313	0.348	0.359	2.4e-17
ZFIN|ZDB-GENE-040426-1630	467	upf3b "UPF3 regulator of nonse	0.311	0.349	0.366	2.7e-17

TAIR|locus:2009026 UPF3 [Arabidopsis thaliana (taxid:3702)]

 Score = 812 (290.9 bits), Expect = 6.6e-81, P = 6.6e-81
 Identities = 192/434 (44%), Positives = 251/434 (57%)

Query:     1 MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKS--SYKHQRYSRAYV 58
             MKEPLQ+ KVV+RHLPPSLSQ+DLL+     F DRYNW  FRPGKS   YK+Q+YSRAYV
Sbjct:     1 MKEPLQKKKVVVRHLPPSLSQSDLLSQIDPRFADRYNWVSFRPGKSRLGYKNQKYSRAYV 60

Query:    59 ELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDY 118
               K P  V+EFA   NGHVFVNEKGAQFKAIVEYAPSQRVPKP  +KD REG+I KDPDY
Sbjct:    61 SFKAPEDVYEFAAFFNGHVFVNEKGAQFKAIVEYAPSQRVPKPSDKKDPREGSISKDPDY 120

Query:   119 LEFLKVIAKPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAAESGAQESLX 178
             LEFLKVIA+P ENLPSAEIQLER+EAE SGA K   +VTPLME++RQKRA   G Q    
Sbjct:   121 LEFLKVIAQPVENLPSAEIQLERREAEQSGASKAAPIVTPLMEFIRQKRATVMGPQGLSD 180

Query:   179 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXYILKDSAKNARRKDKSTFTVVAKRED-QPAS 237
                                          Y+ K+S+KN  RK  +T  V + + D + ++
Sbjct:   181 IRRGGRRTRVVSANKPSPRPSKRNSEKKKYVEKESSKNVPRK--TTADVSSSKPDYRQSN 238

Query:   238 SSGKETSASETICGVEGSV-GIPLTSDTXXXXXXXXXXXEREIPHVPDALLDKQRESSPV 296
             SSGKE   +ET   ++ S  GI LT D+           +R+ P  P    ++  +++  
Sbjct:   239 SSGKELPGNETAAIIDSSPPGIALTMDSGKKKILLLRSKDRDNPDNPPPQPEQHIDTNLS 298

Query:   297 KNSASPTVPKQIQRREAGGRLIRKILLNNETRQTQSVTGVQPQQKMQNLNQENGKPLPGP 356
             +NS   T  +Q Q+ + GGRLI+ ILL N++R +QS T VQ +Q+++    EN K    P
Sbjct:   299 RNS---TDSRQNQKSDVGGRLIKGILLRNDSRPSQSSTFVQSEQRVEPSEAENYKRPSRP 355

Query:   357 TSSPNGHVTNNDSPIFSFDGNTKRSSD--DRFARKVLHGSGAVSEKQEKRTRNKDRPDRV 414
              ++  G   +    I        R+ D  DR         G+  +       N +  DR+
Sbjct:   356 ANTRAGKDYHTSGTISEKQERRTRNKDRPDR-VMWAPRRDGSEDQPLSSAGNNGEVKDRM 414

Query:   415 VWTPRRSDVSQANG 428
              ++ R  +V  ++G
Sbjct:   415 -FSQRSGEVVNSSG 427

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IMP

GO:0005730 "nucleolus" evidence=IDA

GO:0042742 "defense response to bacterium" evidence=IMP

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

ZFIN|ZDB-GENE-060721-2 upf3a "UPF3 regulator of nonsense transcripts homolog A (yeast)" [Danio rerio (taxid:7955)]

 Score = 257 (95.5 bits), Expect = 2.4e-20, Sum P(2) = 2.4e-20
 Identities = 64/176 (36%), Positives = 104/176 (59%)

Query:     8 TKVVIRHLPPSLSQNDLLALFRDHFND--RYNWFCFRPGKSS-YKHQRYSRAYVELKKPA 64
             +KVVIR LPPSLS++ L    ++H +    +++F F P   S Y H  +SRAY+  K P 
Sbjct:    43 SKVVIRRLPPSLSKDQL----QEHLSPLPSFDYFEFFPADQSLYPHL-FSRAYINFKNPE 97

Query:    65 GVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKP-FSRKDSREGTIFKDPDYLEFLK 123
              +  F +  +G+VF++ KG ++ A+VE+AP Q+V K    +KD++ GTI +DP+Y  FL+
Sbjct:    98 DIIIFRDRFDGYVFIDNKGQEYPAVVEFAPFQKVSKKKLKKKDAKAGTIEEDPEYRRFLE 157

Query:   124 VIAKPAE-NLPSAEI---QLERKEAELSGAPKETLVVTPLMEYVRQKRAAESGAQE 175
               +   E ++ + E    ++E K  EL    K T   TPL+EY++ K+  +   +E
Sbjct:   158 NYSCDEEKSMANPETLLGEIEAKTRELIA--KRT---TPLLEYIKNKKLEKQRIRE 208

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q2T9M5 UPF3B "UPF3 regulator of nonsense transcripts homolog B (Yeast)" [Bos taurus (taxid:9913)]

 Score = 230 (86.0 bits), Expect = 1.5e-18, P = 1.5e-18
 Identities = 65/181 (35%), Positives = 102/181 (56%)

Query:     2 KEPLQRTKVVIRHLPPSLSQNDLLALFRDHFND--RYNWFCFRPGKSS-YKHQRYSRAYV 58
             KE L  +KVVIR LPP+L++  L    ++H      +++F F    +S Y H  Y+RAY+
Sbjct:    47 KEAL--SKVVIRRLPPTLTKEQL----QEHLQPMPEHDYFEFFSNDTSLYPHM-YARAYI 99

Query:    59 ELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRK-DSREGTIFKDPD 117
               K    +  F +  +G+VF++ KG ++ AIVE+AP Q+  K  ++K D++ GTI  DP+
Sbjct:   100 NFKNQEDIILFRDRFDGYVFLDNKGQEYPAIVEFAPFQKAAKKKTKKRDTKVGTIDDDPE 159

Query:   118 YLEFLKVIAKPAENLPSA-EIQLERKEAELSGA-PKETLVVTPLMEYVRQK-RAAESGAQ 174
             Y +FL+  A   E + S  E  LE  EA+      K+T   TPL+ +++ K R  E   +
Sbjct:   160 YRKFLESYAADNEKMTSTPETLLEEIEAKNRELIAKKT---TPLLSFLKNKQRMREEKRE 216

Query:   175 E 175
             E
Sbjct:   217 E 217

GO:0045727 "positive regulation of translation" evidence=IEA

GO:0035145 "exon-exon junction complex" evidence=IEA

GO:0003729 "mRNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E1BZ48 UPF3B "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 237 (88.5 bits), Expect = 2.3e-18, Sum P(3) = 2.3e-18
 Identities = 68/182 (37%), Positives = 101/182 (55%)

Query:     2 KEPLQRTKVVIRHLPPSLSQNDLLALFRDHFND--RYNWFCFRPGKSS-YKHQRYSRAYV 58
             KE L  +KVVIR LPPSL++  L     +H      +++F F    SS Y H  +SRAY+
Sbjct:    51 KETL--SKVVIRRLPPSLTREQL----EEHLQPLPEHDYFEFFANDSSLYPHV-FSRAYI 103

Query:    59 ELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRK-DSREGTIFKDPD 117
               +    +  F +  +G+VFV+ KG+++ AIVE+AP Q+  K  S+K D++ GTI  DP+
Sbjct:   104 NFRNQEDIVLFRDRFDGYVFVDHKGSEYAAIVEFAPFQKAAKKKSKKKDAKTGTIEDDPE 163

Query:   118 YLEFLKVIAKPAENLPSA-EIQLERKEAELSGAPKETLV--VTPLMEYVRQK-RAAESGA 173
             Y +FL+  +   E L S  E  LE  EA      KE +    TPL+ +++ K R  E   
Sbjct:   164 YKKFLESYSADDEKLTSTPETLLEEIEAR----NKELIAKKTTPLLNFLKNKQRLREEKR 219

Query:   174 QE 175
             +E
Sbjct:   220 EE 221

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1NQA5 UPF3B "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 235 (87.8 bits), Expect = 4.1e-18, Sum P(3) = 4.1e-18
 Identities = 68/182 (37%), Positives = 100/182 (54%)

Query:     2 KEPLQRTKVVIRHLPPSLSQNDLLALFRDHFND--RYNWFCFRPGKSS-YKHQRYSRAYV 58
             KE L  +KVVIR LPPSL++  L     +H      +++F F    SS Y H  +SRAY+
Sbjct:    51 KETL--SKVVIRRLPPSLTREQL----EEHLQPLPEHDYFEFFANDSSLYPHV-FSRAYI 103

Query:    59 ELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRK-DSREGTIFKDPD 117
               +    +  F +  +G+VFV+ KG ++ AIVE+AP Q+  K  S+K D++ GTI  DP+
Sbjct:   104 NFRNQEDIVLFRDRFDGYVFVDHKGQEYAAIVEFAPFQKAAKKKSKKKDAKTGTIEDDPE 163

Query:   118 YLEFLKVIAKPAENLPSA-EIQLERKEAELSGAPKETLV--VTPLMEYVRQK-RAAESGA 173
             Y +FL+  +   E L S  E  LE  EA      KE +    TPL+ +++ K R  E   
Sbjct:   164 YKKFLESYSADDEKLTSTPETLLEEIEAR----NKELIAKKTTPLLNFLKNKQRLREEKR 219

Query:   174 QE 175
             +E
Sbjct:   220 EE 221

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=IEA

GO:0035145 "exon-exon junction complex" evidence=IEA

GO:0045727 "positive regulation of translation" evidence=IEA

UNIPROTKB|J9NUU8 UPF3B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 230 (86.0 bits), Expect = 9.2e-18, Sum P(3) = 9.2e-18
 Identities = 65/181 (35%), Positives = 102/181 (56%)

Query:     2 KEPLQRTKVVIRHLPPSLSQNDLLALFRDHFND--RYNWFCFRPGKSS-YKHQRYSRAYV 58
             KE L  +KVVIR LPP+L++  L    ++H      +++F F    +S Y H  Y+RAY+
Sbjct:    47 KEAL--SKVVIRRLPPTLTKEQL----QEHLQPMPEHDYFEFFSNDTSLYPHM-YARAYI 99

Query:    59 ELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRK-DSREGTIFKDPD 117
               K    +  F +  +G+VF++ KG ++ AIVE+AP Q+  K  ++K D++ GTI  DP+
Sbjct:   100 NFKNQEDIILFRDRFDGYVFLDNKGQEYPAIVEFAPFQKAAKKKTKKRDTKVGTIDDDPE 159

Query:   118 YLEFLKVIAKPAENLPSA-EIQLERKEAELSGA-PKETLVVTPLMEYVRQK-RAAESGAQ 174
             Y +FL+  A   E + S  E  LE  EA+      K+T   TPL+ +++ K R  E   +
Sbjct:   160 YRKFLESYAADNEKMTSTPETLLEEIEAKNRELIAKKT---TPLLSFLKNKQRMREEKRE 216

Query:   175 E 175
             E
Sbjct:   217 E 217

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1PPT4 UPF3B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 230 (86.0 bits), Expect = 1.4e-17, Sum P(3) = 1.4e-17
 Identities = 65/181 (35%), Positives = 102/181 (56%)

Query:     2 KEPLQRTKVVIRHLPPSLSQNDLLALFRDHFND--RYNWFCFRPGKSS-YKHQRYSRAYV 58
             KE L  +KVVIR LPP+L++  L    ++H      +++F F    +S Y H  Y+RAY+
Sbjct:    47 KEAL--SKVVIRRLPPTLTKEQL----QEHLQPMPEHDYFEFFSNDTSLYPHM-YARAYI 99

Query:    59 ELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRK-DSREGTIFKDPD 117
               K    +  F +  +G+VF++ KG ++ AIVE+AP Q+  K  ++K D++ GTI  DP+
Sbjct:   100 NFKNQEDIILFRDRFDGYVFLDNKGQEYPAIVEFAPFQKAAKKKTKKRDTKVGTIDDDPE 159

Query:   118 YLEFLKVIAKPAENLPSA-EIQLERKEAELSGA-PKETLVVTPLMEYVRQK-RAAESGAQ 174
             Y +FL+  A   E + S  E  LE  EA+      K+T   TPL+ +++ K R  E   +
Sbjct:   160 YRKFLESYAADNEKMTSTPETLLEEIEAKNRELIAKKT---TPLLSFLKNKQRMREEKRE 216

Query:   175 E 175
             E
Sbjct:   217 E 217

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2R5F4 UPF3A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 241 (89.9 bits), Expect = 2.4e-17, Sum P(2) = 2.4e-17
 Identities = 60/180 (33%), Positives = 98/180 (54%)

Query:     2 KEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSS-YKHQRYSRAYVEL 60
             +E    +KVVIR LPP L++  L      H    +++F F P   S Y H  YSRAY+  
Sbjct:    61 EEKTALSKVVIRRLPPGLTKEQLEEQL--HPLPAHDYFEFFPADLSLYPHL-YSRAYINF 117

Query:    61 KKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKP-FSRKDSREGTIFKDPDYL 119
             + P  +  F +  +G++F++ KG ++ A+VE+AP Q++ K    +KD++ G+I  DP+Y 
Sbjct:   118 RNPEDILLFRDRFDGYIFIDSKGLEYPAVVEFAPFQKIAKKKLKKKDAKTGSIEDDPEYK 177

Query:   120 EFLKVIA----KPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAAESGAQE 175
             +FL+       KP  N  +    +E K  EL    + T   TPL+EY+R ++  +   +E
Sbjct:   178 KFLETYCVEEEKPNTNPETLLGDIEAKTRELIA--RRT---TPLLEYIRNRKLEKQRIRE 232

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1RUA3 LOC414433 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 230 (86.0 bits), Expect = 2.4e-17, Sum P(2) = 2.4e-17
 Identities = 65/181 (35%), Positives = 102/181 (56%)

Query:     2 KEPLQRTKVVIRHLPPSLSQNDLLALFRDHFND--RYNWFCFRPGKSS-YKHQRYSRAYV 58
             KE L  +KVVIR LPP+L++  L    ++H      +++F F    +S Y H  Y+RAY+
Sbjct:    47 KEAL--SKVVIRRLPPTLTKEQL----QEHLQPMPEHDYFEFFSNDTSLYPHM-YARAYI 99

Query:    59 ELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRK-DSREGTIFKDPD 117
               K    +  F +  +G+VF++ KG ++ AIVE+AP Q+  K  ++K D++ GTI  DP+
Sbjct:   100 NFKNQEDIILFRDRFDGYVFLDNKGQEYPAIVEFAPFQKAAKKKTKKRDTKVGTIDDDPE 159

Query:   118 YLEFLKVIAKPAENLPSA-EIQLERKEAELSGA-PKETLVVTPLMEYVRQK-RAAESGAQ 174
             Y +FL+  A   E + S  E  LE  EA+      K+T   TPL+ +++ K R  E   +
Sbjct:   160 YRKFLESYAADNEKMTSTPETLLEEIEAKNRELIAKKT---TPLLSFLKNKQRMREEKRE 216

Query:   175 E 175
             E
Sbjct:   217 E 217

GO:0045727 "positive regulation of translation" evidence=IEA

GO:0035145 "exon-exon junction complex" evidence=IEA

GO:0003729 "mRNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

ZFIN|ZDB-GENE-040426-1630 upf3b "UPF3 regulator of nonsense transcripts homolog B (yeast)" [Danio rerio (taxid:7955)]

 Score = 232 (86.7 bits), Expect = 2.7e-17, Sum P(2) = 2.7e-17
 Identities = 63/172 (36%), Positives = 97/172 (56%)

Query:     8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVF 67
             TK+VIR LPP+L++ DL    +      Y  F F    S + H  ++RAY+  K    + 
Sbjct:    37 TKIVIRRLPPTLTKEDLEEQLQPLPELDYLEF-FSSDTSLFPHL-FARAYLNFKNQDDIV 94

Query:    68 EFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRK-DSREGTIFKDPDYLEFLKVIA 126
              F +  +G+VF++ +G ++ AIVE+AP Q+V K  S+K D++ GTI  D DY +FL+   
Sbjct:    95 LFRDRFDGYVFIDNRGQEYPAIVEFAPFQKVAKKRSKKKDAKSGTIDDDADYKKFLEFYN 154

Query:   127 KPAENLPS-AEIQLERKEAELSG-APKETLVVTPLMEYVRQK-RAAESGAQE 175
                E  PS  EI LE  EA+    + K+T   TPL+++++ K R  E   +E
Sbjct:   155 GDEEKSPSNPEILLEEIEAKTKELSSKKT---TPLLDFLKNKQRIREEKKEE 203

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	523
pfam03467	176	pfam03467, Smg4_UPF3, Smg-4/UPF3 family	2e-47
cd12455	88	cd12455, RRM_like_Smg4_UPF3, RNA recognition motif	6e-28
cd12728	89	cd12728, RRM_like_Smg4_UPF3B, RNA recognition moti	4e-13
cd12727	87	cd12727, RRM_like_Smg4_UPF3A, RNA recognition moti	6e-12

>gnl|CDD|217577 pfam03467, Smg4_UPF3, Smg-4/UPF3 family

 Score =  162 bits (411), Expect = 2e-47
 Identities = 75/176 (42%), Positives = 108/176 (61%), Gaps = 8/176 (4%)

Query: 1   MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNW--FCFRPGKSSYKHQRYSRAYV 58
           MK   +  KVV+R LPP+L++ + L        D  NW  F   P   S+K+++YSRAYV
Sbjct: 1   MKSKKEGPKVVVRRLPPTLTEEEFLEQINP-LPDEVNWHYFHGGPATFSFKNEKYSRAYV 59

Query: 59  ELKKPA-GVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRK-DSREGTIFKDP 116
             + P   V EF  + NGH+F++ KG  + AIVE AP Q++PKP   K D+REG+I +DP
Sbjct: 60  NFQNPDDAVLEFFAVFNGHIFIDSKGNTYPAIVELAPYQKIPKPSKVKKDAREGSIEQDP 119

Query: 117 DYLEFLKVIAKPAENL---PSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAA 169
           +++EFLK + +  E+     S E QLE+ E E   A K   V TPL+EY+++K+AA
Sbjct: 120 EFMEFLKQLNEEDESPSQTLSNEDQLEKIELENKTAEKIEKVTTPLVEYLKEKKAA 175

This family contains proteins that are involved in nonsense mediated mRNA decay. A process that is triggered by premature stop codons in mRNA. The family includes Smg-4 and UPF3. Length = 176

>gnl|CDD|240901 cd12455, RRM_like_Smg4_UPF3, RNA recognition motif-like Smg4_UPF3 domain in yeast up-frameshift suppressor 3 (Upf3p), Caenorhabditis elegans SMG-4, their human orthologs Upf3A and Upf3B, and similar proteins

 Score =  106 bits (267), Expect = 6e-28
 Identities = 43/88 (48%), Positives = 55/88 (62%), Gaps = 2/88 (2%)

Query: 9  KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSS--YKHQRYSRAYVELKKPAGV 66
          KVVIR LPPSL++ + L           +W+ F  GKSS  +K   YSRAY+  K P  +
Sbjct: 1  KVVIRRLPPSLTEEEFLEQVSPLIKPTVDWYYFVGGKSSKDFKPPIYSRAYINFKNPEDL 60

Query: 67 FEFAELLNGHVFVNEKGAQFKAIVEYAP 94
           EFA   +GHVFV+ KG ++KAIVEYAP
Sbjct: 61 LEFARRFDGHVFVDSKGNEYKAIVEYAP 88

This subfamily corresponds to the RRM-like Smg4_UPF3 domain found in yeast up-frameshift suppressor 3 (Upf3p), Caenorhabditis elegans SMG-4, their human orthologs Upf3A and Upf3B, and similar proteins. Upf3p, also termed nonsense-mediated mRNA decay protein 3, or Sua6p, a surveillance factor encoded by UPF3 gene from Saccharomyces cerevisiae. It is required for nonsense-mediated mRNA decay (NMD) in yeast. Upf3p is primarily cytoplasmic but accumulates inside the nucleus. Its nuclear import is mediated by the Srp1p (importin-alpha)/beta heterodimer while its nuclear export is mediated by a leucine-rich nuclear export sequence (NES-A), but not the Crm1p exportin. C. elegans SMG-4 is a nuclear shuttling protein that shuttles between the cytoplasm and nucleus through nuclear import and export signals similar to that of the yeast Upf3p. It is regulated by phosphorylation. Human orthologs of yeast Upf3p and C. elegans SMG-4 include Upf3A and Upf3B, which derive from two genes, UPF3A and X-linked UPF3B, respectively. Both, Upf3A (Up-frameshift suppressor 3 homolog A, also termed regulator of nonsense transcripts 3A, or nonsense mRNA reducing factor 3A) and Upf3B (Up-frameshift suppressor 3 homolog B on chromosome X, also termed regulator of nonsense transcripts 3B, or nonsense mRNA reducing factor 3B), are nucleocytoplasmic shuttling proteins. They associate selectively with spliced beta-globin mRNA in vivo, and tethering of any human Upf protein to the 3'UTR of beta-globin mRNA prevents NMD. The function of the Upf proteins in identifying and targeting nonsense mRNAs for rapid decay is conserved among eukaryotes. Besides, all Upf proteins in this family contain a conserved Smg4_UPF3 domain with some similarity to an RNA recognition motif (RRM), indicating that they may be RNA binding proteins. . Length = 88

>gnl|CDD|241172 cd12728, RRM_like_Smg4_UPF3B, RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog B on chromosome X (Upf3B)

 Score = 64.6 bits (157), Expect = 4e-13
 Identities = 34/92 (36%), Positives = 53/92 (57%), Gaps = 6/92 (6%)

Query: 8  TKVVIRHLPPSLSQNDLLALFRDHFND--RYNWFCFRPGKSSYKHQRYSRAYVELKKPAG 65
          +KVVIR LPPSL++  L     +H      +++F F    SS     +SRAY+  K    
Sbjct: 2  SKVVIRRLPPSLTKEQL----EEHLQPLPEHDYFEFFSNDSSLYPHMFSRAYINFKNQED 57

Query: 66 VFEFAELLNGHVFVNEKGAQFKAIVEYAPSQR 97
          +  F +  +G+VF++ KG ++ AIVE+AP Q+
Sbjct: 58 IVLFRDRFDGYVFLDHKGQEYPAIVEFAPFQK 89

This subgroup corresponds to the RRM-like Smg4_UPF3 domain in Upf3B, also termed regulator of nonsense transcripts 3B, or nonsense mRNA reducing factor 3B, a human ortholog of yeast Upf3p and Caenorhabditis elegans SMG-4. It derives from X-linked gene UPF3B and is required for nonsense-mediated mRNA decay (NMD) in human. Upf3B is a nucleocytoplasmic shuttling protein that associates selectively with spliced beta-globin mRNA in vivo. Like other Upf3 proteins, Upf3B contains nuclear import and export signals, and a conserved Smg4_UPF3 domain with some similarity to an RNA recognition motif (RRM), indicating that it may be an RNA binding protein. . Length = 89

>gnl|CDD|241171 cd12727, RRM_like_Smg4_UPF3A, RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog A (Upf3A)

 Score = 61.1 bits (148), Expect = 6e-12
 Identities = 32/87 (36%), Positives = 48/87 (55%), Gaps = 2/87 (2%)

Query: 8  TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVF 67
          +KVVIR LPP L++  L           Y  FC     S Y H  YSRAY+  + P  + 
Sbjct: 3  SKVVIRRLPPGLTKEQLEEQLHPLPAHDYFEFC-TADPSLYPHL-YSRAYINFRNPEDIL 60

Query: 68 EFAELLNGHVFVNEKGAQFKAIVEYAP 94
           F +  +G++F++ KG ++ A+VE+AP
Sbjct: 61 LFRDRFDGYIFIDNKGLEYPAVVEFAP 87

This subgroup corresponds to the RRM-like Smg4_UPF3 domain in Upf3A, also termed regulator of nonsense transcripts 3A, or nonsense mRNA reducing factor 3A, a human ortholog of yeast Upf3p and Caenorhabditis elegans SMG-4. It derives from gene UPF3A and is required for nonsense-mediated mRNA decay (NMD) in human. Upf3A is a nucleocytoplasmic shuttling protein that associates selectively with spliced beta-globin mRNA in vivo. Like other Upf3 proteins, Upf3A contains nuclear import and export signals, and a conserved Smg4_UPF3 domain with some similarity to an RNA recognition motif (RRM), indicating that it may be an RNA binding protein. . Length = 87

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	523
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	100.0
KOG1295	376	consensus Nonsense-mediated decay protein Upf3 [RN	99.94
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.98
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	97.49
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	97.42
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	97.23
smart00362	72	RRM_2 RNA recognition motif.	97.17
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	96.36
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	95.95
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	95.92
smart00360	71	RRM RNA recognition motif.	95.83
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	95.51
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	94.77
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	94.55
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	93.9
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	93.62
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	92.37
COG0724	306	RNA-binding proteins (RRM domain) [General functio	92.19
PLN03120	260	nucleic acid binding protein; Provisional	91.89
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	91.65
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	90.96
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	90.61
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	90.43
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	87.03
PLN03121	243	nucleic acid binding protein; Provisional	86.92
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	86.66
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	85.93
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	85.69
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	85.57
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	80.89

>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=100.00  E-value=1.9e-50  Score=377.70  Aligned_cols=170  Identities=44%  Similarity=0.798  Sum_probs=68.9

Q ss_pred             CCCCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEee--CCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            1 MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFR--PGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         1 mk~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFV--pGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      ||.+..++|||||||||+|||++||++|++++.+.++|.||.  .|+.+.++++||||||+|++.++|..|++.|+||+|
T Consensus         1 ~~~~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F   80 (176)
T PF03467_consen    1 MKKEKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVF   80 (176)
T ss_dssp             --------EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEE
T ss_pred             CCCcccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEE
Confidence            899999999999999999999999999999777667777664  555556889999999999999999999999999999


Q ss_pred             EeCCCCeeeeEEEeccCCCCCC-CCCCCCCCCccccCCHHHHHHHHHHcCCCCCC---CcHHHHhhhHHhhhcCCCCCCc
Q 009860           79 VNEKGAQFKAIVEYAPSQRVPK-PFSRKDSREGTIFKDPDYLEFLKVIAKPAENL---PSAEIQLERKEAELSGAPKETL  154 (523)
Q Consensus        79 vDsKGne~~A~VEfAPYQKvPk-~k~KkD~ReGTIEqDpeYkaFLEsL~~P~e~~---pSaE~~lE~~Eae~a~~~kek~  154 (523)
                      +|++|++++|+|||||||++|. .+.|.|+++||||+|++|++|||+|++|.+.+   .+++..++..|.+...+.+..+
T Consensus        81 ~D~kg~~~~~~VE~Apyqk~p~~~k~k~d~r~GTIe~D~~y~~Fle~L~~~~~~~~~~~s~~~~l~k~e~~~~~~~~~~~  160 (176)
T PF03467_consen   81 VDSKGNEYPAVVEFAPYQKVPKPSKKKKDPREGTIEQDPEYQAFLESLEEPEEKPSQDISAEKSLEKKEKEEKAKEKAEK  160 (176)
T ss_dssp             E-TTS-EEEEEEEE-SS---------------------------------------------------------------
T ss_pred             ECCCCCCcceeEEEcchhcccccccccccccCCCccCCHHHHHHHHHHhccccccccCcchhhhhhhhhhhhhccccccc
Confidence            9999999999999999999998 56789999999999999999999998776543   2344455554444333334455


Q ss_pred             ccChhHHHHHHHHHHh
Q 009860          155 VVTPLMEYVRQKRAAE  170 (523)
Q Consensus       155 ~tTPLlEyLReKKAaK  170 (523)
                      ++||||+|||+||++|
T Consensus       161 ~~TpLie~lk~kk~~k  176 (176)
T PF03467_consen  161 VTTPLIEYLKEKKANK  176 (176)
T ss_dssp             ----------------
T ss_pred             cchHHHHHHHHHhhcC
Confidence            6999999999999885

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.

>KOG1295 consensus Nonsense-mediated decay protein Upf3 [RNA processing and modification]

Probab=99.94  E-value=8.1e-28  Score=246.89  Aligned_cols=176  Identities=34%  Similarity=0.496  Sum_probs=142.7

Q ss_pred             CCCCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            1 MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         1 mk~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      |+.....+|||||||||.||+++|+++|+|. +..+.|.+|.+++.+..++.||||||+|++++++.+|.+.|+||+|+|
T Consensus         1 ~~~~~~~~Kvv~rrlpp~l~~~~~~eqi~p~-~~~v~~~~F~~a~~s~~~~~ysrayinFk~~~dv~ef~~~f~g~ifld   79 (376)
T KOG1295|consen    1 GKKKEAKVKVVVRRLPPKLTEEQLLEQINPF-PEHVNWEFFAKADESLRNHKYSRAYINFKNPEDVEEFRRRFDGYIFLD   79 (376)
T ss_pred             CcccccceeeeeecCCCcccHHHHhhhcCCC-ccccchheeccccccchhhhhhhhhhccccHHHHHHHHhhCCceEEec
Confidence            4455567899999999999999999999995 456999999999999999999999999999999999999999999999


Q ss_pred             CCCCeeeeEEEeccCCCCCCCCCCCCCCCccccCCHHHHHHHHHHcCCCCCCCcHHHHhhhHHhhhcCCCCCCcccChhH
Q 009860           81 EKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLEFLKVIAKPAENLPSAEIQLERKEAELSGAPKETLVVTPLM  160 (523)
Q Consensus        81 sKGne~~A~VEfAPYQKvPk~k~KkD~ReGTIEqDpeYkaFLEsL~~P~e~~pSaE~~lE~~Eae~a~~~kek~~tTPLl  160 (523)
                      .+|                          |||++|++|++||+.++-+.+..++.....+..+.+.....++..++|||+
T Consensus        80 ~Kg--------------------------gti~d~~~yre~~~~~~~~ke~~~s~~~et~~g~~e~d~~~~~fk~~t~~~  133 (376)
T KOG1295|consen   80 NKG--------------------------GTIDDDPAYREFLKNYALAKEDKASKLKETLLGEIEGDTKSLAFKKVTPLL  133 (376)
T ss_pred             CCC--------------------------CCccccHHHHHHHhhccccccCccccchhhhhchhcccccchhhhccchHH
Confidence            999                          999999999999999999988777664443333333333446788899999


Q ss_pred             HHHHHHHHHhhhchhhhhhccccccccccccCCCCCcccccCcccceeEeccccc
Q 009860          161 EYVRQKRAAESGAQESLAVGRVGRRSRAASASKTSSTTTKRGSEKKKYILKDSAK  215 (523)
Q Consensus       161 EyLReKKAaK~k~q~~~~~~k~~rr~~~~~~~~~~~~~~kr~~ek~~yv~rd~~k  215 (523)
                      .||+..     .+|.+..-.+..|+-.-.......       .++++|++++++|
T Consensus       134 ~~~~~~-----~~q~irk~~r~~r~~r~ie~k~~r-------~~vkk~keke~~K  176 (376)
T KOG1295|consen  134 SFIKQA-----DKQRIRKLRREERRRREIEEKENR-------EEVKKDKEKESGK  176 (376)
T ss_pred             Hhhhhh-----hHHHHHHhhccchHHHHHHhccch-------hhhhhhhhccccc
Confidence            999986     355565656555554444332221       7888999999876

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

Probab=97.98  E-value=3e-05  Score=68.00  Aligned_cols=87  Identities=26%  Similarity=0.498  Sum_probs=71.1

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF   86 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~   86 (523)
                      |+-|.||++|..+|.+.+++.|+....+.||++| .|=+... ..-..-|+|+|.+++++..|.+.|+|+.|-.-. ..-
T Consensus         1 RTTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~Y-LPiDf~~-~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~-s~K   77 (97)
T PF04059_consen    1 RTTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFY-LPIDFKN-KCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFN-SKK   77 (97)
T ss_pred             CeeEEEecCCCCCCHHHHHHHHHHhccCcceEEE-eeeeccC-CCceEEEEEEcCCHHHHHHHHHHHcCCccccCC-CCc
Confidence            5679999999999999999999988888999765 4555543 345778999999999999999999999996433 344


Q ss_pred             eeEEEeccCC
Q 009860           87 KAIVEYAPSQ   96 (523)
Q Consensus        87 ~A~VEfAPYQ   96 (523)
                      .+.|-||=.|
T Consensus        78 vc~i~yAriQ   87 (97)
T PF04059_consen   78 VCEISYARIQ   87 (97)
T ss_pred             EEEEehhHhh
Confidence            6788887665

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

>PF00076 RRM_1: RNA recognition motif

Probab=97.49  E-value=0.00031  Score=53.53  Aligned_cols=66  Identities=18%  Similarity=0.296  Sum_probs=52.2

Q ss_pred             EEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860           10 VVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus        10 VVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      |.|.+||+.+|++++.+.+...  +.+....+...   ........|||.|.+.+++....+.++|+.|-+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~--g~i~~~~~~~~---~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~   66 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQF--GKIESIKVMRN---SSGKSKGYAFVEFESEEDAEKALEELNGKKING   66 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTT--STEEEEEEEEE---TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             cEEcCCCCcCCHHHHHHHHHHh--hhccccccccc---ccccccceEEEEEcCHHHHHHHHHHcCCCEECc
Confidence            6899999999999999999984  34544444332   234456789999999999999999999988754

(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 ....

>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=97.42  E-value=0.00079  Score=49.97  Aligned_cols=67  Identities=22%  Similarity=0.359  Sum_probs=53.3

Q ss_pred             eEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      .|+|+.||+.++++++++.+...  +.+....+..-...   .....|||.|.+.++...+.+.+++..|-+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~--g~i~~~~~~~~~~~---~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~   67 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKF--GKVESVRIVRDKDT---KSKGFAFVEFEDEEDAEKALEALNGKELGG   67 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhc--CCEEEEEEeeCCCC---CcceEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            47899999999999999999875  45666555532222   336689999999999999999999998643

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).

>PF14259 RRM_6: RNA recognition motif (a

Probab=97.23  E-value=0.0015  Score=50.85  Aligned_cols=65  Identities=29%  Similarity=0.350  Sum_probs=50.5

Q ss_pred             EEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009860           10 VVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV   79 (523)
Q Consensus        10 VVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv   79 (523)
                      |.|++||++.|++++.+.+...  +.+.-+.+...+.   ......|||.|.+++++..+.+..++..|-
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~--g~v~~v~~~~~~~---~~~~~~a~v~f~~~~~a~~al~~~~~~~~~   65 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRF--GPVEKVRLIKNKD---GQSRGFAFVEFSSEEDAKRALELLNGKEID   65 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTS--SBEEEEEEEESTT---SSEEEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             CEEeCCCCCCCHHHHHHHHHhc--CCcceEEEEeeec---cccCCEEEEEeCCHHHHHHHHHHCCCcEEC
Confidence            6899999999999999999886  3566666654432   234667999999999999999999877763

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 ....

>smart00362 RRM_2 RNA recognition motif

Probab=97.17  E-value=0.0023  Score=47.21  Aligned_cols=65  Identities=22%  Similarity=0.319  Sum_probs=51.2

Q ss_pred             eEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009860            9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV   79 (523)
Q Consensus         9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv   79 (523)
                      +|.|++||+.++++++.+.+...  +.+.+..+....    .....-|||.|.+.++.....+.++++.|-
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~--g~v~~~~~~~~~----~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~   65 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKF--GPIESVKIPKDT----GKSKGFAFVEFESEEDAEKAIEALNGTKLG   65 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhc--CCEEEEEEecCC----CCCCceEEEEeCCHHHHHHHHHHhCCcEEC
Confidence            48999999999999999999864  345555555443    223457999999999999999999998873

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

Probab=96.36  E-value=0.017  Score=53.17  Aligned_cols=80  Identities=14%  Similarity=0.070  Sum_probs=58.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      ...+||.|.+||+.+||+++++.+.+.  +.|.....+.-..+.  ..-.-|||.|.+.+++....+.++++.+.+.   
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~--G~I~~v~i~~d~~tg--~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr---  104 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHF--GDVVDAKVIVDRETG--RSRGFGFVNFNDEGAATAAISEMDGKELNGR---  104 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC--CCeEEEEEEecCCCC--CcceEEEEEECCHHHHHHHHHHcCCCEECCE---
Confidence            346899999999999999999999874  345554444322221  1224699999999999999999999876432   


Q ss_pred             eeeeEEEec
Q 009860           85 QFKAIVEYA   93 (523)
Q Consensus        85 e~~A~VEfA   93 (523)
                        ...|++|
T Consensus       105 --~l~V~~a  111 (144)
T PLN03134        105 --HIRVNPA  111 (144)
T ss_pred             --EEEEEeC
Confidence              4556665

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=95.95  E-value=0.033  Score=58.20  Aligned_cols=82  Identities=23%  Similarity=0.297  Sum_probs=59.8

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .....++|.|.+||+.+||++|.+.+...  +.|.....+.-+.+.+  ...-|||.|.+.+++...++.+++..+.+. 
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~--G~V~~v~i~~d~~tg~--srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr-  177 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTI--GPINTCRIMRDYKTGY--SFGYAFVDFGSEADSQRAIKNLNGITVRNK-  177 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEecCCCCc--cCcEEEEEEccHHHHHHHHHHcCCCccCCc-
Confidence            35678999999999999999999999864  2454444332222111  123499999999999999999999888653 


Q ss_pred             CCeeeeEEEec
Q 009860           83 GAQFKAIVEYA   93 (523)
Q Consensus        83 Gne~~A~VEfA   93 (523)
                          +..|+||
T Consensus       178 ----~i~V~~a  184 (346)
T TIGR01659       178 ----RLKVSYA  184 (346)
T ss_pred             ----eeeeecc
Confidence                4556665

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).

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

Probab=95.92  E-value=0.076  Score=56.16  Aligned_cols=85  Identities=19%  Similarity=0.176  Sum_probs=63.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      +..+|.|.+||+.+|++++.+.|..+  +.|..+.++......+  ...-|||.|.+.+++..-++.++|..|.+.    
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~--G~i~~~~~~~~~~~g~--~~g~afv~f~~~~~a~~A~~~l~g~~~~~~----  365 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESF--GDLKAFNLIKDIATGL--SKGYAFCEYKDPSVTDVAIAALNGKDTGDN----  365 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEEecCCCCC--cCeEEEEEECCHHHHHHHHHHcCCCEECCe----
Confidence            35799999999999999999999874  3455555554322211  234599999999999999999999998544    


Q ss_pred             eeeEEEeccCCCCC
Q 009860           86 FKAIVEYAPSQRVP   99 (523)
Q Consensus        86 ~~A~VEfAPYQKvP   99 (523)
                       ...|++|-+...+
T Consensus       366 -~l~v~~a~~~~~~  378 (509)
T TIGR01642       366 -KLHVQRACVGANQ  378 (509)
T ss_pred             -EEEEEECccCCCC
Confidence             3578888665443

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

>smart00360 RRM RNA recognition motif

Probab=95.83  E-value=0.033  Score=40.72  Aligned_cols=64  Identities=22%  Similarity=0.353  Sum_probs=47.9

Q ss_pred             EecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009860           12 IRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV   79 (523)
Q Consensus        12 IRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv   79 (523)
                      |++||+.++++++.+.+...  +.+....+......  ......|||.|.+.+++..+.+.++++.|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~--g~v~~~~i~~~~~~--~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~   64 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKF--GKIESVRLVRDKDT--GKSKGFAFVEFESEEDAEKALEALNGKELD   64 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhh--CCEeEEEEEeCCCC--CCCCceEEEEeCCHHHHHHHHHHcCCCeeC
Confidence            57899999999999988764  34555544433221  122358999999999999999999998884

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=95.51  E-value=0.068  Score=53.61  Aligned_cols=79  Identities=22%  Similarity=0.339  Sum_probs=59.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      +.+.|.|++||+.+||++|.+.+...  |.|.-...+.-+...  ..-.-|||.|.+.++...-++.++|..+.+.    
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~----   73 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSI--GEIESCKLVRDKVTG--QSLGYGFVNYVRPEDAEKAVNSLNGLRLQNK----   73 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHcc--CCEEEEEEEEcCCCC--ccceEEEEEECcHHHHHHHHhhcccEEECCe----
Confidence            46889999999999999999999874  355544444333221  1235699999999999999999999776533    


Q ss_pred             eeeEEEec
Q 009860           86 FKAIVEYA   93 (523)
Q Consensus        86 ~~A~VEfA   93 (523)
                       ...|+||
T Consensus        74 -~i~v~~a   80 (352)
T TIGR01661        74 -TIKVSYA   80 (352)
T ss_pred             -eEEEEee
Confidence             4667776

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=94.77  E-value=0.18  Score=52.87  Aligned_cols=82  Identities=17%  Similarity=0.154  Sum_probs=59.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      ..++|.|.+||+.+||+++.+.+...  +.|.....+.-+...++  -.-|||.|.+.+++..-++.+++..|...   .
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~f--G~V~~v~i~~d~~tg~~--kG~aFV~F~~~e~A~~Ai~~lng~~~~g~---~  264 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKY--GQIVQKNILRDKLTGTP--RGVAFVRFNKREEAQEAISALNNVIPEGG---S  264 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhc--CCEEEEEEeecCCCCcc--ceEEEEEECCHHHHHHHHHHhCCCccCCC---c
Confidence            46789999999999999999998764  24444333332222111  25799999999999999999999987442   3


Q ss_pred             eeeEEEecc
Q 009860           86 FKAIVEYAP   94 (523)
Q Consensus        86 ~~A~VEfAP   94 (523)
                      .+..|.+|-
T Consensus       265 ~~l~V~~a~  273 (346)
T TIGR01659       265 QPLTVRLAE  273 (346)
T ss_pred             eeEEEEECC
Confidence            456666664

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).

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

Probab=94.55  E-value=0.16  Score=53.13  Aligned_cols=79  Identities=14%  Similarity=0.195  Sum_probs=58.3

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF   86 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~   86 (523)
                      ..+|.|++||+.+||+++.+.+...  +.|.+..++.-....  ..-.-|||.|.+.++...-++.++|..|.+     .
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~--G~i~~v~~~~d~~~g--~~~g~afV~f~~~e~A~~A~~~l~g~~i~g-----~  256 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPF--GDIEDVQLHRDPETG--RSKGFGFIQFHDAEEAKEALEVMNGFELAG-----R  256 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhc--CCeEEEEEEEcCCCC--ccceEEEEEECCHHHHHHHHHhcCCcEECC-----E
Confidence            4789999999999999999988764  356655544322211  112359999999999999999999977633     2


Q ss_pred             eeEEEecc
Q 009860           87 KAIVEYAP   94 (523)
Q Consensus        87 ~A~VEfAP   94 (523)
                      ...|.||-
T Consensus       257 ~i~v~~a~  264 (457)
T TIGR01622       257 PIKVGYAQ  264 (457)
T ss_pred             EEEEEEcc
Confidence            56778765

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.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=93.90  E-value=0.25  Score=49.55  Aligned_cols=78  Identities=15%  Similarity=0.126  Sum_probs=57.5

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeee
Q 009860            8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFK   87 (523)
Q Consensus         8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~   87 (523)
                      ..|.|++||+..||+++++.+.+.  |.|.....+....+.  ..-.-|||.|.+.++...-++.++|..|-+ +    .
T Consensus       270 ~~lfV~NL~~~~~e~~L~~~F~~f--G~v~~v~i~~d~~t~--~skG~aFV~F~~~~~A~~Ai~~lnG~~~~g-r----~  340 (352)
T TIGR01661       270 YCIFVYNLSPDTDETVLWQLFGPF--GAVQNVKIIRDLTTN--QCKGYGFVSMTNYDEAAMAILSLNGYTLGN-R----V  340 (352)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhC--CCeEEEEEeEcCCCC--CccceEEEEECCHHHHHHHHHHhCCCEECC-e----E
Confidence            369999999999999999999975  356665554332221  112348999999999999999999998733 2    4


Q ss_pred             eEEEecc
Q 009860           88 AIVEYAP   94 (523)
Q Consensus        88 A~VEfAP   94 (523)
                      -.|.|+.
T Consensus       341 i~V~~~~  347 (352)
T TIGR01661       341 LQVSFKT  347 (352)
T ss_pred             EEEEEcc
Confidence            5666653

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

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

Probab=93.62  E-value=0.2  Score=54.25  Aligned_cols=67  Identities=16%  Similarity=0.222  Sum_probs=51.3

Q ss_pred             eEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009860            9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV   79 (523)
Q Consensus         9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv   79 (523)
                      -|.|.+||+++||+++.+.+...  +.|.......-+.+.+  ...-|||.|.+.++.....+.+++..|.
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~--G~v~~v~v~~d~~t~~--s~G~afV~F~~~~~A~~Al~~ln~~~i~   68 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPF--GPVLSVRVCRDSVTRR--SLGYGYVNFQNPADAERALETMNFKRLG   68 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEecCCCCC--cceEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            37899999999999999999875  3465555544333222  2346999999999999999999988763

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

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

Probab=92.37  E-value=0.51  Score=53.02  Aligned_cols=72  Identities=14%  Similarity=0.135  Sum_probs=56.8

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeee
Q 009860            8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFK   87 (523)
Q Consensus         8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~   87 (523)
                      .+|.|++||..+||+++.+.+...-.+.|.-...+.|          -|||.|.+.++...-++.+++..|.+     ..
T Consensus       234 k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~rg----------fAFVeF~s~e~A~kAi~~lnG~~i~G-----r~  298 (578)
T TIGR01648       234 KILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD----------YAFVHFEDREDAVKAMDELNGKELEG-----SE  298 (578)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeecC----------eEEEEeCCHHHHHHHHHHhCCCEECC-----EE
Confidence            5699999999999999999998753355654433322          59999999999999999999998844     25


Q ss_pred             eEEEecc
Q 009860           88 AIVEYAP   94 (523)
Q Consensus        88 A~VEfAP   94 (523)
                      ..|++|.
T Consensus       299 I~V~~Ak  305 (578)
T TIGR01648       299 IEVTLAK  305 (578)
T ss_pred             EEEEEcc
Confidence            6788873

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.

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

Probab=92.19  E-value=0.69  Score=41.70  Aligned_cols=72  Identities=18%  Similarity=0.244  Sum_probs=54.8

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      ...|.|.+||+.+|++++.+.+....  .+.+....--+  .......-|||.|.+.+++....+.++|..|.+..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g--~~~~~~~~~d~--~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~  186 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFG--PVKRVRLVRDR--ETGKSRGFAFVEFESEESAEKAIEELNGKELEGRP  186 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcC--ceeEEEeeecc--ccCccCceEEEEecCHHHHHHHHHHcCCCeECCce
Confidence            58999999999999999999998763  23333322111  12234567999999999999999999988887663

>PLN03120 nucleic acid binding protein; Provisional

Probab=91.89  E-value=1.1  Score=46.15  Aligned_cols=75  Identities=20%  Similarity=0.318  Sum_probs=57.7

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF   86 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~   86 (523)
                      ..+|-|.+||+..||+++.+.+..+  |+|.+.......-     .-.-|||.|.+++++.... .++|..|.|.     
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~--G~I~~V~I~~d~~-----~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr-----   70 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFS--GDIEYVEMQSENE-----RSQIAYVTFKDPQGAETAL-LLSGATIVDQ-----   70 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEeecCC-----CCCEEEEEeCcHHHHHHHH-HhcCCeeCCc-----
Confidence            4689999999999999999999764  5777766543221     1357999999999998888 4999988765     


Q ss_pred             eeEEEecc
Q 009860           87 KAIVEYAP   94 (523)
Q Consensus        87 ~A~VEfAP   94 (523)
                      ...|+.+.
T Consensus        71 ~V~Vt~a~   78 (260)
T PLN03120         71 SVTITPAE   78 (260)
T ss_pred             eEEEEecc
Confidence            35666664

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

Probab=91.65  E-value=0.97  Score=48.80  Aligned_cols=84  Identities=21%  Similarity=0.334  Sum_probs=62.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC-
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA-   84 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn-   84 (523)
                      +..+|.|.+||+++||+++.+.+...-...+..+.+++.+-.    ...-|+|.|.+.++...-...++++.+-+..|. 
T Consensus       393 ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~~~----~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~  468 (481)
T TIGR01649       393 PSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDNE----RSKMGLLEWESVEDAVEALIALNHHQLNEPNGSA  468 (481)
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCCCC----cceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCc
Confidence            346799999999999999999998753213555555565532    134599999999999999999999998666542 


Q ss_pred             eeeeEEEec
Q 009860           85 QFKAIVEYA   93 (523)
Q Consensus        85 e~~A~VEfA   93 (523)
                      -+...|.||
T Consensus       469 ~~~lkv~fs  477 (481)
T TIGR01649       469 PYHLKVSFS  477 (481)
T ss_pred             cceEEEEec
Confidence            345566766

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=90.96  E-value=0.92  Score=47.56  Aligned_cols=71  Identities=18%  Similarity=0.243  Sum_probs=52.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      .+...|.|.+||+.+||+++.+.+...  +.|.....+.-+.+.  ..-.-|||.|.+.+++...+. ++|..|.+
T Consensus        87 ~~~~~l~V~nlp~~~~~~~l~~~F~~~--G~v~~v~i~~d~~~~--~skg~afVeF~~~e~A~~Al~-l~g~~~~g  157 (457)
T TIGR01622        87 RDDRTVFVLQLALKARERDLYEFFSKV--GKVRDVQCIKDRNSR--RSKGVAYVEFYDVESVIKALA-LTGQMLLG  157 (457)
T ss_pred             cCCcEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEeecCCCC--CcceEEEEEECCHHHHHHHHH-hCCCEECC
Confidence            346689999999999999999988874  356665555433222  123569999999999998886 78877753

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.

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

Probab=90.61  E-value=0.84  Score=49.61  Aligned_cols=70  Identities=20%  Similarity=0.248  Sum_probs=54.1

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs   81 (523)
                      -+.|.|++||+.+||+++.+.+...  +.|....+.....   ...-..|||.|.+.++.....+.++|..|.+.
T Consensus       178 ~~~l~V~nl~~~~tee~L~~~F~~f--G~i~~~~i~~~~~---g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~  247 (562)
T TIGR01628       178 FTNLYVKNLDPSVNEDKLRELFAKF--GEITSAAVMKDGS---GRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLA  247 (562)
T ss_pred             CCeEEEeCCCCcCCHHHHHHHHHhc--CCEEEEEEEECCC---CCcccEEEEEECCHHHHHHHHHHhCCcEeccc
Confidence            4679999999999999999998864  3466555543321   12245799999999999999999999988643

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

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

Probab=90.43  E-value=0.9  Score=51.11  Aligned_cols=71  Identities=20%  Similarity=0.214  Sum_probs=53.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcce--eEEEEecCcccHHHHHHHhcCCeeEeC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYS--RAYVELKKPAGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~yS--RAYI~Fkn~Edl~~F~d~fdG~vFvDs   81 (523)
                      |...++|-|-+||+.+||+++.+.+...  +.|.-...+.- .+    -.|  -|||.|.+.+++..-++.++++.+.+.
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~--G~I~~vrl~~D-~s----G~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~G  127 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKA--GPIYELRLMMD-FS----GQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPG  127 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhh--CCEEEEEEEEC-CC----CCccceEEEEeCCHHHHHHHHHHcCCCeecCC
Confidence            4456999999999999999999998764  23433333222 11    123  499999999999999999999988643

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.

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

Probab=87.03  E-value=2.1  Score=48.55  Aligned_cols=73  Identities=15%  Similarity=0.153  Sum_probs=54.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs   81 (523)
                      ...++|.|.+||+.+||+++.+.+..+  |.|.-...+.-..+.+  ...-|||.|.+.++...-++.++|..|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~f--G~I~sV~I~~D~~Tgk--skGfAFVeF~s~e~A~~Ai~~lnG~~i~GR  177 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPF--GPIKSINMSWDPATGK--HKGFAFVEYEVPEAAQLALEQMNGQMLGGR  177 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHcc--CCEEEEEEeecCCCCC--cCCeEEEEeCcHHHHHHHHHhcCCeEEecc
Confidence            456799999999999999999999874  3454444332222222  234699999999999999999999887543

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.

>PLN03121 nucleic acid binding protein; Provisional

Probab=86.92  E-value=2.2  Score=43.58  Aligned_cols=69  Identities=20%  Similarity=0.307  Sum_probs=52.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      ...-|.|.+|+|..||+++.+-+..  .|+|...+-+.-.-     .-.-|||.|++++++ +-+-.++|..|+|..
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~--~G~I~~V~I~~D~e-----t~gfAfVtF~d~~aa-etAllLnGa~l~d~~   72 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSH--CGAIEHVEIIRSGE-----YACTAYVTFKDAYAL-ETAVLLSGATIVDQR   72 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHh--cCCeEEEEEecCCC-----cceEEEEEECCHHHH-HHHHhcCCCeeCCce
Confidence            3467899999999999999998885  46777766443211     124799999999999 445589999998874

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

Probab=86.66  E-value=4.7  Score=43.61  Aligned_cols=80  Identities=19%  Similarity=0.150  Sum_probs=62.2

Q ss_pred             CCceEEEecCCC-CCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            6 QRTKVVIRHLPP-SLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         6 ~r~KVVIRrLPP-~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      +...|.|.+||+ .+|++++++.+..+  |.|....++..+       ..-|+|.|.+.++...-.+.++|+.|.+    
T Consensus       274 ~~~~l~v~nL~~~~vt~~~L~~lF~~y--G~V~~vki~~~~-------~g~afV~f~~~~~A~~Ai~~lng~~l~g----  340 (481)
T TIGR01649       274 PGSVLMVSGLHQEKVNCDRLFNLFCVY--GNVERVKFMKNK-------KETALIEMADPYQAQLALTHLNGVKLFG----  340 (481)
T ss_pred             CCCEEEEeCCCCCCCCHHHHHHHHHhc--CCeEEEEEEeCC-------CCEEEEEECCHHHHHHHHHHhCCCEECC----
Confidence            567999999999 69999999999875  456666555432       2469999999999999999999998843    


Q ss_pred             eeeeEEEeccCCCCC
Q 009860           85 QFKAIVEYAPSQRVP   99 (523)
Q Consensus        85 e~~A~VEfAPYQKvP   99 (523)
                       ....|+++-.+.+.
T Consensus       341 -~~l~v~~s~~~~~~  354 (481)
T TIGR01649       341 -KPLRVCPSKQQNVQ  354 (481)
T ss_pred             -ceEEEEEccccccc
Confidence             25667777655543

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).

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

Probab=85.93  E-value=4.4  Score=40.12  Aligned_cols=77  Identities=22%  Similarity=0.288  Sum_probs=61.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      .-.+||-|=+||+.-|+.||...+..+-.-.-.|..+.|         +--|+|.|.++.|..+-...+||..|...   
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP---------PGfAFVEFed~RDA~DAvr~LDG~~~cG~---   75 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP---------PGFAFVEFEDPRDAEDAVRYLDGKDICGS---   75 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC---------CCceEEeccCcccHHHHHhhcCCccccCc---
Confidence            447999999999999999999988765322235765543         34589999999999999999999998876   


Q ss_pred             eeeeEEEeccC
Q 009860           85 QFKAIVEYAPS   95 (523)
Q Consensus        85 e~~A~VEfAPY   95 (523)
                        .+.||++--
T Consensus        76 --r~rVE~S~G   84 (195)
T KOG0107|consen   76 --RIRVELSTG   84 (195)
T ss_pred             --eEEEEeecC
Confidence              578887643

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

Probab=85.69  E-value=2.6  Score=47.92  Aligned_cols=69  Identities=12%  Similarity=0.137  Sum_probs=53.8

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV   79 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv   79 (523)
                      ..+|.|.+||+.++++++.+.+..+  +.|....+.......+  .---|||.|.+.++...-.+.++++.|-
T Consensus       204 ~~rLfVgnLp~~vteedLk~lFs~F--G~I~svrl~~D~~tgk--sKGfGFVeFe~~e~A~kAI~amNg~elg  272 (612)
T TIGR01645       204 FNRIYVASVHPDLSETDIKSVFEAF--GEIVKCQLARAPTGRG--HKGYGFIEYNNLQSQSEAIASMNLFDLG  272 (612)
T ss_pred             cceEEeecCCCCCCHHHHHHHHhhc--CCeeEEEEEecCCCCC--cCCeEEEEECCHHHHHHHHHHhCCCeeC
Confidence            4689999999999999999999874  4566666655433221  1235999999999999999999998664

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.

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

Probab=85.57  E-value=2.3  Score=45.13  Aligned_cols=66  Identities=15%  Similarity=0.297  Sum_probs=46.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCC----------CceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcC
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFN----------DRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNG   75 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~----------gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG   75 (523)
                      ..-+|.|.+||+.+|++++.+.+...+.          ..|....+  +    +.  -.-|||.|.+.+++...+ .++|
T Consensus       174 ~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~--~----~~--kg~afVeF~~~e~A~~Al-~l~g  244 (509)
T TIGR01642       174 QARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI--N----KE--KNFAFLEFRTVEEATFAM-ALDS  244 (509)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE--C----CC--CCEEEEEeCCHHHHhhhh-cCCC
Confidence            3458999999999999999988876421          11111111  1    11  235999999999998887 5999


Q ss_pred             CeeEe
Q 009860           76 HVFVN   80 (523)
Q Consensus        76 ~vFvD   80 (523)
                      ..|.+
T Consensus       245 ~~~~g  249 (509)
T TIGR01642       245 IIYSN  249 (509)
T ss_pred             eEeeC
Confidence            88865

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

>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=80.89  E-value=7.9  Score=34.96  Aligned_cols=72  Identities=21%  Similarity=0.376  Sum_probs=54.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV   79 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv   79 (523)
                      ...++.|.|=..||.|+-..|+-.+...+...+..+..+.-   ..++.| =+-|.|.+.++..+|...|+|..|-
T Consensus         9 ~~~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird---~~pnry-mVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen    9 DERRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRD---GTPNRY-MVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             CCCCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeC---CCCceE-EEEEEECCHHHHHHHHHHhCCCccC
Confidence            34556777779999999999998888877666766555431   123333 3678999999999999999999994

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	523
1uw4_A	91	The Structural Basis Of The Interaction Between Non		1e-09
2l08_A	97	Solution Nmr Structure Of Nonsense Mrna Reducing Fa		3e-09

>pdb|1UW4|A Chain A, The Structural Basis Of The Interaction Between Nonsense Mediated Decay Factors Upf2 And Upf3 Length = 91

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 32/92 (34%), Positives = 54/92 (58%), Gaps = 6/92 (6%)
Query: 8  TKVVIRHLPPSLSQNDLLALFRDHFND--RYNWFCFRPGKSSYKHQRYSRAYVELKKPAG 65
          +KVVIR LPP+L++  L    ++H      +++F F    +S     Y+RAY+  K    
Sbjct: 2  SKVVIRRLPPTLTKEQL----QEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQED 57
Query: 66 VFEFAELLNGHVFVNEKGAQFKAIVEYAPSQR 97
          +  F +  +G+VF++ KG ++ AIVE+AP Q+
Sbjct: 58 IILFRDRFDGYVFLDNKGQEYPAIVEFAPFQK 89

>pdb|2L08|A Chain A, Solution Nmr Structure Of Nonsense Mrna Reducing Factor 3a From H. Sapiens, Northeast Structural Genomics Consortium Target Hr4714b Length = 97

Iteration: 1
 Score = 60.1 bits (144), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 30/88 (34%), Positives = 49/88 (55%), Gaps = 2/88 (2%)
Query: 10 VVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEF 69
          VVIR LPP L++  L    R      +++F F     S     YSRAY+  + P  +  F
Sbjct: 12 VVIRRLPPGLTKEQLEEQLRPL--PAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLF 69
Query: 70 AELLNGHVFVNEKGAQFKAIVEYAPSQR 97
           +  +G++F++ KG ++ A+VE+AP Q+
Sbjct: 70 RDRFDGYIFLDSKGLEYPAVVEFAPFQK 97

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	523
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	2e-31
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	2e-30
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens} Length = 97

 Score =  115 bits (290), Expect = 2e-31
 Identities = 30/92 (32%), Positives = 49/92 (53%), Gaps = 2/92 (2%)

Query: 6  QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAG 65
              VVIR LPP L++  L    R      +++F F     S     YSRAY+  + P  
Sbjct: 8  HSHMVVIRRLPPGLTKEQLEEQLRPLPA--HDYFEFFAADLSLYPHLYSRAYINFRNPDD 65

Query: 66 VFEFAELLNGHVFVNEKGAQFKAIVEYAPSQR 97
          +  F +  +G++F++ KG ++ A+VE+AP Q+
Sbjct: 66 ILLFRDRFDGYIFLDSKGLEYPAVVEFAPFQK 97

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4 Length = 91

 Score =  112 bits (283), Expect = 2e-30
 Identities = 31/91 (34%), Positives = 52/91 (57%), Gaps = 2/91 (2%)

Query: 8  TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVF 67
          +KVVIR LPP+L++  L    +      +++F F    +S     Y+RAY+  K    + 
Sbjct: 2  SKVVIRRLPPTLTKEQLQEHLQPMP--EHDYFEFFSNDTSLYPHMYARAYINFKNQEDII 59

Query: 68 EFAELLNGHVFVNEKGAQFKAIVEYAPSQRV 98
           F +  +G+VF++ KG ++ AIVE+AP Q+ 
Sbjct: 60 LFRDRFDGYVFLDNKGQEYPAIVEFAPFQKA 90

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 44.5 bits (104), Expect = 8e-05
 Identities = 76/466 (16%), Positives = 135/466 (28%), Gaps = 144/466 (30%)

Query: 79  VNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLEFLKVIAKPAE-----NLP 133
             E   Q+K I+           F   +      F   D  +  K I    E        
Sbjct: 11  TGEHQYQYKDILSV-----FEDAF-VDN------FDCKDVQDMPKSILSKEEIDHIIMSK 58

Query: 134 SAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAAESGAQESLAVGRVGRR------SR 187
            A     R                 L   +  K+  E   Q+   V  V R       S 
Sbjct: 59  DAVSGTLR-----------------LFWTLLSKQ--EEMVQK--FVEEVLRINYKFLMSP 97

Query: 188 AASASKTSSTTTKRGSEKKKYILKDSAK----NARRKDKSTFTVVAKREDQPASSSGKET 243
             +  +  S  T+   E++  +  D+      N  R         A  E +PA +     
Sbjct: 98  IKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNV---- 153

Query: 244 SASETICGVEGSVGIPLTSDTGKKKILLLKGKEREIPHVPDALLDKQRESSP-------- 295
                I GV GS         GK   +             D  L  + +           
Sbjct: 154 ----LIDGVLGS---------GKT-WV-----------ALDVCLSYKVQCKMDFKIFWLN 188

Query: 296 VKNSASP-TVPKQIQRREAGGRLIRKILLNNETRQTQSVTGVQP----QQKMQNLNQENG 350
           +KN  SP TV + +Q+      L+ +I  N  +R   S          Q +++ L +   
Sbjct: 189 LKNCNSPETVLEMLQK------LLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKS-- 240

Query: 351 KPLPGPTSSPNG-----HVTNNDSPIF-SFDGNTKRSSDDRFARKVLHGSGAVSEKQEKR 404
           KP        N      +V   ++  + +F+ + K          +L     ++      
Sbjct: 241 KPYE------NCLLVLLNV--QNAKAWNAFNLSCK----------IL-----LT------ 271

Query: 405 TRNKDRPDRVVWTPRRSDVSQANGER-LSSSQPTQLLSDSVEVTRGEMKDDMSYGSKTVD 463
           TR K   D +      + +S  +    L+  +   LL   ++    ++  ++   +    
Sbjct: 272 TRFKQVTDFLS-AATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRL 330

Query: 464 --IAAPTSGGSHR-----HNGRRAATNITKDDGCINMIEGKSSKRR 502
             IA     G        H      T I +    +N++E    ++ 
Sbjct: 331 SIIAESIRDGLATWDNWKHVNCDKLTTIIES--SLNVLEPAEYRKM 374

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 43.3 bits (101), Expect = 2e-04
 Identities = 68/534 (12%), Positives = 127/534 (23%), Gaps = 227/534 (42%)

Query: 14  HLPPSLSQ-----NDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFE 68
           H+     +      D+L++F D F                                   +
Sbjct: 6   HMDFETGEHQYQYKDILSVFEDAF----------------------------VDNFDCKD 37

Query: 69  FAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSR--------KDSREGTIFK------ 114
             ++    +   E   +   I+            S            +E  + K      
Sbjct: 38  VQDMPKS-ILSKE---EIDHIIM------SKDAVSGTLRLFWTLLSKQEEMVQKFVEEVL 87

Query: 115 DPDYLEFLKVIAKPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAAESGAQ 174
             +Y +FL            + I+ E+++  +               Y+ Q+    +  Q
Sbjct: 88  RINY-KFLM-----------SPIKTEQRQPSM-----------MTRMYIEQRDRLYNDNQ 124

Query: 175 ESLAVGRVGRRSRAASASKTSSTTTKRGSEKKKYILKDSAKNARRKD-----------KS 223
              A   V R                    +    L+ +    R              K+
Sbjct: 125 -VFAKYNVSR-------------------LQPYLKLRQALLELRPAKNVLIDGVLGSGKT 164

Query: 224 TFTVVAKREDQPAS---------SSGKETSASETI------C---------GVEGSVGIP 259
              +      +            +     S    +                  + S  I 
Sbjct: 165 WVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIK 224

Query: 260 LTSDTGKKKIL-LLKGKEREIPHVPDAL--LDKQRESSPVKNSASPTVPKQIQRREAGGR 316
           L   + + ++  LLK K    P+  + L  L        V+N+                +
Sbjct: 225 LRIHSIQAELRRLLKSK----PY-ENCLLVLLN------VQNA----------------K 257

Query: 317 LIR------KILLNNETRQTQSVTGVQPQQKMQNLNQENGKPLPGPTSSPNGHVTNNDSP 370
                    KILL   TR  + VT                  L   T++   H++ +   
Sbjct: 258 AWNAFNLSCKILLT--TRF-KQVTDF----------------LSAATTT---HISLDHHS 295

Query: 371 IFSFDGNTKRSSDDRFARKVLHGSGAVSEKQEKRTRN-----------KDRPDRVVWTPR 419
                  T          K L         +E  T N           +D      W   
Sbjct: 296 ----MTLTPDEVKSLLL-KYL-DCRPQDLPREVLTTNPRRLSIIAESIRDGLAT--WDNW 347

Query: 420 RSDVSQANGERLSSSQPTQLLSDSVEV-TRGEMK---DDMSYGSKTVDIAAPTS 469
           +      N ++L     T ++  S+ V    E +   D +S    +  I  PT 
Sbjct: 348 K----HVNCDKL-----TTIIESSLNVLEPAEYRKMFDRLSVFPPSAHI--PTI 390

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	523
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	100.0
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	100.0
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	97.79
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	97.74
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	97.69
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	97.61
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	97.6
2div_A	99	TRNA selenocysteine associated protein; structural	97.57
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	97.55
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	97.52
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	97.51
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	97.5
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	97.49
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	97.49
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	97.48
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	97.47
1x4e_A	85	RNA binding motif, single-stranded interacting pro	97.46
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	97.46
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	97.46
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	97.46
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	97.46
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	97.45
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	97.44
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	97.44
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	97.43
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	97.43
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	97.42
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	97.42
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	97.42
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	97.41
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	97.41
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	97.4
1x5o_A	114	RNA binding motif, single-stranded interacting pro	97.39
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	97.37
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	97.37
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	97.36
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	97.35
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	97.35
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	97.35
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	97.35
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	97.35
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	97.34
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	97.34
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	97.32
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	97.29
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	97.28
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	97.27
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	97.27
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	97.25
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	97.24
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	97.24
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	97.24
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	97.24
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	97.24
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	97.21
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	97.21
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	97.19
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	97.18
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	97.18
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	97.18
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	97.16
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	97.14
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	97.14
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	97.14
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	97.13
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	97.12
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	97.11
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	97.11
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	97.1
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	97.07
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	97.06
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	97.05
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	97.05
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	97.04
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	97.03
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	97.02
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	97.02
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	97.01
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	97.0
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	97.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	96.99
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	96.98
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	96.97
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	96.96
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	96.92
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	96.91
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	96.91
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.9
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	96.89
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	96.88
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	96.88
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	96.87
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	96.85
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	96.83
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	96.83
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	96.81
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	96.81
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	96.8
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	96.77
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	96.75
2dis_A	109	Unnamed protein product; structural genomics, RRM	96.75
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	96.75
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	96.74
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	96.73
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	96.73
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	96.72
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	96.71
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	96.71
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	96.71
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	96.69
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	96.68
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	96.64
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	96.64
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	96.63
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	96.62
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	96.61
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	96.6
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	96.58
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	96.53
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	96.52
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	96.52
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	96.51
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	96.48
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	96.47
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	96.43
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	96.4
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	96.4
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	96.38
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	96.36
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	96.35
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	96.33
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	96.29
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	96.28
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	96.26
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	96.23
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	96.23
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	96.23
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	96.2
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	96.19
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	96.17
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	96.15
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	96.15
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	96.12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	96.11
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	96.09
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	96.08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	96.05
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	96.04
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	96.04
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	96.03
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	95.99
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	95.99
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	95.93
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	95.87
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	95.83
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	95.81
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	95.78
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	95.74
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	95.73
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	95.68
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	95.61
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	95.57
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	95.53
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	95.52
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	95.5
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	95.45
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	95.42
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	95.41
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	95.39
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	95.38
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	95.28
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	95.27
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	95.16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	95.14
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	95.14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	95.12
1x5p_A	97	Negative elongation factor E; structure genomics,	95.1
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	95.03
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	94.9
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	94.85
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	94.78
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	94.71
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	94.66
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	94.51
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	93.54
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	94.43
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	94.31
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	94.0
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	93.76
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	93.44
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	93.33
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	93.27
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	93.26
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	93.07
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	92.59
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	91.92
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	90.2
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	89.26
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	88.41
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	87.3
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	86.72
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	85.41
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	80.7

>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=100.00  E-value=3.6e-36  Score=255.54  Aligned_cols=90  Identities=34%  Similarity=0.649  Sum_probs=87.3

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeee
Q 009860            8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFK   87 (523)
Q Consensus         8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~   87 (523)
                      +|||||||||+|||++|+++|+++|  .++|+||++|+++.++++||||||+|++.|+|.+|.+.|+|++|+|++|++++
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~--~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~   79 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMP--EHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYP   79 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCC--CEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcc--cceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEee
Confidence            7999999999999999999999987  58999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEeccCCCCC
Q 009860           88 AIVEYAPSQRVP   99 (523)
Q Consensus        88 A~VEfAPYQKvP   99 (523)
                      |+||||||||||
T Consensus        80 a~VE~AP~qkvP   91 (91)
T 1uw4_A           80 AIVEFAPFQKAA   91 (91)
T ss_dssp             CEEEECSSCCC-
T ss_pred             eEEEEcCCCcCc
Confidence            999999999997

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=100.00  E-value=2.4e-35  Score=253.73  Aligned_cols=91  Identities=33%  Similarity=0.621  Sum_probs=87.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      -..+|||||||||+|||++|+++|+++|.  ++|+||++|+++.++++||||||+|+++|+|.+|.+.|+|++|+|++|+
T Consensus         7 ~~~~KvVIRrLPP~Ltee~F~~~l~~~~~--~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~   84 (97)
T 2l08_A            7 HHSHMVVIRRLPPGLTKEQLEEQLRPLPA--HDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGL   84 (97)
T ss_dssp             CCCCCEEEECCCSCSCHHHHTTTTSCCSS--EEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCC
T ss_pred             ccceeEEEeCCCCCCCHHHHHHHhCCcCc--cceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCC
Confidence            34689999999999999999999999875  6999999999999999999999999999999999999999999999999


Q ss_pred             eeeeEEEeccCCC
Q 009860           85 QFKAIVEYAPSQR   97 (523)
Q Consensus        85 e~~A~VEfAPYQK   97 (523)
                      +++|+||||||||
T Consensus        85 ~~~a~VE~APyqK   97 (97)
T 2l08_A           85 EYPAVVEFAPFQK   97 (97)
T ss_dssp             EEEEEEEECCCCC
T ss_pred             EeeeEEEecCCCC
Confidence            9999999999997

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.79  E-value=0.00019  Score=59.51  Aligned_cols=81  Identities=20%  Similarity=0.194  Sum_probs=66.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +....+|.|.+||+.+||+++.+.+..+  +.|.....+..         .-|||.|.+.+++...++.++++.|.+..+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~~~i~~~---------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~   80 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREA--GDVCYADVYRD---------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEG   80 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGG--SCEEEEEEETT---------TEEEEEESSHHHHHHHHHHSSSEEEECTTS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEeEEEEecC---------CEEEEEECCHHHHHHHHHHHCcCCccCCcC
Confidence            4567899999999999999999999875  34555444332         579999999999999999999999987676


Q ss_pred             CeeeeEEEeccC
Q 009860           84 AQFKAIVEYAPS   95 (523)
Q Consensus        84 ne~~A~VEfAPY   95 (523)
                      ......|++|--
T Consensus        81 ~~~~i~V~~a~~   92 (108)
T 1x4c_A           81 ETAYIRVKVDGP   92 (108)
T ss_dssp             CEEEEEEEESSC
T ss_pred             cceEEEEEeCCC
Confidence            667888998854

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.74  E-value=0.00021  Score=56.88  Aligned_cols=82  Identities=17%  Similarity=0.193  Sum_probs=61.4

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+..+|.|++||+.+|++++.+.+...  +.|........+...+  ...-|||.|.+.+++....+.++|+.|.+  
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~--G~v~~v~i~~~~~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~g--   85 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKY--GKVVKVTIMKDKDTRK--SKGVAFILFLDKDSAQNCTRAINNKQLFG--   85 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTT--SCEEEEEECCCSSSCC--CTTCEEEEESCHHHHHHHHHHTTTEEETT--
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhc--CCeEEEEEEeCCCCCC--cccEEEEEECCHHHHHHHHHHcCCCeeCC--
Confidence            35677899999999999999999999875  3465555544333221  12359999999999999999999988742  


Q ss_pred             CCeeeeEEEec
Q 009860           83 GAQFKAIVEYA   93 (523)
Q Consensus        83 Gne~~A~VEfA   93 (523)
                         ....|+||
T Consensus        86 ---~~l~v~~a   93 (94)
T 2e5h_A           86 ---RVIKASIA   93 (94)
T ss_dssp             ---EEEEEEEC
T ss_pred             ---cEEEEEec
Confidence               34566665

>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=97.69  E-value=0.00021  Score=59.08  Aligned_cols=80  Identities=20%  Similarity=0.249  Sum_probs=59.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      .++++|.|++||+.+||+++.+.+...  |.|.....+.-+.+.+  .-.-|||.|.+.+++....+.++|..|-+    
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~--G~I~~v~i~~d~~tg~--~kG~afV~f~~~~~A~~Ai~~lng~~~~g----   88 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSI--GEVESAKLIRDKVAGH--SLGYGFVNYVTAKDAERAINTLNGLRLQS----   88 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTT--SCEEEEEEEECSSSCC--EEEEEEEEESSHHHHHHHHHHHTTCEETT----
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEeEeeecCCCCc--ccccEEEEECCHHHHHHHHHHhCCCEECC----
Confidence            356899999999999999999999874  4565555543322221  12349999999999999999999998842    


Q ss_pred             eeeeEEEec
Q 009860           85 QFKAIVEYA   93 (523)
Q Consensus        85 e~~A~VEfA   93 (523)
                       ..-.|+||
T Consensus        89 -r~l~V~~A   96 (99)
T 4fxv_A           89 -KTIKVSYA   96 (99)
T ss_dssp             -EECEEEEC
T ss_pred             -EEEEEEEe
Confidence             25677777

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.61  E-value=0.0007  Score=53.95  Aligned_cols=85  Identities=9%  Similarity=0.116  Sum_probs=63.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +.+..+|.|++||+.+|++++.+.+...  +.|........+.+.+  ...-|||.|.+.+++...++.++|+.|.+   
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~--G~v~~v~i~~~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g---   74 (95)
T 2dnz_A            2 SSGSSGLYVGSLHFNITEDMLRGIFEPF--GKIDNIVLMKDSDTGR--SKGYGFITFSDSECARRALEQLNGFELAG---   74 (95)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTT--SCEEEEEEECCSSSCC--CCSEEEEEESCHHHHHHHHHHHTTCCSSS---
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhc--CCEeEEEEeecCCCCc--eeeEEEEEECCHHHHHHHHHHhCCCeeCC---
Confidence            5677899999999999999999999875  3455555544333221  23469999999999999999999988743   


Q ss_pred             CeeeeEEEeccCCC
Q 009860           84 AQFKAIVEYAPSQR   97 (523)
Q Consensus        84 ne~~A~VEfAPYQK   97 (523)
                        ....|++|.-+.
T Consensus        75 --~~l~V~~a~~~~   86 (95)
T 2dnz_A           75 --RPMRVGHVTERL   86 (95)
T ss_dssp             --SCCEEEESSCCC
T ss_pred             --cEEEEEEccccc
Confidence              356788875443

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.60  E-value=0.00029  Score=56.28  Aligned_cols=75  Identities=16%  Similarity=0.194  Sum_probs=61.4

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+..+|.|++||+.+|++++.+.+...  +.|.......|          -|||.|.+.+++....+.++|+.|.+  
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~v~~v~~~~~----------~afV~f~~~~~a~~A~~~l~g~~~~g--   71 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEY--GPVIECDIVKD----------YAFVHMERAEDAVEAIRGLDNTEFQG--   71 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTT--SCCCEEEECSS----------EEEEEESCHHHHHHHHHHHTTEEETT--
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEECC----------EEEEEECCHHHHHHHHHHhCCCeeCC--
Confidence            35677899999999999999999999874  34655555543          79999999999999999999998842  


Q ss_pred             CCeeeeEEEecc
Q 009860           83 GAQFKAIVEYAP   94 (523)
Q Consensus        83 Gne~~A~VEfAP   94 (523)
                         ....|+||-
T Consensus        72 ---~~l~V~~a~   80 (92)
T 2dgt_A           72 ---KRMHVQLST   80 (92)
T ss_dssp             ---EEEEEEESS
T ss_pred             ---cEEEEEEcc
Confidence               467788884

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.57  E-value=0.00035  Score=56.25  Aligned_cols=92  Identities=12%  Similarity=0.042  Sum_probs=65.7

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCcee-EEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYN-WFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvd-wfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs   81 (523)
                      ...+..+|.|.+||+.+||+++.+.+...-  .|. ....+..+...  ....-|||.|.+.+++....+.++|+.|.+.
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G--~i~~~v~i~~~~~~g--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   80 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMG--ETVMSVKIIRNRLTG--IPAGYCFVEFADLATAEKCLHKINGKPLPGA   80 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTT--CCCCEEEEEECSSSC--CEEEEEEEECSCHHHHHHHHHTTTTSEESSC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhC--CcceEEEEeecCCCC--CcCCEEEEEeCCHHHHHHHHHHHcCCccCCC
Confidence            356778999999999999999999998752  333 33333322221  1224599999999999999999999987544


Q ss_pred             CCCeeeeEEEeccCCCCC
Q 009860           82 KGAQFKAIVEYAPSQRVP   99 (523)
Q Consensus        82 KGne~~A~VEfAPYQKvP   99 (523)
                      .. .-.-.|+||-.++.+
T Consensus        81 ~~-~~~l~v~~a~~~~~~   97 (99)
T 2div_A           81 TP-AKRFKLNYATYSGPS   97 (99)
T ss_dssp             SS-CEECCEEETTCCSSS
T ss_pred             Cc-ceeEEEeecCCCCCC
Confidence            32 223678988776654

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.55  E-value=0.00047  Score=56.10  Aligned_cols=85  Identities=15%  Similarity=0.062  Sum_probs=63.7

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+..+|.|.+||+.+|++++.+.+..+  +.|.....+..+...  ....-|||.|.+.+++...++.++++.|.+  
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--   84 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQA--GPVVNTHMPKDRVTG--QHQGYGFVEFLSEEDADYAIKIMDMIKLYG--   84 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTT--SCEEEEECCBCSSSC--SBCSCEEEEESSHHHHHHHHHHSSSCBCSS--
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEecCCCC--cCCcEEEEEECCHHHHHHHHHHhCCCeECC--
Confidence            46678999999999999999999999875  356555544332221  122359999999999999999999988743  


Q ss_pred             CCeeeeEEEeccCC
Q 009860           83 GAQFKAIVEYAPSQ   96 (523)
Q Consensus        83 Gne~~A~VEfAPYQ   96 (523)
                         ....|++|--.
T Consensus        85 ---~~l~v~~a~~~   95 (105)
T 1x5u_A           85 ---KPIRVNKASAH   95 (105)
T ss_dssp             ---CBCEEEETTTT
T ss_pred             ---eEEEEEECCCC
Confidence               35678887443

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.52  E-value=0.00048  Score=54.84  Aligned_cols=77  Identities=18%  Similarity=0.178  Sum_probs=62.1

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+..+|.|.+||+.+|++++.+.+...  +.|.......|          .|||.|.+.+++...++.++|+.|.+  
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~v~~~~~~~~----------~afV~f~~~~~a~~A~~~l~g~~~~g--   70 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERR--GRVIECDVVKD----------YAFVHMEKEADAKAAIAQLNGKEVKG--   70 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHH--SCEEEEEECSS----------CEEEEESCHHHHHHHHHHHTTCEETT--
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcC--CCEEEEEEECC----------EEEEEECCHHHHHHHHHHhCCCEECC--
Confidence            35677899999999999999999999875  34666555544          79999999999999999999988742  


Q ss_pred             CCeeeeEEEeccCC
Q 009860           83 GAQFKAIVEYAPSQ   96 (523)
Q Consensus        83 Gne~~A~VEfAPYQ   96 (523)
                         ....|++|--+
T Consensus        71 ---~~l~v~~a~~~   81 (90)
T 2dnp_A           71 ---KRINVELSTKG   81 (90)
T ss_dssp             ---EECEEEESCCC
T ss_pred             ---cEEEEEECCCC
Confidence               35678887543

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.51  E-value=0.0014  Score=53.23  Aligned_cols=85  Identities=15%  Similarity=0.145  Sum_probs=64.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +.+..+|.|++||+.+||+++.+.+..+  +.|.....+....    ..-.-|||.|.+.+++...++.++++.|.+   
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~--G~v~~v~i~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g---   82 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQF--GKILDVEIIFNER----GSKGFGFVTFENSADADRAREKLHGTVVEG---   82 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGT--SCEEEEEEECCTT----TTCCEEEEEESCHHHHHHHHHHHTTCEETT---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEecCC----CCcEEEEEEECCHHHHHHHHHHhCCCEECC---
Confidence            5667899999999999999999999875  3565555543321    123479999999999999999999998743   


Q ss_pred             CeeeeEEEeccCCCCC
Q 009860           84 AQFKAIVEYAPSQRVP   99 (523)
Q Consensus        84 ne~~A~VEfAPYQKvP   99 (523)
                        ....|++|--....
T Consensus        83 --~~l~v~~a~~~~~~   96 (103)
T 2cq3_A           83 --RKIEVNNATARVMT   96 (103)
T ss_dssp             --EECEEEECCSSCCC
T ss_pred             --EEEEEEEcccCCCC
Confidence              35788887655433

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=97.50  E-value=0.00055  Score=53.35  Aligned_cols=81  Identities=12%  Similarity=0.067  Sum_probs=59.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +.+..+|.|++||+.+||+++.+.+...  +.|.....+......  ....-|||.|.+.+++....+.++|+.|.+   
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~--G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g---   76 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPF--GDITDIQIPLDYETE--KHRGFAFVEFELAEDAAAAIDNMNESELFG---   76 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGG--SCEEEEECCEETTTT--EECSEEEEEESSHHHHHHHHHHHTTCEETT---
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcc--CCEEEEEEEECCCCC--ccccEEEEEECCHHHHHHHHHHhCCCEECC---
Confidence            4577899999999999999999999875  345544433221111  123459999999999999999999998832   


Q ss_pred             CeeeeEEEec
Q 009860           84 AQFKAIVEYA   93 (523)
Q Consensus        84 ne~~A~VEfA   93 (523)
                        ....|+||
T Consensus        77 --~~l~v~~a   84 (85)
T 3mdf_A           77 --RTIRVNLA   84 (85)
T ss_dssp             --EECEEEEC
T ss_pred             --cEEEEEEc
Confidence              24556654

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.49  E-value=0.00076  Score=54.79  Aligned_cols=83  Identities=16%  Similarity=0.202  Sum_probs=63.1

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009860            2 KEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         2 k~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs   81 (523)
                      ....+..+|.|.+||+.+||+++.+.+..+  +.|.....+.-...    .-.-|||.|.+.+++...++.++++.|.  
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~--   81 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQI--GPCKSCKMITEHTS----NDPYCFVEFYEHRDAAAALAAMNGRKIL--   81 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHH--SCEEEEEEECCCCS----SCCEEEEEESSHHHHHHHHHHHTTEEET--
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhc--CCEeEEEEEecCCC----CCCEEEEEECCHHHHHHHHHHhCCCCcC--
Confidence            456678999999999999999999999875  34554444433211    1347999999999999999999999874  


Q ss_pred             CCCeeeeEEEeccC
Q 009860           82 KGAQFKAIVEYAPS   95 (523)
Q Consensus        82 KGne~~A~VEfAPY   95 (523)
                       |  ....|+||--
T Consensus        82 -g--~~l~V~~a~~   92 (103)
T 2cqi_A           82 -G--KEVKVNWATT   92 (103)
T ss_dssp             -T--EEEEEEECCC
T ss_pred             -C--CeEEEEECCC
Confidence             2  3577888754

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.49  E-value=0.00065  Score=54.91  Aligned_cols=81  Identities=17%  Similarity=0.224  Sum_probs=61.2

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+..+|.|++||+.+|++++.+.+..+  +.|.....+..+ .  .....-|||.|.+.+++...++.++|+.|.+  
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~-~--g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--   85 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAH--GTVKDLRLVTNR-A--GKPKGLAYVEYENESQASQAVMKMDGMTIKE--   85 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTT--SCEEEEEEEECT-T--SCEEEEEEEEESSHHHHHHHHHHHTTEESSS--
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhC--CCeEEEEEEECC-C--CCEEeEEEEEECCHHHHHHHHHHhCCCEECC--
Confidence            35667899999999999999999999875  345555554433 1  1123469999999999999999999988743  


Q ss_pred             CCeeeeEEEec
Q 009860           83 GAQFKAIVEYA   93 (523)
Q Consensus        83 Gne~~A~VEfA   93 (523)
                         ....|+||
T Consensus        86 ---~~l~v~~a   93 (100)
T 2do4_A           86 ---NIIKVAIS   93 (100)
T ss_dssp             ---CEEEEEEC
T ss_pred             ---EEEEEEEC
Confidence               24667776

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.48  E-value=0.0011  Score=53.73  Aligned_cols=85  Identities=13%  Similarity=0.071  Sum_probs=64.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+..+|.|.+||+.+||+++.+.+...  +.|....+...+...  ..-.-|||.|.+.+++...++.++|+.|.+   
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~--G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~g---   82 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKY--GRVGDVYIPREPHTK--APRGFAFVRFHDRRDAQDAEAAMDGAELDG---   82 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTT--SCEEEEECCBCSSSC--SBCSCEEEEESSSSHHHHHHHHHSSCCBTT---
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEeCCCCC--CCCeEEEEEECCHHHHHHHHHHcCCCEECC---
Confidence            4567899999999999999999999875  356655544333221  123469999999999999999999998743   


Q ss_pred             CeeeeEEEeccCCC
Q 009860           84 AQFKAIVEYAPSQR   97 (523)
Q Consensus        84 ne~~A~VEfAPYQK   97 (523)
                        ....|++|-..+
T Consensus        83 --~~l~V~~a~~~~   94 (103)
T 2dnm_A           83 --RELRVQVARYGR   94 (103)
T ss_dssp             --BCCEEEECSSCC
T ss_pred             --cEEEEEECCcCC
Confidence              356888886544

>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=97.47  E-value=0.00082  Score=54.89  Aligned_cols=77  Identities=13%  Similarity=0.188  Sum_probs=61.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+..+|.|++||+.+||+++.+.+..+  +.|.......|          -|||.|.+.+++...++.++++.|.+   
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~--G~i~~v~~~~~----------~afV~f~~~~~a~~A~~~l~g~~~~g---   72 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQF--GKLERVKKLKD----------YAFIHFDERDGAVKAMEEMNGKDLEG---   72 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHH--SCEEEEEECSS----------CEEEEESSHHHHHHHHHHHTTEEETT---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEECC----------EEEEEeCCHHHHHHHHHHHCCCccCC---
Confidence            3456899999999999999999999875  34555555443          69999999999999999999998642   


Q ss_pred             CeeeeEEEeccCCC
Q 009860           84 AQFKAIVEYAPSQR   97 (523)
Q Consensus        84 ne~~A~VEfAPYQK   97 (523)
                        ....|+||--..
T Consensus        73 --~~l~v~~a~~~~   84 (103)
T 2dgu_A           73 --ENIEIVFAKPPD   84 (103)
T ss_dssp             --EEEEEEECCCCC
T ss_pred             --CEEEEEEcCCCc
Confidence              367888885443

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.46  E-value=0.00028  Score=55.32  Aligned_cols=74  Identities=16%  Similarity=0.164  Sum_probs=56.2

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      ++.+..+|.|.+||+.+||+++.+.+...  +.|.....+..+...+  .-.-|||.|.+.+++....+.++|+.|..
T Consensus         1 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~--G~i~~~~i~~~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g   74 (85)
T 1x4e_A            1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPY--GKIVSTKAILDKTTNK--CKGYGFVDFDSPSAAQKAVTALKASGVQA   74 (85)
T ss_dssp             CCCCCCEEEEESCCTTCCHHHHHTTSTTT--SCEEEEEEECCSSSCS--CCSEEEEEESCHHHHHHHHHHHHHHTCCE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEecCCCCC--cCcEEEEEECCHHHHHHHHHHhcCCeEee
Confidence            35678899999999999999999888864  3565555544433221  12359999999999999999999987654

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.46  E-value=0.0005  Score=54.93  Aligned_cols=82  Identities=16%  Similarity=0.117  Sum_probs=59.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEE-EeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWF-CFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwf-yFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      +.+..+|.|++||+.+|++++.+.+..+-  .|... .....+...  ....-|||.|.+.+++...++.++|+.|.+  
T Consensus         2 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G--~i~~~~~i~~~~~~g--~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--   75 (96)
T 1x5t_A            2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFG--VILQTPKIMRDPDTG--NSKGYAFINFASFDASDAAIEAMNGQYLCN--   75 (96)
T ss_dssp             CSCCCEEEEECCCTTCCHHHHHHHHHTTS--CBSSCCEECCCTTTC--SCCSEEEEEBSSHHHHHHHHHTTTTCEETT--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC--CeeEEEEEEEcCCCC--CcCeEEEEEECCHHHHHHHHHHcCCCEECC--
Confidence            45678999999999999999999998752  33222 222221111  123469999999999999999999999732  


Q ss_pred             CCeeeeEEEecc
Q 009860           83 GAQFKAIVEYAP   94 (523)
Q Consensus        83 Gne~~A~VEfAP   94 (523)
                         ....|+||-
T Consensus        76 ---~~l~v~~a~   84 (96)
T 1x5t_A           76 ---RPITVSYAF   84 (96)
T ss_dssp             ---EECEEEESC
T ss_pred             ---EEEEEEEec
Confidence               356788874

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.46  E-value=0.00044  Score=54.96  Aligned_cols=82  Identities=16%  Similarity=0.056  Sum_probs=60.4

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+..+|.|.+||+.+|++++.+.+...  +.|....++..+...  ....-|||.|.+.+++...++.++|+.|.+  
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~--G~v~~v~i~~~~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--   84 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKY--GPIADVSIVYDQQSR--RSRGFAFVYFENVDDAKEAKERANGMELDG--   84 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTT--SCEEEEEEEECSSSS--SEEEEEEEEESSHHHHHHHHHHHTTEEETT--
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhc--CCeeEEEEEEcCCCC--CcccEEEEEECCHHHHHHHHHHhCCCEECC--
Confidence            46677899999999999999999999874  345544444322211  123469999999999999999999988732  


Q ss_pred             CCeeeeEEEec
Q 009860           83 GAQFKAIVEYA   93 (523)
Q Consensus        83 Gne~~A~VEfA   93 (523)
                         ....|+||
T Consensus        85 ---~~l~v~~a   92 (95)
T 2cqc_A           85 ---RRIRVSGP   92 (95)
T ss_dssp             ---EEEEEECC
T ss_pred             ---EEEEEEec
Confidence               34566665

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=97.46  E-value=0.00055  Score=53.59  Aligned_cols=81  Identities=11%  Similarity=0.082  Sum_probs=58.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+..+|.|++||+.+|++++.+.+...  +.|.....+..+...  ....-|||.|.+.+++....+.++|+.|.+   
T Consensus         3 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~g---   75 (87)
T 3bs9_A            3 LGSHFHVFVGDLSPEITTAAIAAAFAPF--GRISDARVVKDMATG--KSKGYGFVSFFNKWDAENAIQQMGGQWLGG---   75 (87)
T ss_dssp             ---CEEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTC--CEEEEEEEEESSHHHHHHHHHHHTTCEETT---
T ss_pred             CCCceEEEEeCCCCCCCHHHHHHHHHhc--CCEeEEEEEecCCCC--ccceEEEEEECCHHHHHHHHHHcCCCEECC---
Confidence            3467899999999999999999999875  345555544332221  123469999999999999999999988742   


Q ss_pred             CeeeeEEEec
Q 009860           84 AQFKAIVEYA   93 (523)
Q Consensus        84 ne~~A~VEfA   93 (523)
                        ....|+||
T Consensus        76 --~~l~v~~a   83 (87)
T 3bs9_A           76 --RQIRTNWA   83 (87)
T ss_dssp             --EECEEEEE
T ss_pred             --eEEEEEec
Confidence              34566665

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.46  E-value=0.00055  Score=55.18  Aligned_cols=78  Identities=17%  Similarity=0.156  Sum_probs=60.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +.+..+|.|.+||+.+||+++.+.+...  +.|....+..+        ..-|||.|.+.+++...++.++++.|..   
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~v~~v~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~~---   80 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRF--GSIRTIDHVKG--------DSFAYIQYESLDAAQAACAKMRGFPLGG---   80 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTT--SCEEEEEECSS--------SCCEEEEESSHHHHHHHHHHHTTCBCSS---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEeCC--------CCEEEEEECCHHHHHHHHHHHCCCEeCC---
Confidence            4566899999999999999999999875  34665555544        2479999999999999999999998742   


Q ss_pred             CeeeeEEEecc
Q 009860           84 AQFKAIVEYAP   94 (523)
Q Consensus        84 ne~~A~VEfAP   94 (523)
                      .-....|+||-
T Consensus        81 ~g~~l~V~~a~   91 (97)
T 1why_A           81 PDRRLRVDFAK   91 (97)
T ss_dssp             SSCBCEEEECC
T ss_pred             CCcEEEEEECC
Confidence            11356777763

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.45  E-value=0.0011  Score=53.24  Aligned_cols=86  Identities=16%  Similarity=0.165  Sum_probs=63.9

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      ...+..+|.|++||+.+|++++.+.+..+  +.|........+...  ....-|||.|.+.+++...++.++|+.|.+  
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--   77 (99)
T 1whw_A            4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAY--GPLSELHYPIDSLTK--KPKGFAFVTFMFPEHAVKAYAEVDGQVFQG--   77 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTT--SCEEEEECCCCTTTC--CCCSEEEEEESSHHHHHHHHHHTTTEESSS--
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEeEEEEEecCCCC--CcCeEEEEEECCHHHHHHHHHHhCCCEECC--
Confidence            45677899999999999999999999875  356554444332221  123469999999999999999999988753  


Q ss_pred             CCeeeeEEEeccCCC
Q 009860           83 GAQFKAIVEYAPSQR   97 (523)
Q Consensus        83 Gne~~A~VEfAPYQK   97 (523)
                         ....|++|--++
T Consensus        78 ---~~l~V~~a~~~~   89 (99)
T 1whw_A           78 ---RMLHVLPSTIKK   89 (99)
T ss_dssp             ---CEEEEEECCCCS
T ss_pred             ---cEEEEEEcCCCc
Confidence               356788875544

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.44  E-value=0.00063  Score=55.03  Aligned_cols=82  Identities=11%  Similarity=0.101  Sum_probs=60.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +.+..+|.|++||+.+||+++.+.+..+  +.|....++......  ....-|||.|.+.+++...++.++++.|.+   
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~--G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~g---   81 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKY--GQISEVVVVKDRETQ--RSRGFGFVTFENIDDAKDAMMAMNGKSVDG---   81 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHH--SCCCEEEECCCSSSC--SCCSEEEEECSSHHHHHHHHHHHTTCCTTS---
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhc--CCeEEEEEEeCCCCC--CcccEEEEEECCHHHHHHHHHHhCCCEECC---
Confidence            4567899999999999999999999875  245444444322211  123469999999999999999999998743   


Q ss_pred             CeeeeEEEecc
Q 009860           84 AQFKAIVEYAP   94 (523)
Q Consensus        84 ne~~A~VEfAP   94 (523)
                        ....|+||-
T Consensus        82 --~~l~v~~a~   90 (102)
T 1x5s_A           82 --RQIRVDQAG   90 (102)
T ss_dssp             --CCCEEEEEE
T ss_pred             --eEEEEEECC
Confidence              346777774

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=97.44  E-value=0.0014  Score=55.27  Aligned_cols=87  Identities=21%  Similarity=0.206  Sum_probs=66.7

Q ss_pred             CCCCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            1 MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         1 mk~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      |-.+.+..+|.|.+||+.+|++++.+.+...  +.|....+...+ ..  ..-.-|||.|.+.+++...++.++|..|.+
T Consensus         1 m~e~~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~-~g--~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g   75 (116)
T 2fy1_A            1 MVEADHPGKLFIGGLNRETNEKMLKAVFGKH--GPISEVLLIKDR-TS--KSRGFAFITFENPADAKNAAKDMNGKSLHG   75 (116)
T ss_dssp             CCTTCSCCEEEEECCTTTCCHHHHHHHHHTS--SCCSEEEEECST-TT--TCCCEEEEECSSHHHHHHHHHHCSSCBCSS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEECC-CC--CcccEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            6677888999999999999999999999875  345555555443 21  123579999999999999999999998843


Q ss_pred             CCCCeeeeEEEeccCCC
Q 009860           81 EKGAQFKAIVEYAPSQR   97 (523)
Q Consensus        81 sKGne~~A~VEfAPYQK   97 (523)
                           ....|++|--..
T Consensus        76 -----~~l~V~~a~~~~   87 (116)
T 2fy1_A           76 -----KAIKVEQAKKPS   87 (116)
T ss_dssp             -----SBCEEEECCCSS
T ss_pred             -----EEEEEEECCCCC
Confidence                 256788885443

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=97.43  E-value=0.00062  Score=55.44  Aligned_cols=87  Identities=15%  Similarity=0.157  Sum_probs=63.9

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+..+|.|.+||+.+||+++.+.+...  +.|.....+..+.+.+  .-.-|||.|.+.+++...++.+++..|.+..
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~g~--~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~   84 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEF--GKIYELTVLKDRFTGM--HKGCAFLTYCERESALKAQSALHEQKTLPGM   84 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHH--SCCCEEECCCCSSSCS--CCSEEEEEESSHHHHHHHHHHHTTTCCCTTC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEEecCCCCC--cceEEEEEECCHHHHHHHHHHhcCCcccCCC
Confidence            45677899999999999999999999875  3455544443322221  1246999999999999999999999876543


Q ss_pred             CCeeeeEEEeccC
Q 009860           83 GAQFKAIVEYAPS   95 (523)
Q Consensus        83 Gne~~A~VEfAPY   95 (523)
                      |  ....|+||--
T Consensus        85 g--~~l~v~~a~~   95 (106)
T 2dgp_A           85 N--RPIQVKPADS   95 (106)
T ss_dssp             S--SCCEEEECCC
T ss_pred             C--ceEEEEECCc
Confidence            3  3567777743

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.43  E-value=0.0011  Score=53.91  Aligned_cols=83  Identities=12%  Similarity=0.124  Sum_probs=62.6

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+..+|.|++||+.+|++++.+.+..+  +.|....++..    ......-|||.|.+.+++...++.++|+.|.+  
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~----~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--   82 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPF--GTITSAKVMME----GGRSKGFGFVCFSSPEEATKAVTEMNGRIVAT--   82 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTT--SCEEEEEEEEC----SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSS--
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEcC----CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCC--
Confidence            35678999999999999999999998864  34554444432    11223469999999999999999999998832  


Q ss_pred             CCeeeeEEEeccCC
Q 009860           83 GAQFKAIVEYAPSQ   96 (523)
Q Consensus        83 Gne~~A~VEfAPYQ   96 (523)
                         ....|+||--+
T Consensus        83 ---~~l~V~~a~~~   93 (103)
T 2d9p_A           83 ---KPLYVALAQRK   93 (103)
T ss_dssp             ---SBCEEEECSSC
T ss_pred             ---cEEEEEEeccc
Confidence               35778887543

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=97.42  E-value=0.00082  Score=54.07  Aligned_cols=83  Identities=12%  Similarity=0.098  Sum_probs=62.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      +..+|.|++||+.+|++++.+.+...  +.|........+.+.  ....-|||.|.+.+++....+.++|+.|.+     
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~g--~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g-----   71 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNV--GPVINLKMMFDPQTG--RSKGYAFIEFRDLESSASAVRNLNGYQLGS-----   71 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTT--SCEEEEECCBCTTTC--CBCSEEEEEESSHHHHHHHHHHHTTCEETT-----
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhc--CCEEEEEEEeCCCCC--ccceEEEEEECCHHHHHHHHHHhCCCeECC-----
Confidence            35789999999999999999999875  346555544332221  223469999999999999999999998743     


Q ss_pred             eeeEEEeccCCC
Q 009860           86 FKAIVEYAPSQR   97 (523)
Q Consensus        86 ~~A~VEfAPYQK   97 (523)
                      ....|+||--..
T Consensus        72 ~~l~V~~a~~~~   83 (96)
T 2x1f_A           72 RFLKCGYSSNSD   83 (96)
T ss_dssp             EECEEEECSCSS
T ss_pred             eEEEEEEcCCCC
Confidence            467788875443

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.42  E-value=0.00072  Score=53.78  Aligned_cols=77  Identities=13%  Similarity=0.135  Sum_probs=61.2

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+..+|.|++||+.+||+++.+.+..+  +.|.......          .-|||.|.+.+++....+.++++.|.+. 
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~~~~----------g~afV~f~~~~~A~~A~~~l~g~~~~g~-   70 (90)
T 2dnq_A            4 GSSGMVKLFIGNLPREATEQEIRSLFEQY--GKVLECDIIK----------NYGFVHIEDKTAAEDAIRNLHHYKLHGV-   70 (90)
T ss_dssp             CSSCCEEEEEESCCSSCCHHHHHHHHHTS--SCEEEEEEET----------TEEEEEESSHHHHHHHHHHHTTCBCSSC-
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhC--CCEEEEEEEC----------CEEEEEECCHHHHHHHHHHhcCCccCCc-
Confidence            45678999999999999999999999875  3465555552          2699999999999999999999887432 


Q ss_pred             CCeeeeEEEeccCC
Q 009860           83 GAQFKAIVEYAPSQ   96 (523)
Q Consensus        83 Gne~~A~VEfAPYQ   96 (523)
                          ...|++|--+
T Consensus        71 ----~l~v~~a~~~   80 (90)
T 2dnq_A           71 ----NINVEASKNK   80 (90)
T ss_dssp             ----BCEEECSSCC
T ss_pred             ----EEEEEECCCC
Confidence                4678877443

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=97.42  E-value=0.00098  Score=53.10  Aligned_cols=81  Identities=19%  Similarity=0.155  Sum_probs=60.9

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+..+|.|++||+.+|++++.+.+...  +.|........+.   .....-|||.|.+.+++...++.++++.|.+  
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~--G~i~~v~i~~~~~---g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--   84 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQA--GPLTKVTICKDRE---GKPKSFGFVCFKHPESVSYAIALLNGIRLYG--   84 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGG--SCEEEEEEEECTT---SCEEEEEEEEESSTHHHHHHHHHHTTCEETT--
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhc--CCEEEEEEEECCC---CCCceEEEEEECCHHHHHHHHHHhCCCEECC--
Confidence            35567899999999999999999999875  3465555443321   1223469999999999999999999998742  


Q ss_pred             CCeeeeEEEec
Q 009860           83 GAQFKAIVEYA   93 (523)
Q Consensus        83 Gne~~A~VEfA   93 (523)
                         ....|+||
T Consensus        85 ---~~l~V~~a   92 (95)
T 2ywk_A           85 ---RPINVSGP   92 (95)
T ss_dssp             ---EECEEECC
T ss_pred             ---CEEEEEEc
Confidence               34566665

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.41  E-value=0.00084  Score=54.60  Aligned_cols=84  Identities=13%  Similarity=0.229  Sum_probs=62.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCC-CCCCCCCcceeEEEEecCcccHHHHHHHh-cCCeeEeC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPG-KSSYKHQRYSRAYVELKKPAGVFEFAELL-NGHVFVNE   81 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpG-K~S~Kp~~ySRAYI~Fkn~Edl~~F~d~f-dG~vFvDs   81 (523)
                      ..+..+|.|.+||+.+||+++.+.+..+  +.|........ +...  ....-|||.|.+.+++...++.+ +++.|.+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~~--~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~   87 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTF--GELKTVRLPKKMTGTG--AHRGFGFVDFITKQDAKKAFNALCHSTHLYGR   87 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTT--SCEEEEECCCCCSSSC--SSCSEEEEEESSHHHHHHHHHHHHTCCBSSSC
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHcc--CCeEEEEEecCCCCCC--CcCceEEEEECCHHHHHHHHHHhccCCeECCC
Confidence            4567899999999999999999999875  34655554433 2221  12346999999999999999999 88887532


Q ss_pred             CCCeeeeEEEeccCC
Q 009860           82 KGAQFKAIVEYAPSQ   96 (523)
Q Consensus        82 KGne~~A~VEfAPYQ   96 (523)
                           ...|+||--+
T Consensus        88 -----~l~v~~a~~~   97 (107)
T 2cph_A           88 -----RLVLEWADSE   97 (107)
T ss_dssp             -----BCEEEECCCC
T ss_pred             -----EEEEEeCCCC
Confidence                 5678887543

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=97.41  E-value=0.00095  Score=54.26  Aligned_cols=86  Identities=17%  Similarity=0.198  Sum_probs=64.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+..+|.|.+||+.+||+++.+.+..+  +.|....++..+ .  ...-.-|||.|.+.+++...++.++|..|.+.  
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~-~--g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg--   84 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPF--GVIDECTVLRGP-D--GSSKGCAFVKFSSHTEAQAAIHALHGSQTMPG--   84 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTT--SCEEEEEEEECS-S--SCEEEEEEEEESSHHHHHHHHHHHSSCCCCTT--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEECC-C--CCcCcEEEEEeCCHHHHHHHHHHHcCCccCCC--
Confidence            3457899999999999999999999865  346555554433 1  12234699999999999999999999988663  


Q ss_pred             CeeeeEEEeccCC
Q 009860           84 AQFKAIVEYAPSQ   96 (523)
Q Consensus        84 ne~~A~VEfAPYQ   96 (523)
                      ......|+||--.
T Consensus        85 ~~~~l~V~~a~~~   97 (105)
T 2dnh_A           85 ASSSLVVKFADTD   97 (105)
T ss_dssp             CSSCCEEEESCSS
T ss_pred             CCccEEEEECccC
Confidence            2235678877543

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.40  E-value=0.0012  Score=54.22  Aligned_cols=81  Identities=16%  Similarity=0.254  Sum_probs=61.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +.+..+|.|.+||+.+||+++.+.+..+  +.|....+....     ....-|||.|.+.+++...++.++++.|.+   
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~v~~~~i~~~~-----~~~g~afV~f~~~~~A~~A~~~l~g~~~~g---   88 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKY--GAIRDIDLKNRR-----GGPPFAFVEFEDPRDAEDAVYGRDGYDYDG---   88 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEECCSS-----SSSCCEEEEESCHHHHHHHHHHHTTCEETT---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEECC-----CCCcEEEEEECCHHHHHHHHHHcCCCEECC---
Confidence            4567899999999999999999999875  345554443221     123469999999999999999999998732   


Q ss_pred             CeeeeEEEeccCC
Q 009860           84 AQFKAIVEYAPSQ   96 (523)
Q Consensus        84 ne~~A~VEfAPYQ   96 (523)
                        ....|+||--.
T Consensus        89 --~~l~V~~a~~~   99 (109)
T 1x4a_A           89 --YRLRVEFPRSG   99 (109)
T ss_dssp             --EECEEECCCCC
T ss_pred             --eEEEEEEcccC
Confidence              36678887443

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.39  E-value=0.001  Score=54.96  Aligned_cols=86  Identities=12%  Similarity=0.159  Sum_probs=64.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+..+|.|++||+.+|++++.+.+...  +.|.....+..+ ..  ....-|||.|.+.+++...++.++|+.|.....
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~~~i~~~~-~g--~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~   96 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPF--GQVISTRILRDS-SG--TSRGVGFARMESTEKCEAVIGHFNGKFIKTPPG   96 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTT--SCEEEEEEEECS-SS--CEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEECC-CC--CcceEEEEEECCHHHHHHHHHHhCCCEEcCCcc
Confidence            4567899999999999999999988874  345555544433 11  123469999999999999999999999866553


Q ss_pred             ---CeeeeEEEecc
Q 009860           84 ---AQFKAIVEYAP   94 (523)
Q Consensus        84 ---ne~~A~VEfAP   94 (523)
                         ...+..|.||-
T Consensus        97 ~~~~~~~l~v~~a~  110 (114)
T 1x5o_A           97 VSAPTEPLLCKFSG  110 (114)
T ss_dssp             SCCCSSCBEEEECC
T ss_pred             ccCCCCceeEEccC
Confidence               23356777774

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=97.37  E-value=0.00092  Score=58.46  Aligned_cols=82  Identities=11%  Similarity=0.094  Sum_probs=62.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+..+|.|.+||+.+||+++.+.+..+  +.|.....+.-+...  ..-.-|||.|.+.+++...++.++++.|.   |
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~A~~Ai~~l~g~~~~---g  108 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKS--GDIKKIIMGLDKMKK--TACGFCFVEYYSRADAENAMRYINGTRLD---D  108 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTC--CEEEEEEEEESSHHHHHHHHHHTTTSEET---T
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEecCCCC--ccceEEEEEECCHHHHHHHHHHhCCCEEC---C
Confidence            4567899999999999999999999875  345554444332221  12346999999999999999999999983   2


Q ss_pred             CeeeeEEEecc
Q 009860           84 AQFKAIVEYAP   94 (523)
Q Consensus        84 ne~~A~VEfAP   94 (523)
                        ....|++|.
T Consensus       109 --~~l~V~~a~  117 (156)
T 1h2v_Z          109 --RIIRTDWDA  117 (156)
T ss_dssp             --EECEEEEES
T ss_pred             --eEEEEEECC
Confidence              467888885

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=97.37  E-value=0.0013  Score=54.49  Aligned_cols=86  Identities=12%  Similarity=0.130  Sum_probs=64.8

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+..+|.|++||+.+||+++.+.+..+  +.|....++..+...  ....-|||.|.+.+++...++.++|+.|.+  
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--   84 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPF--GRISDARVVKDMATG--KSKGYGFVSFFNKWDAENAIQQMGGQWLGG--   84 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTC--CEEEEEEEEESSHHHHHHHHHHTTTCEETT--
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEEcCCCC--CcceEEEEEECCHHHHHHHHHHhCCCEECC--
Confidence            56778999999999999999999999865  345554544332211  123479999999999999999999988743  


Q ss_pred             CCeeeeEEEeccCCC
Q 009860           83 GAQFKAIVEYAPSQR   97 (523)
Q Consensus        83 Gne~~A~VEfAPYQK   97 (523)
                         ....|+||--..
T Consensus        85 ---~~l~V~~a~~~~   96 (115)
T 2dgo_A           85 ---RQIRTNWATRKP   96 (115)
T ss_dssp             ---EECEEEESSCCC
T ss_pred             ---EEEEEEEccCCC
Confidence               367888885543

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=97.36  E-value=0.00094  Score=56.14  Aligned_cols=87  Identities=11%  Similarity=0.096  Sum_probs=64.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+..+|.|.+||+.+||+++.+.+..+  +.|....++..+...+  .-.-|||.|.+.+++...++.++|+.|.+   
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g---   91 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEY--GEIKNIHLNLDRRTGY--LKGYTLVEYETYKEAQAAMEGLNGQDLMG---   91 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTT--SCEEEEECCBCTTTSS--BCSCEEEEESSHHHHHHHHHHHTTCBSSS---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEecCCCCc--cceEEEEEECCHHHHHHHHHHhCCCeeCC---
Confidence            3456799999999999999999999864  3565555543332221  13469999999999999999999999833   


Q ss_pred             CeeeeEEEeccCCCCC
Q 009860           84 AQFKAIVEYAPSQRVP   99 (523)
Q Consensus        84 ne~~A~VEfAPYQKvP   99 (523)
                        ....|+||--+.-+
T Consensus        92 --~~l~v~~a~~~~~~  105 (126)
T 3ex7_B           92 --QPISVDWCFVRGPP  105 (126)
T ss_dssp             --SBCEEEESEESSSC
T ss_pred             --eEEEEEEecCCCCC
Confidence              25678888655444

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.35  E-value=0.0013  Score=53.14  Aligned_cols=85  Identities=13%  Similarity=0.078  Sum_probs=62.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +.+..+|.|++||+.+||+++.+.+..+  +.|....++..+...  ....-|||.|.+.+++...++.++++.|.+   
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~--G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~g---   81 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPF--GDITDIQIPLDYETE--KHRGFAFVEFELAEDAAAAIDNMNESELFG---   81 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTT--SCCCCEECCCCSSSC--CCSSEEEECCSSHHHHHHHHHHHTTEEETT---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcc--CCEEEEEEEecCCCC--CcceEEEEEECCHHHHHHHHHHhCCCEECC---
Confidence            4567899999999999999999999874  244444443322221  123469999999999999999999988742   


Q ss_pred             CeeeeEEEeccCCC
Q 009860           84 AQFKAIVEYAPSQR   97 (523)
Q Consensus        84 ne~~A~VEfAPYQK   97 (523)
                        ....|+||--++
T Consensus        82 --~~l~V~~a~~~~   93 (102)
T 2cqb_A           82 --RTIRVNLAKPMR   93 (102)
T ss_dssp             --EEEEEEECCCCC
T ss_pred             --cEEEEEeCCCCC
Confidence              367788875443

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.35  E-value=0.0014  Score=54.42  Aligned_cols=89  Identities=17%  Similarity=0.134  Sum_probs=65.3

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      ...+..+|.|.+||+.+||+++.+.+..+  +.|.....+..+...+  ...-|||.|.+.+++...++.+++ .| +. 
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~~--~~g~afV~f~~~~~a~~Ai~~~~~-~~-~g-   85 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGF--GDIEEAVVITDRQTGK--SRGYGFVTMADRAAAERACKDPNP-II-DG-   85 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTT--SCEEEEEESCCSSSCC--CCSEEEEEESSHHHHHHHHTCSSC-EE-TT-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhC--CCeeEEEEEEcCCCCc--cceEEEEEECCHHHHHHHHHhCCC-cC-CC-
Confidence            34567899999999999999999999864  3466555544333221  224699999999999999999997 44 32 


Q ss_pred             CCeeeeEEEeccCCCCCCC
Q 009860           83 GAQFKAIVEYAPSQRVPKP  101 (523)
Q Consensus        83 Gne~~A~VEfAPYQKvPk~  101 (523)
                         ....|++|--...|..
T Consensus        86 ---~~l~V~~a~~~~~~~~  101 (116)
T 2cqd_A           86 ---RKANVNLAYLGAKPRS  101 (116)
T ss_dssp             ---EECEEEESTTTCCCCC
T ss_pred             ---EEEEEEEcccCCCccc
Confidence               4678999876555543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.35  E-value=0.0016  Score=52.51  Aligned_cols=83  Identities=11%  Similarity=0.160  Sum_probs=61.6

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+..+|.|++||+.+||+++.+.+..+  +.|....++..+...+  .-.-|||.|.+.+++...++ ++++.|.+. 
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~~--~~g~afV~f~~~~~a~~A~~-~~~~~~~g~-   79 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKF--GVVTEVVMIYDAEKQR--PRGFGFITFEDEQSVDQAVN-MHFHDIMGK-   79 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSS--SCEEEEEECCCTTTCS--CCSEEEEEESSHHHHHHHHH-HCCCBSSSC-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEeCCCCCC--CCceEEEEECCHHHHHHHHH-hCCCEECCe-
Confidence            45677899999999999999999999874  3566555543322221  12459999999999999998 899877432 


Q ss_pred             CCeeeeEEEeccC
Q 009860           83 GAQFKAIVEYAPS   95 (523)
Q Consensus        83 Gne~~A~VEfAPY   95 (523)
                          ...|++|--
T Consensus        80 ----~l~V~~a~~   88 (99)
T 2dgs_A           80 ----KVEVKRAEP   88 (99)
T ss_dssp             ----BCEEEECCC
T ss_pred             ----EEEEEECCC
Confidence                567787753

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=97.35  E-value=0.00094  Score=55.47  Aligned_cols=84  Identities=13%  Similarity=0.204  Sum_probs=57.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCe---eEe
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHV---FVN   80 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~v---FvD   80 (523)
                      ....-.|.||+|||..||+++.+.+.+.-.-.+.....+.-+.+.+  .-.-|||.|.+.+++....+.++|..   .+|
T Consensus         6 ~~~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            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQ--NRGFAFVQLSSAMDASQLLQILQSLHPPLKID   83 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSS--CSSEEEEECSSSHHHHHHHHHHHSSSSCEEET
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCC--CceEeEEEECCHHHHHHHHHHhcCCCCCceEC
Confidence            3455679999999999999999999875321222233332222211  12359999999999999999999863   345


Q ss_pred             CCCCeeeeEEEec
Q 009860           81 EKGAQFKAIVEYA   93 (523)
Q Consensus        81 sKGne~~A~VEfA   93 (523)
                      .+    .-.|+||
T Consensus        84 Gr----~i~V~~A   92 (95)
T 2lkz_A           84 GK----TIGVDFA   92 (95)
T ss_dssp             TE----EEEEEEC
T ss_pred             CE----EEEEEEc
Confidence            43    5667776

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.35  E-value=0.0012  Score=53.66  Aligned_cols=85  Identities=15%  Similarity=0.219  Sum_probs=63.3

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+..+|.|.+||+.+||+++.+.+..+  +.|.....+..+...  ....-|||.|.+.+++...++.++|+.|.+  
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~--G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--   84 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPF--GSISRIYLAKDKTTG--QSKGFAFISFHRREDAARAIAGVSGFGYDH--   84 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTT--CCEEEEEEEECSSSC--SEEEEEEEEESSHHHHHHHHHHTTTCEETT--
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhC--CCeEEEEEeecCCCC--ceeeEEEEEECCHHHHHHHHHHcCCCeeCC--
Confidence            35677999999999999999999888864  345555544332222  123469999999999999999999998742  


Q ss_pred             CCeeeeEEEeccCC
Q 009860           83 GAQFKAIVEYAPSQ   96 (523)
Q Consensus        83 Gne~~A~VEfAPYQ   96 (523)
                         ....|+||--.
T Consensus        85 ---~~l~v~~a~~~   95 (103)
T 2cq0_A           85 ---LILNVEWAKPS   95 (103)
T ss_dssp             ---EECEEEESSCC
T ss_pred             ---cEEEEEECCCC
Confidence               35678887543

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=97.34  E-value=0.0013  Score=53.62  Aligned_cols=81  Identities=15%  Similarity=0.169  Sum_probs=60.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+..+|.|++||+.+||+++.+.+...  +.|....++..+ .  .....-|||.|.+.+++...++.++|+.|.+   
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~-~--g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g---   97 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEF--GTLKKAAVHYDR-S--GRSLGTADVHFERKADALKAMKQYNGVPLDG---   97 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTT--SCEEEEEEEECT-T--SCEEEEEEEEESSHHHHHHHHHHHTTCEETT---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEECC-C--CCcceEEEEEECCHHHHHHHHHHhCCCEeCC---
Confidence            4567899999999999999999999864  345554544333 1  1224469999999999999999999998832   


Q ss_pred             CeeeeEEEecc
Q 009860           84 AQFKAIVEYAP   94 (523)
Q Consensus        84 ne~~A~VEfAP   94 (523)
                        ....|+||.
T Consensus        98 --~~l~V~~a~  106 (107)
T 3ulh_A           98 --RPMNIQLVT  106 (107)
T ss_dssp             --EECEEEEEC
T ss_pred             --cEEEEEEeC
Confidence              345677764

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.34  E-value=0.0016  Score=53.59  Aligned_cols=84  Identities=11%  Similarity=0.080  Sum_probs=62.8

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      +..+..+|.|++||+.+||+++.+.+..+  +.|.....+..+.   .....-|||.|.+.+++...++.++++.|.+  
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~--G~i~~~~i~~~~~---g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--   83 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMA--GVVVRADILEDKD---GKSRGIGTVTFEQSIEAVQAISMFNGQLLFD--   83 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTT--SCEEEEEEEECTT---CSEEEEEEEEESSHHHHHHHHHHHTTCEETT--
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEECCC---CCeeeEEEEEECCHHHHHHHHHHhCCCEeCC--
Confidence            34567899999999999999999999865  3555544443321   1223469999999999999999999998842  


Q ss_pred             CCeeeeEEEeccCC
Q 009860           83 GAQFKAIVEYAPSQ   96 (523)
Q Consensus        83 Gne~~A~VEfAPYQ   96 (523)
                         ....|++|-..
T Consensus        84 ---~~l~v~~a~~~   94 (114)
T 2do0_A           84 ---RPMHVKMDERA   94 (114)
T ss_dssp             ---EECEEEECSCC
T ss_pred             ---CEEEEEEcccC
Confidence               35678887543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.32  E-value=0.00097  Score=53.94  Aligned_cols=76  Identities=20%  Similarity=0.118  Sum_probs=60.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+..+|.|++||+.+|++++.+.+..+-.+.|.......|          -|||.|.+.+++...++.++|+.|.   |
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~~g----------~afV~f~~~~~A~~A~~~l~g~~~~---g   78 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD----------YAFVHFSNREDAVEAMKALNGKVLD---G   78 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECSS----------EEEEEESSHHHHHHHHHHHSSEEET---T
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEeCC----------eEEEEeCCHHHHHHHHHHhCCCEeC---C
Confidence            34567999999999999999999998763355655544333          7999999999999999999999874   2


Q ss_pred             CeeeeEEEecc
Q 009860           84 AQFKAIVEYAP   94 (523)
Q Consensus        84 ne~~A~VEfAP   94 (523)
                        ....|+||-
T Consensus        79 --~~l~v~~a~   87 (99)
T 2cpd_A           79 --SPIEVTLAK   87 (99)
T ss_dssp             --EEEEEECCC
T ss_pred             --cEEEEEECC
Confidence              356788773

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.29  E-value=0.0012  Score=54.05  Aligned_cols=83  Identities=11%  Similarity=0.097  Sum_probs=61.0

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhc------CC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLN------GH   76 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fd------G~   76 (523)
                      .+.+..+|.|++||+.+||+++.+.+..+  +.|.....+.-+.+.  ....-|||.|.+.+++...++.++      ++
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~g--~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~   86 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQF--GDLKYVRVVLHPDTE--HSKGCAFAQFMTQEAAQKCLAAASLEAEGGGL   86 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTT--SCEEEEECCBCSSSC--CBCSEEEEEESSHHHHHHHHHHHCTTTTTCCE
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhc--CCeEEEEEEecCCCC--CCccEEEEEECCHHHHHHHHHHhccccccCCc
Confidence            35667899999999999999999999864  346554443322221  123469999999999999999999      77


Q ss_pred             eeEeCCCCeeeeEEEecc
Q 009860           77 VFVNEKGAQFKAIVEYAP   94 (523)
Q Consensus        77 vFvDsKGne~~A~VEfAP   94 (523)
                      .|.+     ....|+||-
T Consensus        87 ~~~g-----~~l~v~~a~   99 (111)
T 1x4h_A           87 KLDG-----RQLKVDLAV   99 (111)
T ss_dssp             ESSS-----CEEEEECCC
T ss_pred             EEcC-----EEEEEEECC
Confidence            7632     256778774

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=97.28  E-value=0.001  Score=54.12  Aligned_cols=82  Identities=18%  Similarity=0.176  Sum_probs=60.8

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      ++.+..+|.|.+||+.+||+++.+.+..+  + |.....+..+...  ....-|||.|.+.+++...+ .++|+.|.+  
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~--g-i~~v~i~~~~~~g--~~~g~afV~f~~~~~a~~A~-~l~g~~~~g--   82 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDL--S-IRSVRLVRDKDTD--KFKGFCYVEFDEVDSLKEAL-TYDGALLGD--   82 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTS--C-EEEEEEEECSSSC--SEEEEEEEEESSHHHHHHHG-GGTTCEETT--
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhC--C-ceEEEEeecCCCC--ccceEEEEEECCHHHHHHHH-hhCCCeECC--
Confidence            35677899999999999999999999886  3 5554444332211  12346999999999999999 899988732  


Q ss_pred             CCeeeeEEEeccC
Q 009860           83 GAQFKAIVEYAPS   95 (523)
Q Consensus        83 Gne~~A~VEfAPY   95 (523)
                         ....|++|--
T Consensus        83 ---~~l~V~~a~~   92 (103)
T 2dng_A           83 ---RSLRVDIAEG   92 (103)
T ss_dssp             ---EECEEEECCC
T ss_pred             ---eEEEEEEecC
Confidence               3567888753

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.27  E-value=0.0013  Score=53.18  Aligned_cols=78  Identities=14%  Similarity=0.195  Sum_probs=60.7

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      ...+..+|.|.+||+.+||+++.+.+...  +.|....+...        -.-|||.|.+.+++...++.++|+.|.+  
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~~~~~--------kg~afV~f~~~~~a~~a~~~l~g~~~~g--   78 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKY--GKAGEVFIHKD--------KGFGFIRLETRTLAEIAKVELDNMPLRG--   78 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTT--CCCSEEEEETT--------TTEEEEECSSSHHHHHHHHHHTTCCBTT--
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhc--CCeEEEEEecC--------CCEEEEEECCHHHHHHHHHHhCCCEeCC--
Confidence            34567899999999999999999999875  24544444421        2479999999999999999999998743  


Q ss_pred             CCeeeeEEEeccC
Q 009860           83 GAQFKAIVEYAPS   95 (523)
Q Consensus        83 Gne~~A~VEfAPY   95 (523)
                         ....|+||--
T Consensus        79 ---~~l~v~~a~~   88 (99)
T 2cpj_A           79 ---KQLRVRFACH   88 (99)
T ss_dssp             ---BCCEEEESSC
T ss_pred             ---ceEEEEEcCC
Confidence               3567888744

>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=97.27  E-value=0.0011  Score=56.77  Aligned_cols=82  Identities=18%  Similarity=0.189  Sum_probs=62.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      .+..+|.|++||+.+|++++.+.+...  +.|........+...+  .-.-|||.|.+.++.....+.++|..|.   |.
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~--G~i~~~~i~~~~~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~---g~  159 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKY--GSIVQKNILRDKLTGR--PRGVAFVRYNKREEAQEAISALNNVIPE---GG  159 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSS--SCEEEEEEEECTTTCC--EEEEEEEEESSHHHHHHHHHHHTTCCCT---TC
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcC--CcEEEEEEEEcCCCCC--cceEEEEEECCHHHHHHHHHHhcCCEec---CC
Confidence            456899999999999999999999875  3566666554433221  1235999999999999999999999873   33


Q ss_pred             eeeeEEEec
Q 009860           85 QFKAIVEYA   93 (523)
Q Consensus        85 e~~A~VEfA   93 (523)
                      ..+-.|+||
T Consensus       160 ~~~l~V~~A  168 (168)
T 1b7f_A          160 SQPLSVRLA  168 (168)
T ss_dssp             SSCCEEEEC
T ss_pred             CeEEEEEeC
Confidence            456667775

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=97.25  E-value=0.0016  Score=50.53  Aligned_cols=77  Identities=12%  Similarity=0.130  Sum_probs=56.9

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeee
Q 009860            8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFK   87 (523)
Q Consensus         8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~   87 (523)
                      ++|.|++||+.+|++++.+.+...  +.|.....+......  ....-|||.|.+.+++....+.++|+.|.   |  ..
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~--G~i~~~~i~~~~~~~--~~~g~afV~f~~~~~a~~a~~~l~g~~~~---g--~~   72 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDF--PSYLSGHVMWDMQTG--SSRGYGFVSFTSQDDAQNAMDSMQGQDLN---G--RP   72 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTS--TTEEEEEEEECTTTC--CEEEEEEEEESCHHHHHHHHHHHTTCEET---T--EE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEEEcCCCC--CccceEEEEECCHHHHHHHHHHhcCCeeC---C--cE
Confidence            579999999999999999999875  345544444332221  12346999999999999999999999873   2  24


Q ss_pred             eEEEec
Q 009860           88 AIVEYA   93 (523)
Q Consensus        88 A~VEfA   93 (523)
                      -.|++|
T Consensus        73 l~v~~a   78 (83)
T 3md1_A           73 LRINWA   78 (83)
T ss_dssp             CEEEEC
T ss_pred             EEEEec
Confidence            566666

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=97.24  E-value=0.0011  Score=53.56  Aligned_cols=82  Identities=11%  Similarity=0.194  Sum_probs=59.2

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeE--------EEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhc
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNW--------FCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLN   74 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdw--------fyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fd   74 (523)
                      ++.+..+|.|++||+.+|++++.+.+...  +.|..        ...+..+...  ....-|||.|.+.+++...++.++
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~~~~~~~~~v~i~~~~~~g--~~~G~afV~f~~~~~a~~Ai~~l~   84 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQI--GIIKTNKKTGQPMINLYTDRETG--KLKGEATVSFDDPPSAKAAIDWFD   84 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTT--SCBCEETTTTEESEEEEECTTTC--SEEEEEEEEBSSHHHHHHHHHHHT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHh--CCEeeccccccccEEEEecCCCC--CeeeEEEEEECCHHHHHHHHHHhC
Confidence            46778999999999999999999999864  23433        2322221111  123469999999999999999999


Q ss_pred             CCeeEeCCCCeeeeEEEec
Q 009860           75 GHVFVNEKGAQFKAIVEYA   93 (523)
Q Consensus        75 G~vFvDsKGne~~A~VEfA   93 (523)
                      |..|.+.     .-.|++|
T Consensus        85 g~~~~g~-----~l~V~~A   98 (99)
T 2la6_A           85 GKEFSGN-----PIKVSFA   98 (99)
T ss_dssp             TCBSSSS-----BCEEEEC
T ss_pred             CCEeCCc-----EEEEEec
Confidence            9987532     4566665

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=97.24  E-value=0.00077  Score=56.28  Aligned_cols=83  Identities=12%  Similarity=0.137  Sum_probs=61.0

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009860            2 KEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         2 k~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs   81 (523)
                      +++.+..+|.|++||+.+|++++.+.+...  +.|.....+..+...  ....-|||.|.+.+++...++.++|+.|-+.
T Consensus        21 ~~~~~~~~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           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPF--GRIESIQLMMDSETG--RSKGYGFITFSDSECAKKALEQLNGFELAGR   96 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTT--SCEEEEEEEEETTTT--EEEEEEEEEESCHHHHHHHHHHHTTCCSSSS
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEEcCCCC--ccceEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            356678899999999999999999999865  345544444322211  1234699999999999999999999887432


Q ss_pred             CCCeeeeEEEec
Q 009860           82 KGAQFKAIVEYA   93 (523)
Q Consensus        82 KGne~~A~VEfA   93 (523)
                           ...|++|
T Consensus        97 -----~l~V~~a  103 (108)
T 2jrs_A           97 -----PMKVGHV  103 (108)
T ss_dssp             -----CCEEECS
T ss_pred             -----EEEEEEc
Confidence                 3566665

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=97.24  E-value=0.0012  Score=54.68  Aligned_cols=82  Identities=17%  Similarity=0.176  Sum_probs=60.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+..+|.|++||+.+||+++.+.+..+  +.|.....+..+...  ....-|||.|.+.+++...++.++++.|.+   
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~g--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g---   94 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPF--GNVVSAKVFIDKQTN--LSKCFGFVSYDNPVSAQAAIQSMNGFQIGM---   94 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGG--SCCSEEEEEECSSSC--SEEEEEEEECSSHHHHHHHHHHHTTCEETT---
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEECCCCC--CcCccEEEEECCHHHHHHHHHHcCCCEECC---
Confidence            3456899999999999999999999875  234444443322211  122359999999999999999999988742   


Q ss_pred             CeeeeEEEecc
Q 009860           84 AQFKAIVEYAP   94 (523)
Q Consensus        84 ne~~A~VEfAP   94 (523)
                        ....|+||-
T Consensus        95 --~~l~V~~a~  103 (115)
T 2cpz_A           95 --KRLKVQLKR  103 (115)
T ss_dssp             --EECEEECCC
T ss_pred             --EEEEEEEcC
Confidence              356788774

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=97.24  E-value=0.00076  Score=54.68  Aligned_cols=80  Identities=20%  Similarity=0.207  Sum_probs=53.3

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeee
Q 009860            8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFK   87 (523)
Q Consensus         8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~   87 (523)
                      ..|.||+||+.+||+++.+.+...-. .|.....+.-+.+.  ..-.-|||.|.+.+++...++..++...++.    ..
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~-~v~~v~i~~d~~t~--~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~g----r~   74 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGV-QAREVRLMRNKSSG--QSRGFAFVEFSHLQDATRWMEANQHSLNILG----QK   74 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTC-CCSBCCSSSCSSSC--CCSSEEEEECSSHHHHHHHHHTTTTEEEETT----EE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCC-EeEEEEEEecCCCC--CcCceEEEEecCHHHHHHHHHhcCCCeEECC----EE
Confidence            36899999999999999999987521 23322222211111  1123499999999999998887765544443    26


Q ss_pred             eEEEecc
Q 009860           88 AIVEYAP   94 (523)
Q Consensus        88 A~VEfAP   94 (523)
                      ..|+||-
T Consensus        75 i~V~~a~   81 (91)
T 2lxi_A           75 VSMHYSD   81 (91)
T ss_dssp             EEEECCC
T ss_pred             EEEEEcC
Confidence            7788873

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=97.24  E-value=0.0012  Score=55.78  Aligned_cols=81  Identities=14%  Similarity=0.092  Sum_probs=59.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +.+..+|.|++||+.+|++++.+.+...  +.|.....+..+...  ..-.-|||.|.+.+++....+.++|+.|-   |
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~--G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~---g  132 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPF--GDITDIQIPLDYETE--KHRGFAFVEFELAEDAAAAIDNMNESELF---G  132 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGG--SCEEEEECCCCTTTC--CCCSEEEEEESCHHHHHHHHHHSTEEEET---T
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhc--CCEEEEEEeecCCCC--CcCcEEEEEECCHHHHHHHHHHhCCCEEC---C
Confidence            4567899999999999999999999875  346555543332221  12346999999999999999999998764   2


Q ss_pred             CeeeeEEEec
Q 009860           84 AQFKAIVEYA   93 (523)
Q Consensus        84 ne~~A~VEfA   93 (523)
                        ....|+||
T Consensus       133 --~~l~v~~A  140 (140)
T 2ku7_A          133 --RTIRVNLA  140 (140)
T ss_dssp             --EEEEEEC-
T ss_pred             --EEEEEEeC
Confidence              24456654

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.21  E-value=0.0011  Score=53.96  Aligned_cols=83  Identities=16%  Similarity=0.078  Sum_probs=59.9

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009860            2 KEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         2 k~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs   81 (523)
                      ..+.+..+|.|++||+.+||+++.+.+..+  +.|.....+..+...  ....-|||.|.+.+++...++. +++.|.+.
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~v~~v~i~~~~~~g--~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~   85 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQY--GEVVDCVIMKDKTTN--QSRGFGFVKFKDPNCVGTVLAS-RPHTLDGR   85 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTT--SCEEEEEEEECSSSC--CEEEEEEEEESSTTHHHHHHHH-CSEEETTE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEeeCCCCC--CcceEEEEEECCHHHHHHHHHh-CCCeECCE
Confidence            356778999999999999999999999874  345554544332221  1223599999999999999998 88776432


Q ss_pred             CCCeeeeEEEecc
Q 009860           82 KGAQFKAIVEYAP   94 (523)
Q Consensus        82 KGne~~A~VEfAP   94 (523)
                           ...|++|-
T Consensus        86 -----~l~V~~a~   93 (105)
T 2dh8_A           86 -----NIDPKPCT   93 (105)
T ss_dssp             -----EEBCCCSC
T ss_pred             -----EEEEEEcc
Confidence                 45566653

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.21  E-value=0.0022  Score=52.23  Aligned_cols=81  Identities=15%  Similarity=0.165  Sum_probs=59.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+..+|.|++||+.+||+++.+.+..+  + |.....+..+... .....-|||.|.+.+++...+ .++++.|.+   
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G-i~~v~i~~~~~~~-g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g---   83 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGL--N-ISAVRLPREPSNP-ERLKGFGYAEFEDLDSLLSAL-SLNEESLGN---   83 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTS--C-EEEEECCBCSSCT-TSBCSCEEEEESSHHHHHHHH-GGGTCEETT---
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHC--C-ceEEEEecCCCCC-CCcCeEEEEEECCHHHHHHHH-hcCCCEeCC---
Confidence            4567899999999999999999999875  4 6555544322210 111235999999999999999 999998732   


Q ss_pred             CeeeeEEEecc
Q 009860           84 AQFKAIVEYAP   94 (523)
Q Consensus        84 ne~~A~VEfAP   94 (523)
                        ....|+||-
T Consensus        84 --~~l~V~~a~   92 (104)
T 1wi8_A           84 --KRIRVDVAD   92 (104)
T ss_dssp             --EECEEEECC
T ss_pred             --cEEEEEEcc
Confidence              356788774

>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=97.19  E-value=0.0025  Score=52.53  Aligned_cols=79  Identities=9%  Similarity=0.065  Sum_probs=62.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +....+|.|.+||+.+|++++.+.+...  +.|....+...        -.-|||.|.+.+++...++.++|+.|.+   
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~--G~i~~v~i~~~--------~g~afV~f~~~~~a~~A~~~l~g~~~~g---   88 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPF--GQIMEIRVFPE--------KGYSFVRFSTHESAAHAIVSVNGTTIEG---   88 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHH--SCEEEEEEETT--------TTEEEEEESSHHHHHHHHHHHTTCEETT---
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEeCC--------CCEEEEEECCHHHHHHHHHHcCCCEECC---
Confidence            5567899999999999999999999875  35655555543        3479999999999999999999998743   


Q ss_pred             CeeeeEEEeccCCC
Q 009860           84 AQFKAIVEYAPSQR   97 (523)
Q Consensus        84 ne~~A~VEfAPYQK   97 (523)
                        ....|+||--+.
T Consensus        89 --~~l~v~~a~~~~  100 (109)
T 1x4g_A           89 --HVVKCYWGKESP  100 (109)
T ss_dssp             --EECEEECCCCCC
T ss_pred             --cEEEEEecCCCC
Confidence              356788875443

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=97.18  E-value=0.0016  Score=54.50  Aligned_cols=74  Identities=19%  Similarity=0.291  Sum_probs=58.9

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+..+|.|.+||+.+||+++.+.+...  |.|.....+          -.-|||.|.+.+++....+.++|+.|   .
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~--G~i~~v~i~----------kg~afV~f~~~~~A~~Ai~~l~g~~~---~   91 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPF--GPMKEVKIL----------NGFAFVEFEEAESAAKAIEEVHGKSF---A   91 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTT--SCCCEEEEE----------TTEEEEECSSHHHHHHHHHHHTTCEE---T
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhc--CCEEEEEEE----------CCEEEEEECCHHHHHHHHHHcCCCEE---C
Confidence            45678899999999999999999999875  245444444          24799999999999999999999998   2


Q ss_pred             CCeeeeEEEec
Q 009860           83 GAQFKAIVEYA   93 (523)
Q Consensus        83 Gne~~A~VEfA   93 (523)
                      |  ....|+||
T Consensus        92 g--~~l~V~~a  100 (108)
T 2jvo_A           92 N--QPLEVVYS  100 (108)
T ss_dssp             T--EECEEESC
T ss_pred             C--eEEEEEEe
Confidence            2  35677776

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=97.18  E-value=0.0026  Score=52.24  Aligned_cols=81  Identities=14%  Similarity=0.158  Sum_probs=60.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      .+..+|.|.+||+.+|++++.+.+..+  +.|........+...  ..-.-|||.|.+.+++....+.++|+.|.   | 
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~A~~Ai~~l~g~~~~---g-   95 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDY--GEIKNIHLNLDRRTG--FSKGYALVEYETHKQALAAKEALNGAEIM---G-   95 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGG--SCEEEEECCBCTTTS--SBCSEEEEEESSHHHHHHHHHHHTTCEET---T-
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEecCCCC--CcceEEEEEECCHHHHHHHHHHcCCCEEC---C-
Confidence            456789999999999999999999875  356555544332221  12346999999999999999999999873   2 


Q ss_pred             eeeeEEEecc
Q 009860           85 QFKAIVEYAP   94 (523)
Q Consensus        85 e~~A~VEfAP   94 (523)
                       ....|+||-
T Consensus        96 -~~l~V~~a~  104 (110)
T 1oo0_B           96 -QTIQVDWCF  104 (110)
T ss_dssp             -EECEEEESE
T ss_pred             -cEEEEEEcc
Confidence             356777763

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=97.18  E-value=0.0015  Score=53.20  Aligned_cols=81  Identities=11%  Similarity=0.081  Sum_probs=60.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      .+..+|.|.+||+.+|++++.+.+..+  +.|........+.+.  ..-.-|||.|.+.+++....+.++|+.|.+    
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~--G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----   92 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEY--GEIKNIHLNLDRRTG--YLKGYTLVEYETYKEAQAAMEGLNGQDLMG----   92 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTS--SEEEEEEEEESCHHHHHHHHHHHTTCBSSS----
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcc--CCeEEEEEEecCCCC--ceeeEEEEEECCHHHHHHHHHHhcCCEECC----
Confidence            455789999999999999999999875  356555544332221  123469999999999999999999987753    


Q ss_pred             eeeeEEEecc
Q 009860           85 QFKAIVEYAP   94 (523)
Q Consensus        85 e~~A~VEfAP   94 (523)
                       ....|+||-
T Consensus        93 -~~l~V~~a~  101 (106)
T 1p27_B           93 -QPISVDWCF  101 (106)
T ss_dssp             -SBCEEEESE
T ss_pred             -cEEEEEeec
Confidence             245677763

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=97.16  E-value=0.0023  Score=52.87  Aligned_cols=80  Identities=18%  Similarity=0.198  Sum_probs=61.0

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      ++.+..+|.|++||+.+|++++.+.+...  |.|.....+..     .....-|||.|.+.+++....+.++|+.|.+  
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~v~~v~i~~~-----~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--   74 (115)
T 3lqv_A            4 PPEVNRILYIRNLPYKITAEEMYDIFGKY--GPIRQIRVGNT-----PETRGTAYVVYEDIFDAKNAVDHLSGFNVSN--   74 (115)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTT--SCEEEEEEECS-----TTTTTCEEEEESSHHHHHHHHHHHTTCBSSS--
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEeeC-----CCCCcEEEEEECCHHHHHHHHHHcCCCEECC--
Confidence            45677899999999999999999999875  34554444321     1124579999999999999999999998832  


Q ss_pred             CCeeeeEEEecc
Q 009860           83 GAQFKAIVEYAP   94 (523)
Q Consensus        83 Gne~~A~VEfAP   94 (523)
                         ....|+||-
T Consensus        75 ---~~l~v~~a~   83 (115)
T 3lqv_A           75 ---RYLVVLYYN   83 (115)
T ss_dssp             ---CBCEEEECC
T ss_pred             ---eEEEEEEec
Confidence               256788774

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=97.14  E-value=0.0029  Score=53.28  Aligned_cols=87  Identities=15%  Similarity=0.129  Sum_probs=65.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +.+..+|.|++||+.+||+++.+.+...  +.|......... ..  ....-|||.|.+.+++....+.++|+.|.+   
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~v~~v~i~~~~-~g--~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g---  103 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEF--GTLKKAAVDYDR-SG--RSLGTADVHFERRADALKAMKQYKGVPLDG---  103 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTT--SCCSEEEEECCS-SS--SCCSEEEEEESSHHHHHHHHHHHTTEESSS---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEEECC-CC--CEeeEEEEEECCHHHHHHHHHHcCCCEECC---
Confidence            4567899999999999999999999874  345544444333 21  123469999999999999999999998743   


Q ss_pred             CeeeeEEEeccCCCCCC
Q 009860           84 AQFKAIVEYAPSQRVPK  100 (523)
Q Consensus        84 ne~~A~VEfAPYQKvPk  100 (523)
                        ....|+||.-...+.
T Consensus       104 --~~l~V~~a~~~~~~~  118 (124)
T 2kt5_A          104 --RPMDIQLVASQIDLE  118 (124)
T ss_dssp             --CEEEEEEECCTTCCC
T ss_pred             --cEEEEEEeCCCCCCC
Confidence              357889887666554

>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=97.14  E-value=0.0017  Score=55.06  Aligned_cols=81  Identities=20%  Similarity=0.212  Sum_probs=60.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      ...+|.|++||+.+|++++.+.+...  +.+....+.......  ..-.-|||.|.+.++.....+.++|..|.   |..
T Consensus        87 ~~~~l~v~nl~~~~t~~~l~~~f~~~--G~i~~~~i~~~~~~g--~~~g~afV~f~~~~~A~~A~~~l~g~~~~---g~~  159 (167)
T 1fxl_A           87 RDANLYVSGLPKTMTQKELEQLFSQY--GRIITSRILVDQVTG--VSRGVGFIRFDKRIEAEEAIKGLNGQKPS---GAT  159 (167)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTC--CEEEEEEEEESSHHHHHHHHHHHTTCCCT---TCS
T ss_pred             CCCcEEECCCCCcCCHHHHHHHHHhc--CCEeEEEEEecCCCC--CccceEEEEeCCHHHHHHHHHHhcCCccC---CCc
Confidence            45789999999999999999999875  346555554433221  12345999999999999999999999873   334


Q ss_pred             eeeEEEec
Q 009860           86 FKAIVEYA   93 (523)
Q Consensus        86 ~~A~VEfA   93 (523)
                      .+..|.||
T Consensus       160 ~~i~v~~A  167 (167)
T 1fxl_A          160 EPITVKFA  167 (167)
T ss_dssp             SCCEEEEC
T ss_pred             cceEEEeC
Confidence            45677776

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.14  E-value=0.0021  Score=53.84  Aligned_cols=77  Identities=18%  Similarity=0.215  Sum_probs=60.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      ...+|.|++||+.+||+++.+.+..+  +.|......+.        -.-|||.|.+.++...-++.++|+.|.+.    
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 SKTVILAKNLPAGTLAAEIQETFSRF--GSLGRVLLPEG--------GITAIVEFLEPLEARKAFRHLAYSKFHHV----   74 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTT--SCEEEEECCSS--------SSCEEEEESCHHHHHHHHHHHTTCBSSSS----
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEeCC--------CCEEEEEeCCHHHHHHHHHHhCCCEECCe----
Confidence            45799999999999999999999874  35655444321        12499999999999999999999987532    


Q ss_pred             eeeEEEeccCCC
Q 009860           86 FKAIVEYAPSQR   97 (523)
Q Consensus        86 ~~A~VEfAPYQK   97 (523)
                       ...|+||+-..
T Consensus        75 -~l~V~~a~~~~   85 (111)
T 1whx_A           75 -PLYLEWAPIGV   85 (111)
T ss_dssp             -BCEEEEEETTT
T ss_pred             -EEEEEECCCCc
Confidence             56799997543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=97.13  E-value=0.0022  Score=53.29  Aligned_cols=81  Identities=16%  Similarity=0.150  Sum_probs=59.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+..+|.|++||+.+||+++.+.+..+  +.|.....+..+.+.  ....-|||.|.+.++....++.++|+.|.+   
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~~~i~~~~~~g--~~~g~afV~f~~~~~A~~A~~~l~g~~~~g---  109 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPF--GNVISAKVFIDKQTS--LSKCFGFVSFDNPDSAQVAIKAMNGFQVGT---  109 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTS--CEEEEEEECCCSSSS--CCCCEEEEEEESSHHHHHHHHHCCCCEETT---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEeCCCCC--CcCcEEEEEECCHHHHHHHHHHcCCCEECC---
Confidence            4456899999999999999999999864  356555544332221  123579999999999999999999988742   


Q ss_pred             CeeeeEEEec
Q 009860           84 AQFKAIVEYA   93 (523)
Q Consensus        84 ne~~A~VEfA   93 (523)
                        ....|+||
T Consensus       110 --~~l~V~~a  117 (118)
T 2khc_A          110 --KRLKVQLK  117 (118)
T ss_dssp             --EECCEEEC
T ss_pred             --EEEEEEec
Confidence              23455554

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.12  E-value=0.0019  Score=53.32  Aligned_cols=82  Identities=18%  Similarity=0.189  Sum_probs=58.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCcee--------EEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYN--------WFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNG   75 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvd--------wfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG   75 (523)
                      ..+..+|.|.+||+.+|++++.+.+...-  .|.        ....+..+...  ....-|||.|.+.+++...++.++|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G--~i~~~~~~~~~~v~i~~~~~~g--~~~g~afV~f~~~~~A~~Ai~~l~g   87 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCG--VVKMNKRTGQPMIHIYLDKETG--KPKGDATVSYEDPPTAKAAVEWFDG   87 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTS--CBCBCSSSCCBSEECCBCTTTC--SBCSEEEEEBSSHHHHHHHHHHHTT
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcC--CEeEccccCccCEEEEEeCCCC--CeeeEEEEEECCHHHHHHHHHHcCC
Confidence            45678999999999999999999998752  332        12222211111  1234699999999999999999999


Q ss_pred             CeeEeCCCCeeeeEEEecc
Q 009860           76 HVFVNEKGAQFKAIVEYAP   94 (523)
Q Consensus        76 ~vFvDsKGne~~A~VEfAP   94 (523)
                      +.|.+     ....|++|-
T Consensus        88 ~~~~g-----~~l~V~~a~  101 (113)
T 2cpe_A           88 KDFQG-----SKLKVSLAR  101 (113)
T ss_dssp             CEETT-----EECEEECSS
T ss_pred             CccCC-----CEEEEEECC
Confidence            99842     356777763

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.11  E-value=0.0017  Score=51.88  Aligned_cols=80  Identities=23%  Similarity=0.212  Sum_probs=59.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +....+|.|.+||+.+|++++.+.+..+  +.|....++.-+.     ...+|||.|.+.++....++.++|+.|.+   
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~v~~~~~i~~~~-----~~~~afV~f~~~~~a~~Ai~~l~g~~~~g---   81 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQY--GVVESCEQVNTDS-----ETAVVNVTYSSKDQARQALDKLNGFQLEN---   81 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHH--SCEEEEEEECCSS-----SSEEEEEEESSHHHHHHHHHHHTTCBCSS---
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhc--CCeEEEEEeecCC-----CCCEEEEEECCHHHHHHHHHHhCCCEECC---
Confidence            3457899999999999999999999875  3455442222211     12239999999999999999999998842   


Q ss_pred             CeeeeEEEeccC
Q 009860           84 AQFKAIVEYAPS   95 (523)
Q Consensus        84 ne~~A~VEfAPY   95 (523)
                        ....|+||.-
T Consensus        82 --~~l~V~~a~~   91 (96)
T 2e44_A           82 --FTLKVAYIPD   91 (96)
T ss_dssp             --CBCEEEECCC
T ss_pred             --cEEEEEEcCc
Confidence              2467777753

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=97.11  E-value=0.002  Score=51.02  Aligned_cols=82  Identities=12%  Similarity=0.154  Sum_probs=60.6

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      +..+..+|.|++||+.+|++++.+.+...  +.|....... +  . ......|||.|.+.+++...++.++++.|.+. 
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~--G~v~~~~i~~-~--~-g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~-   76 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTWKMLKDKFNEC--GHVLYADIKM-E--N-GKSKGCGVVKFESPEVAERACRMMNGMKLSGR-   76 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHHHHHHHHTT--SCEEEEEEEE-S--S-SCEEEEEEEEESSHHHHHHHHHHHTTCCBTTB-
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEc-c--C-CCcceEEEEEECCHHHHHHHHHHhCCCEECCc-
Confidence            34677899999999999999999999875  3455444442 1  1 11234699999999999999999999987432 


Q ss_pred             CCeeeeEEEeccC
Q 009860           83 GAQFKAIVEYAPS   95 (523)
Q Consensus        83 Gne~~A~VEfAPY   95 (523)
                          ...|++|--
T Consensus        77 ----~l~v~~a~~   85 (92)
T 2dgv_A           77 ----EIDVRIDRN   85 (92)
T ss_dssp             ----CCCCEECSC
T ss_pred             ----EEEEEEcCC
Confidence                455666643

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=97.10  E-value=0.0021  Score=51.99  Aligned_cols=81  Identities=19%  Similarity=0.323  Sum_probs=59.9

Q ss_pred             CCCCCCceEEEecCCC-CCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            2 KEPLQRTKVVIRHLPP-SLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         2 k~p~~r~KVVIRrLPP-~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      ....+..+|.|.+||+ .+||+++.+.+..+  +.|......          -.-|||.|.+.+++....+.++|..|.+
T Consensus         5 ~~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~--G~v~~v~i~----------~g~afV~f~~~~~A~~A~~~l~g~~~~g   72 (96)
T 2kvi_A            5 HNIPPKSRLFIGNLPLKNVSKEDLFRIFSPY--GHIMQINIK----------NAFGFIQFDNPQSVRDAIECESQEMNFG   72 (96)
T ss_dssp             ----CCEEEEEESSTTSCCCHHHHHHHHTTT--CCCCEEEEE----------TTEEEEEESCHHHHHHHHHHHTCSSCBT
T ss_pred             ccCCCCCEEEEeCCCcccCCHHHHHHHHHhc--CCEEEEEEe----------CCEEEEEECCHHHHHHHHHHcCCCeeCC
Confidence            3456788999999999 99999999999875  334444432          2379999999999999999999998764


Q ss_pred             CCCCeeeeEEEeccCCCCC
Q 009860           81 EKGAQFKAIVEYAPSQRVP   99 (523)
Q Consensus        81 sKGne~~A~VEfAPYQKvP   99 (523)
                      .     ...|++|.-..-+
T Consensus        73 ~-----~l~V~~a~~~~~~   86 (96)
T 2kvi_A           73 K-----KLILEVSSSNARP   86 (96)
T ss_dssp             T-----TBCEEEEECCCC-
T ss_pred             c-----EEEEEEcCcCCCC
Confidence            3     4578887544433

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=97.07  E-value=0.0017  Score=56.22  Aligned_cols=82  Identities=16%  Similarity=0.120  Sum_probs=60.8

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+..+|.|++||+.+||+++.+.+..+  +.|.....+..+...  ..-.-|||.|.+.+++...++.++|..|-+. 
T Consensus        42 ~~~~~~~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           42 NPDPNCCLGVFGLSLYTTERDLREVFSKY--GPIADVSIVYDQQSR--RSRGFAFVYFENVDDAKEAKERANGMELDGR-  116 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTT--SCEEEEEEECCSSSS--CCCCEEEEEESCHHHHHHHHHHHTTCCSSSS-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEecCCCC--ccceEEEEEECCHHHHHHHHHHhCCCEECCE-
Confidence            45677899999999999999999999874  346555554333221  1234699999999999999999999887432 


Q ss_pred             CCeeeeEEEec
Q 009860           83 GAQFKAIVEYA   93 (523)
Q Consensus        83 Gne~~A~VEfA   93 (523)
                          ...|+||
T Consensus       117 ----~l~V~~a  123 (129)
T 2kxn_B          117 ----RIRVDFS  123 (129)
T ss_dssp             ----CCEESCC
T ss_pred             ----EEEEEEe
Confidence                4566665

>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=97.06  E-value=0.0028  Score=54.07  Aligned_cols=83  Identities=23%  Similarity=0.309  Sum_probs=60.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      ++..+|.|++||+.+||+++.+.+...  +.|....++..+...  ....-|||.|.+.++.....+.++|..|.+    
T Consensus         1 ~~~~~l~v~nlp~~~~~~~l~~~f~~~--G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~A~~a~~~l~~~~~~g----   72 (168)
T 1b7f_A            1 ASNTNLIVNYLPQDMTDRELYALFRAI--GPINTCRIMRDYKTG--YSYGYAFVDFTSEMDSQRAIKVLNGITVRN----   72 (168)
T ss_dssp             -CCSEEEEECCCTTCCHHHHHHHHHTT--SCEEEEECCEETTTT--EECSEEEEEESSHHHHHHHHHHHTTCEETT----
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEEEeCCCC--ccceEEEEEECCHHHHHHHHHhcCCCEeCC----
Confidence            356899999999999999999999874  345444443222111  122469999999999999999999998832    


Q ss_pred             eeeeEEEeccCC
Q 009860           85 QFKAIVEYAPSQ   96 (523)
Q Consensus        85 e~~A~VEfAPYQ   96 (523)
                       ....|+++.-+
T Consensus        73 -~~l~v~~~~~~   83 (168)
T 1b7f_A           73 -KRLKVSYARPG   83 (168)
T ss_dssp             -EECEEEECCCC
T ss_pred             -cEEEEEecCCC
Confidence             35667777544

>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=97.05  E-value=0.0016  Score=55.27  Aligned_cols=80  Identities=20%  Similarity=0.274  Sum_probs=60.0

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF   86 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~   86 (523)
                      .++|.|++||+.+||+++.+.+...  +.|.....+..+.+.  ....-|||.|.+.++.....+.++|..|.+     .
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~--G~i~~v~~~~~~~~~--~~~g~afV~f~~~~~A~~a~~~l~~~~~~g-----~   72 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSI--GEIESCKLVRDKITG--QSLGYGFVNYIDPKDAEKAINTLNGLRLQT-----K   72 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTT--SCEEEEEEEECTTTC--CEEEEEEEEESSHHHHHHHHHHHTTCEETT-----E
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhc--CCeEEEEEEeCCCCC--cceeEEEEEECCHHHHHHHHHHcCCCccCC-----c
Confidence            5789999999999999999999875  346555554433222  123469999999999999999999988843     3


Q ss_pred             eeEEEeccC
Q 009860           87 KAIVEYAPS   95 (523)
Q Consensus        87 ~A~VEfAPY   95 (523)
                      ...|+++.-
T Consensus        73 ~l~v~~~~~   81 (167)
T 1fxl_A           73 TIKVSYARP   81 (167)
T ss_dssp             ECEEEECCC
T ss_pred             eEEEEecCC
Confidence            556777753

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=97.05  E-value=0.0023  Score=53.98  Aligned_cols=83  Identities=11%  Similarity=0.006  Sum_probs=60.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +.+..+|.|++||+.+||+++.+.+...  +.|.....+.-..+.  ..-.-|||.|.+.+++..-++.++|..|..   
T Consensus         3 ~~p~~~lfV~nL~~~~te~~L~~~F~~~--G~i~~v~i~~d~~tg--~~rG~aFV~f~~~~~A~~Ai~~lng~~~~g---   75 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETFLKDMCRKY--GEVEEVEILLHPRTR--KHLGLARVLFTSTRGAKETVKNLHLTSVMG---   75 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTT--SCEEEEEEEECTTTC--CEEEEEEEEESSHHHHHHHHHHHTTCEETT---
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhc--CCeeEEEEEECCCCC--ceeeEEEEEECCHHHHHHHHHHhCCCEECC---
Confidence            5677899999999999999999999874  345443332221111  112359999999999999999999998743   


Q ss_pred             CeeeeEEEeccC
Q 009860           84 AQFKAIVEYAPS   95 (523)
Q Consensus        84 ne~~A~VEfAPY   95 (523)
                        ..-.|++|+.
T Consensus        76 --r~i~V~~a~~   85 (110)
T 3s8s_A           76 --NIIHAQLDIK   85 (110)
T ss_dssp             --EECEEEECST
T ss_pred             --eEEEEEECCC
Confidence              2567888853

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=97.04  E-value=0.0019  Score=54.38  Aligned_cols=78  Identities=21%  Similarity=0.211  Sum_probs=59.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      ....+|.|.+||+.+||+++.+.+...  +.|.....+..         .-|||.|.+.+++...++.++|+.|.+....
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~--G~v~~~~i~~~---------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~   82 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREA--GDVCYADVYRD---------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGE   82 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGG--SCEEEEEECTT---------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEecC---------CEEEEEECCHHHHHHHHHHhCCCEECCcEee
Confidence            356899999999999999999999875  34554433221         6799999999999999999999998776654


Q ss_pred             eeeeEEEec
Q 009860           85 QFKAIVEYA   93 (523)
Q Consensus        85 e~~A~VEfA   93 (523)
                      .....|+.+
T Consensus        83 ~~~i~v~~~   91 (115)
T 3beg_B           83 TAYIRVKVD   91 (115)
T ss_dssp             CCBCEEEEC
T ss_pred             eEEEEeccC
Confidence            444556554

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=97.03  E-value=0.0019  Score=51.40  Aligned_cols=78  Identities=14%  Similarity=0.290  Sum_probs=60.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      ....+|.|++||+.+||+++.+.+... .  |......        ..-.-|||.|.+.+++....+.++|+.|.+    
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~--v~~~~i~--------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g----   67 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-D--LKYCYVD--------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRG----   67 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-C--CCCEEEE--------GGGTEEEECCSCHHHHHHHHHHHTTEEETT----
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-C--eEEEEEe--------CCCcEEEEEECCHHHHHHHHHHhCCCeECC----
Confidence            456899999999999999999999876 2  3332221        123469999999999999999999998743    


Q ss_pred             eeeeEEEeccCCCC
Q 009860           85 QFKAIVEYAPSQRV   98 (523)
Q Consensus        85 e~~A~VEfAPYQKv   98 (523)
                       ....|++||-..+
T Consensus        68 -~~l~V~~a~~~~~   80 (88)
T 1wg1_A           68 -KDLIVQLQPTDAL   80 (88)
T ss_dssp             -EEEEEEECCCCCC
T ss_pred             -cEEEEEEcCCCce
Confidence             3578999876543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.02  E-value=0.0018  Score=52.27  Aligned_cols=79  Identities=10%  Similarity=0.141  Sum_probs=58.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +.+..+|.|.+||+.+||+++.+.+....  .+..   +.-+...  ....-|||.|.+.+++...++.++++.|.+   
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~--~~~~---~~~~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~g---   81 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV--RARI---VTDRETG--SSKGFGFVDFNSEEDAKAAKEAMEDGEIDG---   81 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS--EEEE---EECSSSC--SEEEEEEEECSSHHHHHHHHHHHTTCEETT---
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe--EEEE---EecCCCC--CcCcEEEEEECCHHHHHHHHHHhCCCeECC---
Confidence            56778999999999999999999888541  2322   2111111  123469999999999999999999998742   


Q ss_pred             CeeeeEEEecc
Q 009860           84 AQFKAIVEYAP   94 (523)
Q Consensus        84 ne~~A~VEfAP   94 (523)
                        ....|+||-
T Consensus        82 --~~l~V~~a~   90 (102)
T 2fc8_A           82 --NKVTLDWAK   90 (102)
T ss_dssp             --EECEEEECC
T ss_pred             --eEEEEEEec
Confidence              357888874

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=97.02  E-value=0.0043  Score=50.66  Aligned_cols=74  Identities=18%  Similarity=0.302  Sum_probs=58.6

Q ss_pred             CCCCCceEEEecCCC-CCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009860            3 EPLQRTKVVIRHLPP-SLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP-~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs   81 (523)
                      .+.+..+|.|++||+ .+|++++.+.+..+  |.|......          -.-|||.|.+.+++....+.++|..|.+ 
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~--G~v~~v~i~----------~g~afV~f~~~~~A~~Ai~~l~g~~~~g-   84 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPY--GHIMQINIK----------NAFGFIQFDNPQSVRDAIEXESQEMNFG-   84 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGG--SCEEEEEEC----------SSEEEEEESSHHHHHHHHHHHTTSEETT-
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhc--CCEEEEEEe----------CCEEEEEECCHHHHHHHHHHcCCCEECC-
Confidence            356788999999999 99999999999875  345554442          2469999999999999999999998742 


Q ss_pred             CCCeeeeEEEec
Q 009860           82 KGAQFKAIVEYA   93 (523)
Q Consensus        82 KGne~~A~VEfA   93 (523)
                          ....|+||
T Consensus        85 ----~~l~V~~a   92 (97)
T 2xnq_A           85 ----KKLILEVS   92 (97)
T ss_dssp             ----EECEEEEC
T ss_pred             ----EEEEEEec
Confidence                34677776

>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=97.01  E-value=0.0028  Score=49.46  Aligned_cols=75  Identities=13%  Similarity=0.105  Sum_probs=57.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHh-cCCeeEeCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELL-NGHVFVNEK   82 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~f-dG~vFvDsK   82 (523)
                      ..+..+|.|.+||+.+|++++.+.+...  +.|....+...        -.-|||.|.+.++.....+.+ +|+.|.+  
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~--G~i~~~~~~~~--------kg~afV~f~~~~~A~~a~~~l~~~~~~~g--   76 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQF--GEIRTITVVQR--------QQCAFIQFATRQAAEVAAEKSFNKLIVNG--   76 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTT--SCEEEEEEEGG--------GTEEEEEESSHHHHHHHHHTTTTTCEETT--
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhC--CCEeEEEEECC--------CCEEEEEECCHHHHHHHHHHhcCCeeECC--
Confidence            4566899999999999999999999875  34655555531        247999999999999999988 8877643  


Q ss_pred             CCeeeeEEEec
Q 009860           83 GAQFKAIVEYA   93 (523)
Q Consensus        83 Gne~~A~VEfA   93 (523)
                         ....|+||
T Consensus        77 ---~~l~v~~a   84 (85)
T 2ytc_A           77 ---RRLNVKWG   84 (85)
T ss_dssp             ---EECCEEEC
T ss_pred             ---CEEEEEec
Confidence               24556665

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=97.00  E-value=0.0016  Score=54.72  Aligned_cols=80  Identities=16%  Similarity=0.177  Sum_probs=57.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      |...++|.|++||+.+||+++.+.+..+  |.|.....+..+  .  ..-.-|||.|.+.+++...++.++|+.|.+   
T Consensus         2 P~~~~~lfV~nLp~~~te~~L~~~F~~~--G~v~~v~i~~d~--~--~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g---   72 (115)
T 4f25_A            2 PLGSGNIFIKNLDKSIDNKALYDTFSAF--GNILSCKVVCDE--N--GSKGYGFVHFETQEAAERAIEKMNGMLLND---   72 (115)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEEET--T--EEEEEEEEEESCHHHHHHHHHHHTTCEETT---
T ss_pred             CCCCCEEEECCCCCCCCHHHHHHHHhcc--CCEEEEEEeecC--C--CCCceEEEEECCHHHHHHHHHHcCCCEECC---
Confidence            5567899999999999999999999875  345544333211  1  112359999999999999999999998743   


Q ss_pred             CeeeeEEEecc
Q 009860           84 AQFKAIVEYAP   94 (523)
Q Consensus        84 ne~~A~VEfAP   94 (523)
                        ....|++|-
T Consensus        73 --~~i~V~~a~   81 (115)
T 4f25_A           73 --RKVFVGRFK   81 (115)
T ss_dssp             --EECEEEESS
T ss_pred             --EEEEEEECC
Confidence              255677764

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=97.00  E-value=0.0026  Score=54.31  Aligned_cols=83  Identities=17%  Similarity=0.221  Sum_probs=61.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +.+..+|.|.+||+.+||+++.+.+..+  +.|.....+..+.+.  ....-|||.|.+.+++...++.++|..|.+.  
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~--G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~--  112 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERY--GPIESVKIVCDRETR--QSRGYGFVKFQSGSSAQQAIAGLNGFNILNK--  112 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHH--SCEEEEEEEEETTTT--EEEEEEEEEESSHHHHHHHHHHTTTEECSSC--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEEcCCCC--CcceEEEEEECCHHHHHHHHHHhCCCEECCe--
Confidence            4456899999999999999999999875  345554444332221  1234699999999999999999999887532  


Q ss_pred             CeeeeEEEeccC
Q 009860           84 AQFKAIVEYAPS   95 (523)
Q Consensus        84 ne~~A~VEfAPY   95 (523)
                         ...|+||--
T Consensus       113 ---~l~v~~a~~  121 (139)
T 1u6f_A          113 ---RLKVALAAS  121 (139)
T ss_dssp             ---EEEEEESSC
T ss_pred             ---EEEEEECCC
Confidence               567887743

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=96.99  E-value=0.0057  Score=51.79  Aligned_cols=81  Identities=11%  Similarity=0.112  Sum_probs=59.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+...|.|++||+.+|++++.+.+...  +.|.....+......  ....-|||.|.+.+++....+.++|..|-   |
T Consensus        84 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~--G~i~~~~i~~~~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~---g  156 (166)
T 3md3_A           84 SDDTFNLFVGDLNVNVDDETLRNAFKDF--PSYLSGHVMWDMQTG--SSRGYGFVSFTSQDDAQNAMDSMQGQDLN---G  156 (166)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHTTS--TTEEEEEEEECTTTC--CEEEEEEEEESCHHHHHHHHHHHTTCEET---T
T ss_pred             CCCCceEEECCCCCCCCHHHHHHHHhcc--CCeeEEEEEecCCCC--CcceEEEEEeCCHHHHHHHHHHhCCCccC---C
Confidence            4456789999999999999999999874  356555554332221  11235999999999999999999999873   2


Q ss_pred             CeeeeEEEec
Q 009860           84 AQFKAIVEYA   93 (523)
Q Consensus        84 ne~~A~VEfA   93 (523)
                        ..-.|+||
T Consensus       157 --~~i~v~~a  164 (166)
T 3md3_A          157 --RPLRINWA  164 (166)
T ss_dssp             --EECEEEES
T ss_pred             --cEEEEEec
Confidence              34556665

>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=96.98  E-value=0.0048  Score=49.94  Aligned_cols=79  Identities=16%  Similarity=0.173  Sum_probs=59.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHH----HHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLL----ALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV   79 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~----eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv   79 (523)
                      ..+.++|.|.+||+.+||+++.    +.+...  +.|.....+..+..     -..|||.|.+.+++..-++.++|+.|.
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~--G~v~~v~i~~~~~~-----rg~afV~f~~~~~A~~Ai~~l~g~~~~   78 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARH--GKVKSVELSPHTDY-----QLKAVVQMENLQDAIGAVNSLHRYKIG   78 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHH--SCEEEEEECSCCST-----TCCEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccc--CcEEEEEEEeCCCC-----CeEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            4577899999999999999999    555543  35655444433222     236999999999999999999999874


Q ss_pred             eCCCCeeeeEEEecc
Q 009860           80 NEKGAQFKAIVEYAP   94 (523)
Q Consensus        80 DsKGne~~A~VEfAP   94 (523)
                      +     ....|++|-
T Consensus        79 g-----r~l~V~~a~   88 (96)
T 2dgx_A           79 S-----KKILVSLAT   88 (96)
T ss_dssp             T-----EEEEEEECC
T ss_pred             C-----eEEEEEEcC
Confidence            2     256788873

>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=96.97  E-value=0.0021  Score=55.15  Aligned_cols=76  Identities=16%  Similarity=0.173  Sum_probs=56.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +..+|.|++||+.+||+++.+.+...  +.|.....+............-|||.|.+.+++....+.+++..+.+..+
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~--G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~   77 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQY--GAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMH   77 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTT--SCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCS
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhC--CCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCc
Confidence            46799999999999999999999875  34655554433222111233469999999999999999999998876544

>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=96.96  E-value=0.0032  Score=49.38  Aligned_cols=77  Identities=17%  Similarity=0.105  Sum_probs=56.9

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF   86 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~   86 (523)
                      ..+|.|++||+.+|++++.+.+...  +.|............+  ...-|||.|.+.+++.... .++|+.|.+     .
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 ARSIYVGNVDYGATAEELEAHFHGC--GSVNRVTILCDKFSGH--PKGFAYIEFSDKESVRTSL-ALDESLFRG-----R   75 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGG--CCEEEEEEEESCSSSS--CCEEEEEEESSTHHHHHHG-GGTTCEETT-----E
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhC--CCEEEEEEEecCCCCC--cceEEEEEECCHHHHHHHH-hcCCCEECC-----c
Confidence            4689999999999999999999875  3465555443322221  2346999999999999998 999998743     2


Q ss_pred             eeEEEec
Q 009860           87 KAIVEYA   93 (523)
Q Consensus        87 ~A~VEfA   93 (523)
                      .-.|++|
T Consensus        76 ~l~V~~a   82 (89)
T 3ucg_A           76 QIKVIPK   82 (89)
T ss_dssp             ECEEEET
T ss_pred             EEEEEEc
Confidence            4566665

>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=96.92  E-value=0.007  Score=50.04  Aligned_cols=77  Identities=19%  Similarity=0.180  Sum_probs=56.3

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF   86 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~   86 (523)
                      ..+|.|.+||+.+|++++.+.+..+  +.|.....+..+...  ..-.-|||.|.+.+++...+ .++|+.|.+     .
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~g--~~~g~afV~f~~~~~a~~A~-~l~g~~~~g-----~   94 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAV--GKVRDVRIISDRNSR--RSKGIAYVEFCEIQSVPLAI-GLTGQRLLG-----V   94 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTT--SCEEEEEECCSCCSS--SCCCCEEEEESCGGGHHHHH-HHTTEEETT-----E
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhC--CCEeEEEEEecCCCC--ccCcEEEEEeCcHHHHHHHH-HcCCCEeCC-----e
Confidence            3589999999999999999999864  356555544322211  11235999999999999999 999998832     3


Q ss_pred             eeEEEec
Q 009860           87 KAIVEYA   93 (523)
Q Consensus        87 ~A~VEfA   93 (523)
                      ...|++|
T Consensus        95 ~l~V~~a  101 (114)
T 2cq4_A           95 PIIVQAS  101 (114)
T ss_dssp             EEEEEEH
T ss_pred             EEEEEec
Confidence            5667765

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.91  E-value=0.0031  Score=50.04  Aligned_cols=80  Identities=9%  Similarity=0.040  Sum_probs=58.2

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+....+|.|++||+.+||+++.+.+... .  +.....+.. . . ...-.-|||.|.+.+++....+ ++|..|.+. 
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~--i~~v~i~~~-~-~-g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr-   77 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-K--PVAIRIVRN-A-H-GNKTGYIFVDFSNEEEVKQALK-CNREYMGGR-   77 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-C--CSEEEEEEC-T-T-SCEEEEEEEECSSHHHHHHHHH-SCSEEETTE-
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-C--ceEEEEEEC-C-C-CCCceEEEEEECCHHHHHHHHH-hCCceeCCc-
Confidence            45677899999999999999999999876 2  444343322 1 1 1123579999999999999999 999887322 


Q ss_pred             CCeeeeEEEecc
Q 009860           83 GAQFKAIVEYAP   94 (523)
Q Consensus        83 Gne~~A~VEfAP   94 (523)
                          .-.|++|-
T Consensus        78 ----~i~v~~a~   85 (91)
T 2dgw_A           78 ----YIEVFREK   85 (91)
T ss_dssp             ----EEEEEEES
T ss_pred             ----EEEEEECC
Confidence                45666653

>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=96.91  E-value=0.0068  Score=49.94  Aligned_cols=76  Identities=16%  Similarity=0.142  Sum_probs=58.4

Q ss_pred             CCCceEEEecCCCC-CCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            5 LQRTKVVIRHLPPS-LSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         5 ~~r~KVVIRrLPP~-LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ....+|.|.+||+. +||+++.+.+..+-  .|.....          .-.-|||.|.+.+++...++.++|+.|.+   
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G--~v~~v~i----------~~g~afV~f~~~~~A~~A~~~l~g~~~~g---   89 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYG--RVAGCSV----------HKGYAFVQYSNERHARAAVLGENGRVLAG---   89 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGS--CCSEEEE----------ETTEEEEECSSSHHHHHHHHHHTTCEETT---
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCC--CeEEEEE----------eCCEEEEEECCHHHHHHHHHHcCCCEECC---
Confidence            34579999999999 99999999998752  3433333          12469999999999999999999998842   


Q ss_pred             CeeeeEEEeccCCC
Q 009860           84 AQFKAIVEYAPSQR   97 (523)
Q Consensus        84 ne~~A~VEfAPYQK   97 (523)
                        ....|+||--.+
T Consensus        90 --~~l~V~~a~~~~  101 (110)
T 1wf1_A           90 --QTLDINMAGEPK  101 (110)
T ss_dssp             --EECCEEESCCCC
T ss_pred             --eEEEEEECCCCC
Confidence              356788875433

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=96.90  E-value=0.0062  Score=52.89  Aligned_cols=85  Identities=15%  Similarity=0.134  Sum_probs=62.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+..+|.|++||+.+||+++.+.+..+  +.|........+...  ..-.-|||.|.+.+++...++.++|+.|.+   
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~--G~v~~~~i~~~~~~g--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g---  139 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKY--GRVGDVYIPRDRYTK--ESRGFAFVRFHDKRDAEDAMDAMDGAVLDG---  139 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHH--SCEEEEECCCCSSCT--TSCCEEEEEESBHHHHHHHHHHSTTEESSS---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEeecCCCC--ccceEEEEEECCHHHHHHHHHHhCCCEECC---
Confidence            3456899999999999999999999775  346554443322221  123469999999999999999999988743   


Q ss_pred             CeeeeEEEeccCCC
Q 009860           84 AQFKAIVEYAPSQR   97 (523)
Q Consensus        84 ne~~A~VEfAPYQK   97 (523)
                        ....|+||--++
T Consensus       140 --~~l~v~~a~~~~  151 (158)
T 2kn4_A          140 --RELRVQMARYGR  151 (158)
T ss_dssp             --SEEEEEEECCSS
T ss_pred             --eEEEEEECCCCC
Confidence              357888886554

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=96.89  E-value=0.0021  Score=51.94  Aligned_cols=75  Identities=19%  Similarity=0.218  Sum_probs=57.9

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeee
Q 009860            8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFK   87 (523)
Q Consensus         8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~   87 (523)
                      ++|.|.+||+.+||+++.+.+...  +.|........       .-.-|||.|.+.+++....+.++|+.|.+.     .
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~-------~~g~afV~f~~~~~a~~A~~~l~g~~~~g~-----~   66 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYY--GPLRTVWIARN-------PPGFAFVEFEDPRDAEDAVRGLDGKVICGS-----R   66 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHH--CCCSEEEEESS-------SSSEEEEECSSHHHHHHHHHHHHHSCSSSC-----C
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEeeC-------CCCEEEEEECCHHHHHHHHHHHCCCeECCc-----E
Confidence            479999999999999999998875  24554454433       234799999999999999999999987432     3


Q ss_pred             eEEEeccCC
Q 009860           88 AIVEYAPSQ   96 (523)
Q Consensus        88 A~VEfAPYQ   96 (523)
                      ..|++|--.
T Consensus        67 l~V~~a~~~   75 (101)
T 2hvz_A           67 VRVELSTGM   75 (101)
T ss_dssp             CEEEESSSC
T ss_pred             EEEEEccCC
Confidence            678877544

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=96.88  E-value=0.0048  Score=51.28  Aligned_cols=79  Identities=18%  Similarity=0.157  Sum_probs=58.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+..+|.|++||+.+||+++.+.+...  |.|.....+..+.    ..-.-|||.|.+.+++....+.++|+.|.+   
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~--G~i~~v~i~~~~~----~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g---   96 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQF--GKILDVEIIFNER----GSKGFGFVTFENSADADRAREKLHGTVVEG---   96 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGT--CCCSCEEECCBTT----BCTTEEEEECCCSHHHHHHHHHHTTCEETT---
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhc--CCEEEEEEEECCC----CCceEEEEEECCHHHHHHHHHHcCCCEECC---
Confidence            4567899999999999999999999875  2344334332211    123469999999999999999999998743   


Q ss_pred             CeeeeEEEec
Q 009860           84 AQFKAIVEYA   93 (523)
Q Consensus        84 ne~~A~VEfA   93 (523)
                        ....|++|
T Consensus        97 --~~l~V~~a  104 (109)
T 2err_A           97 --RKIEVNNA  104 (109)
T ss_dssp             --EECEEEEC
T ss_pred             --EEEEEEEC
Confidence              35567776

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=96.88  E-value=0.0019  Score=49.36  Aligned_cols=67  Identities=15%  Similarity=0.170  Sum_probs=48.1

Q ss_pred             eEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      ||.|.+||+.+|++++.+.+...  +.|........+.+.  ....-|||.|.+.+++....+ ++++.|-+
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~a~~a~~-~~~~~~~g   67 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQF--GKVDDAMLMFDKTTN--RHRGFGFVTFESEDIVEKVCE-IHFHEINN   67 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTT--SCCSEECCCBCSSST--TSCBEEEEECSCHHHHHHHHS-SSCCCSSS
T ss_pred             CEEEecCCCCCCHHHHHHHHHhc--CCEEEEEEEecCCCC--CcCcEEEEEECCHHHHHHHHH-CCCCEECC
Confidence            68999999999999999999874  345443333222211  123469999999999988877 88887743

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=96.87  E-value=0.0039  Score=50.37  Aligned_cols=66  Identities=18%  Similarity=0.239  Sum_probs=53.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV   79 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv   79 (523)
                      +....+|.|.+||+.+|++++.+.+...  +.|.......        .-.-|||.|.+.+++...++.++|+.|.
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~--G~i~~~~~~~--------~~g~afV~f~~~~~A~~Ai~~l~g~~~~   89 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNF--GFILDFKHYP--------EKGCCFIKYDTHEQAAVCIVALANFPFQ   89 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTT--SCCSEEEEET--------TTTEEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhC--CCEEEEEEec--------CCCEEEEEECCHHHHHHHHHHhCCCeEC
Confidence            4457899999999999999999999875  3454444441        1246999999999999999999999874

>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=96.85  E-value=0.0048  Score=54.76  Aligned_cols=82  Identities=13%  Similarity=0.152  Sum_probs=60.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      .+..+|.|.+||+.+|++++.+.+..+  +.|....++..+...  ....-|||.|.+.+++...++.++|+.|.   | 
T Consensus        70 ~~~~~l~V~nLp~~~t~~~L~~~F~~~--G~i~~v~i~~~~~~g--~~~g~afV~f~~~~~A~~Ai~~l~g~~~~---g-  141 (165)
T 1rk8_A           70 VEGWILFVTSIHEEAQEDEIQEKFCDY--GEIKNIHLNLDRRTG--FSKGYALVEYETHKQALAAKEALNGAEIM---G-  141 (165)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTS--SEEEEEEEEESSHHHHHHHHHHHTTCEET---T-
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhcC--CCEEEEEEEecCCCC--cEeeEEEEEECCHHHHHHHHHHhCCCEEC---C-
Confidence            345689999999999999999999875  356555554332221  12346999999999999999999999883   2 


Q ss_pred             eeeeEEEeccC
Q 009860           85 QFKAIVEYAPS   95 (523)
Q Consensus        85 e~~A~VEfAPY   95 (523)
                       ....|+||--
T Consensus       142 -~~l~V~~a~~  151 (165)
T 1rk8_A          142 -QTIQVDWCFV  151 (165)
T ss_dssp             -EECEEEESEE
T ss_pred             -EEEEEEEecC
Confidence             3567888743

>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=96.83  E-value=0.0058  Score=52.48  Aligned_cols=80  Identities=19%  Similarity=0.142  Sum_probs=59.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      ....+|.|++||+.+|++++.+.+...  +.|............  ..-.-|||.|.+.++.....+.++|+.|-+    
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~--G~v~~v~i~~~~~~g--~~~g~afV~f~~~~~A~~A~~~l~g~~~~g----  163 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSF--GPLKAFNLVKDSATG--LSKGYAFCEYVDINVTDQAIAGLNGMQLGD----  163 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTT--SCEEEEEEEECTTTC--SEEEEEEEEESSTTHHHHHHHHHTTCEETT----
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhc--CCceEEEEEecCCCC--CcceEEEEEeCCHHHHHHHHHHcCCCEECC----
Confidence            346889999999999999999999874  356655554433221  112359999999999999999999998832    


Q ss_pred             eeeeEEEec
Q 009860           85 QFKAIVEYA   93 (523)
Q Consensus        85 e~~A~VEfA   93 (523)
                       ..-.|+||
T Consensus       164 -~~l~V~~A  171 (172)
T 2g4b_A          164 -KKLLVQRA  171 (172)
T ss_dssp             -EECEEEEC
T ss_pred             -eEEEEEeC
Confidence             24566665

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.83  E-value=0.0048  Score=49.99  Aligned_cols=82  Identities=10%  Similarity=0.051  Sum_probs=60.1

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCe-eEeC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHV-FVNE   81 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~v-FvDs   81 (523)
                      .+.+..+|.|.+||+.+||+++.+.+...+. .|.....+... ..  ..-.-|||.|.+.+++...++.++++. |.+.
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G-~v~~v~i~~~~-~g--~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~   80 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYP-SCRGGKVVLDQ-TG--VSKGYGFVKFTDELEQKRALTECQGAVGLGSK   80 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCT-TEEEEEEEECT-TC--CEEEEEEEEESCHHHHHHHHHHTTTCCSSSSS
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCC-CeEEEEEEECC-CC--CccceEEEEECCHHHHHHHHHHccCCcccCCE
Confidence            4567799999999999999999999987332 45444444332 11  123469999999999999999999988 5432


Q ss_pred             CCCeeeeEEEec
Q 009860           82 KGAQFKAIVEYA   93 (523)
Q Consensus        82 KGne~~A~VEfA   93 (523)
                           ...|++|
T Consensus        81 -----~l~v~~a   87 (104)
T 2dhg_A           81 -----PVRLSVA   87 (104)
T ss_dssp             -----CCCCCBC
T ss_pred             -----eEEEEEc
Confidence                 3456665

>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=96.81  E-value=0.0019  Score=52.28  Aligned_cols=81  Identities=16%  Similarity=0.201  Sum_probs=58.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      +..+|.|++||+.+|++++.+.+...  +.|............  ....-|||.|.+.+++....+.++|+.|.+     
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~--G~i~~~~i~~~~~~g--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----   77 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEV--GPVVSFRLVYDRETG--KPKGYGFCEYQDQETALSAMRNLNGREFSG-----   77 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTT--SCCSEEEEEEETTTT--EEEEEEEEECSCHHHHHHHHHHSSSBSCSS-----
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhc--CCeeEEEEEeCCCCC--ccceEEEEEECCHHHHHHHHHHhCCCeeCC-----
Confidence            34689999999999999999999874  234333333222111  123469999999999999999999998833     


Q ss_pred             eeeEEEeccC
Q 009860           86 FKAIVEYAPS   95 (523)
Q Consensus        86 ~~A~VEfAPY   95 (523)
                      ....|+||--
T Consensus        78 ~~l~v~~a~~   87 (104)
T 1p1t_A           78 RALRVDNAAS   87 (104)
T ss_dssp             SCBEEEETTC
T ss_pred             cEEEEEeCCC
Confidence            2467887753

>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=96.81  E-value=0.0097  Score=50.11  Aligned_cols=82  Identities=18%  Similarity=0.254  Sum_probs=61.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCe-eEeCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHV-FVNEK   82 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~v-FvDsK   82 (523)
                      ..+..+|.|++||+.+||+++.+.+.++  +.|.....+++        -.-|||.|.+.++...-++.+++.. .++.+
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~f--G~V~~v~i~~~--------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr   81 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKF--GTICYVMMMPF--------KRQALVEFENIDSAKECVTFAADVPVYIAGQ   81 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTT--SCEEEEEEETT--------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhC--CCEEEEEEECC--------CCEEEEEECCHHHHHHHHHHhccCCceECCE
Confidence            3456789999999999999999999875  45666555543        2469999999999999998887653 22322


Q ss_pred             CCeeeeEEEeccCCCCC
Q 009860           83 GAQFKAIVEYAPSQRVP   99 (523)
Q Consensus        83 Gne~~A~VEfAPYQKvP   99 (523)
                          ...|+||-.+.+-
T Consensus        82 ----~l~V~~a~~~~~~   94 (104)
T 1wex_A           82 ----QAFFNYSTSKRIT   94 (104)
T ss_dssp             ----BCEEEECSSSSCC
T ss_pred             ----EEEEEEccCcccc
Confidence                5679998766543

>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=96.80  E-value=0.0026  Score=50.80  Aligned_cols=81  Identities=16%  Similarity=0.219  Sum_probs=57.0

Q ss_pred             CCCCCceEEEecCCCCCCHHHHH----HHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLL----ALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~----eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      ...+..+|.|++||+.+|++++.    +.+...  +.|.......    . .....-|||.|.+.++.....+.++|+.|
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~--G~i~~v~i~~----~-~~~~g~afV~f~~~~~A~~A~~~l~g~~~   76 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRF--GQILDILVSR----S-LKMRGQAFVIFKEVSSATNALRSMQGFPF   76 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGG--SCEEEEECCH----H-HHHTTCEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhC--CCEEEEEEEc----C-CCcCcEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            45677899999999999999998    555543  3454433321    0 01123699999999999999999999988


Q ss_pred             EeCCCCeeeeEEEeccC
Q 009860           79 VNEKGAQFKAIVEYAPS   95 (523)
Q Consensus        79 vDsKGne~~A~VEfAPY   95 (523)
                      .   |  ....|+||--
T Consensus        77 ~---g--~~l~v~~a~~   88 (97)
T 1nu4_A           77 Y---D--KPMRIQYAKT   88 (97)
T ss_dssp             T---T--EECEEEECSS
T ss_pred             C---C--cEEEEEEccC
Confidence            2   3  4567787743

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.77  E-value=0.0084  Score=48.41  Aligned_cols=80  Identities=13%  Similarity=0.104  Sum_probs=59.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +.+..+|.|++||+.+||+++.+.+..+  +.|.   .+. +.  ......-|||.|.+.+++...++.++++.|.+   
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~--g~v~---~~~-~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g---   80 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKA--TFIK---VPQ-NQ--NGKSKGYAFIEFASFEDAKEALNSCNKREIEG---   80 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSC--SEEE---CCB-CS--SSCBCSEEEEECSSHHHHHHHHHHTSSEEETT---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhC--CEEE---EEE-CC--CCCEeeEEEEEECCHHHHHHHHHHhCCCEeCC---
Confidence            4567899999999999999999998874  3341   111 11  11123479999999999999999999988752   


Q ss_pred             CeeeeEEEeccCC
Q 009860           84 AQFKAIVEYAPSQ   96 (523)
Q Consensus        84 ne~~A~VEfAPYQ   96 (523)
                        ....|+||--+
T Consensus        81 --~~l~v~~a~~~   91 (101)
T 2fc9_A           81 --RAIRLELQGPR   91 (101)
T ss_dssp             --EEEEEEECSSC
T ss_pred             --eEEEEEEcCCC
Confidence              35678887544

>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=96.75  E-value=0.0026  Score=49.61  Aligned_cols=80  Identities=16%  Similarity=0.233  Sum_probs=57.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      ...+|.|++||+.+||+++.+.+...  +.|............ .....-|||.|.+.+++....+.++|+.|.+     
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~~~i~~~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----   74 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTY--GKIKMIDMPVERMHP-HLSKGYAYVEFENPDEAEKALKHMDGGQIDG-----   74 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTT--SCEEEEECCEETTEE-EEECSEEEEEESSHHHHHHHHHHHTTCEETT-----
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhC--CCEEEEEEEeCCCCC-CCCCcEEEEEEecHHHHHHHHHHcCCCeECC-----
Confidence            45789999999999999999999874  345444332211110 1123479999999999999999999999843     


Q ss_pred             eeeEEEec
Q 009860           86 FKAIVEYA   93 (523)
Q Consensus        86 ~~A~VEfA   93 (523)
                      ....|++|
T Consensus        75 ~~l~v~~a   82 (88)
T 4a8x_A           75 QEITATAV   82 (88)
T ss_dssp             EECEEEEE
T ss_pred             eEEEEEEC
Confidence            24567776

>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=96.75  E-value=0.008  Score=49.05  Aligned_cols=90  Identities=10%  Similarity=0.032  Sum_probs=62.5

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhc--CCeeEe
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLN--GHVFVN   80 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fd--G~vFvD   80 (523)
                      ...+..+|.|.+||+.+|++++.+.+..+-. .|.....+.-+... ...-.-|||.|.+.+++...++.++  ++.|.+
T Consensus         4 ~s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~-~v~~v~i~~~~~~~-g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g   81 (109)
T 2dis_A            4 GSSGNCRLFIGGIPKMKKREEILEEIAKVTE-GVLDVIVYASAADK-MKNRGFAFVEYESHRAAAMARRKLMPGRIQLWG   81 (109)
T ss_dssp             CCCCSEEEEEECCCTTSCHHHHHHHHHHHST-TEEEEECCSSSCTT-TTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTT
T ss_pred             cccCCCEEEEeCCCCcCCHHHHHHHHHHhcC-CceEEEEEccCCCC-CCcCcEEEEEecCHHHHHHHHHHhhCCCceecC
Confidence            3456789999999999999999999987522 15544443121111 1223579999999999999999996  455533


Q ss_pred             CCCCeeeeEEEeccCCCCC
Q 009860           81 EKGAQFKAIVEYAPSQRVP   99 (523)
Q Consensus        81 sKGne~~A~VEfAPYQKvP   99 (523)
                           ....|+||--...+
T Consensus        82 -----~~l~V~~a~~~~~~   95 (109)
T 2dis_A           82 -----HQIAVDWAEPEIDV   95 (109)
T ss_dssp             -----BCCEEEESCSSCST
T ss_pred             -----CeEEEEEcCCCCCc
Confidence                 25688888655444

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=96.75  E-value=0.0033  Score=50.39  Aligned_cols=85  Identities=19%  Similarity=0.183  Sum_probs=61.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCC-CCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSY-KHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~-Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      .+..+|.|++||+.+||+++.+.+...  +.|.....+...... ......-|||.|.+.+++...++.++|+.|.+   
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g---   77 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKV--GAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDG---   77 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTT--SCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETT---
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCC---
Confidence            467899999999999999999999864  345444443222100 00123469999999999999999999998752   


Q ss_pred             CeeeeEEEeccCC
Q 009860           84 AQFKAIVEYAPSQ   96 (523)
Q Consensus        84 ne~~A~VEfAPYQ   96 (523)
                        ....|++|--.
T Consensus        78 --~~l~V~~a~~~   88 (98)
T 2cpf_A           78 --HKLEVRISERA   88 (98)
T ss_dssp             --EECEEECSSCS
T ss_pred             --eEEEEEEccCC
Confidence              25678877443

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=96.74  E-value=0.0036  Score=54.40  Aligned_cols=88  Identities=16%  Similarity=0.165  Sum_probs=63.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +.+..+|.|++||+.+|++++.+.+...  +.|.....+..+...+  .-.-|||.|.+.+++...++.++|+.|.+.  
T Consensus        44 ~~~~~~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           44 VEGMTSLKVDNLTYRTSPDTLRRVFEKY--GRVGDVYIPRDRYTKE--SRGFAFVRFHDKRDAEDAMDAMDGAVLDGR--  117 (135)
T ss_dssp             GGGCCCEEEECCCSSCHHHHHHHHHGGG--SCCSEEECCCCSSSSS--CCSCCEEECSCHHHHHHHHTTTTTCCSSSS--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEecCCCCc--cceEEEEEECCHHHHHHHHHHcCCCEECCE--
Confidence            3456789999999999999999999875  2454444433222211  123599999999999999999999987432  


Q ss_pred             CeeeeEEEeccCCCCCC
Q 009860           84 AQFKAIVEYAPSQRVPK  100 (523)
Q Consensus        84 ne~~A~VEfAPYQKvPk  100 (523)
                         ...|++|--++-+.
T Consensus       118 ---~l~V~~a~~~~~~~  131 (135)
T 2lea_A          118 ---ELRVQMARYGRPPD  131 (135)
T ss_dssp             ---CCEEEECCCCCCCT
T ss_pred             ---EEEEEECCCCCCCc
Confidence               56888886655443

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=96.73  E-value=0.0025  Score=50.90  Aligned_cols=77  Identities=18%  Similarity=0.242  Sum_probs=56.8

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      ...+..+|.|++||+.+|++++.+.+...  +.|... ...|      ..-.-|||.|.+.+++....+.++|+.|.   
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~--g~v~~~-~~~~------~~~g~afV~f~~~~~a~~A~~~l~g~~~~---   79 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDA--LEIRLV-SQDG------KSKGIAYIEFKSEADAEKNLEEKQGAEID---   79 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSE--EEECCE-EETT------EEEEEEEEEESSHHHHHHHHHHTTEEEET---
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhC--CcEEEe-CCCC------CcceEEEEEECCHHHHHHHHHHhCCCEEC---
Confidence            45567899999999999999999988874  233222 1111      12346999999999999999999998873   


Q ss_pred             CCeeeeEEEec
Q 009860           83 GAQFKAIVEYA   93 (523)
Q Consensus        83 Gne~~A~VEfA   93 (523)
                      |  ....|++|
T Consensus        80 g--~~l~v~~a   88 (96)
T 1fjc_A           80 G--RSVSLYYT   88 (96)
T ss_dssp             T--EEEEEEEC
T ss_pred             C--eEEEEEEc
Confidence            2  24677776

>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=96.73  E-value=0.0047  Score=49.21  Aligned_cols=77  Identities=21%  Similarity=0.221  Sum_probs=57.0

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcC-CeeEeC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNG-HVFVNE   81 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG-~vFvDs   81 (523)
                      .+.+..+|.|.+||+.+||+++.+.+..+-. -+......         ...-|||.|.+.+++...++.++| +.|.+ 
T Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~-vv~~~~~~---------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g-   72 (93)
T 2cqh_A            4 GSSGMNKLYIGNLSPAVTADDLRQLFGDRKL-PLAGQVLL---------KSGYAFVDYPDQNWAIRAIETLSGKVELHG-   72 (93)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHTTC-CCSSCEEE---------ETTEEEECCSCHHHHHHHHHHHTTTCEETT-
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCC-ceEEEEEc---------CCCEEEEEECCHHHHHHHHHHccCCeeECC-
Confidence            4566789999999999999999998877522 01111111         124699999999999999999999 77632 


Q ss_pred             CCCeeeeEEEecc
Q 009860           82 KGAQFKAIVEYAP   94 (523)
Q Consensus        82 KGne~~A~VEfAP   94 (523)
                          ....|++|-
T Consensus        73 ----~~l~v~~a~   81 (93)
T 2cqh_A           73 ----KIMEVDYSV   81 (93)
T ss_dssp             ----EECEEEECC
T ss_pred             ----EEEEEEEcc
Confidence                467788874

>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=96.72  E-value=0.0083  Score=48.04  Aligned_cols=81  Identities=12%  Similarity=0.078  Sum_probs=57.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCC-CceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFN-DRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~-gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      +....+|.|++||+.+||+++.+.+..+-. ..+.+....   ..  .....-|||.|.+.+++...++.++|+.|.+  
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~---~~--g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g--   84 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN---EK--GMPTGEAMVAFESRDEATAAVIDLNDRPIGS--   84 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC---SS--SCEEEEEEEEESCHHHHHHHHHHTTTCEETT--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEEC---CC--CCeeeEEEEEECCHHHHHHHHHHhCCCeeCC--
Confidence            455689999999999999999999886521 112222221   10  1123569999999999999999999998743  


Q ss_pred             CCeeeeEEEecc
Q 009860           83 GAQFKAIVEYAP   94 (523)
Q Consensus        83 Gne~~A~VEfAP   94 (523)
                         ....|++|-
T Consensus        85 ---~~l~V~~a~   93 (98)
T 2cqp_A           85 ---RKVKLVLGS   93 (98)
T ss_dssp             ---EECEEEESS
T ss_pred             ---eEEEEEEcC
Confidence               356777763

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=96.71  E-value=0.0053  Score=54.64  Aligned_cols=70  Identities=13%  Similarity=0.123  Sum_probs=53.2

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      ..+|.|++||+.+||+++.+.+..+  +.|....++.-+...  ....-|||.|.+.+++...++.+++..|.+
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~--G~i~~v~i~~~~~~g--~~~g~afV~f~~~~~A~~A~~~l~~~~~~g   97 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPF--GPIKSIDMSWDSVTM--KHKGFAFVEYEVPEAAQLALEQMNSVMLGG   97 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGG--SCEEEEEECCC-CC---CCCSEEEEEESSHHHHHHHHHHHSSCCCC-
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhC--CCEEEEEEeecCCCC--ccCceEEEEeCCHHHHHHHHHHccCCeeCC
Confidence            4689999999999999999999875  356655554322211  123469999999999999999999988743

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=96.71  E-value=0.0034  Score=53.77  Aligned_cols=81  Identities=22%  Similarity=0.215  Sum_probs=59.2

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009860            2 KEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         2 k~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs   81 (523)
                      +.|...++|.|++||+..||+++.+.+...- ..|.+..-..++      ...-|||.|.+.+++..-++.++|..|.+.
T Consensus        23 ~~p~~~~~l~VgnLp~~~te~dL~~~F~~~G-~~v~~v~i~~~~------~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr   95 (111)
T 2jvr_A           23 KLPAKRYRITMKNLPEGCSWQDLKDLARENS-LETTFSSVNTRD------FDGTGALEFPSEEILVEALERLNNIEFRGS   95 (111)
T ss_dssp             --CCCCEEEEEECSSCCCCHHHHHHHHHHHT-CCCSEEECSSCS------SSCCEEEEESSHHHHHHHHHHTTTEEETTE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHhC-CeeEEEEEEcCC------CCCEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            3577889999999999999999999887652 145543322221      234699999999999999999999887432


Q ss_pred             CCCeeeeEEEecc
Q 009860           82 KGAQFKAIVEYAP   94 (523)
Q Consensus        82 KGne~~A~VEfAP   94 (523)
                           .-.|++|-
T Consensus        96 -----~i~V~~a~  103 (111)
T 2jvr_A           96 -----VITVERDD  103 (111)
T ss_dssp             -----EEEEEESC
T ss_pred             -----EEEEEECC
Confidence                 45677663

>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=96.71  E-value=0.0094  Score=49.08  Aligned_cols=83  Identities=17%  Similarity=0.343  Sum_probs=58.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCC-Cce-eEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFN-DRY-NWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~-gkv-dwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs   81 (523)
                      +.+..+|.|++||+.+|++++.+.+..+-. ..+ -......|+.      -.-|||.|.+.+++...++.++|+.|.  
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~------~g~afV~f~~~~~a~~Ai~~l~g~~~~--   93 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRM------RGQAFITFPNKEIAWQALHLVNGYKLY--   93 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSS------CSEEEEECSSHHHHHHHHHHSTTCBCS--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCcc------ceEEEEEECCHHHHHHHHHHhCCCEeC--
Confidence            345689999999999999999988876421 001 1122233321      246999999999999999999999883  


Q ss_pred             CCCeeeeEEEeccCCC
Q 009860           82 KGAQFKAIVEYAPSQR   97 (523)
Q Consensus        82 KGne~~A~VEfAPYQK   97 (523)
                       |  ....|+||--.+
T Consensus        94 -g--~~l~v~~a~~~~  106 (115)
T 2cpx_A           94 -G--KILVIEFGKNKK  106 (115)
T ss_dssp             -S--CBCEEEECCCCS
T ss_pred             -C--cEEEEEEccCCC
Confidence             2  256888875443

>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=96.69  E-value=0.0065  Score=50.51  Aligned_cols=84  Identities=15%  Similarity=0.188  Sum_probs=60.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHH---HHhcccCCCceeEEEeeCCCCCCC-CCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLL---ALFRDHFNDRYNWFCFRPGKSSYK-HQRYSRAYVELKKPAGVFEFAELLNGHVFV   79 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~---eqL~p~~~gkvdwfyFVpGK~S~K-p~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv   79 (523)
                      ..+..+|.|.+||+.+||++++   +.+..+  +.|........+...+ .....-|||.|.+.+++...++.++|+.|.
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~--G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   89 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKF--GKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD   89 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTT--SCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhcc--CCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEEC
Confidence            3467899999999999999998   666653  3565555443322111 122357999999999999999999999873


Q ss_pred             eCCCCeeeeEEEecc
Q 009860           80 NEKGAQFKAIVEYAP   94 (523)
Q Consensus        80 DsKGne~~A~VEfAP   94 (523)
                         |  ....|+||-
T Consensus        90 ---g--r~l~V~~a~   99 (111)
T 2cpi_A           90 ---G--RTLKASLGT   99 (111)
T ss_dssp             ---T--EEEEEESCC
T ss_pred             ---C--EEEEEEecc
Confidence               2  256788774

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=96.68  E-value=0.0086  Score=53.31  Aligned_cols=85  Identities=13%  Similarity=0.154  Sum_probs=63.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      ...+|.|++||+.+|++++.+.+..+  +.|....++..+...+  ...-|||.|.+.++.....+.++|+.|-+     
T Consensus       124 ~~~~l~v~nlp~~~t~~~l~~~f~~~--G~v~~v~i~~~~~~g~--~~g~afV~F~~~~~A~~A~~~l~g~~~~g-----  194 (216)
T 2qfj_A          124 AFNRIYVASVHQDLSDDDIKSVFEAF--GKIKSATLARDPTTGK--HKGYGFIEYEKAQSSQDAVSSMNLFDLGG-----  194 (216)
T ss_dssp             TSCEEEEECCCTTCCHHHHHHHHTTS--SCEEEEEEEECTTTCC--EEEEEEEEESSHHHHHHHHHHHTTCBCSS-----
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhcc--CCeeEEEEEecCCCCC--cCceEEEEecCHHHHHHHHHHccCCEeCC-----
Confidence            45789999999999999999999875  3576666654433221  13359999999999999999999998732     


Q ss_pred             eeeEEEeccCCCCC
Q 009860           86 FKAIVEYAPSQRVP   99 (523)
Q Consensus        86 ~~A~VEfAPYQKvP   99 (523)
                      ..-.|+||--...|
T Consensus       195 ~~i~V~~a~~~~~~  208 (216)
T 2qfj_A          195 QYLRVGKAVTPPMP  208 (216)
T ss_dssp             SBCEEEECSSCSST
T ss_pred             cEEEEEEecCCCCC
Confidence            24678887655433

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=96.64  E-value=0.0064  Score=55.43  Aligned_cols=86  Identities=15%  Similarity=0.126  Sum_probs=62.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +.+.++|.|.+||+.+|++++.+.+..+  +.|.....+... ..  ..-.-|||.|.+.+++...++.++|+.|.+   
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~--G~I~~v~i~~d~-~g--~~kG~afV~F~~~~~A~~Ai~~lng~~l~G---  156 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEF--GTLKKAAVDYDR-SG--RSLGTADVHFERRADALKAMKQYKGVPLDG---  156 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHT--SCCSEEEECCCT-TS--SCSCCEEEEESCHHHHHHHHHHSTTCBCSS---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEECC-CC--CEeeEEEEEeCCHHHHHHHHHHhCCCEECC---
Confidence            4457899999999999999999988874  234443333222 11  123469999999999999999999998743   


Q ss_pred             CeeeeEEEeccCCCCC
Q 009860           84 AQFKAIVEYAPSQRVP   99 (523)
Q Consensus        84 ne~~A~VEfAPYQKvP   99 (523)
                        ....|+||.-...+
T Consensus       157 --r~l~V~~a~~~~~~  170 (177)
T 2f3j_A          157 --RPMDIQLVASQIDL  170 (177)
T ss_dssp             --SBCEEEEESSGGGG
T ss_pred             --EEEEEEEecCCCCC
Confidence              25678888655433

>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=96.64  E-value=0.0084  Score=51.32  Aligned_cols=82  Identities=13%  Similarity=0.163  Sum_probs=60.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      .+..+|.|++||+.+|++++.+.+...  +.|..........   ...-.-|||.|.+.++.....+.++|..+.+..  
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~~--G~i~~v~~~~~~~---g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~--  165 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSSF--GQIEECRILRGPD---GLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGC--  165 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTT---SCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTC--
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHhC--CCEEEEEEEECCC---CCEEEEEEEEECCHHHHHHHHHHhcCCcccCCC--
Confidence            356789999999999999999999875  3465555443321   111234999999999999999999998876532  


Q ss_pred             eeeeEEEec
Q 009860           85 QFKAIVEYA   93 (523)
Q Consensus        85 e~~A~VEfA   93 (523)
                      ..+-.|.||
T Consensus       166 ~~~l~V~~a  174 (175)
T 3nmr_A          166 SSPMVVKFA  174 (175)
T ss_dssp             SSCCEEEEC
T ss_pred             CCCeEEEec
Confidence            234566665

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.63  E-value=0.0044  Score=50.00  Aligned_cols=75  Identities=17%  Similarity=0.148  Sum_probs=55.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      ....+|.|.+||+.+|++++.+.+..+-  .|. ...+.+      ....-|||.|.+.+++...++.++|..|.+.   
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 PLAADVYVGNLPRDARVSDLKRALRELG--SVP-LRLTWQ------GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTD---   84 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTT--CCC-SEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCCSSSS---
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcC--CEE-EEEEcC------CCCcEEEEEECCHHHHHHHHHHhCCCEECCc---
Confidence            4468999999999999999999887652  222 122222      1123699999999999999999999987532   


Q ss_pred             eeeeEEEec
Q 009860           85 QFKAIVEYA   93 (523)
Q Consensus        85 e~~A~VEfA   93 (523)
                        ...|++|
T Consensus        85 --~l~V~~a   91 (97)
T 2e5j_A           85 --TLRVALA   91 (97)
T ss_dssp             --CCEEEEC
T ss_pred             --EEEEEEc
Confidence              4667776

>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=96.62  E-value=0.0063  Score=47.72  Aligned_cols=71  Identities=14%  Similarity=0.129  Sum_probs=51.6

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      .+.+..+|.|++||+.+||+++.+.+...  +.|.....+..+.+.  ....-|||.|.+.+++....+. +++.|
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~g--~~~g~afV~f~~~~~a~~A~~~-~~~~~   77 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKF--GEVVDCTIKMDPNTG--RSRGFGFILFKDAASVEKVLDQ-KEHRL   77 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTT--SCEEEEEEEECTTTC--CEEEEEEEEESSTHHHHHHHHS-SCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhC--CCEEEEEEeecCCCC--ccccEEEEEECCHHHHHHHHHh-CCCEE
Confidence            45678899999999999999999999764  356555544332221  1233599999999999988865 55543

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=96.61  E-value=0.0078  Score=49.91  Aligned_cols=78  Identities=13%  Similarity=0.027  Sum_probs=56.3

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF   86 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~   86 (523)
                      ..+|.|.+||+.+||+++.+.+..+  +.|.....+..+...+  ...-|||.|.+.+++...++. +++.|.+     .
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~--G~i~~v~i~~~~~~g~--~~g~afV~f~~~~~a~~Ai~~-~~~~~~g-----~   96 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQW--GKLTDCVVMRDPASKR--SRGFGFVTFSSMAEVDAAMAA-RPHSIDG-----R   96 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSS--CCCSEEEEECCTTTSS--CCSEEEEECSSHHHHHHHHTS-CSEEETT-----E
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEECCCCCC--cCceEEEEeCCHHHHHHHHHh-CCcEECC-----E
Confidence            4789999999999999999999764  3454444443322221  224699999999999999888 8777632     3


Q ss_pred             eeEEEecc
Q 009860           87 KAIVEYAP   94 (523)
Q Consensus        87 ~A~VEfAP   94 (523)
                      ...|++|-
T Consensus        97 ~l~V~~a~  104 (116)
T 1x4b_A           97 VVEPKRAV  104 (116)
T ss_dssp             EEEEECCS
T ss_pred             EEEEEECC
Confidence            56777764

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=96.60  E-value=0.01  Score=52.09  Aligned_cols=80  Identities=19%  Similarity=0.132  Sum_probs=59.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      .+..+|.|++||+.+|++++.+.+...  +.|............  ....-|||.|.+.++.....+.++|+.|.   | 
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~--G~v~~~~~~~~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~---g-  183 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSF--GPLKAFNLVKDSATG--LSKGYAFCEYVDINVTDQAIAGLNGMQLG---D-  183 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTB--SCEEEEEEEECTTTC--SEEEEEEEEESSSSHHHHHHHHHTTCEET---T-
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHc--CCccEEEEeecCCCC--CcceEEEEEECCHHHHHHHHHHcCCCEEC---C-
Confidence            566899999999999999999999875  345555544332211  12346999999999999999999999882   2 


Q ss_pred             eeeeEEEec
Q 009860           85 QFKAIVEYA   93 (523)
Q Consensus        85 e~~A~VEfA   93 (523)
                       ..-.|+||
T Consensus       184 -~~l~v~~a  191 (198)
T 2yh0_A          184 -KKLLVQRA  191 (198)
T ss_dssp             -EECEEEES
T ss_pred             -EEEEEEEC
Confidence             25667776

>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=96.58  E-value=0.0039  Score=52.06  Aligned_cols=80  Identities=15%  Similarity=0.130  Sum_probs=55.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCce-eEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRY-NWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkv-dwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      +.+..+|.|++||+.+||+++.+.+...  +.+ .....+..+ ..+  .-.-|||.|.+.+++...++. +++.|.+  
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~--g~v~~~v~i~~d~-~g~--~~G~afV~F~~~~~a~~Al~~-~~~~~~g--   83 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGI--PVDENAVHVLVDN-NGQ--GLGQALVQFKNEDDARKSERL-HRKKLNG--   83 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTS--CCCSTTEEECCCT-TSS--CSSCEEEECSSHHHHHHHGGG-CSEEETT--
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhC--CCcCCeEEEEECC-CCC--cceEEEEEECCHHHHHHHHHh-CCCccCC--
Confidence            5677899999999999999999999875  334 222333222 111  123599999999999998887 8766632  


Q ss_pred             CCeeeeEEEecc
Q 009860           83 GAQFKAIVEYAP   94 (523)
Q Consensus        83 Gne~~A~VEfAP   94 (523)
                         ....|++|-
T Consensus        84 ---r~i~v~~a~   92 (114)
T 2cpy_A           84 ---REAFVHVVT   92 (114)
T ss_dssp             ---EEEEEEEEC
T ss_pred             ---eEEEEEECC
Confidence               245666663

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.53  E-value=0.011  Score=47.45  Aligned_cols=75  Identities=13%  Similarity=0.038  Sum_probs=54.3

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      ....+|.|.+||+.+||+++.+.+..+  +.|...  +.-+...+     -|||.|.+.+++...++ ++|+.|.+.   
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~--G~v~~v--~~~~~~g~-----~afV~f~~~~~a~~ai~-l~g~~~~g~---   72 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAF--GPVASV--VMDKDKGV-----FAIVEMGDVGAREAVLS-QSQHSLGGH---   72 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGT--SCEEEE--EECSSSCC-----EEEEEESSHHHHHHHHT-CSCCEETTE---
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhc--CCeEEE--EEcCCCCc-----EEEEEECCHHHHHHHHh-cCCeEECCE---
Confidence            445699999999999999999999864  344432  11111111     89999999999999999 999987532   


Q ss_pred             eeeeEEEecc
Q 009860           85 QFKAIVEYAP   94 (523)
Q Consensus        85 e~~A~VEfAP   94 (523)
                        ...|++|.
T Consensus        73 --~l~V~~a~   80 (94)
T 2e5g_A           73 --RLRVRPRE   80 (94)
T ss_dssp             --ECCCBCSC
T ss_pred             --EEEEEECC
Confidence              44556554

>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=96.52  E-value=0.0075  Score=52.29  Aligned_cols=77  Identities=17%  Similarity=0.159  Sum_probs=59.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+..+|.|.+||+.+||+++.+.+...  +.|.....+..       .-.-|||.|.+.++.....+.++|+.|.+   
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~--G~i~~v~i~~~-------~~g~afV~f~~~~~a~~A~~~l~g~~~~g---  137 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYY--GPLRSVWVARN-------PPGFAFVEFEDPRDAADAVRELDGRTLCG---  137 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHH--SCEEEEEECSS-------SCSEEEEEESSHHHHHHHHHHHSSSCSSS---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhh--CCEEEEEEeeC-------CCcEEEEEECCHHHHHHHHHHcCCCEECC---
Confidence            4567899999999999999999999875  35655554432       13479999999999999999999998732   


Q ss_pred             CeeeeEEEecc
Q 009860           84 AQFKAIVEYAP   94 (523)
Q Consensus        84 ne~~A~VEfAP   94 (523)
                        ....|+||-
T Consensus       138 --~~l~v~~a~  146 (150)
T 2i2y_A          138 --CRVRVELSN  146 (150)
T ss_dssp             --SCCEEEECC
T ss_pred             --eEEEEEEcC
Confidence              245677763

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=96.52  E-value=0.02  Score=48.33  Aligned_cols=78  Identities=15%  Similarity=0.150  Sum_probs=58.7

Q ss_pred             eEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeeee
Q 009860            9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKA   88 (523)
Q Consensus         9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~A   88 (523)
                      +|.|++||+.+||+++.+.+...  +.|....++..+..   ....-|||.|.+.+++....+.++|..|.+     ...
T Consensus         2 ~l~V~nlp~~~t~~~l~~~f~~~--G~i~~v~i~~~~~~---~~~g~afV~f~~~~~a~~A~~~l~~~~~~g-----~~i   71 (166)
T 3md3_A            2 VLYVGNLDKAITEDILKQYFQVG--GPIANIKIMIDKNN---KNVNYAFVEYHQSHDANIALQTLNGKQIEN-----NIV   71 (166)
T ss_dssp             EEEEEEEETTCCHHHHHHHHGGG--SCEEEEEEECCCC----CCEEEEEEEESSHHHHHHHHHHHTTCEETT-----EEC
T ss_pred             EEEECCCCCcCCHHHHHHHHHhc--CCeEEEEEEECCCC---CCCCEEEEEeCCHHHHHHHHHHcCCCccCC-----Cee
Confidence            68999999999999999999875  35665555543321   123469999999999999999999998832     355


Q ss_pred             EEEeccCC
Q 009860           89 IVEYAPSQ   96 (523)
Q Consensus        89 ~VEfAPYQ   96 (523)
                      .|+++.-.
T Consensus        72 ~v~~~~~~   79 (166)
T 3md3_A           72 KINWAFQS   79 (166)
T ss_dssp             EEEECCCC
T ss_pred             EEEEcCCC
Confidence            67776443

>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=96.51  E-value=0.011  Score=55.57  Aligned_cols=75  Identities=17%  Similarity=0.270  Sum_probs=60.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      +...|.|++||+.+|++++.+.+..+  +.|....+++++       ..-|||.|.+.++...-++.++|+.|.+.    
T Consensus       206 ~~~~l~v~nl~~~~~~~~l~~~F~~~--G~i~~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~~g----  272 (282)
T 3pgw_A          206 PNHILFLTNLPEETNELMLSMLFNQF--PGFKEVRLVPGR-------HDIAFVEFDNEVQAGAARDALQGFKITQN----  272 (282)
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhc--CCeEEEEEecCC-------CcEEEEEeCCHHHHHHHHHHcCCcEeCCC----
Confidence            56789999999999999999999875  456666666544       24899999999999999999999888732    


Q ss_pred             eeeEEEec
Q 009860           86 FKAIVEYA   93 (523)
Q Consensus        86 ~~A~VEfA   93 (523)
                      ..-.|+||
T Consensus       273 ~~l~v~~a  280 (282)
T 3pgw_A          273 NAMKISFA  280 (282)
T ss_pred             CEEEEEEe
Confidence            25566765

>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=96.48  E-value=0.0084  Score=47.61  Aligned_cols=80  Identities=13%  Similarity=0.070  Sum_probs=54.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCC-CceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFN-DRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~-gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      +.+..+|.|++||+.+||+++.+.+...-. ..+......   ..  .....-|||.|.+.+++...++.++++.|.+  
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~---~~--g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g--   84 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN---EK--GMPTGEAMVAFESRDEATAAVIDLNDRPIGS--   84 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEEC---TT--SCEEEEEEEEESSHHHHHHHHHHHTTCEETT--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeC---CC--CCEeeEEEEEECCHHHHHHHHHHhCCCeECC--
Confidence            345689999999999999999998876421 112222211   10  1122459999999999999999999998743  


Q ss_pred             CCeeeeEEEec
Q 009860           83 GAQFKAIVEYA   93 (523)
Q Consensus        83 Gne~~A~VEfA   93 (523)
                         ....|++|
T Consensus        85 ---r~l~v~~a   92 (95)
T 2ek1_A           85 ---RKVKLSGP   92 (95)
T ss_dssp             ---EECEEECC
T ss_pred             ---cEEEEEec
Confidence               24566665

>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=96.47  E-value=0.015  Score=53.67  Aligned_cols=81  Identities=17%  Similarity=0.167  Sum_probs=62.8

Q ss_pred             CCCCceEEEecCCC-CCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            4 PLQRTKVVIRHLPP-SLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         4 p~~r~KVVIRrLPP-~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      +.+..+|.|++||+ .+||+++.+.+...  +.|....++..+       ..-|||.|.+.+++....+.++|..|.+  
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~--G~i~~v~i~~~~-------~g~afV~F~~~~~A~~Ai~~l~g~~~~g--   99 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVY--GDVQRVKILFNK-------KENALVQMADGNQAQLAMSHLNGHKLHG--   99 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHH--TCEEEEEECCTT-------SCCEEEEESCHHHHHHHHHHHTTCBCSS--
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhC--CCeEEEEEEECC-------CCEEEEEECCHHHHHHHHHHhCCCeECC--
Confidence            45678999999999 99999999999865  346555554332       2349999999999999999999998843  


Q ss_pred             CCeeeeEEEeccCCCC
Q 009860           83 GAQFKAIVEYAPSQRV   98 (523)
Q Consensus        83 Gne~~A~VEfAPYQKv   98 (523)
                         ....|++|..+..
T Consensus       100 ---~~l~v~~a~~~~~  112 (229)
T 2adc_A          100 ---KPIRITLSKHQNV  112 (229)
T ss_dssp             ---SBCEEECCSCCCC
T ss_pred             ---eEEEEEEecCccc
Confidence               3567888865543

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=96.43  E-value=0.0091  Score=46.54  Aligned_cols=68  Identities=9%  Similarity=0.218  Sum_probs=52.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccC--CC-------ceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhc
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHF--ND-------RYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLN   74 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~--~g-------kvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fd   74 (523)
                      ..+..+|.|.+||+.+|++++.+.+....  .+       .+........        -.-|||.|.+.+++.... .++
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~--------kg~afV~f~~~~~a~~A~-~l~   73 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD--------KNFAFLEFRSVDETTQAM-AFD   73 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS--------SSEEEEEESSHHHHHHHG-GGT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC--------CcEEEEEcCCHHHHHHHH-hcC
Confidence            34568999999999999999999887651  12       4554443321        357999999999999999 999


Q ss_pred             CCeeEe
Q 009860           75 GHVFVN   80 (523)
Q Consensus        75 G~vFvD   80 (523)
                      |+.|.+
T Consensus        74 g~~~~g   79 (87)
T 2hzc_A           74 GIIFQG   79 (87)
T ss_dssp             TCEETT
T ss_pred             CCEECC
Confidence            998743

>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=96.40  E-value=0.02  Score=48.00  Aligned_cols=82  Identities=13%  Similarity=0.251  Sum_probs=60.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcC--CeeEeC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNG--HVFVNE   81 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG--~vFvDs   81 (523)
                      ..+..+|.|++||+.+||+++.+.+.+.  +.|.....+.+        -.-|||.|.+.++....++.+++  ..| + 
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~f--G~v~~v~i~~~--------kg~aFVef~~~~~A~~Ai~~l~~~~~~~-~-   79 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPF--GKVTNILMLKG--------KNQAFLELATEEAAITMVNYYSAVTPHL-R-   79 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTT--SCEEEEEEETT--------TTEEEEEESSHHHHHHHHHHHHHSCCEE-T-
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEECC--------CCEEEEEECCHHHHHHHHHHhccCCceE-C-
Confidence            3456789999999999999999988875  35655555443        34699999999999988887764  333 2 


Q ss_pred             CCCeeeeEEEeccCCCCCC
Q 009860           82 KGAQFKAIVEYAPSQRVPK  100 (523)
Q Consensus        82 KGne~~A~VEfAPYQKvPk  100 (523)
                       |  ....|+||-.+.+-.
T Consensus        80 -G--r~l~V~~a~~~~~~~   95 (101)
T 2cq1_A           80 -N--QPIYIQYSNHKELKT   95 (101)
T ss_dssp             -T--EECEEEECSCSSCCC
T ss_pred             -C--cEEEEEEcCcccCcC
Confidence             2  256899987665443

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=96.40  E-value=0.013  Score=50.25  Aligned_cols=83  Identities=11%  Similarity=0.254  Sum_probs=63.1

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcC--CeeEe
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNG--HVFVN   80 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG--~vFvD   80 (523)
                      .+.+..+|-|++||+.+||+++.+.+.+.  |.|.....+.+        -.-|||.|.+.++...-++.+++  ..| +
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~f--G~V~~v~i~~~--------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l-~   80 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPF--GKVTNLLMLKG--------KNQAFIEMNTEEAANTMVNYYTSVTPVL-R   80 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHH--CCEEEEEEETT--------TTEEEEEESSHHHHHHHHHHHTTSCCEE-T
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEcC--------CCEEEEEECCHHHHHHHHHHhccCCceE-C
Confidence            36788999999999999999999999875  35666665554        24699999999999999998875  333 2


Q ss_pred             CCCCeeeeEEEeccCCCCCC
Q 009860           81 EKGAQFKAIVEYAPSQRVPK  100 (523)
Q Consensus        81 sKGne~~A~VEfAPYQKvPk  100 (523)
                      .    .+..|+||-.+.+..
T Consensus        81 G----r~l~V~~A~~~~~~~   96 (105)
T 1sjq_A           81 G----QPIYIQFSNHKELKT   96 (105)
T ss_dssp             T----EECCBCCCSSSSCCC
T ss_pred             C----EEEEEEEcCCCCCCc
Confidence            2    256688886655443

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=96.38  E-value=0.021  Score=48.68  Aligned_cols=81  Identities=21%  Similarity=0.333  Sum_probs=63.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee-EeCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF-VNEK   82 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF-vDsK   82 (523)
                      ..|...|-|++||+..||+++.+.+.+.  |.|.....++.+        .-|+|.|.+.++...-.+.+++..+ ++.+
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~f--G~V~~v~i~~~k--------g~AFVef~~~~~A~~Av~~ln~~~~~i~Gr   87 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEF--GPISYVVVMPKK--------RQALVEFEDVLGACNAVNYAADNQIYIAGH   87 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEETTT--------TEEEEEESSHHHHHHHHHHHHHSCEEETTE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcc--CCEEEEEEEcCC--------CEEEEEECCHHHHHHHHHHhcCCCceeCCc
Confidence            4566789999999999999999999885  467766665432        3699999999999999999998753 4433


Q ss_pred             CCeeeeEEEeccCCCC
Q 009860           83 GAQFKAIVEYAPSQRV   98 (523)
Q Consensus        83 Gne~~A~VEfAPYQKv   98 (523)
                          +..|+||=.+.+
T Consensus        88 ----~i~V~~S~~k~l   99 (100)
T 3r27_A           88 ----PAFVNYSTSQKI   99 (100)
T ss_dssp             ----EEEEEECSCSCC
T ss_pred             ----EEEEEecccccc
Confidence                678888865543

>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=96.36  E-value=0.011  Score=61.21  Aligned_cols=82  Identities=11%  Similarity=0.098  Sum_probs=60.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      +..+|.|.+||+.+|+++|.+.|..+  +.|....++..+...+  .-.-|||.|.+.+++...++.++|+.|.+     
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~--G~I~~v~i~~d~~tg~--~kG~aFV~F~~~e~A~~Ai~~lng~~i~g-----  171 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVY--GPIKRIHMVYSKRSGK--PRGYAFIEYEHERDMHSAYKHADGKKIDG-----  171 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHc--CCeeEEEeeccCCCCC--ccceEEEeeccHHHHHHHHHHcCCCEECC-----
Confidence            44799999999999999999999874  3455544443322221  23469999999999999999999998832     


Q ss_pred             eeeEEEeccCC
Q 009860           86 FKAIVEYAPSQ   96 (523)
Q Consensus        86 ~~A~VEfAPYQ   96 (523)
                      ....|+||--.
T Consensus       172 r~i~V~~a~~~  182 (437)
T 3pgw_S          172 RRVLVDVERGR  182 (437)
T ss_pred             EEEEEEEeCCC
Confidence            35778887643

>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=96.35  E-value=0.0072  Score=49.22  Aligned_cols=71  Identities=13%  Similarity=0.171  Sum_probs=51.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCC-CCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGK-SSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK-~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      +....+|.|++||+.+||+++.+.+...  + |.....+..+ .+.+  .-.-|||.|.+.+++.... .++|+.|.+
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~--G-i~~v~i~~~~~~~g~--~~g~afV~f~~~~~a~~Ai-~l~g~~~~g   87 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGL--N-ISAVRLPREPSNPER--LKGFGYAEFEDLDSLLSAL-SLNEESLGN   87 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSS--C-EEEEECSCCTTTTCC--CCSCEEEEECCHHHHHHHH-HTTTCCBTT
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhc--C-CeEEEEEecCCcCCc--cCeEEEEEECCHHHHHHHH-hcCCCEECC
Confidence            4567899999999999999999999875  4 6655554332 1111  1236999999999999999 899998743

>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=96.33  E-value=0.012  Score=51.03  Aligned_cols=76  Identities=16%  Similarity=0.190  Sum_probs=57.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+..+|.|++||+.+|++++.+.+...  +.|...     ...  ...-.-|||.|.+.++.....+.++|+.|-+   
T Consensus        96 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~--g~v~~~-----~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g---  163 (175)
T 1fje_B           96 VRAARTLLAKNLSFNITEDELKEVFEDA--LEIRLV-----SQD--GKSKGIAYIEFKSEADAEKNLEEKQGAEIDG---  163 (175)
T ss_dssp             TGGGGEEEEESCCSSCCHHHHHHHCTTC--SEEEEE-----CSS--SSCCSEEEEECSSHHHHHHHHHHHTEEEETT---
T ss_pred             cccCCEEEEeCCCCCCCHHHHHHHHHhc--CeEEEe-----cCC--CCCceEEEEEECCHHHHHHHHHHhCCCEECC---
Confidence            3456899999999999999999999874  345433     111  1123469999999999999999999987742   


Q ss_pred             CeeeeEEEec
Q 009860           84 AQFKAIVEYA   93 (523)
Q Consensus        84 ne~~A~VEfA   93 (523)
                        ..-.|+||
T Consensus       164 --~~i~v~~a  171 (175)
T 1fje_B          164 --RSVSLYYT  171 (175)
T ss_dssp             --EEEEEEEC
T ss_pred             --eEEEEEec
Confidence              34677777

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=96.29  E-value=0.01  Score=51.87  Aligned_cols=80  Identities=16%  Similarity=0.248  Sum_probs=55.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCC--CceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFN--DRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~--gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+..+|.|++||+.+|++++.+.|...+.  |.|.......   ..  ..-..|||.|.+.++....++.++|+.|.+. 
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 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SD--DNSGKAYIVFATQESAQAFVEAFQGYPFQGN-  100 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CC--SSCCCEEEEESSHHHHHHHHHHSTTCCCTTS-
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CC--CcCCEEEEEECCHHHHHHHHHHHCCCEeCCC-
Confidence            45689999999999999987654443331  3453332211   11  1134599999999999999999999987543 


Q ss_pred             CCeeeeEEEecc
Q 009860           83 GAQFKAIVEYAP   94 (523)
Q Consensus        83 Gne~~A~VEfAP   94 (523)
                          .-.|+||-
T Consensus       101 ----~l~V~~a~  108 (127)
T 2a3j_A          101 ----PLVITFSE  108 (127)
T ss_dssp             ----CCEEEECC
T ss_pred             ----EEEEEEcc
Confidence                55788774

>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=96.28  E-value=0.0071  Score=57.27  Aligned_cols=81  Identities=15%  Similarity=0.081  Sum_probs=58.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      ..++|.|.+||+.+||+++.+.+..+-...|.....+.-+.+.+  .-.-|||.|.+.+++...++.++++.|...    
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 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQ--SKGFALVGVGSEASSKKLMDLLPKRELHGQ----  140 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCC--EEEEEEEEESCTTHHHHHHTTSTTSCBTTB----
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCc--cceEEEEEECCHHHHHHHHHHcCCCeECCE----
Confidence            56789999999999999999999764211565555543332221  123599999999999999999999987532    


Q ss_pred             eeeEEEec
Q 009860           86 FKAIVEYA   93 (523)
Q Consensus        86 ~~A~VEfA   93 (523)
                       ...|++|
T Consensus       141 -~l~V~~a  147 (229)
T 3q2s_C          141 -NPVVTPV  147 (229)
T ss_dssp             -CCEEEEC
T ss_pred             -EeEEEEC
Confidence             4567776

>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=96.26  E-value=0.011  Score=51.90  Aligned_cols=82  Identities=15%  Similarity=0.037  Sum_probs=56.9

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+..+|.|++||+.+||+++.+.+..+  +.|.....+.-+...  ....-|||.|.+.+++....+. +++.|.+  
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~--G~i~~v~i~~~~~~g--~~~g~afV~f~~~~~A~~A~~~-~~~~~~g--   81 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQW--GTLTDCVVMRDPNTK--RSRGFGFVTYATVEEVDAAMNA-RPHKVDG--   81 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTC--CEEEEEEEEESSHHHHHHHHHT-CSCEETT--
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhC--CCEEEEEEEEcCCCC--CccceEEEEeCCHHHHHHHHhc-CCCEECC--
Confidence            35567899999999999999999999875  345554444322211  1234699999999999998877 6665522  


Q ss_pred             CCeeeeEEEecc
Q 009860           83 GAQFKAIVEYAP   94 (523)
Q Consensus        83 Gne~~A~VEfAP   94 (523)
                         ....|+++.
T Consensus        82 ---~~l~v~~~~   90 (196)
T 1l3k_A           82 ---RVVEPKRAV   90 (196)
T ss_dssp             ---EECEEEECC
T ss_pred             ---EEeeeeccc
Confidence               234566554

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=96.23  E-value=0.022  Score=50.56  Aligned_cols=78  Identities=17%  Similarity=0.171  Sum_probs=59.8

Q ss_pred             CCceEEEecCCC-CCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            6 QRTKVVIRHLPP-SLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         6 ~r~KVVIRrLPP-~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      ...+|.|++||+ .+||+++.+.+..+  +.|.....+..+       ..-|||.|.+.+++....+.++|..|.+    
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~--G~i~~v~i~~~~-------~g~afV~f~~~~~a~~A~~~l~~~~~~g----   68 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVY--GDVQRVKILFNK-------KENALVQMADGNQAQLAMSHLNGHKLHG----   68 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTT--CCCSEEECSTTC-------SSCCEEECTTTHHHHHHHHHHTTCCCSS----
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhc--CCEEEEEEEeCC-------CCEEEEEECCHHHHHHHHHHhCCCeecC----
Confidence            357899999999 99999999999864  345544444322       2359999999999999999999998833    


Q ss_pred             eeeeEEEeccCCC
Q 009860           85 QFKAIVEYAPSQR   97 (523)
Q Consensus        85 e~~A~VEfAPYQK   97 (523)
                       ....|++|..+.
T Consensus        69 -~~l~v~~a~~~~   80 (198)
T 1qm9_A           69 -KPIRITLSKHQN   80 (198)
T ss_dssp             -CCCEEEECCCCS
T ss_pred             -eEEEEEEecCCC
Confidence             356788876554

>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=96.23  E-value=0.0062  Score=48.56  Aligned_cols=72  Identities=17%  Similarity=0.061  Sum_probs=49.1

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      +.+|.|++||+.+||+++.+.+...-...+.....+..+...  ..-.-|||.|.+.+++...++.++|+.|..
T Consensus         1 r~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g--~~kG~afV~f~~~~~a~~Ai~~l~g~~~~g   72 (90)
T 3p5t_L            1 RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANG--QSKGFALVGVGSEASSKKLMDLLPKRELHG   72 (90)
T ss_dssp             ---CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTC--CEEEEEEECC-CHHHHHHHHHHGGGSCSSS
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCC--ccCcEEEEEECCHHHHHHHHHHcCCCeeCC
Confidence            468999999999999999999876521134333333322221  113459999999999999999999998743

>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=96.23  E-value=0.02  Score=49.94  Aligned_cols=80  Identities=15%  Similarity=0.271  Sum_probs=62.3

Q ss_pred             CCCceEEEec--CCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            5 LQRTKVVIRH--LPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         5 ~~r~KVVIRr--LPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+..+|.|++  ||..+||+++.+.+..+  |.|......++        -.-|||.|.+.++...-++.++|..|.+.-
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~f--G~v~~v~i~~~--------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~l   92 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKC--GLVDALLMPPN--------KPYSFARYRTTEESKRAYVTLNGKEVVDDL   92 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHH--SCEEEEECCTT--------CSCEEEEESSHHHHHHHHHHTTTCEEECTT
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhc--CCeEEEEEeCC--------CCEEEEEECCHHHHHHHHHHhCCCEEcccc
Confidence            3456799955  99999999999999876  35665554433        247999999999999999999999986555


Q ss_pred             CCeeeeEEEecc
Q 009860           83 GAQFKAIVEYAP   94 (523)
Q Consensus        83 Gne~~A~VEfAP   94 (523)
                      |.-.+..|.||-
T Consensus        93 g~g~~l~v~~a~  104 (114)
T 2cq2_A           93 GQKITLYLNFVE  104 (114)
T ss_dssp             SCEEECEEEEES
T ss_pred             CCCcEEEEEecc
Confidence            555667788774

>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=96.20  E-value=0.0071  Score=46.02  Aligned_cols=65  Identities=14%  Similarity=0.215  Sum_probs=45.3

Q ss_pred             eEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      +|.|++||+.+||+++.+.+...  +.+........+.+.  ....-|||.|.+.+++....+. +++.|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~a~~Ai~~-~~~~~   65 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGF--GEVESIELPMDNKTN--KRRGFCFITFKEEEPVKKIMEK-KYHNV   65 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHH--SCCSEECCCCSCCCS--SSCCCEEEECSSSHHHHHHHTT-SSCCB
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEecCCCC--CcCCEEEEEECCHHHHHHHHHh-CCCeE
Confidence            58899999999999999988875  234333322221111  1233599999999999988875 66665

>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=96.19  E-value=0.011  Score=51.55  Aligned_cols=82  Identities=10%  Similarity=0.248  Sum_probs=60.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCC-eeEeCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGH-VFVNEK   82 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~-vFvDsK   82 (523)
                      ..+..+|.|++||+..||+++.+.+.+.  |.|.....+.+        -.-|||.|.+.++....++.+++. ..++.+
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~f--G~V~~v~i~~~--------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr   97 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPF--GKVTNLLMLKG--------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQ   97 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTT--SCCCEEEEEGG--------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEeCC--------CCEEEEEECCHHHHHHHHHHhccCCceECCe
Confidence            4566889999999999999999999875  34655555543        246999999999999988888753 122222


Q ss_pred             CCeeeeEEEeccCCCCC
Q 009860           83 GAQFKAIVEYAPSQRVP   99 (523)
Q Consensus        83 Gne~~A~VEfAPYQKvP   99 (523)
                          ...|+||-.+.+-
T Consensus        98 ----~l~V~~a~~k~~~  110 (119)
T 2ad9_A           98 ----PIYIQFSNHKELK  110 (119)
T ss_dssp             ----CCEEEECSSSSCC
T ss_pred             ----EEEEEEccCCCCC
Confidence                5688988655443

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=96.17  E-value=0.0093  Score=45.45  Aligned_cols=66  Identities=17%  Similarity=0.119  Sum_probs=47.7

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      ++|.|++||+.+|++++.+.+...  +.+........+.+.  ....-|||.|.+.+++....+.++ +.|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~--G~v~~v~i~~~~~~~--~~~g~afV~f~~~~~a~~a~~~~~-~~~   66 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQF--GEVKECLVMRDPLTK--RSRGFGFVTFMDQAGVDKVLAQSR-HEL   66 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTT--SCCCCEEEECCCCSS--SCSSEEEECCCCTTHHHHHHHTTT-CCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEecCCCCC--CcCceEEEEEcCHHHHHHHHHhCC-Ccc
Confidence            478999999999999999988875  234333333322211  123479999999999999999888 544

>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=96.15  E-value=0.027  Score=45.56  Aligned_cols=83  Identities=11%  Similarity=0.115  Sum_probs=56.5

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      +..+..+|.|++||+.+||+++.+.+..+  +.|.....+..+...  ..-.-|||.|.+.+++...++  +++.|.   
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~g--~~~g~afV~f~~~~~a~~A~~--~~~~~~---   81 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTF--GEVLMVQVKKDLKTG--HSKGFGFVRFTEYETQVKVMS--QRHMID---   81 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGG--SCEEEEEEEECSSSC--SEEEEEEEEESSHHHHHHHHH--SCEEET---
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhc--CCeEEEEEEecCCCC--CccceEEEEECCHHHHHHHHH--cCCeeC---
Confidence            35567899999999999999999999875  345544444332221  122459999999999988877  344332   


Q ss_pred             CCeeeeEEEeccCC
Q 009860           83 GAQFKAIVEYAPSQ   96 (523)
Q Consensus        83 Gne~~A~VEfAPYQ   96 (523)
                      |  ....|++|--.
T Consensus        82 g--~~l~v~~a~~~   93 (103)
T 2cqg_A           82 G--RWCDCKLPNSK   93 (103)
T ss_dssp             T--EEEEEECCCTT
T ss_pred             C--eEEEEEecCCC
Confidence            1  25677877544

>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=96.15  E-value=0.013  Score=50.07  Aligned_cols=63  Identities=14%  Similarity=0.172  Sum_probs=46.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHH
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAEL   72 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~   72 (523)
                      +..+|.|++||+.+||+++.+.+...  |.|.....+..+.+.+  .-.-|||.|.+.+++....+.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~g~--~~g~afV~f~~~~~a~~A~~~   64 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKY--GTVTDLKIMKDPATGR--SRGFGFLSFEKPSSVDEVVKT   64 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTT--CCEEEEECCCCTTTSS--CCSCEEEEESSTHHHHHHHHS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhC--CCEEEEEEEECCCCCC--ccceEEEEEccHHHHHHHHhc
Confidence            45799999999999999999999875  3566555443322211  123599999999999988885

>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=96.12  E-value=0.0075  Score=47.57  Aligned_cols=79  Identities=15%  Similarity=0.167  Sum_probs=54.8

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeee
Q 009860            8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFK   87 (523)
Q Consensus         8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~   87 (523)
                      .+|.|++||+.+||+++.+.+...  +.|........+.+.  ..-.-|||.|.+.+ ....++.++|+.|.+.     .
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~--~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~-----~   71 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQF--GKVFNVKLIYDRETK--KPKGFGFVEMQEES-VSEAIAKLDNTDFMGR-----T   71 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHH--TCCSEEEECCCSSSC--CCCEEEEEEECTTH-HHHHHHTSCSSCCSSS-----S
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhc--CCEEEEEEEEcCCCC--CcceEEEEEECCHH-HHHHHHHhCCCEECCe-----E
Confidence            478999999999999998888764  245444443322221  12356999999999 9999999999987532     4


Q ss_pred             eEEEeccCC
Q 009860           88 AIVEYAPSQ   96 (523)
Q Consensus        88 A~VEfAPYQ   96 (523)
                      ..|++|.-.
T Consensus        72 l~V~~a~~~   80 (90)
T 2ki2_A           72 IRVTEANPK   80 (90)
T ss_dssp             CSEEEC---
T ss_pred             EEEEEcCCC
Confidence            566666443

>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=96.11  E-value=0.024  Score=53.17  Aligned_cols=81  Identities=15%  Similarity=0.189  Sum_probs=57.8

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCC--CceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFN--DRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~--gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      ...+..+|.|++||+.+||+++.+.|..++.  +.|.......    . ...-.-|||.|.+.++....++.++|..|.+
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~----~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   79 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR----S-LKMRGQAFVIFKEVSSATNALRSMQGFPFYD   79 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC----C-CCcceEEEEEECCHHHHHHHHHHhcCCeeCC
Confidence            3566789999999999999996643433331  3454444332    1 1123469999999999999999999988854


Q ss_pred             CCCCeeeeEEEec
Q 009860           81 EKGAQFKAIVEYA   93 (523)
Q Consensus        81 sKGne~~A~VEfA   93 (523)
                           ....|+||
T Consensus        80 -----~~l~v~~a   87 (282)
T 3pgw_A           80 -----KPMRIQYA   87 (282)
T ss_pred             -----cEEEEEEe
Confidence                 35678887

>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=96.09  E-value=0.023  Score=48.12  Aligned_cols=77  Identities=13%  Similarity=0.054  Sum_probs=58.7

Q ss_pred             CCCCceEEEecCCC-CCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCe-eEeC
Q 009860            4 PLQRTKVVIRHLPP-SLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHV-FVNE   81 (523)
Q Consensus         4 p~~r~KVVIRrLPP-~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~v-FvDs   81 (523)
                      +.+..+|-|++||+ .+||+++.+.+.++  |.|.....+..+        .-|||.|.+.++....++.+++.. -++.
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~f--G~V~~v~i~~~k--------g~aFVef~~~~~A~~Ai~~l~~~~~~~~G   81 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPF--GVISNHLILNKI--------NEAFIEMATTEDAQAAVDYYTTTPALVFG   81 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGG--SCEEEEEECSSS--------SCEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhc--CCEEEEEEEcCC--------CEEEEEECCHHHHHHHHHHHcCCCceECC
Confidence            45678999999999 99999999988875  457666655432        249999999999999999888653 1222


Q ss_pred             CCCeeeeEEEecc
Q 009860           82 KGAQFKAIVEYAP   94 (523)
Q Consensus        82 KGne~~A~VEfAP   94 (523)
                          .+..|+||-
T Consensus        82 ----r~l~V~~a~   90 (102)
T 1x4d_A           82 ----KPVRVHLSQ   90 (102)
T ss_dssp             ----EECEEEEEC
T ss_pred             ----cEEEEEECC
Confidence                256788886

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=96.08  E-value=0.031  Score=46.42  Aligned_cols=82  Identities=15%  Similarity=0.031  Sum_probs=53.5

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+..+|.|.+||+.+||+++.+.+...  |.|.....+..+.+.  ..-.-|||.|.+.+++...++.. ++.| +. 
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~--G~i~~v~i~~~~~tg--~~kg~afV~f~~~~~A~~Ai~~~-~~~l-~g-   93 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQF--GEVKECLVMRDPLTK--RSRGFGFVTFMDQAGVDKVLAQS-RHEL-DS-   93 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTT--SCEEEEEECCCTTTC--CCTTCEEEEESSHHHHHHHHHSS-CEEE-TT-
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHcc--CCeEEEEEEECCCCC--CcCcEEEEEECCHHHHHHHHHHC-CCcC-CC-
Confidence            45677899999999999999999999875  345554443322211  12346999999999999988875 3333 22 


Q ss_pred             CCeeeeEEEecc
Q 009860           83 GAQFKAIVEYAP   94 (523)
Q Consensus        83 Gne~~A~VEfAP   94 (523)
                         ....|++|-
T Consensus        94 ---~~l~V~~a~  102 (109)
T 2rs2_A           94 ---KTIDPKVAF  102 (109)
T ss_dssp             ---EEEEEEECC
T ss_pred             ---EEEEEEEcc
Confidence               245677663

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=96.05  E-value=0.016  Score=51.48  Aligned_cols=75  Identities=19%  Similarity=0.275  Sum_probs=58.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCC-ceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFND-RYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~g-kvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      +...|.|++||+.+|++++.+.+...  + .+.....++-.       -.-|||.|.+.++.....+.++|..|-+.   
T Consensus       119 ~~~~l~v~nl~~~~~~~~l~~~f~~~--G~~v~~v~i~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~~g---  186 (198)
T 1qm9_A          119 PSATLHLSNIPPSVSEEDLKVLFSSN--GGVVKGFKFFQKD-------RKMALIQMGSVEEAVQALIDLHNHDLGEN---  186 (198)
T ss_dssp             CCCEEEECCCCTTCCHHHHHHHHHHT--TSCCCEEEESSTT-------SSCEEEECSSHHHHHHHHHHHTSSCCSSC---
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHc--CCCceEEEEEeCC-------CcEEEEEeCCHHHHHHHHHHhcCCccCCC---
Confidence            46789999999999999999999876  4 56655654421       24799999999999999999999988312   


Q ss_pred             eeeeEEEec
Q 009860           85 QFKAIVEYA   93 (523)
Q Consensus        85 e~~A~VEfA   93 (523)
                       ..-.|+||
T Consensus       187 -~~l~v~~a  194 (198)
T 1qm9_A          187 -HHLRVSFS  194 (198)
T ss_dssp             -CSCCEEEE
T ss_pred             -CeEEEEee
Confidence             24556665

>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=96.04  E-value=0.036  Score=47.58  Aligned_cols=81  Identities=17%  Similarity=0.327  Sum_probs=59.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCC-Cc------eeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFN-DR------YNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGH   76 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~-gk------vdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~   76 (523)
                      ..+..+|.|++||+.+|++++.+.+..+-. ..      ++......|+      ...-|||.|.+.+++...++.++|+
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~------~~g~afV~f~~~~~A~~Ai~~lng~  115 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGR------MKGQAFIGLPNEKAAAKALKEANGY  115 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETT------TEEEEEEECSSHHHHHHHHHHHTTB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCC------cccEEEEEeCCHHHHHHHHHHhCCC
Confidence            456789999999999999999999987531 01      1222222222      2457999999999999999999999


Q ss_pred             eeEeCCCCeeeeEEEeccC
Q 009860           77 VFVNEKGAQFKAIVEYAPS   95 (523)
Q Consensus        77 vFvDsKGne~~A~VEfAPY   95 (523)
                      .|.   |  ....|+||-.
T Consensus       116 ~~~---g--~~l~V~~a~~  129 (143)
T 3egn_A          116 VLF---G--KPMVVQFARS  129 (143)
T ss_dssp             EET---T--EECEEEECCC
T ss_pred             EeC---C--cEEEEEECCC
Confidence            983   2  3567888843

>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=96.04  E-value=0.022  Score=52.62  Aligned_cols=75  Identities=19%  Similarity=0.275  Sum_probs=59.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCC-ceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFND-RYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~g-kvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      +..+|.|++||+.+|++++.+.+...  + .|....+++-.       -..|||.|.+.++.....+.++|..|-+.   
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~--G~~i~~v~i~~~~-------~g~afV~f~~~~~A~~Ai~~l~g~~~~~g---  217 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSN--GGVVKGFKFFQKD-------RKMALIQMGSVEEAVQALIDLHNHDLGEN---  217 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTT--SCCEEEEEECSSS-------TTCEEEEESSHHHHHHHHHHHTTCBSSSS---
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHc--CCCeeEEEEEECC-------CcEEEEEECCHHHHHHHHHHHCCCccCCC---
Confidence            35789999999999999999999876  4 67666665521       24799999999999999999999988412   


Q ss_pred             eeeeEEEec
Q 009860           85 QFKAIVEYA   93 (523)
Q Consensus        85 e~~A~VEfA   93 (523)
                       ..-.|+||
T Consensus       218 -~~l~v~~a  225 (229)
T 2adc_A          218 -HHLRVSFS  225 (229)
T ss_dssp             -CBCEEEEC
T ss_pred             -CeEEEEEe
Confidence             24567766

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=96.03  E-value=0.015  Score=52.00  Aligned_cols=81  Identities=20%  Similarity=0.140  Sum_probs=58.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      ...+|.|++||+.+||+++.+.+..+-.-.|....++..+...+  .-.-|||.|.+.+++...++.++|+.|.+     
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~--skGfaFV~f~~~~~A~~Ai~~lng~~~~G-----  126 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQ--SKGYAEVVVASENSVHKLLELLPGKVLNG-----  126 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCC--EEEEEEEEESCHHHHHHHHHHSTTCEETT-----
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCc--cceEEEEEECCHHHHHHHHHHcCCCEECC-----
Confidence            45799999999999999999999765211455555543333221  23459999999999999999999998743     


Q ss_pred             eeeEEEec
Q 009860           86 FKAIVEYA   93 (523)
Q Consensus        86 ~~A~VEfA   93 (523)
                      ....|++|
T Consensus       127 r~l~V~~a  134 (156)
T 3n9u_C          127 EKVDVRPA  134 (156)
T ss_dssp             EECEEEEC
T ss_pred             eEeEEEEc
Confidence            24567766

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=95.99  E-value=0.018  Score=47.97  Aligned_cols=75  Identities=16%  Similarity=0.282  Sum_probs=52.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCC-CCCcceeEEEEecCcccHHHHHHHh---cCCeeE
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSY-KHQRYSRAYVELKKPAGVFEFAELL---NGHVFV   79 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~-Kp~~ySRAYI~Fkn~Edl~~F~d~f---dG~vFv   79 (523)
                      .....+|.|.+||+.+||+++.+.+...  +.|. ...+.-+... .-..-.-|||.|.+.+++...++.+   +|+.|+
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~--G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~~~G~~~~   81 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRF--GPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLYL   81 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTT--CCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEEETTEEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhc--CCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhhcCCcEEE
Confidence            4566899999999999999999999875  3454 3333221111 0112346999999999999888887   787665


Q ss_pred             eC
Q 009860           80 NE   81 (523)
Q Consensus        80 Ds   81 (523)
                      -.
T Consensus        82 ~~   83 (114)
T 2dnl_A           82 CV   83 (114)
T ss_dssp             EE
T ss_pred             ec
Confidence            43

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=95.99  E-value=0.012  Score=49.26  Aligned_cols=78  Identities=19%  Similarity=0.127  Sum_probs=57.0

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF   86 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~   86 (523)
                      ..+|.|++||+.+||+++.+.+..+  +.|........+...  ....-|||.|.+.+++.... .++|+.|.+     .
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 KRSVYVGNVDYGSTAQDLEAHFSSC--GSINRITILCDKFSG--HPKGYAYIEFAERNSVDAAV-AMDETVFRG-----R  105 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTT--SCEEEEEEEEECTTS--SCEEEEEEEESSHHHHHHHH-TTTTCEETT-----E
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEecCCCC--CcccEEEEEECCHHHHHHHH-hcCCCeECC-----e
Confidence            4689999999999999999999875  345444433322211  12457999999999999988 799998832     3


Q ss_pred             eeEEEecc
Q 009860           87 KAIVEYAP   94 (523)
Q Consensus        87 ~A~VEfAP   94 (523)
                      ...|++|-
T Consensus       106 ~l~V~~a~  113 (124)
T 2jwn_A          106 TIKVLPKR  113 (124)
T ss_dssp             ECEEEESS
T ss_pred             EEEEEECC
Confidence            56778774

>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=95.93  E-value=0.018  Score=53.26  Aligned_cols=84  Identities=10%  Similarity=0.097  Sum_probs=62.3

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      +|..-++|.|++||+.+||+++.+.+..+  |.|.....+..     . .---|||.|.+.++...-++.++|+.|.+. 
T Consensus        42 ~ps~vl~l~VgNL~~~vted~L~~~Fs~f--G~V~~V~i~~k-----~-~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~-  112 (164)
T 1sjr_A           42 GQSPVLRIIVENLFYPVTLDVLHQIFSKF--GTVLKIITFTK-----N-NQFQALLQYADPVSAQHAKLSLDGQNIYNA-  112 (164)
T ss_dssp             CCCCEEEEEECSCCSCCCHHHHHHHHHHH--SCEEEEEEEES-----S-SCEEEEEEESCHHHHHHHHHHSTTBCSSSS-
T ss_pred             CCCceEEEEEeCcCCCCCHHHHHHHHHhc--CCEEEEEEEeC-----C-CCCEEEEEECCHHHHHHHHHHhCCCEecCC-
Confidence            45566888999999999999999999876  34544332211     1 123599999999999999999999998753 


Q ss_pred             CCeeeeEEEeccCCC
Q 009860           83 GAQFKAIVEYAPSQR   97 (523)
Q Consensus        83 Gne~~A~VEfAPYQK   97 (523)
                        ...-.|+||--..
T Consensus       113 --g~~L~V~~Ak~~~  125 (164)
T 1sjr_A          113 --CCTLRIDFSKLTS  125 (164)
T ss_dssp             --CSCEEEEECSSSS
T ss_pred             --CcEEEEEEecCCc
Confidence              2256889885443

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=95.87  E-value=0.0029  Score=51.14  Aligned_cols=78  Identities=19%  Similarity=0.216  Sum_probs=53.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCC--CceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFN--DRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~--gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs   81 (523)
                      +.+..+|.|.+||+.+||+++.+.+...-.  ..+- ..-..|.      ...-|||.|.+.+++...++ ++|+.|.+ 
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~-~~~~~g~------~~g~afV~f~~~~~a~~A~~-l~g~~~~g-   84 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGT------NRKFGYVDFESAEDLEKALE-LTGLKVFG-   84 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCC-CEEEEET------TTTEEEEEESSHHHHHHHHH-GGGCCBTT-
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEE-ecCCCCC------cCcEEEEEECCHHHHHHHHh-cCCcEECC-
Confidence            346789999999999999999888876421  1110 0000111      12359999999999999998 99998752 


Q ss_pred             CCCeeeeEEEecc
Q 009860           82 KGAQFKAIVEYAP   94 (523)
Q Consensus        82 KGne~~A~VEfAP   94 (523)
                          ....|++|-
T Consensus        85 ----~~l~V~~a~   93 (101)
T 1fj7_A           85 ----NEIKLEKPK   93 (101)
T ss_dssp             ----BCCEEECCS
T ss_pred             ----cEEEEEEcC
Confidence                245677763

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=95.83  E-value=0.028  Score=46.93  Aligned_cols=72  Identities=14%  Similarity=0.210  Sum_probs=53.1

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      ...+..+|-|.+||+.+||+++.+.+.+.  |.|.....+..+. .  ..-.-|||.|.+.+++...++ .+++.|-+
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~--G~v~~v~i~~d~~-g--~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~g   78 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDK--GQVLNIQMRRTLH-K--AFKGSIFVVFDSIESAKKFVE-TPGQKYKE   78 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTS--SCEEEEEEECCCT-T--SCCCEEEEEESSHHHHHHHHT-SSCCCCTT
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhc--CCEEEEEEEECCC-C--CCccEEEEEECCHHHHHHHHH-cCCCEECC
Confidence            35567899999999999999999999874  3565544443222 1  112359999999999999888 78887643

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=95.81  E-value=0.024  Score=51.77  Aligned_cols=72  Identities=15%  Similarity=0.166  Sum_probs=52.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV   79 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv   79 (523)
                      ..+...|-|++||+.+||+++.+.+...  |.|.....+.-+.+.  ....-|||.|.+.+++..-++.+++..|.
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~--G~I~~v~i~~d~~tg--~~~G~afV~F~~~~~A~~Ai~~~~~~~~~   83 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPA--GPILSIRVCRDMITR--RSLGYAYVNFQQPADAERALDTMNFDVIK   83 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTC--CEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhh--CCEEEEEEecccCCC--CccccccceeCCHHHHHHHHHHhhhhhcC
Confidence            3456789999999999999999999875  355554443322221  12346999999999999999999998764

>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=95.78  E-value=0.032  Score=52.36  Aligned_cols=73  Identities=19%  Similarity=0.294  Sum_probs=56.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      +..+|.|++||+.+||+++.+.+...  | +.....  |+.      -.-|||.|.+.++.....+.++|..|.+     
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~--G-i~~~~~--~~~------~g~afV~f~~~~~A~~A~~~l~~~~~~g-----   84 (284)
T 3smz_A           21 NRRKILIRGLPGDVTNQEVHDLLSDY--E-LKYCFV--DKY------KGTAFVTLLNGEQAEAAINAFHQSRLRE-----   84 (284)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHTTTS--C-EEEEEE--ETT------TTEEEEEESSHHHHHHHHHHHTTCEETT-----
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHc--C-CEEEEE--ecC------CCEEEEEeCCHHHHHHHHHHcCCCeeCC-----
Confidence            56889999999999999999998875  3 444333  221      2369999999999999999999998743     


Q ss_pred             eeeEEEecc
Q 009860           86 FKAIVEYAP   94 (523)
Q Consensus        86 ~~A~VEfAP   94 (523)
                      ....|+++|
T Consensus        85 ~~i~v~~~~   93 (284)
T 3smz_A           85 RELSVQLQP   93 (284)
T ss_dssp             EECEEEECC
T ss_pred             eEEEEEecC
Confidence            355677765

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=95.74  E-value=0.033  Score=45.73  Aligned_cols=77  Identities=13%  Similarity=0.202  Sum_probs=56.3

Q ss_pred             CceEEEecCCCCC------CHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            7 RTKVVIRHLPPSL------SQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         7 r~KVVIRrLPP~L------TEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      ..+|.|.+||+..      |++++.+.+...  |.|..... + ....  ..-.-|||.|.+.+++..-++.++|+.|..
T Consensus        15 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~--G~v~~v~i-~-~~~g--~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g   88 (105)
T 2nlw_A           15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKF--GKITNDFY-P-EEDG--KTKGYIFLEYASPAHAVDAVKNADGYKLDK   88 (105)
T ss_dssp             CSEEEEESCCCCCTTTTTHHHHHHHHHHGGG--SCEEEEEC-C-CBTT--BSCCEEEEEECSSSHHHHHHHHCSSEECST
T ss_pred             CCEEEEeCCCcchhhhhHHHHHHHHHHHhcC--CCEEEEEe-e-CCCC--CeeeEEEEEECCHHHHHHHHHHhCCcccCC
Confidence            5799999999999      789999988875  34555443 3 2111  123469999999999999999999988743


Q ss_pred             CCCCeeeeEEEec
Q 009860           81 EKGAQFKAIVEYA   93 (523)
Q Consensus        81 sKGne~~A~VEfA   93 (523)
                      .    ..-.|++|
T Consensus        89 ~----~~l~V~~a   97 (105)
T 2nlw_A           89 Q----HTFRVNLF   97 (105)
T ss_dssp             T----CEEEEECS
T ss_pred             C----ceEEEEEc
Confidence            2    14566666

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=95.73  E-value=0.017  Score=48.77  Aligned_cols=71  Identities=21%  Similarity=0.127  Sum_probs=49.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCC-CceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFN-DRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~-gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      +.+..+|.|++||+..||+++.+.+..+-. +.|.....+..+. .  ..-.-|||.|.+.+++...++ ++++.|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g--~~~G~afV~F~~~~~a~~Al~-~~g~~~   85 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-G--RQSGEAFVELESEDDVKLALK-KDRESM   85 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-S--CEEEEEEEEBSSHHHHHHHGG-GTTEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-C--CCCeEEEEEECCHHHHHHHHh-cCCCeE
Confidence            456788999999999999999999876421 1122222222221 1  123469999999999999888 888665

>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=95.68  E-value=0.036  Score=45.44  Aligned_cols=69  Identities=12%  Similarity=0.094  Sum_probs=49.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeE-EEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNW-FCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdw-fyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      +.+..+|.|++||+..||+++.+.+...  +.|.. ...+. +...  ..-.-|||.|.+.+++...++. +++.|
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~--G~v~~~v~i~~-~~~g--~~~G~afV~F~~~~~a~~A~~~-~~~~~   81 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGL--EIVPNGMTLPV-DFQG--RSTGEAFVQFASQEIAEKALKK-HKERI   81 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTC--CEEEEEEECCB-CSSS--CBCSEEEEEESSHHHHHHHHTT-TTCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCcceeEEEEE-CCCC--CcceEEEEEECCHHHHHHHHHh-Ccchh
Confidence            4567899999999999999999998874  34433 22221 1111  1124699999999999999887 77665

>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=95.61  E-value=0.028  Score=49.18  Aligned_cols=81  Identities=14%  Similarity=0.129  Sum_probs=55.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      +..+|.|++||+.+|++++.+.+...  +.|.....+......  ..-.-|||.|.+.+++....+. +++.|-+     
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~g--~~~g~afV~F~~~~~A~~A~~~-~~~~~~G-----  172 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQY--GKIEVIEIMTDRGSG--KKRGFAFVTFDDHDSVDKIVIQ-KYHTVNG-----  172 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTT--SCEEEEEEEECTTTC--CEEEEEEEEESSHHHHHHHHHC-SCCEETT-----
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcC--CCeEEEEEeecCCCC--CccceEEEEECCHHHHHHHHHh-CCcEECC-----
Confidence            44789999999999999999999864  456665555432221  1123599999999999888776 6665532     


Q ss_pred             eeeEEEeccCC
Q 009860           86 FKAIVEYAPSQ   96 (523)
Q Consensus        86 ~~A~VEfAPYQ   96 (523)
                      ....|.+|.-.
T Consensus       173 ~~i~v~~a~~k  183 (196)
T 1l3k_A          173 HNCEVRKALSK  183 (196)
T ss_dssp             EECEEEECC--
T ss_pred             EEEEEEecCCh
Confidence            24667776433

>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=95.57  E-value=0.037  Score=52.18  Aligned_cols=76  Identities=14%  Similarity=0.220  Sum_probs=58.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+..+|.|++||+.+||+++.+.+...  +.|........        -.-|||.|.+.+++......++|..|.+   
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~--G~i~~v~i~~~--------kg~afV~f~~~~~A~~A~~~l~g~~i~g---   85 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERY--GEPSEVFINRD--------RGFGFIRLESRTLAEIAKAELDGTILKS---   85 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGG--CCCSEEEEETT--------TTEEEEECSSHHHHHHHHHHHTTCEETT---
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhc--CCEEEEEEeCC--------CcEEEEEECCHHHHHHHHHHcCCcEECC---
Confidence            4566899999999999999999999875  33444433211        2469999999999999999999998732   


Q ss_pred             CeeeeEEEecc
Q 009860           84 AQFKAIVEYAP   94 (523)
Q Consensus        84 ne~~A~VEfAP   94 (523)
                        ....|++|.
T Consensus        86 --~~l~v~~a~   94 (261)
T 3sde_A           86 --RPLRIRFAT   94 (261)
T ss_dssp             --EECEEEECC
T ss_pred             --ceeEeeecc
Confidence              355677764

>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=95.53  E-value=0.019  Score=47.36  Aligned_cols=72  Identities=21%  Similarity=0.162  Sum_probs=50.3

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCC-CceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFN-DRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~-gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      ++....+|.|++||+..||+++.+.+...-. +.|.....+..+. .  ..-.-|||.|.+.+++...++ +++..|
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g--~~~G~afV~F~~~~~a~~Al~-~~~~~~   79 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-G--KRRGDALIEMESEQDVQKALE-KHRMYM   79 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-S--TTCSEEEEEBSSHHHHHHHHT-TTTCCS
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-C--CEeeEEEEEECCHHHHHHHHH-hCccee
Confidence            3567889999999999999999998886421 1133333332221 1  112469999999999999888 787665

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=95.52  E-value=0.02  Score=46.28  Aligned_cols=67  Identities=9%  Similarity=0.147  Sum_probs=49.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      .+..+|.|.+||+.+|++++.+.+...  +.|........+ .  ...-.-|||.|.+.+++....+  +++.|
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~-~--g~~~g~afV~f~~~~~a~~Ai~--~~~~~   73 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARY--GSVKEVKIITDR-T--GVSKGYGFVSFYNDVDVQKIVE--SQINF   73 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGG--SCEEEEEEEECT-T--SCEEEEEEEEESSCCCHHHHTT--CCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhC--CCeEEEEEEECC-C--CCccceEEEEECCHHHHHHHHh--CCCeE
Confidence            345789999999999999999999875  345555544433 2  1223569999999999998888  55544

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=95.50  E-value=0.098  Score=46.55  Aligned_cols=87  Identities=10%  Similarity=0.092  Sum_probs=63.4

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009860            2 KEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         2 k~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs   81 (523)
                      .+|..-++|.|++||..+||+++.+.+..+-  .|.-..-+. +    . .---|||.|.+.++...-++.++|..|.+.
T Consensus        23 ~~ps~VL~I~V~NL~~~vte~~L~~lFs~yG--~V~~V~i~~-~----~-~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~   94 (130)
T 3zzy_A           23 AGQSPVLRIIVENLFYPVTLDVLHQIFSKFG--TVLKIITFT-K----N-NQFQALLQYADPVSAQHAKLSLDGQNIYNA   94 (130)
T ss_dssp             --CCSEEEEEEESCCSCCCHHHHHHHHTTSS--CEEEEEEEE-E----T-TEEEEEEEESCHHHHHHHHHHHTTCEEETT
T ss_pred             CCCCceEEEEECCCCCCCCHHHHHHHHhCcC--CEEEEEEEc-C----C-CCcEEEEEECCHHHHHHHHHHcCCCeecCC
Confidence            3567779999999999999999999998752  343322111 1    1 111399999999999999999999999872


Q ss_pred             CCCeeeeEEEeccCCCCC
Q 009860           82 KGAQFKAIVEYAPSQRVP   99 (523)
Q Consensus        82 KGne~~A~VEfAPYQKvP   99 (523)
                         .-.-.|+||--..+.
T Consensus        95 ---~~~LrI~~ak~~~l~  109 (130)
T 3zzy_A           95 ---CCTLRIDFSKLTSLN  109 (130)
T ss_dssp             ---EEEEEEEECSCSSCC
T ss_pred             ---CcEEEEEecCCCcee
Confidence               346689999655443

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=95.45  E-value=0.022  Score=48.62  Aligned_cols=79  Identities=14%  Similarity=0.195  Sum_probs=54.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeE--EEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCC----ee
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNW--FCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGH----VF   78 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdw--fyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~----vF   78 (523)
                      .+..+|.|++||+.+||+++.+.+..+-  .|..  ...+..+...  ..-.-|||.|.+. +....++.++|+    .|
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G--~v~~~~v~i~~d~~tg--~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~   95 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYA--VLSSSNVRVIKDKQTQ--LNRGFAFIQLSTI-EAAQLLQILQALHPPLTI   95 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGC--CCCTTTEECCBCSSSS--SBCSCEEEECCHH-HHHHHHHHHTTCCCSCCG
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhC--CcceeeEEEEEcCCCC--CcceEEEEEECCH-HHHHHHHHhcCCCCCccC
Confidence            4678999999999999999999998752  2321  2222222111  1124599999999 999999999998    54


Q ss_pred             EeCCCCeeeeEEEec
Q 009860           79 VNEKGAQFKAIVEYA   93 (523)
Q Consensus        79 vDsKGne~~A~VEfA   93 (523)
                      ...     ...|+||
T Consensus        96 ~gr-----~l~V~~a  105 (131)
T 2m2b_A           96 DGK-----TINVEFA  105 (131)
T ss_dssp             GGC-----CCCCEEC
T ss_pred             CCE-----EEEEEEC
Confidence            322     3456666

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=95.42  E-value=0.029  Score=43.69  Aligned_cols=67  Identities=13%  Similarity=0.238  Sum_probs=50.2

Q ss_pred             ceEEEecCCCCC------CHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            8 TKVVIRHLPPSL------SQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         8 ~KVVIRrLPP~L------TEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      .+|.|.+||+..      ||+++.+.+...  +.|..... + +...  ..-.-|||.|.+.+++....+.++|+.|..
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~--G~i~~v~i-~-~~~g--~~~g~afV~f~~~~~A~~Ai~~lng~~~~g   74 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKF--GKITNDFY-P-EEDG--KTKGYIFLEYASPAHAVDAVKNADGYKLDK   74 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTT--CCEEEEEC-C-CBTT--BCCCEEEEEESSHHHHHHHHTTSSSCCCSS
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhc--CCeEEEEe-c-CCCC--cEeEEEEEEECCHHHHHHHHHHhcCcccCC
Confidence            579999999999      789998888764  34554443 3 1111  123469999999999999999999988743

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.41  E-value=0.031  Score=47.42  Aligned_cols=66  Identities=18%  Similarity=0.213  Sum_probs=48.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      +..+|.|++||+..||+++.+.+.+.   .|.....+..+. . . .-.-|||.|.+.+++...+ .++++.|
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~---~v~~v~i~~d~~-g-~-~~G~afV~F~~~~~a~~Al-~~~~~~~   80 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL---RVDAVHLLKDHV-G-R-NNGNGLVKFLSPQDTFEAL-KRNRMLM   80 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS---CCCEEEECCCTT-C-C-CCSEEEEECSSHHHHHHHH-HTTTEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC---CeeEEEEEECCC-C-C-CCeEEEEEECCHHHHHHHH-hcCCCeE
Confidence            35799999999999999999999886   244444443221 1 1 1246999999999999887 5787655

>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=95.39  E-value=0.039  Score=45.61  Aligned_cols=70  Identities=16%  Similarity=0.120  Sum_probs=49.4

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV   79 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv   79 (523)
                      .+....+|.|++||+.+||+++.+.+.+.-  .+ ....+..+ ..  ..---|||.|.+.+++...++ .+++.|-
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G--~~-~v~i~~d~-~g--~~~G~afV~F~~~~~a~~Al~-~~~~~~~   80 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN--PM-RVHIEIGP-DG--RVTGEADVEFATHEDAVAAMA-KDKANMQ   80 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC--CS-EEEEEESS-SS--CEEEEEEEECSSSHHHHHHHT-TSSCCSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcC--ce-EEEEEECC-CC--CEeeEEEEEECCHHHHHHHHH-hCCCeEC
Confidence            356778999999999999999999888753  22 22222222 11  112359999999999998885 5776653

>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=95.38  E-value=0.078  Score=49.74  Aligned_cols=80  Identities=16%  Similarity=0.198  Sum_probs=60.3

Q ss_pred             CCCceEEEecCCCCC-CHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            5 LQRTKVVIRHLPPSL-SQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         5 ~~r~KVVIRrLPP~L-TEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      .+...|.|++||+.+ |++++.+.+...  +.|..........   .....-|||.|.+.++.......++|+.|   .|
T Consensus       182 ~~~~~l~v~nlp~~~~~~~~l~~~f~~~--G~i~~v~i~~~~~---g~~~g~afV~f~~~~~A~~A~~~l~g~~~---~g  253 (284)
T 3smz_A          182 LHSRCLCVDRLPPGFNDVDALCRALSAV--HSPTFCQLACGQD---GQLKGFAVLEYETAEMAEEAQQQADGLSL---GG  253 (284)
T ss_dssp             TSCSEEEEECCCTTCCCHHHHHHHTCSS--SCCSEEEEEECSS---CCEEEEEEEECSSHHHHHHHHHHHTTCEE---TT
T ss_pred             CCccEEEEecCCcccCCHHHHHHHhhCC--CCeEEEEEEECCC---CCcccEEEEEeCCHHHHHHHHHHhCCCcc---CC
Confidence            456789999999997 999999999875  3455444443321   12345799999999999999999999998   22


Q ss_pred             CeeeeEEEecc
Q 009860           84 AQFKAIVEYAP   94 (523)
Q Consensus        84 ne~~A~VEfAP   94 (523)
                        ..-.|.||.
T Consensus       254 --~~l~v~~a~  262 (284)
T 3smz_A          254 --SHLRVSFCA  262 (284)
T ss_dssp             --EECEEEECC
T ss_pred             --eEEEEEEec
Confidence              266788873

>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=95.28  E-value=0.053  Score=50.17  Aligned_cols=81  Identities=14%  Similarity=0.160  Sum_probs=60.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCce--eEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRY--NWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkv--dwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      +..+|.|++||+.+||+++.+.+.+.-  .|  .-...++.+ . +  ...-|||.|.+.++...-+..++|+.+... +
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G--~v~~~~v~~~~~~-~-~--~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~-~  194 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELG--VKRPTSVKVFSGK-S-E--RSSSGLLEWDSKSDALETLGFLNHYQMKNP-N  194 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHT--CCCCSEEEECSCC-S-S--SSEEEEEECSSHHHHHHHHHHHTTCEECCS-S
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcC--CcceEEEEEEcCC-C-C--CceEEEEEeCCHHHHHHHHHHhCCCCccCC-C
Confidence            345799999999999999999998753  23  334444443 1 1  126899999999999999999999987544 4


Q ss_pred             CeeeeEEEec
Q 009860           84 AQFKAIVEYA   93 (523)
Q Consensus        84 ne~~A~VEfA   93 (523)
                      ..++-+|.||
T Consensus       195 ~~~p~~vk~~  204 (205)
T 3tyt_A          195 GPYPYTLKLC  204 (205)
T ss_dssp             SSSCEECEEE
T ss_pred             CCcceEEEec
Confidence            4666666665

>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=95.27  E-value=0.033  Score=48.17  Aligned_cols=77  Identities=13%  Similarity=0.193  Sum_probs=56.0

Q ss_pred             CCCCceEEEecCCCC-CCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCe-eEeC
Q 009860            4 PLQRTKVVIRHLPPS-LSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHV-FVNE   81 (523)
Q Consensus         4 p~~r~KVVIRrLPP~-LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~v-FvDs   81 (523)
                      ..+..+|-|++||+. +||+++.+.+.++  +.|.....+..        -.-|||.|.+.++....++.+++.. .++.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~f--G~V~~v~i~~~--------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~G   91 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPY--GKIKNYILMRM--------KSQAFIEMETREDAMAMVDHCLKKALWFQG   91 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTT--SCCSEEEEETT--------TTEEEEECSSHHHHHHHHHHHHHSCCCSSS
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhc--CCEEEEEEecC--------CCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            456789999999998 9999999888875  34555555432        1369999999999999998886532 1222


Q ss_pred             CCCeeeeEEEecc
Q 009860           82 KGAQFKAIVEYAP   94 (523)
Q Consensus        82 KGne~~A~VEfAP   94 (523)
                      +    ...|+||-
T Consensus        92 r----~l~V~~a~  100 (112)
T 1x4f_A           92 R----CVKVDLSE  100 (112)
T ss_dssp             S----CCEEEEEC
T ss_pred             E----EEEEEECc
Confidence            2    46788873

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=95.16  E-value=0.02  Score=46.82  Aligned_cols=81  Identities=11%  Similarity=0.107  Sum_probs=56.8

Q ss_pred             CCCceEEEecCCC------CCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            5 LQRTKVVIRHLPP------SLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         5 ~~r~KVVIRrLPP------~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      .....|.|.+||+      .+|++++.+.+...  +.|........+.+.  ..-.-|||.|.+.+++...++.++|+.|
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~--G~i~~v~i~~d~~tg--~~kG~afV~f~~~~~A~~Ai~~lng~~~   79 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKA--GKVVNMEFPIDEATG--KTKGFLFVECGSMNDAKKIIKSFHGKRL   79 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTT--SCEEEEECCEETTTT--EECSEEEEEESSHHHHHHHHHHHTTCBS
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhc--CCEeEEEEEEcCCCC--ccceEEEEEECCHHHHHHHHHHhCCccc
Confidence            3457899999999      99999999999874  345543322111111  1124599999999999999999999988


Q ss_pred             EeCCCCeeeeEEEec
Q 009860           79 VNEKGAQFKAIVEYA   93 (523)
Q Consensus        79 vDsKGne~~A~VEfA   93 (523)
                      ...+    .-.|++|
T Consensus        80 ~g~r----~l~V~~a   90 (100)
T 3ns6_A           80 DLKH----RLFLYTM   90 (100)
T ss_dssp             SSSC----BCEEEES
T ss_pred             CCCe----EEEEEEC
Confidence            5422    4455554

>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=95.14  E-value=0.058  Score=50.80  Aligned_cols=83  Identities=16%  Similarity=0.191  Sum_probs=59.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      ....+|.|++||+.+|++++.+.+...- ..|....++.-..   ...-.-|||.|.+.+++....+.++|+.|.+    
T Consensus       115 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G-~~i~~v~i~~~~~---~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----  186 (292)
T 2ghp_A          115 LTECTLWMTNFPPSYTQRNIRDLLQDIN-VVALSIRLPSLRF---NTSRRFAYIDVTSKEDARYCVEKLNGLKIEG----  186 (292)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHHTT-CCCCEEECC----------CCEEEEECSSHHHHHHHHHHHTTCEETT----
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhC-CCeEEEEEEeCCC---CCcceEEEEEECCHHHHHHHHHHhCCCEeCC----
Confidence            3567899999999999999999998752 1455444432221   1123469999999999999999999998832    


Q ss_pred             eeeeEEEeccCC
Q 009860           85 QFKAIVEYAPSQ   96 (523)
Q Consensus        85 e~~A~VEfAPYQ   96 (523)
                       ....|++|.-+
T Consensus       187 -~~l~v~~a~~~  197 (292)
T 2ghp_A          187 -YTLVTKVSNPL  197 (292)
T ss_dssp             -EECEEEECCCC
T ss_pred             -cEEEEEECCCC
Confidence             45677877533

>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=95.14  E-value=0.038  Score=47.16  Aligned_cols=77  Identities=13%  Similarity=0.088  Sum_probs=53.4

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF   86 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~   86 (523)
                      ..+|.|++||+.+|++++.+.+...  +.|........+...  ..-.-|||.|.+.+++....+ .+|..|-+     .
T Consensus        87 ~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~~~i~~~~~~g--~~~g~afV~f~~~~~a~~A~~-~~~~~~~g-----~  156 (167)
T 2cjk_A           87 TGKIFVGGIGPDVRPKEFEEFFSQW--GTIIDAQLMLDKDTG--QSRGFGFVTYDSADAVDRVCQ-NKFIDFKD-----R  156 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTT--SCCSEEECCCSSSSS--TTSEEEEEEESSHHHHHHHHH-CSEECSSS-----S
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhC--ccEEEEEEEEcCCCC--ccceEEEEEECCHHHHHHHHh-CCCEEeCC-----e
Confidence            4589999999999999999999875  345555544332221  122469999999999988877 56655532     2


Q ss_pred             eeEEEec
Q 009860           87 KAIVEYA   93 (523)
Q Consensus        87 ~A~VEfA   93 (523)
                      ...|+||
T Consensus       157 ~i~V~~a  163 (167)
T 2cjk_A          157 KIEIKRA  163 (167)
T ss_dssp             CEEEEEC
T ss_pred             EEEEeec
Confidence            4566665

>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=95.12  E-value=0.045  Score=51.58  Aligned_cols=82  Identities=17%  Similarity=0.187  Sum_probs=56.4

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+...|.|++||+.+||+++.+.+...  |.|.....+.....    ...-|||.|.+.+++....+ ++|..|.+  
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~----~~g~afV~f~~~~~A~~A~~-~~~~~~~g--  107 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHC--GPIIHVDVADSLKK----NFRFARIEFARYDGALAAIT-KTHKVVGQ--  107 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGG--SCEEEEEEEECTTS----SSEEEEEEESSHHHHHHHHT-TTTCEETT--
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEECCCC----CcEEEEEEECCHHHHHHHHH-hCCcEeCC--
Confidence            45668899999999999999999999875  34544444432211    13689999999999999985 88887733  


Q ss_pred             CCeeeeEEEeccCC
Q 009860           83 GAQFKAIVEYAPSQ   96 (523)
Q Consensus        83 Gne~~A~VEfAPYQ   96 (523)
                         ....|++++..
T Consensus       108 ---~~i~v~~~~~~  118 (292)
T 2ghp_A          108 ---NEIIVSHLTEC  118 (292)
T ss_dssp             ---EECEEEECCSC
T ss_pred             ---cEEEEEECCCC
Confidence               24566766433

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=95.10  E-value=0.15  Score=40.89  Aligned_cols=76  Identities=14%  Similarity=0.106  Sum_probs=57.5

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+.+..+|.|.+|  .+||+++.+.+...  +.|......        ..-..|||.|.+.+++...++.++|+.|.   
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~--G~i~~v~i~--------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~---   75 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPF--GNIIDLSMD--------PPRNCAFVTYEKMESADQAVAELNGTQVE---   75 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTT--SCEEEEEEE--------TTTTEEEEEESSHHHHHHHHHHTTTEEET---
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhC--CCEEEEEec--------CCCCEEEEEECCHHHHHHHHHHhCCCeEC---
Confidence            3556789999997  99999999999875  345444332        11236999999999999999999999882   


Q ss_pred             CCeeeeEEEeccC
Q 009860           83 GAQFKAIVEYAPS   95 (523)
Q Consensus        83 Gne~~A~VEfAPY   95 (523)
                      |  ....|+||--
T Consensus        76 g--~~l~v~~a~~   86 (97)
T 1x5p_A           76 S--VQLKVNIARK   86 (97)
T ss_dssp             T--EEEEEECCSS
T ss_pred             C--eEEEEEECCC
Confidence            2  3567888743

>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=95.03  E-value=0.059  Score=45.40  Aligned_cols=79  Identities=13%  Similarity=0.130  Sum_probs=53.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCC-CceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFN-DRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~-gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      +.+..+|.|++||+.+||+++.+.+..+-. ..+.......   .  -..-.-|||.|.+.+++...++ ++++.|-+- 
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~---~--g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr-   94 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGP---N--GKATGEGFVEFRNEADYKAALC-RHKQYMGNR-   94 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECT---T--SSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTS-
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECC---C--CCCCeEEEEEECCHHHHHHHHH-hCCCeECCc-
Confidence            456689999999999999999998886421 1111222111   1  1113469999999999999988 888776332 


Q ss_pred             CCeeeeEEEec
Q 009860           83 GAQFKAIVEYA   93 (523)
Q Consensus        83 Gne~~A~VEfA   93 (523)
                          ...|++|
T Consensus        95 ----~i~V~~a  101 (124)
T 1wel_A           95 ----FIQVHPI  101 (124)
T ss_dssp             ----CBEEEEE
T ss_pred             ----EEEEEEC
Confidence                3455555

>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=94.90  E-value=0.034  Score=49.08  Aligned_cols=71  Identities=20%  Similarity=0.096  Sum_probs=49.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCC-ceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFND-RYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~g-kvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      +.+.++|.|++||+..||+++.+.+...-.- .|.....+..+. .  ..-.-|||.|.+.+++..-++ ++++.|
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g--~srG~aFV~F~~~e~a~~Al~-~~g~~l  112 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-G--RQSGEAFVELGSEDDVKMALK-KDRESM  112 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-S--CEEEEEEEECSSHHHHHHHHT-TTEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-C--CCCeEEEEEECCHHHHHHHHh-cCCCEE
Confidence            4567899999999999999999999875210 022222222211 1  113369999999999999888 888665

>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=94.85  E-value=0.092  Score=46.01  Aligned_cols=69  Identities=12%  Similarity=0.085  Sum_probs=48.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCcee-EEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYN-WFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvd-wfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      +.+..+|.|++||+..||+++.+.+.+.  +-+. ....+..+. .+  .-.-|||.|.+.+++...++. ++..|
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~--~i~~~~v~i~~d~~-Gr--srGfaFV~F~~~e~A~~Al~~-~~~~l  108 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL--EIVPNGITLPVDPE-GK--ITGEAFVQFASQELAEKALGK-HKERI  108 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS--CEEEEEEECCCCSS-SS--SCSEEEEEESSTTHHHHHHTT-TTCCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC--CceeeEEEEEECCC-CC--CceEEEEEECCHHHHHHHHHH-CCCEE
Confidence            4567899999999999999999999986  2221 333322221 11  124699999999999988875 55443

>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=94.78  E-value=0.16  Score=40.80  Aligned_cols=75  Identities=13%  Similarity=0.107  Sum_probs=49.3

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      ++.+..+|.|.+||+.+||+++.+.+...  |.|.....+. +      .-.-|||.|.+.+++.    .+++..|.- +
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~--G~i~~v~i~~-~------srGfaFV~F~~~~~A~----~~~~~~~~~-~   72 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQY--GEVVDVFIPK-P------FRAFAFVTFADDKVAQ----SLCGEDLII-K   72 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTT--SCEEEEECCS-S------CCSEEEEEESCHHHHH----HHTTCEEEE-T
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcc--CCEEEEEEee-C------CCCEEEEEECCHHHHH----HHcCCCccc-C
Confidence            46778999999999999999999999875  4565543322 1      1236999999999876    466664431 1


Q ss_pred             CCeeeeEEEec
Q 009860           83 GAQFKAIVEYA   93 (523)
Q Consensus        83 Gne~~A~VEfA   93 (523)
                        -....|.+|
T Consensus        73 --g~~v~v~~a   81 (89)
T 3d2w_A           73 --GISVHISNA   81 (89)
T ss_dssp             --TEEEEEEEC
T ss_pred             --CEEEEEEEc
Confidence              234556655

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=94.71  E-value=0.079  Score=46.87  Aligned_cols=60  Identities=18%  Similarity=0.227  Sum_probs=52.1

Q ss_pred             CCCceEEEecCCCC-CCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecC-cccHHHHHHHhc
Q 009860            5 LQRTKVVIRHLPPS-LSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKK-PAGVFEFAELLN   74 (523)
Q Consensus         5 ~~r~KVVIRrLPP~-LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn-~Edl~~F~d~fd   74 (523)
                      ..++-|.|..||+. .|+++|.+.+..+  +.|.|..|+.|...        |||.|.+ .++...++..++
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~--G~V~~Vd~~~g~~t--------gfVrf~~~~~~A~~av~~ln   77 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNH--GEIKWIDFVRGAKE--------GIILFKEKAKEALGKAKDAN   77 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSS--CCEEEEECCTTCSE--------EEEEESSCHHHHHHHHHHTT
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhc--CCEEEEEEecCCCE--------EEEEECCChHHHHHHHHHhh
Confidence            46788999999999 9999999999974  47999999988763        9999999 688888888763

>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=94.66  E-value=0.074  Score=45.55  Aligned_cols=75  Identities=8%  Similarity=0.206  Sum_probs=53.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccC--CC-------ceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCC
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHF--ND-------RYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGH   76 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~--~g-------kvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~   76 (523)
                      +..+|.|++||+.+||+++.+.+....  .+       .+........        -.-|||.|.+.+++.... .++|.
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~--------~g~afV~f~~~~~A~~A~-~~~~~   73 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD--------KNFAFLEFRSVDETTQAM-AFDGI   73 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETT--------TTEEEEEESSHHHHHHHG-GGTTC
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCC--------CCEEEEEeCCHHHHHHHH-HhCCc
Confidence            457899999999999999999887751  11       3332222111        357999999999999998 89998


Q ss_pred             eeEeCCCCeeeeEEEecc
Q 009860           77 VFVNEKGAQFKAIVEYAP   94 (523)
Q Consensus        77 vFvDsKGne~~A~VEfAP   94 (523)
                      .|.+     ....|+++.
T Consensus        74 ~~~g-----~~i~v~~~~   86 (172)
T 2g4b_A           74 IFQG-----QSLKIRRPH   86 (172)
T ss_dssp             EETT-----EECEEECCS
T ss_pred             EecC-----ceeeecCCc
Confidence            8732     244566543

>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=94.51  E-value=0.035  Score=47.97  Aligned_cols=80  Identities=20%  Similarity=0.245  Sum_probs=56.0

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCC--C-ceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFN--D-RYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV   79 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~--g-kvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv   79 (523)
                      .+.+..+|.|++||+.+||+++.+.+.....  + .+.  ....|+      .-.-|||.|.+.+++....+ ++|..|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~--~~~~~~------~~g~afV~f~~~~~a~~A~~-l~g~~~~   79 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV--DVRTGT------NRKFGYVDFESAEDLEKALE-LTGLKVF   79 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCC--EEEEET------TTTEEEEEESSHHHHHHHHH-GGGEEET
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEE--ECCCCc------cccEEEEEECCHHHHHHHHh-cCCCEeC
Confidence            5778899999999999999998887766531  1 111  111111      13479999999999999884 9988776


Q ss_pred             eCCCCeeeeEEEeccCC
Q 009860           80 NEKGAQFKAIVEYAPSQ   96 (523)
Q Consensus        80 DsKGne~~A~VEfAPYQ   96 (523)
                      +     ....|++|.-.
T Consensus        80 g-----~~l~v~~~~~~   91 (175)
T 1fje_B           80 G-----NEIKLEKPKGR   91 (175)
T ss_dssp             T-----EEEEEECCCCS
T ss_pred             C-----eEEEEecCCCc
Confidence            2     24567776543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=93.54  E-value=0.0065  Score=50.53  Aligned_cols=82  Identities=11%  Similarity=0.184  Sum_probs=55.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeE--------EEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNW--------FCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNG   75 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdw--------fyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG   75 (523)
                      ..+..+|.|.+||+.+|++++.+.+..+-  .|..        ...+..+..  .....-|||.|.+.+++...++.++|
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G--~i~~~~~~~~~~v~i~~~~~~--g~~~g~afV~f~~~~~A~~Ai~~l~g   79 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIG--IIKTNKKTGQPMINLYTDRET--GKLKGEATVSFDDPPSAKAAIDWFDG   79 (116)
Confidence            34668899999999999999988887642  2321        111111010  11123699999999999999999999


Q ss_pred             CeeEeCCCCeeeeEEEecc
Q 009860           76 HVFVNEKGAQFKAIVEYAP   94 (523)
Q Consensus        76 ~vFvDsKGne~~A~VEfAP   94 (523)
                      +.|.+.     ...|++|-
T Consensus        80 ~~~~g~-----~l~V~~a~   93 (116)
T 2lcw_A           80 KEFSGN-----PIKVSFAT   93 (116)
Confidence            887532     45666653

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=94.43  E-value=0.18  Score=44.20  Aligned_cols=81  Identities=15%  Similarity=0.119  Sum_probs=59.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcce-eEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYS-RAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~yS-RAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      |..-++|.|.+||..+|++++.+.+..+  |.|.-..-+. +    .   . .|+|.|.+.++...-++.++|..|.+. 
T Consensus        22 ps~vl~l~V~NL~~~vt~~~L~~~Fs~y--G~V~~v~i~~-~----~---Gf~aFVef~~~~~A~~A~~~LnG~~i~g~-   90 (124)
T 2e5i_A           22 GNKVLLLSIQNPLYPITVDVLYTVCNPV--GKVQRIVIFK-R----N---GIQAMVEFESVLCAQKAKAALNGADIYAG-   90 (124)
T ss_dssp             CCSEEEEEEESCCSCCCHHHHHHHHTTT--SCEEEEEEEE-S----S---SEEEEEEESSHHHHHHHHHHHTTCCCBTT-
T ss_pred             CCcEEEEEEcCcCCCCCHHHHHHHHHhc--CCEEEEEEEe-C----C---CCEEEEEECCHHHHHHHHHHhCCCEecCC-
Confidence            3444667799999999999999999875  2343322222 1    1   4 599999999999999999999988652 


Q ss_pred             CCeeeeEEEeccCCC
Q 009860           83 GAQFKAIVEYAPSQR   97 (523)
Q Consensus        83 Gne~~A~VEfAPYQK   97 (523)
                        ...-.|+||--..
T Consensus        91 --~~~l~V~~Ak~~~  103 (124)
T 2e5i_A           91 --CCTLKIEYARPTR  103 (124)
T ss_dssp             --BSEEEEECCSCSC
T ss_pred             --CeEEEEEEecCCc
Confidence              3356788885443

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=94.31  E-value=0.11  Score=47.48  Aligned_cols=76  Identities=14%  Similarity=0.146  Sum_probs=56.3

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF   86 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~   86 (523)
                      ..+|.|++||+.+||+++.+.+...  +.|.....+.-.    ...-.-|||.|.+.+++..-++.++|+.|-+     .
T Consensus       103 ~~~l~v~nl~~~~t~~~l~~~F~~~--G~i~~~~i~~d~----~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g-----~  171 (213)
T 4f02_A          103 VGNIFIKNLDKSIDNKALYDTFSAF--GNILSCKVVCDE----NGSKGYGFVHFETQEAAERAIEKMNGMLLND-----R  171 (213)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEEET----TEEEEEEEEEESSHHHHHHHHHHHTTCEETT-----E
T ss_pred             cccceECCcccccHHHHHHHHHhhc--CCeEEEEeeccC----CCCceEEEEEeCCHHHHHHHHHHhCCCEECC-----E
Confidence            4689999999999999999999875  345444332211    1112359999999999999999999998732     2


Q ss_pred             eeEEEec
Q 009860           87 KAIVEYA   93 (523)
Q Consensus        87 ~A~VEfA   93 (523)
                      .-.|++|
T Consensus       172 ~i~V~~a  178 (213)
T 4f02_A          172 KVFVGRF  178 (213)
T ss_dssp             ECEEEEC
T ss_pred             EEEEEEc
Confidence            5677776

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=94.00  E-value=0.091  Score=45.99  Aligned_cols=74  Identities=8%  Similarity=0.215  Sum_probs=51.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccC--CC-------ceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCC
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHF--ND-------RYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGH   76 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~--~g-------kvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~   76 (523)
                      ...+|.|++||+.+||+++.+.+...-  .+       .+.....  |.      .-.-|||.|.+.+++.... .++|.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~--~~------~~g~afV~F~~~~~A~~Al-~l~g~   73 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI--NQ------DKNFAFLEFRSVDETTQAM-AFDGI   73 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE--ET------TTTEEEEEESCSHHHHHHG-GGTTE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe--cC------CCCEEEEEeCCHHHHHHHH-HhcCC
Confidence            357899999999999999999887651  01       2322222  11      1246999999999999999 89998


Q ss_pred             eeEeCCCCeeeeEEEec
Q 009860           77 VFVNEKGAQFKAIVEYA   93 (523)
Q Consensus        77 vFvDsKGne~~A~VEfA   93 (523)
                      .|.+     ....|+++
T Consensus        74 ~~~g-----~~i~v~~~   85 (198)
T 2yh0_A           74 IFQG-----QSLKIRRP   85 (198)
T ss_dssp             EETT-----EEEEEECC
T ss_pred             EEcC-----ceEEEeCC
Confidence            8732     24556655

>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=93.76  E-value=0.24  Score=46.57  Aligned_cols=85  Identities=14%  Similarity=0.127  Sum_probs=59.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      .+..+|.|++||+.+|++++.+.+...  +.|.....+....   ...-.-|||.|.+.+++...++.+++..|..... 
T Consensus        94 ~~~~~l~v~nl~~~~t~~~l~~~F~~~--G~i~~v~i~~~~~---g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~-  167 (261)
T 3sde_A           94 THGAALTVKNLSPVVSNELLEQAFSQF--GPVEKAVVVVDDR---GRATGKGFVEFAAKPPARKALERCGDGAFLLTTT-  167 (261)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEEETT---SCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSS-
T ss_pred             ccCCcccccCCCCCCCHHHHHHHHHhc--CCeEEEEeeeCCC---CCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCC-
Confidence            356789999999999999999999875  3565555443321   1123469999999999999999996655554221 


Q ss_pred             eeeeEEEeccC
Q 009860           85 QFKAIVEYAPS   95 (523)
Q Consensus        85 e~~A~VEfAPY   95 (523)
                      -.+..|++|--
T Consensus       168 ~r~i~v~~~~~  178 (261)
T 3sde_A          168 PRPVIVEPMEQ  178 (261)
T ss_dssp             CCBCEEEECCC
T ss_pred             CceEEEeeccc
Confidence            23567777653

>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=93.44  E-value=0.29  Score=49.92  Aligned_cols=80  Identities=15%  Similarity=0.274  Sum_probs=64.4

Q ss_pred             CCCCceEEEec--CCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009860            4 PLQRTKVVIRH--LPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         4 p~~r~KVVIRr--LPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs   81 (523)
                      ..+..+|.|.+  |+.++||+++.+.+..+  |.|.-....++        -+.|||.|.+.++....++.++|..+.+.
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~--G~V~~v~~~~~--------kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~   84 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKC--GLVDALLMPPN--------KPYSFARYRTTEESKRAYVTLNGKEVVDD   84 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTT--SCEEEEECCTT--------CSEEEEEESSHHHHHHHHHHTTTCEEECT
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhc--CCeEEEEEeCC--------CCEEEEEECCHHHHHHHHHHhCCCccccc
Confidence            45567899999  57899999999999985  46765555442        26999999999999999999999999888


Q ss_pred             CCCeeeeEEEec
Q 009860           82 KGAQFKAIVEYA   93 (523)
Q Consensus        82 KGne~~A~VEfA   93 (523)
                      .|......|.|+
T Consensus        85 ~g~~~~ly~~~~   96 (345)
T 3tht_A           85 LGQKITLYLNFV   96 (345)
T ss_dssp             TSCEEECEEEEC
T ss_pred             cCCceEEEEEEe
Confidence            786555566666

>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=93.33  E-value=0.14  Score=40.27  Aligned_cols=74  Identities=11%  Similarity=0.073  Sum_probs=49.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      .+..+|.|.+||+.+||+++.+.+...  +.|.....+ .+      .-.-|||.|.+.+++.    .+++..+.-   .
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~--G~i~~v~i~-~~------~~g~afV~f~~~~~a~----~~~~~~~~~---~   66 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQY--GDVMDVFIP-KP------FRAFAFVTFADDQIAQ----SLCGEDLII---K   66 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTT--SCCCEEECC-SS------CCSCCEEECSCHHHHH----HTTTCEEEE---T
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHc--CCeeEEEEe-cC------CCCEEEEEECCHHHHH----HHhcCCcee---C
Confidence            456899999999999999999998875  334443332 11      1235999999998885    355554322   1


Q ss_pred             eeeeEEEecc
Q 009860           85 QFKAIVEYAP   94 (523)
Q Consensus        85 e~~A~VEfAP   94 (523)
                      -....|++|.
T Consensus        67 g~~l~v~~a~   76 (88)
T 1wf0_A           67 GISVHISNAE   76 (88)
T ss_dssp             TEEEEEECCC
T ss_pred             CEEEEEEecC
Confidence            2355677664

>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=93.27  E-value=0.45  Score=43.92  Aligned_cols=79  Identities=15%  Similarity=0.113  Sum_probs=61.1

Q ss_pred             CCceEEEecCC-CCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            6 QRTKVVIRHLP-PSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         6 ~r~KVVIRrLP-P~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      +...|-|.+|| +.+|++++.+.+..+  |.|.....+..+       -.-|||.|.+.++...-++.++|..|.+    
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~--G~v~~v~i~~~~-------~g~afV~f~~~~~A~~Ai~~lng~~~~g----   69 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLY--GNVEKVKFMKSK-------PGAAMVEMADGYAVDRAITHLNNNFMFG----   69 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTT--SCEEEEEECTTS-------TTCEEEEESSHHHHHHHHHHHTTCEETT----
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhc--CCeEEEEEecCC-------CCEEEEEECCHHHHHHHHHHhCCCEECC----
Confidence            56789999999 699999999999875  356555444321       2459999999999999999999998854    


Q ss_pred             eeeeEEEeccCCCC
Q 009860           85 QFKAIVEYAPSQRV   98 (523)
Q Consensus        85 e~~A~VEfAPYQKv   98 (523)
                       ..-.|+||-.+.+
T Consensus        70 -~~l~v~~s~~~~~   82 (205)
T 3tyt_A           70 -QKMNVCVSKQPAI   82 (205)
T ss_dssp             -EECEEEECSCSCC
T ss_pred             -ceEEEEEccCCcc
Confidence             2467888866553

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=93.26  E-value=0.11  Score=45.11  Aligned_cols=70  Identities=14%  Similarity=0.125  Sum_probs=47.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCC--CceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFN--DRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~--gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      .+..+|.|++||...||+++.+.+..+-.  +.+.-...+..+ ..  ..---|||.|.+.+++..-++. +++.|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~g--r~~G~aFV~F~~~~~A~~Al~~-~~~~l   92 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DG--RPTGDAFVLFACEEYAQNALRK-HKDLL   92 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TS--CEEEEEEECCSSHHHHHHHHTT-TTEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CC--CEeeEEEEEECCHHHHHHHHHh-CCCee
Confidence            45689999999999999999998887532  112222222211 11  1134699999999999988876 76543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=93.07  E-value=0.19  Score=42.56  Aligned_cols=64  Identities=16%  Similarity=0.126  Sum_probs=52.4

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      ..-|+||+|+|..||+.+++.+...  |.|..+..+.        .-.-|++.|.+.++...-++.+++..+.+
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~--G~V~~~~l~~--------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~g   70 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQH--GPLVSFHPYL--------NQGIALCKYTTREEANKAQMALNNCVLAN   70 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHH--SCEEEEEEET--------TTTEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhh--CCEEEEEEcC--------CCcEEEEEECCHHHHHHHHHHhcCCEECC
Confidence            4678999999999999999999875  3566666543        24679999999999999999999876543

>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=91.92  E-value=0.078  Score=47.06  Aligned_cols=68  Identities=16%  Similarity=0.089  Sum_probs=47.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      +....+|.|++||+..||+++.+.+..+-   +.....+..+. .  ..---|||.|.+.+++...+ ..+++.|
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G---i~~v~i~~d~~-g--~srGfaFV~F~~~e~A~~Al-~~~g~~l  110 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN---PVRVHIEIGPD-G--RVTGEADVEFATHEEAVAAM-SKDRANM  110 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC---CSEEECCCSSS-S--CSSCCCEEECSHHHHHHHHT-TCCSCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC---CeEEEEEECCC-C--CCceEEEEEeCCHHHHHHHH-hhCCCEE
Confidence            45668999999999999999999998753   22333222211 1  11235999999999999888 6677655

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=90.20  E-value=0.38  Score=46.79  Aligned_cols=82  Identities=10%  Similarity=0.174  Sum_probs=62.0

Q ss_pred             CCCceEEEecCCCCC---------CHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcC
Q 009860            5 LQRTKVVIRHLPPSL---------SQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNG   75 (523)
Q Consensus         5 ~~r~KVVIRrLPP~L---------TEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG   75 (523)
                      ....+|-|.+||+.+         ||+++.+.+..+  |.|.....++.        -.-|||.|.+.++...-++.++|
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~f--G~I~~v~v~~~--------kG~AFV~F~~~~~Ae~A~~am~g  201 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRL--GDIDRIRYVES--------KNCGFVKFKYQANAEFAKEAMSN  201 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTT--SCEEEEEEEGG--------GTEEEEEESSHHHHHHHHHHHTT
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHcc--CCEEEEEEECC--------CCEEEEEeCCHHHHHHHHHHhCC
Confidence            356789999999998         799999998875  46776666532        24699999999999999999999


Q ss_pred             CeeE-------eCCCCeeeeEEEeccCC
Q 009860           76 HVFV-------NEKGAQFKAIVEYAPSQ   96 (523)
Q Consensus        76 ~vFv-------DsKGne~~A~VEfAPYQ   96 (523)
                      ..|.       |..+.-....|.||--.
T Consensus       202 ~~l~~~~~~e~~~~~~gr~L~V~wA~~~  229 (240)
T 3u1l_A          202 QTLLLPSDKEWDDRREGTGLLVKWANED  229 (240)
T ss_dssp             CCCCCTTSTTGGGGGGSCCCEEEECC--
T ss_pred             CEEeccccccccccCCCCEEEEEEccCC
Confidence            9883       22233456788888433

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=89.26  E-value=0.99  Score=38.82  Aligned_cols=71  Identities=13%  Similarity=0.218  Sum_probs=55.1

Q ss_pred             EEEecCCCCCCHHHHHHHhcccC---CCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009860           10 VVIRHLPPSLSQNDLLALFRDHF---NDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF   86 (523)
Q Consensus        10 VVIRrLPP~LTEEeF~eqL~p~~---~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~   86 (523)
                      |-|++||-.++++++...|..++   .|+|-..   -|         ..|||.|.+.++...-.+.++|..|.+.     
T Consensus        12 lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V---tg---------G~AfV~F~~~esA~~A~~~l~G~~l~gr-----   74 (96)
T 2diu_A           12 LYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI---TG---------CSAILRFINQDSAERAQKRMENEDVFGN-----   74 (96)
T ss_dssp             EEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC---CT---------TCEEEEESSHHHHHHHHHHHTTCCSSSS-----
T ss_pred             EEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE---ec---------CEEEEEECCHHHHHHHHHHhcCCccCCc-----
Confidence            55999999999999877665554   2355322   22         8899999999999999999999987654     


Q ss_pred             eeEEEeccCCC
Q 009860           87 KAIVEYAPSQR   97 (523)
Q Consensus        87 ~A~VEfAPYQK   97 (523)
                      +-.|.||+...
T Consensus        75 ~i~v~~A~~~s   85 (96)
T 2diu_A           75 RIIVSFTPKNR   85 (96)
T ss_dssp             CCEEESSCCSC
T ss_pred             eEEEEecCCCc
Confidence            46788887664

>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=88.41  E-value=3.3  Score=34.11  Aligned_cols=78  Identities=15%  Similarity=0.183  Sum_probs=51.9

Q ss_pred             CCCCCceEEEecC--CCCCC---------HHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHH
Q 009860            3 EPLQRTKVVIRHL--PPSLS---------QNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAE   71 (523)
Q Consensus         3 ~p~~r~KVVIRrL--PP~LT---------EEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d   71 (523)
                      .|.+..-|+|++|  |+.|.         |+++.+.+..+  +.|... ++.-+     ..-.-|||.|.+.++...-++
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~--G~v~~v-~i~~~-----~~~G~afV~f~~~~~A~~Ai~   82 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKF--GQIRKL-LLFDR-----HPDGVASVSFRDPEEADYCIQ   82 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGT--SCCSEE-EEETT-----CTTCEEEEECSCHHHHHHHHH
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHcc--CCEeEE-EEecC-----CCCEEEEEEECCHHHHHHHHH
Confidence            4566677999999  44332         45565555543  345444 33211     124569999999999999999


Q ss_pred             HhcCCeeEeCCCCeeeeEEEec
Q 009860           72 LLNGHVFVNEKGAQFKAIVEYA   93 (523)
Q Consensus        72 ~fdG~vFvDsKGne~~A~VEfA   93 (523)
                      .++|+.|-   |  ....|+||
T Consensus        83 ~lng~~~~---g--r~l~v~~a   99 (112)
T 2dit_A           83 TLDGRWFG---G--RQITAQAW   99 (112)
T ss_dssp             HSTTCEET---T--EECEEEEC
T ss_pred             HcCCCEEC---C--cEEEEEEe
Confidence            99999882   2  35677876

>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=87.30  E-value=1.8  Score=39.70  Aligned_cols=62  Identities=15%  Similarity=0.177  Sum_probs=45.5

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhc
Q 009860            8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLN   74 (523)
Q Consensus         8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fd   74 (523)
                      .+|.|++||+..|++++.+.+...  |.|..........   ...-.-|||.|.+.+++....+..+
T Consensus       110 ~~l~V~nLp~~~t~~~L~~~F~~~--G~v~~v~i~~~~~---~~~kG~aFVeF~~~e~A~~A~~~~~  171 (193)
T 2voo_A          110 RSVYIKGFPTDATLDDIKEWLEDK--GQVLNIQMRRTLH---KAFKGSIFVVFDSIESAKKFVETPG  171 (193)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTS--CCEEEEEEEECTT---CCEEEEEEEEESSHHHHHHHHHCTT
T ss_pred             CEEEecCCCCcCCHHHHHHHHhcC--CCEEEEEEEECCC---CCcccEEEEEECCHHHHHHHHHhCC
Confidence            579999999999999999999874  3455444332211   1123469999999999999887653

>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=86.72  E-value=1.9  Score=36.04  Aligned_cols=84  Identities=12%  Similarity=0.148  Sum_probs=50.9

Q ss_pred             CceEEEecC--CCCCCHHHHH----HHhcccC--CCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            7 RTKVVIRHL--PPSLSQNDLL----ALFRDHF--NDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         7 r~KVVIRrL--PP~LTEEeF~----eqL~p~~--~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      -.=|||+++  |-.|.+++.+    +.|...+  -|.|.-..-..............|||.|.+.++...-++.++|..|
T Consensus         5 s~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~f   84 (105)
T 3v4m_A            5 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF   84 (105)
T ss_dssp             CSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCEe
Confidence            345788988  6667654332    2232222  1456544322111111123457899999999999999999999998


Q ss_pred             EeCCCCeeeeEEEeccC
Q 009860           79 VNEKGAQFKAIVEYAPS   95 (523)
Q Consensus        79 vDsKGne~~A~VEfAPY   95 (523)
                      -   |  -.-.|+|++-
T Consensus        85 ~---G--R~i~v~~~~~   96 (105)
T 3v4m_A           85 A---N--RVVVTKYCDP   96 (105)
T ss_dssp             T---T--EECEEEEECH
T ss_pred             C---C--CEEEEEEeCH
Confidence            3   2  2456777653

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=85.41  E-value=8.9  Score=31.91  Aligned_cols=83  Identities=11%  Similarity=0.084  Sum_probs=54.3

Q ss_pred             CCCceEEEecCCC--CC---CHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009860            5 LQRTKVVIRHLPP--SL---SQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV   79 (523)
Q Consensus         5 ~~r~KVVIRrLPP--~L---TEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv   79 (523)
                      .+..-|+|++|..  .|   +++++.+.+..+  |.|....-..-... ....-..|||.|.+.++...-++.++|..|-
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~--G~V~~v~i~~~~~~-~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~   82 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKY--GKVGKCVIFEIPGA-PDDEAVRIFLEFERVESAIKAVVDLNGRYFG   82 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGG--SCEEEEEEEECSSC-CTTTSEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhc--CCEEEEEEecCCCC-CCCCcEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            4456789999962  23   567777777653  34544332221111 1123468999999999999999999999983


Q ss_pred             eCCCCeeeeEEEeccC
Q 009860           80 NEKGAQFKAIVEYAPS   95 (523)
Q Consensus        80 DsKGne~~A~VEfAPY   95 (523)
                         |  -.-.|+||+-
T Consensus        83 ---G--r~i~v~~a~~   93 (105)
T 2pe8_A           83 ---G--RVVKACFYNL   93 (105)
T ss_dssp             ---T--EECEEEECCH
T ss_pred             ---C--cEEEEEEcCH
Confidence               2  3567777753

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=80.70  E-value=4.4  Score=35.45  Aligned_cols=65  Identities=15%  Similarity=0.156  Sum_probs=44.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccc---CCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDH---FNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~---~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      .-+.+|.|+.|||.+.++-+.--+...   ..+.+....|.+          ..|+|.|.+.+.+......- .|.|.+
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~----------~~AvItF~d~~va~rVL~k~-~H~L~~   73 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG----------CGGVLTFREPADAERVLAQA-DHELHG   73 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET----------TEEEEEESSHHHHHHHHTCS-CCBSSS
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC----------CcEEEEEcChHHHHHHhcCC-cceecC
Confidence            456899999999999987554455442   346776666644          57899999998887665541 244443

---

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	523
d1uw4a_	91	d.58.7.4 (A:) RNA processing protein UPF3x, RRM do	7e-32
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-05
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-05
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	7e-05
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-04
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-04
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-04
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	0.001
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	0.002
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	0.004

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]} Length = 91

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]

 Score =  115 bits (290), Expect = 7e-32
 Identities = 31/91 (34%), Positives = 52/91 (57%), Gaps = 2/91 (2%)

Query: 8  TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVF 67
          +KVVIR LPP+L++  L    +      +++F F    +S     Y+RAY+  K    + 
Sbjct: 2  SKVVIRRLPPTLTKEQLQEHLQPM--PEHDYFEFFSNDTSLYPHMYARAYINFKNQEDII 59

Query: 68 EFAELLNGHVFVNEKGAQFKAIVEYAPSQRV 98
           F +  +G+VF++ KG ++ AIVE+AP Q+ 
Sbjct: 60 LFRDRFDGYVFLDNKGQEYPAIVEFAPFQKA 90

>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 = 41.1 bits (96), Expect = 2e-05
 Identities = 15/91 (16%), Positives = 31/91 (34%), Gaps = 7/91 (7%)

Query: 3  EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKK 62
          E ++ T + + +LP +++ + L  +F  + +                 +    A+V   K
Sbjct: 2  ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK----LTGRPRGVAFVRYNK 57

Query: 63 PAGVFEFAELLNGHVFVNEKGAQFKAIVEYA 93
               E    LN  +    +G      V  A
Sbjct: 58 REEAQEAISALNNVIP---EGGSQPLSVRLA 85

>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 = 40.4 bits (94), Expect = 3e-05
 Identities = 14/77 (18%), Positives = 20/77 (25%), Gaps = 5/77 (6%)

Query: 2  KEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELK 61
          KEP Q  K+ I  L    +   L + F              P     +       +V   
Sbjct: 1  KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGF----GFVTYA 56

Query: 62 KPAGVFEFAELLNGHVF 78
              V + A     H  
Sbjct: 57 TVEEV-DAAMNARPHKV 72

>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 = 39.5 bits (92), Expect = 7e-05
 Identities = 9/97 (9%), Positives = 26/97 (26%), Gaps = 9/97 (9%)

Query: 6   QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAG 65
           +   + + +L    ++  +  LF    + +             K       +VE    A 
Sbjct: 6   KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK----MKKTACGFCFVEYYSRAD 61

Query: 66  VFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPF 102
                  +NG           +   ++    +  + +
Sbjct: 62  AENAMRYINGTRL---DDRIIR--TDWDAGFKEGRQY 93

>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 = 37.8 bits (87), Expect = 2e-04
 Identities = 18/90 (20%), Positives = 31/90 (34%), Gaps = 10/90 (11%)

Query: 7  RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGV 66
          +T +++ +LP +++Q +  +LF                      Q     +V    P   
Sbjct: 2  KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDK----ITGQSLGYGFVNYIDPKDA 57

Query: 67 FEFAELLNGHVFVNEKGAQFKAIVEYA-PS 95
           +    LNG      +    K  V YA PS
Sbjct: 58 EKAINTLNGLRL---QTKTIK--VSYARPS 82

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.6 bits (87), Expect = 3e-04
 Identities = 13/87 (14%), Positives = 29/87 (33%), Gaps = 10/87 (11%)

Query: 9  KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFE 68
          K+++ +L   +S  D+  LF +    +     +         +    A V  ++ A   +
Sbjct: 2  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-----RSGRSLGTADVHFERKADALK 56

Query: 69 FAELLNGHVFVNEKGAQFKAIVEYAPS 95
            +  NG       G      ++   S
Sbjct: 57 AMKQYNGVPL---DGRPMN--IQLVTS 78

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.9 bits (85), Expect = 6e-04
 Identities = 19/90 (21%), Positives = 34/90 (37%), Gaps = 8/90 (8%)

Query: 12  IRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAE 71
           I++L  S ++  L  +F      +      +  K+          +VE KKP    +  +
Sbjct: 3   IKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGF-GFVEYKKPEQAQKALK 61

Query: 72  LLNGHVFVNEKGAQFKAIVEYAPSQRVPKP 101
            L GH      G + +  V  +  +R  KP
Sbjct: 62  QLQGHTV---DGHKLE--VRIS--ERATKP 84

>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 = 36.2 bits (83), Expect = 0.001
 Identities = 15/86 (17%), Positives = 28/86 (32%), Gaps = 7/86 (8%)

Query: 8  TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVF 67
            + +  LP +++Q +L  LF  +     +                   ++   K     
Sbjct: 7  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ----VTGVSRGVGFIRFDKRIEAE 62

Query: 68 EFAELLNGHVFVNEKGAQFKAIVEYA 93
          E  + LNG       GA     V++A
Sbjct: 63 EAIKGLNGQKP---SGATEPITVKFA 85

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 12/77 (15%), Positives = 20/77 (25%), Gaps = 5/77 (6%)

Query: 2  KEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELK 61
          +E  Q  K+ I  L    ++  L   +              P     +       +V   
Sbjct: 15 REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGF----GFVTFS 70

Query: 62 KPAGVFEFAELLNGHVF 78
            A V + A     H  
Sbjct: 71 SMAEV-DAAMAARPHSI 86

>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 = 34.6 bits (79), Expect = 0.004
 Identities = 11/78 (14%), Positives = 20/78 (25%), Gaps = 4/78 (5%)

Query: 1  MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVEL 60
          + E  Q   V +  L   +S+  L  LF                      Q     +VE 
Sbjct: 3  ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDR----VTGQHQGYGFVEF 58

Query: 61 KKPAGVFEFAELLNGHVF 78
                    ++++    
Sbjct: 59 LSEEDADYAIKIMDMIKL 76

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	523
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	100.0
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	97.88
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	97.86
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	97.72
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	97.67
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	97.65
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	97.62
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	97.54
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	97.52
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	97.52
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	97.51
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	97.5
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	97.47
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	97.47
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	97.45
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	97.44
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	97.36
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	97.33
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	97.31
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	97.31
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	97.3
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	97.29
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	97.28
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	97.27
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	97.26
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	97.25
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	97.24
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	97.17
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	97.16
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	97.1
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	97.07
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	97.06
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	97.02
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	96.98
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	96.98
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	96.94
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	96.93
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	96.9
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	96.9
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	96.9
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	96.9
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	96.88
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	96.84
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	96.82
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	96.8
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	96.78
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	96.77
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	96.76
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	96.73
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	96.71
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	96.61
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	96.57
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	96.55
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	96.54
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	96.54
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	96.53
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	96.49
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	96.46
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	96.45
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	96.45
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	96.42
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	96.39
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	96.36
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	96.28
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	96.28
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	96.19
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	96.1
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	96.04
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	96.01
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	95.89
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	95.88
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	95.77
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	95.7
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	95.51
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	95.45
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	95.41
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	95.4
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	95.38
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	94.93
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	94.77
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	94.4
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	93.93
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	93.31
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	92.14
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	85.55
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	84.94
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	84.88

>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=100.00  E-value=4.7e-36  Score=253.37  Aligned_cols=90  Identities=34%  Similarity=0.661  Sum_probs=86.7

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeee
Q 009860            8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFK   87 (523)
Q Consensus         8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~   87 (523)
                      +|||||||||+|||++|+++|+++  ++++|+||++||.+.++++||||||+|++.|+|.+|++.|+|++|+|++|++++
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~--~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~   79 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPM--PEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYP   79 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSC--CCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCc--CceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEee
Confidence            799999999999999999999985  468999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEeccCCCCC
Q 009860           88 AIVEYAPSQRVP   99 (523)
Q Consensus        88 A~VEfAPYQKvP   99 (523)
                      |+|||||||||.
T Consensus        80 a~VE~AP~qkv~   91 (91)
T d1uw4a_          80 AIVEFAPFQKAA   91 (91)
T ss_dssp             CEEEECSSCCC-
T ss_pred             eEEEEcCccccC
Confidence            999999999983

>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=97.88  E-value=2.3e-05  Score=60.42  Aligned_cols=78  Identities=21%  Similarity=0.283  Sum_probs=58.8

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF   86 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~   86 (523)
                      +++|.|.+||+.+||+++.+.+...  |.|.....+.-....  ..-.-|||.|.+.+++....+.++|+.|.+     .
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~--G~v~~v~i~~~~~~~--~~~g~afv~f~~~~~a~~a~~~l~g~~~~g-----~   72 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSI--GEIESCKLVRDKITG--QSLGYGFVNYIDPKDAEKAINTLNGLRLQT-----K   72 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTT--SCEEEEEEEECTTTC--CEEEEEEEEESSHHHHHHHHHHHTTCEETT-----E
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHh--CCcccccceeeccCC--CceeeEEEEECCHHHHHHHHHHhCCCEECC-----E
Confidence            6789999999999999999999874  346555544222211  122349999999999999999999998843     3


Q ss_pred             eeEEEec
Q 009860           87 KAIVEYA   93 (523)
Q Consensus        87 ~A~VEfA   93 (523)
                      ...|+||
T Consensus        73 ~l~v~~A   79 (82)
T d1fxla1          73 TIKVSYA   79 (82)
T ss_dssp             ECEEEEC
T ss_pred             EEEEEEe
Confidence            5778877

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.86  E-value=2.2e-05  Score=63.47  Aligned_cols=79  Identities=18%  Similarity=0.203  Sum_probs=62.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      ..+.|.|++||+.+|++++.+.+...  |.|......+.        -.-|||.|.+.+++..-++.++|+.|.+.    
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~f--G~I~~v~l~~~--------kg~afV~f~~~~~A~~A~~~lng~~~~gr----   74 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRF--GSLGRVLLPEG--------GITAIVEFLEPLEARKAFRHLAYSKFHHV----   74 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTT--SCEEEEECCSS--------SSCEEEEESCHHHHHHHHHHHTTCBSSSS----
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhcc--CCccEEEeecc--------CceEEEEEcCHHHHHHHHHHHcCCccCCC----
Confidence            34679999999999999999999864  46766543211        23699999999999999999999999642    


Q ss_pred             eeeEEEeccCCCCC
Q 009860           86 FKAIVEYAPSQRVP   99 (523)
Q Consensus        86 ~~A~VEfAPYQKvP   99 (523)
                       +..|+||+.+...
T Consensus        75 -~l~v~~a~~~~~~   87 (111)
T d1whxa_          75 -PLYLEWAPIGVFG   87 (111)
T ss_dssp             -BCEEEEEETTTTC
T ss_pred             -eEEEEECCCCccc
Confidence             5578999876544

>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=97.72  E-value=7.3e-05  Score=58.35  Aligned_cols=83  Identities=17%  Similarity=0.158  Sum_probs=61.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ....++|-|.+||+.+||+++.+.+...  +.|.....+.-+.+.+  .-.-|||.|.+.+++...++.++|..|...  
T Consensus         3 ~~~~t~lfV~nlp~~~te~~l~~~F~~~--G~i~~~~~~~d~~~g~--~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~--   76 (85)
T d1b7fa2           3 SIKDTNLYVTNLPRTITDDQLDTIFGKY--GSIVQKNILRDKLTGR--PRGVAFVRYNKREEAQEAISALNNVIPEGG--   76 (85)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSS--SCEEEEEEEECTTTCC--EEEEEEEEESSHHHHHHHHHHHTTCCCTTC--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhh--CCEeeeeeeccccccc--CceeEEEEECCHHHHHHHHHHHCCCEeCCC--
Confidence            3467889999999999999999999874  3565444433222221  123599999999999999999999887543  


Q ss_pred             CeeeeEEEec
Q 009860           84 AQFKAIVEYA   93 (523)
Q Consensus        84 ne~~A~VEfA   93 (523)
                       ..+..|+||
T Consensus        77 -~~~l~V~~A   85 (85)
T d1b7fa2          77 -SQPLSVRLA   85 (85)
T ss_dssp             -SSCCEEEEC
T ss_pred             -CeEEEEEEC
Confidence             346778776

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.67  E-value=0.00016  Score=57.54  Aligned_cols=78  Identities=15%  Similarity=0.256  Sum_probs=59.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      .+.++|.|.+||+++|++++.+.+...  +.|.......-     ...-..|||.|.+.+++..-++.++|+.|.+    
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~v~~~~~~~~-----~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g----   80 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKY--GAIRDIDLKNR-----RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDG----   80 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEECCS-----SSSSCCEEEEESCHHHHHHHHHHHTTCEETT----
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcC--CceEEEEeccc-----ccccceEEEEECCHHHHHHHHHHhCCCEECC----
Confidence            567899999999999999999999875  34555443211     1112459999999999999999999999833    


Q ss_pred             eeeeEEEecc
Q 009860           85 QFKAIVEYAP   94 (523)
Q Consensus        85 e~~A~VEfAP   94 (523)
                       ..-.|+||-
T Consensus        81 -~~l~V~~a~   89 (95)
T d1x4aa1          81 -YRLRVEFPR   89 (95)
T ss_dssp             -EECEEECCC
T ss_pred             -EEEEEEecc
Confidence             356788874

>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=97.65  E-value=7.8e-05  Score=57.41  Aligned_cols=78  Identities=24%  Similarity=0.338  Sum_probs=56.5

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF   86 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~   86 (523)
                      ++.|.|.+||+.+||+++.+.+...  +.|.....+.-+.+.+  ...-|||.|.+.+++....+.++|+.|.+     .
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 NTNLIVNYLPQDMTDRELYALFRAI--GPINTCRIMRDYKTGY--SYGYAFVDFTSEMDSQRAIKVLNGITVRN-----K   72 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTT--SCEEEEECCEETTTTE--ECSEEEEEESSHHHHHHHHHHHTTCEETT-----E
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHh--CCcceeeeeeecccCC--ccccceEEECCHHHHHHHHHHhCCCEECC-----E
Confidence            5789999999999999999999875  3454433222111111  12249999999999999999999998732     2


Q ss_pred             eeEEEec
Q 009860           87 KAIVEYA   93 (523)
Q Consensus        87 ~A~VEfA   93 (523)
                      .-.|+||
T Consensus        73 ~l~v~~a   79 (82)
T d1b7fa1          73 RLKVSYA   79 (82)
T ss_dssp             ECEEEEC
T ss_pred             EEEEEEc
Confidence            5567776

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.62  E-value=0.00014  Score=58.16  Aligned_cols=77  Identities=18%  Similarity=0.198  Sum_probs=61.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      .|...|.|.+||+++||++|.+.+...  +.|..+.+++++        ..|||.|.+.++.....+.+++..|.   |.
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~--G~i~~~~~~~~~--------~~afV~f~~~~~A~~A~~~l~~~~i~---g~   81 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRF--GSIRTIDHVKGD--------SFAYIQYESLDAAQAACAKMRGFPLG---GP   81 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTT--SCEEEEEECSSS--------CCEEEEESSHHHHHHHHHHHTTCBCS---SS
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhh--cccceEeeeccc--------cEEEeccCCHHHHHHHHHHhCCCEeC---CC
Confidence            455789999999999999999999875  356655555432        36999999999999999999999873   33


Q ss_pred             eeeeEEEecc
Q 009860           85 QFKAIVEYAP   94 (523)
Q Consensus        85 e~~A~VEfAP   94 (523)
                      ..+-.|+||-
T Consensus        82 ~~~l~v~~ak   91 (97)
T d1whya_          82 DRRLRVDFAK   91 (97)
T ss_dssp             SCBCEEEECC
T ss_pred             ceEEEEEeCC
Confidence            4578899884

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=97.54  E-value=0.00025  Score=55.11  Aligned_cols=75  Identities=17%  Similarity=0.259  Sum_probs=58.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      |...|-|++||+.+|++++.+.+..+  |.|....+++++-       .-|||.|.+.++...-.+.++|+.|.+.+   
T Consensus         7 P~~tl~V~nLp~~~t~~~l~~~f~~~--G~i~~v~~~~~~~-------g~afV~f~~~~~A~~A~~~l~g~~~~~~~---   74 (83)
T d2b0ga1           7 PNQILFLTNLPEETNEMMLSMLFNQF--PGFKEVRLVPNRH-------DIAFVEFTTELQSNAAKEALQGFKITPTH---   74 (83)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTS--TTEEEEEECTTTC-------SCEEEEESSHHHHHHHHHHHTTCBSSTTC---
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhccC--ccEEEeeeecccc-------eeEEEecCCHHHHHHHHHHhCCcEeCCCc---
Confidence            45668899999999999999999875  3565556655431       24999999999999999999999986532   


Q ss_pred             eeeEEEec
Q 009860           86 FKAIVEYA   93 (523)
Q Consensus        86 ~~A~VEfA   93 (523)
                       .-.|+||
T Consensus        75 -~i~v~~a   81 (83)
T d2b0ga1          75 -AMKITFA   81 (83)
T ss_dssp             -BCEEEEC
T ss_pred             -EEEEEEe
Confidence             4577776

>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=97.52  E-value=0.00032  Score=56.01  Aligned_cols=86  Identities=17%  Similarity=0.184  Sum_probs=62.9

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      ......||.|.+||+..||+++.+.+..+  +.|....+..-+...++  -.-|||.|.+.+++...++.++++.|.+. 
T Consensus         4 ~~~~~~~lfV~nL~~~~t~~~l~~~F~~~--g~v~~v~i~~d~~tg~~--~g~afV~f~~~~~a~~A~~~l~g~~~~gr-   78 (99)
T d1whwa_           4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAY--GPLSELHYPIDSLTKKP--KGFAFVTFMFPEHAVKAYAEVDGQVFQGR-   78 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTT--SCEEEEECCCCTTTCCC--CSEEEEEESSHHHHHHHHHHTTTEESSSC-
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhc--CCceeeeeccccccccc--CcceEEEECCHHHHHHHHHHcCCCEECCE-
Confidence            45667899999999999999999999764  34554443322222221  23499999999999999999999987432 


Q ss_pred             CCeeeeEEEeccCCC
Q 009860           83 GAQFKAIVEYAPSQR   97 (523)
Q Consensus        83 Gne~~A~VEfAPYQK   97 (523)
                          .-.|++|-..+
T Consensus        79 ----~i~V~~a~~~~   89 (99)
T d1whwa_          79 ----MLHVLPSTIKK   89 (99)
T ss_dssp             ----EEEEEECCCCS
T ss_pred             ----EEEEEECCCCC
Confidence                46788877654

>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=97.52  E-value=0.00024  Score=55.59  Aligned_cols=81  Identities=20%  Similarity=0.212  Sum_probs=59.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      ..++|.|.+||+.+||+++.+.+...  |.|.....+.-+.+.  ..-.-|||.|.+.+++....+.++|..|.   |..
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~--G~v~~v~i~~d~~~g--~~kg~afV~f~~~~~a~~Ai~~lng~~~~---G~~   77 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQY--GRIITSRILVDQVTG--VSRGVGFIRFDKRIEAEEAIKGLNGQKPS---GAT   77 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTC--CEEEEEEEEESSHHHHHHHHHHHTTCCCT---TCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHh--CCccccccccccccc--cCCCeeEEEEcCHHHHHHHHHHhCCCEeC---CCC
Confidence            46789999999999999999999875  345554444322211  12235999999999999999999998763   444


Q ss_pred             eeeEEEec
Q 009860           86 FKAIVEYA   93 (523)
Q Consensus        86 ~~A~VEfA   93 (523)
                      .+-.|.||
T Consensus        78 ~~i~V~~A   85 (85)
T d1fxla2          78 EPITVKFA   85 (85)
T ss_dssp             SCCEEEEC
T ss_pred             EEEEEEeC
Confidence            45667776

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.51  E-value=0.00043  Score=55.04  Aligned_cols=83  Identities=11%  Similarity=0.121  Sum_probs=62.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      +.+.|.|.+||+++||+++.+.+...  |.|.....+.-+....  .-.-|||.|.+.+++..-.+.++|..|-+     
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~--G~i~~v~i~~~~~~~~--~kg~afV~f~~~~~A~~Ai~~l~g~~~~g-----   76 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKS--GDIKKIIMGLDKMKKT--ACGFCFVEYYSRADAENAMRYINGTRLDD-----   76 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTCC--EEEEEEEEESSHHHHHHHHHHTTTSEETT-----
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHH--CCcceecccccccccc--ccceEEEEECCHHHHHHHHHHhCCCEECC-----
Confidence            45789999999999999999999875  3566555554333221  11249999999999999999999998732     


Q ss_pred             eeeEEEeccCCC
Q 009860           86 FKAIVEYAPSQR   97 (523)
Q Consensus        86 ~~A~VEfAPYQK   97 (523)
                      ..-.|+||+-.+
T Consensus        77 r~i~V~~a~~~~   88 (93)
T d1h2vz_          77 RIIRTDWDAGFK   88 (93)
T ss_dssp             EECEEEEESCCC
T ss_pred             EEEEEEEcCCCC
Confidence            366799987443

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.50  E-value=0.00019  Score=56.19  Aligned_cols=80  Identities=11%  Similarity=0.130  Sum_probs=59.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      +.-||.|.+||+++||+++.+.+...  +.|....++..+....+.  .-|||.|.+.+++..-.+.++|+.|-+     
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~--G~i~~~~~~~~~~~~~~~--g~afV~f~~~~~a~~Ai~~l~~~~~~g-----   74 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKY--GQISEVVVVKDRETQRSR--GFGFVTFENIDDAKDAMMAMNGKSVDG-----   74 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHH--SCCCEEEECCCSSSCSCC--SEEEEECSSHHHHHHHHHHHTTCCTTS-----
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhcc--ccccceeecccccccccc--ceEEEEECCHHHHHHHHHHcCCCEECC-----
Confidence            45789999999999999999999875  345544444443333222  249999999999999999999998743     


Q ss_pred             eeeEEEecc
Q 009860           86 FKAIVEYAP   94 (523)
Q Consensus        86 ~~A~VEfAP   94 (523)
                      ..-.|++|.
T Consensus        75 ~~l~V~~a~   83 (90)
T d1x5sa1          75 RQIRVDQAG   83 (90)
T ss_dssp             CCCEEEEEE
T ss_pred             EEEEEEEcC
Confidence            256688774

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.47  E-value=0.00049  Score=54.53  Aligned_cols=80  Identities=16%  Similarity=0.150  Sum_probs=61.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      .....+|.|.+||+.+|++++.+.+...  +.|.+...+...-.    .-..|||.|.+.+++..-.+.++|+.|-+   
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~--G~v~~v~~~~~~~~----~kg~afV~f~~~~~a~~Ai~~l~~~~~~g---   78 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQF--GKILDVEIIFNERG----SKGFGFVTFENSADADRAREKLHGTVVEG---   78 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGT--SCEEEEEEECCTTT----TCCEEEEEESCHHHHHHHHHHHTTCEETT---
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhc--ceeeeccccccccC----CcceeEEEECCHHHHHHHHHHcCCCEECC---
Confidence            4566789999999999999999999876  35666555433221    13469999999999999999999998843   


Q ss_pred             CeeeeEEEecc
Q 009860           84 AQFKAIVEYAP   94 (523)
Q Consensus        84 ne~~A~VEfAP   94 (523)
                        ..-.|++|-
T Consensus        79 --~~l~V~~A~   87 (93)
T d2cq3a1          79 --RKIEVNNAT   87 (93)
T ss_dssp             --EECEEEECC
T ss_pred             --EEEEEEecC
Confidence              367788873

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.47  E-value=0.0003  Score=55.28  Aligned_cols=78  Identities=14%  Similarity=0.197  Sum_probs=61.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      -.++.+|.|.+||+.+|++++.+.+.+.  |.|......+.        ..-|||.|.+.++...-...++|..|.+   
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~--G~i~~i~~~~~--------k~~afV~f~~~~~A~~A~~~l~g~~i~g---   71 (86)
T d2cpja1           5 FTQRSRLFVGNLPPDITEEEMRKLFEKY--GKAGEVFIHKD--------KGFGFIRLETRTLAEIAKVELDNMPLRG---   71 (86)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTT--CCCSEEEEETT--------TTEEEEECSSSHHHHHHHHHHTTCCBTT---
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHh--CCceEeeeecc--------cceEEEEECCHHHHHHHHHHhCCCEECC---
Confidence            3467899999999999999999999874  34554444432        1369999999999999999999999853   


Q ss_pred             CeeeeEEEeccCC
Q 009860           84 AQFKAIVEYAPSQ   96 (523)
Q Consensus        84 ne~~A~VEfAPYQ   96 (523)
                        ....|+||+..
T Consensus        72 --~~l~V~~A~~~   82 (86)
T d2cpja1          72 --KQLRVRFACHS   82 (86)
T ss_dssp             --BCCEEEESSCC
T ss_pred             --EEEEEEECCCc
Confidence              26788888754

>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=97.45  E-value=0.00029  Score=55.40  Aligned_cols=81  Identities=14%  Similarity=0.156  Sum_probs=59.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      .+...|.|++||+.+||+++.+.+...  +.|....++.-..+.++  -.-|||.|.+.+++....+.++|..|.   | 
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~--G~i~~v~i~~d~~tg~~--~g~afV~f~~~~~A~~A~~~lng~~l~---g-   76 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDY--GEIKNIHLNLDRRTGFS--KGYALVEYETHKQALAAKEALNGAEIM---G-   76 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTSSE--EEEEEEEESSHHHHHHHHHHHTTCEET---T-
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHc--CCccccccccccccccc--ccceeEEECCHHHHHHHHHHcCCCEEC---C-
Confidence            456789999999999999999999875  34654454432222211  123999999999999999999998773   2 


Q ss_pred             eeeeEEEecc
Q 009860           85 QFKAIVEYAP   94 (523)
Q Consensus        85 e~~A~VEfAP   94 (523)
                       ..-.|+||-
T Consensus        77 -~~l~V~~a~   85 (88)
T d1rk8a_          77 -QTIQVDWCF   85 (88)
T ss_dssp             -EECEEEESE
T ss_pred             -EEEEEEEec
Confidence             356788874

>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=97.44  E-value=0.00029  Score=55.46  Aligned_cols=79  Identities=16%  Similarity=0.263  Sum_probs=59.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCccee--EEEEecCcccHHHHHHHhcCCeeEeC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSR--AYVELKKPAGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySR--AYI~Fkn~Edl~~F~d~fdG~vFvDs   81 (523)
                      ..+...|.|.+||+.+||+++.+.+...  |.|....++.-+.    ...+|  |||.|.+.++...-++.++|+.|-+ 
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~--G~v~~v~i~~d~~----t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g-   77 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPF--GSISRIYLAKDKT----TGQSKGFAFISFHRREDAARAIAGVSGFGYDH-   77 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTT--CCEEEEEEEECSS----SCSEEEEEEEEESSHHHHHHHHHHTTTCEETT-
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHh--ccccccccccccc----ccccccceeEEECCHHHHHHHHHHhCCCEECC-
Confidence            3456789999999999999999988774  3566555443222    12344  9999999999999999999998832 


Q ss_pred             CCCeeeeEEEec
Q 009860           82 KGAQFKAIVEYA   93 (523)
Q Consensus        82 KGne~~A~VEfA   93 (523)
                          ..-.|+||
T Consensus        78 ----~~i~v~~a   85 (90)
T d2cq0a1          78 ----LILNVEWA   85 (90)
T ss_dssp             ----EECEEEES
T ss_pred             ----EEEEEEee
Confidence                25677877

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.36  E-value=0.0002  Score=55.02  Aligned_cols=77  Identities=17%  Similarity=0.239  Sum_probs=52.7

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeee
Q 009860            8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFK   87 (523)
Q Consensus         8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~   87 (523)
                      ++|.|++||+.+||+++.+.+...  |.+.....+.-+...+  ...-|||.|.+.++.....+.++|+.|-+     ..
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~--G~v~~~~~~~~~~~~~--~~g~afV~f~~~e~A~~Ai~~l~g~~~~g-----~~   72 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDI--NVVALSIRLPSLRFNT--SRRFAYIDVTSKEDARYCVEKLNGLKIEG-----YT   72 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHT--TCCCCEEECC---------CCEEEEECSSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHh--CcEEeeeeeccccccc--ccceeEEEECCHHHHHHHHHHhCCCEECC-----EE
Confidence            689999999999999999999875  2332222221111111  12359999999999999999999998843     24


Q ss_pred             eEEEec
Q 009860           88 AIVEYA   93 (523)
Q Consensus        88 A~VEfA   93 (523)
                      -.|+||
T Consensus        73 i~V~~a   78 (81)
T d2ghpa1          73 LVTKVS   78 (81)
T ss_dssp             CEEEEC
T ss_pred             EEEEEc
Confidence            455554

>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=97.33  E-value=0.00023  Score=55.06  Aligned_cols=73  Identities=16%  Similarity=0.053  Sum_probs=54.1

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV   79 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv   79 (523)
                      .|.+...|.|.+||+.+||+++.+.+...-  .|.....+.-+.+.  ....-|||.|.+.+++....+.++|+.|-
T Consensus         5 ~p~~~~~l~V~nL~~~~te~~l~~~F~~~G--~i~~v~i~~~~~~~--~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   77 (83)
T d2cqca1           5 NPDPNCCLGVFGLSLYTTERDLREVFSKYG--PIADVSIVYDQQSR--RSRGFAFVYFENVDDAKEAKERANGMELD   77 (83)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTS--CEEEEEEEECSSSS--SEEEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhC--CCcccccccccccc--ccccceEEEECCHHHHHHHHHHcCCCEEC
Confidence            366778899999999999999999998752  45444333211111  11234999999999999999999998874

>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=97.31  E-value=0.00064  Score=54.07  Aligned_cols=85  Identities=15%  Similarity=0.239  Sum_probs=59.5

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHh-cCCeeEeC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELL-NGHVFVNE   81 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~f-dG~vFvDs   81 (523)
                      ...+..+|.|++||+.+||+++.+.+...  |.|....... +.......-.-|||.|.+.++....++.+ +|..|.  
T Consensus         4 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~--G~i~~v~i~~-~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~--   78 (94)
T d2cpha1           4 KKQTTSKILVRNIPFQANQREIRELFSTF--GELKTVRLPK-KMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLY--   78 (94)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTT--SCEEEEECCC-CCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSS--
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHh--CCceEEEEEe-ccccCCCcccEEEEEECCHHHHHHHHHHccCCcEEC--
Confidence            34566889999999999999999999875  3565444322 21111112346999999999999998887 776653  


Q ss_pred             CCCeeeeEEEeccC
Q 009860           82 KGAQFKAIVEYAPS   95 (523)
Q Consensus        82 KGne~~A~VEfAPY   95 (523)
                       |  .+-.|+||--
T Consensus        79 -G--r~l~V~~A~~   89 (94)
T d2cpha1          79 -G--RRLVLEWADS   89 (94)
T ss_dssp             -S--CBCEEEECCC
T ss_pred             -C--EEEEEEEcCC
Confidence             2  2567888853

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.31  E-value=0.00039  Score=53.80  Aligned_cols=77  Identities=22%  Similarity=0.231  Sum_probs=56.6

Q ss_pred             EEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCccee--EEEEecCcccHHHHHHHhcCCeeEeCCCCeee
Q 009860           10 VVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSR--AYVELKKPAGVFEFAELLNGHVFVNEKGAQFK   87 (523)
Q Consensus        10 VVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySR--AYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~   87 (523)
                      |-|++||+++|++++.+.+...  |.|.....+.-+. ......||  |||.|.+.+++...++.++|+.|.+     ..
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~--G~v~~v~i~~~~~-~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g-----~~   72 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKV--GAIKSCTISKKKN-KAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDG-----HK   72 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTT--SCEEEEEEEEEEC-TTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETT-----EE
T ss_pred             CEEcCCCCCCCHHHHHHHHHHh--CCccccceecccc-cccccccceEEEEEECCHHHHHHHHHHhCCCEECC-----EE
Confidence            5799999999999999999875  3455444332222 12233455  9999999999999999999998732     25


Q ss_pred             eEEEecc
Q 009860           88 AIVEYAP   94 (523)
Q Consensus        88 A~VEfAP   94 (523)
                      -.|++|.
T Consensus        73 i~V~~a~   79 (85)
T d2cpfa1          73 LEVRISE   79 (85)
T ss_dssp             CEEECSS
T ss_pred             EEEEECC
Confidence            6788874

>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=97.30  E-value=0.00066  Score=52.12  Aligned_cols=76  Identities=16%  Similarity=0.194  Sum_probs=56.7

Q ss_pred             eEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeeee
Q 009860            9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKA   88 (523)
Q Consensus         9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~A   88 (523)
                      ||.|.+|||.+||+++.+.+...  +.|........+ .. . ...-|||.|.+.+++....+.++|+.|.+     ..-
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~--G~v~~~~i~~~~-~g-~-~~g~afV~f~~~~~A~~Ai~~l~g~~l~g-----~~l   71 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEF--GTLKKAAVHYDR-SG-R-SLGTADVHFERKADALKAMKQYNGVPLDG-----RPM   71 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHH--SCEEEEEESCSS-CC-C-SCCEEEEEESCHHHHHHHHHHHTTCEETT-----EEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHh--CCCeEEEEEEee-cc-c-cceeEEEEECCHHHHHHHHHHhCCCEECC-----EEE
Confidence            79999999999999999999875  345554443332 11 1 23469999999999999999999998743     245


Q ss_pred             EEEecc
Q 009860           89 IVEYAP   94 (523)
Q Consensus        89 ~VEfAP   94 (523)
                      .|++|.
T Consensus        72 ~V~~a~   77 (78)
T d1no8a_          72 NIQLVT   77 (78)
T ss_dssp             EEEEEC
T ss_pred             EEEEee
Confidence            667664

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.29  E-value=0.00086  Score=52.66  Aligned_cols=82  Identities=16%  Similarity=0.184  Sum_probs=61.2

Q ss_pred             CCCCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            1 MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         1 mk~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      |....+...|-|.+||+++||+++.+.+...  |.|.-...+.-+...    -.-|||.|.+.+++..-.+.++|+.|.+
T Consensus         2 m~d~~~~~tl~V~nLp~~~te~~l~~~F~~~--G~i~~v~i~~d~~~~----~~~afV~f~~~~~A~~A~~~l~~~~~~g   75 (90)
T d2cqia1           2 MEDDGQPRTLYVGNLSRDVTEVLILQLFSQI--GPCKSCKMITEHTSN----DPYCFVEFYEHRDAAAALAAMNGRKILG   75 (90)
T ss_dssp             CCCSCCCCEEEEESCCTTCCHHHHHHHHHHH--SCEEEEEEECCCCSS----CCEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhc--CCceeeeeecccCcc----ceeeEEEECCHHHHHHHHHHcCCCEECC
Confidence            5666677789999999999999999998875  345444443322221    2359999999999999999999998743


Q ss_pred             CCCCeeeeEEEec
Q 009860           81 EKGAQFKAIVEYA   93 (523)
Q Consensus        81 sKGne~~A~VEfA   93 (523)
                           ..-.|.||
T Consensus        76 -----~~i~v~~a   83 (90)
T d2cqia1          76 -----KEVKVNWA   83 (90)
T ss_dssp             -----EEEEEEEC
T ss_pred             -----EEEEEEEc
Confidence                 25667776

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.28  E-value=0.00017  Score=58.10  Aligned_cols=78  Identities=18%  Similarity=0.239  Sum_probs=57.6

Q ss_pred             eEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeeee
Q 009860            9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKA   88 (523)
Q Consensus         9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~A   88 (523)
                      +|.|++||+.+||+++.+.++.+  |.|........+.+.+.  -.-|||.|.+.+++....+.++|+.|.+.     ..
T Consensus        10 tl~V~nLp~~~te~~l~~~f~~~--G~i~~v~i~~~~~tg~~--~g~afV~f~~~~~a~~ai~~l~~~~~~g~-----~i   80 (104)
T d1p1ta_          10 SVFVGNIPYEATEEQLKDIFSEV--GPVVSFRLVYDRETGKP--KGYGFCEYQDQETALSAMRNLNGREFSGR-----AL   80 (104)
T ss_dssp             CEEEESCCTTSCHHHHHHHHHTT--SCCSEEEEEEETTTTEE--EEEEEEECSCHHHHHHHHHHSSSBSCSSS-----CB
T ss_pred             EEEEECCCCcCCHHHHHHhhhcc--ccccccccccccceecc--CCceEEEECCHHHHHHHHHHcCCCEECCE-----EE
Confidence            58999999999999999999875  34555444433332211  12399999999999999999999988542     45


Q ss_pred             EEEeccC
Q 009860           89 IVEYAPS   95 (523)
Q Consensus        89 ~VEfAPY   95 (523)
                      .|++|.-
T Consensus        81 ~V~~a~~   87 (104)
T d1p1ta_          81 RVDNAAS   87 (104)
T ss_dssp             EEEETTC
T ss_pred             EEEECCC
Confidence            7888743

>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=97.27  E-value=0.00053  Score=55.31  Aligned_cols=78  Identities=21%  Similarity=0.232  Sum_probs=56.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcce--eEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYS--RAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~yS--RAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+..+|.|.+||+.+||+++.+.+...-. -+.+ ..+.-+    ..-.+  -|||.|.+.+++..-++.++|+.|-+  
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~-i~~~-~~~~~~----~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g--   87 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGN-VVSA-KVFIDK----QTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGM--   87 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSC-CSEE-EEEECS----SSCSEEEEEEEECSSHHHHHHHHHHHTTCEETT--
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhcc-cccc-ceeeec----ccCCCccceEEEeCCHHHHHHHHHHhCCCEECC--
Confidence            45689999999999999999999987532 1222 222111    11133  49999999999999999999998843  


Q ss_pred             CCeeeeEEEec
Q 009860           83 GAQFKAIVEYA   93 (523)
Q Consensus        83 Gne~~A~VEfA   93 (523)
                         -.-.|+||
T Consensus        88 ---~~i~V~~a   95 (102)
T d2cpza1          88 ---KRLKVQLK   95 (102)
T ss_dssp             ---EECEEECC
T ss_pred             ---EEEEEEEe
Confidence               24567776

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.26  E-value=0.00096  Score=53.82  Aligned_cols=83  Identities=20%  Similarity=0.255  Sum_probs=62.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE-eCCCC
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV-NEKGA   84 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv-DsKGn   84 (523)
                      +...|.|++||+.+||+++.+.+...  +.|....+.+.+        .-|||.|.+.++....++.+++..+. +.   
T Consensus        14 ps~~l~v~nlp~~~te~~l~~~F~~f--G~I~~~~~~~~k--------~~AfV~f~~~e~A~~ai~~~~~~~~~~~g---   80 (104)
T d1wexa_          14 VSPVVHVRGLCESVVEADLVEALEKF--GTICYVMMMPFK--------RQALVEFENIDSAKECVTFAADVPVYIAG---   80 (104)
T ss_dssp             CCSEEEEESCCSSCCHHHHHHHHTTT--SCEEEEEEETTT--------TEEEEEESSHHHHHHHHHHHHHSCCBSSS---
T ss_pred             CCCEEEEeCCCCCCCHHHHHHhhhhc--ccceEEEEEecc--------eeEEEEeCCHHHHHHHHHHHcCCCcEEee---
Confidence            34567899999999999999999875  356666554321        23999999999999999988765432 22   


Q ss_pred             eeeeEEEeccCCCCCCCC
Q 009860           85 QFKAIVEYAPSQRVPKPF  102 (523)
Q Consensus        85 e~~A~VEfAPYQKvPk~k  102 (523)
                       .+..|.||-++++....
T Consensus        81 -~~l~v~~s~~~~~~~~~   97 (104)
T d1wexa_          81 -QQAFFNYSTSKRITRPG   97 (104)
T ss_dssp             -SBCEEEECSSSSCCCSC
T ss_pred             -EEEEEEEcCCCccCCCC
Confidence             26889999988877654

>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=97.25  E-value=0.00061  Score=55.39  Aligned_cols=79  Identities=16%  Similarity=0.299  Sum_probs=63.6

Q ss_pred             CCCceEEEec--CCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            5 LQRTKVVIRH--LPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         5 ~~r~KVVIRr--LPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+...++|.+  ||+++||+++.+.+.+.  |.+....+.+++        ..|||.|.+.++....++.++|+.+.|..
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~--G~i~~i~~~~~k--------~~aFV~f~~~e~A~~A~~~lng~~i~~~~   85 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKC--GLVDALLMPPNK--------PYSFARYRTTEESKRAYVTLNGKEVVDDL   85 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHH--SCEEEEECCTTC--------SCEEEEESSHHHHHHHHHHTTTCEEECTT
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhh--CcccEEeeccCc--------cEEEEEECCHHHHHHHHHHhCCCCCCCCC
Confidence            3456788877  99999999999999986  456666665543        36999999999999999999999999988


Q ss_pred             CCeeeeEEEec
Q 009860           83 GAQFKAIVEYA   93 (523)
Q Consensus        83 Gne~~A~VEfA   93 (523)
                      +.....-+.|+
T Consensus        86 ~~~i~~~~~~~   96 (101)
T d2cq2a1          86 GQKITLYLNFV   96 (101)
T ss_dssp             SCEEECEEEEE
T ss_pred             CcEEEEEEEee
Confidence            86655555554

>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=97.24  E-value=0.001  Score=53.93  Aligned_cols=79  Identities=18%  Similarity=0.210  Sum_probs=60.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      |.....|.|++||+.+||+++.+.+..+  |.|.........     ..-.-|||.|.+.+++...++.++|+.|.+   
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~--G~v~~i~~~~~~-----~~kG~afV~f~~~~~A~~Ai~~l~g~~~~g---   73 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKY--GPIRQIRVGNTP-----ETRGTAYVVYEDIFDAKNACDHLSGFNVCN---   73 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTT--SCEEEEEEECST-----TTTTEEEEEESSHHHHHHHHHHHTTCEETT---
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhc--CCeEeecccccC-----CcCCeEEEEECCHHHHHHHHHHhCCCEECC---
Confidence            4455679999999999999999999875  456555443211     112359999999999999999999999853   


Q ss_pred             CeeeeEEEecc
Q 009860           84 AQFKAIVEYAP   94 (523)
Q Consensus        84 ne~~A~VEfAP   94 (523)
                        ....|+||.
T Consensus        74 --r~l~V~~a~   82 (114)
T d2f9da1          74 --RYLVVLYYN   82 (114)
T ss_dssp             --EECEEEECC
T ss_pred             --EEEEEEEcC
Confidence              356788874

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.17  E-value=0.00038  Score=52.32  Aligned_cols=67  Identities=15%  Similarity=0.143  Sum_probs=48.6

Q ss_pred             eEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      ||-|.+||+++||+++.+.+...-  .+.-...+..+.+.  ....-|||.|.+.+++....+ ++|+.|-+
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G--~i~~~~~~~~~~~~--~~~~~afV~F~~~~~a~~al~-~~~~~l~g   67 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFG--KVDDAMLMFDKTTN--RHRGFGFVTFESEDIVEKVCE-IHFHEINN   67 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTS--CCSEECCBCCTTCT--TSCCEEEEECSCHHHHHHHHH-CSSCCBTT
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhC--Ccceeeeeeecccc--ccCceeEEEECCHHHHHHHHh-cCCCEECC
Confidence            689999999999999999998752  33333333322222  223469999999999988876 89998743

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.16  E-value=0.0011  Score=52.47  Aligned_cols=83  Identities=16%  Similarity=0.088  Sum_probs=59.0

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009860            2 KEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         2 k~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs   81 (523)
                      ....+...|.|.+||+.+|++++.+.+...  +.|.-...+.-..+...  -.-|||.|.+.+++....+.++|+.|.+-
T Consensus         4 ~~~~~~~tlfV~nLp~~~t~~~l~~~F~~~--G~v~~v~~~~d~~tg~~--kg~afV~f~~~~~A~~Ai~~l~g~~~~g~   79 (93)
T d1x5ua1           4 SERNQDATVYVGGLDEKVSEPLLWELFLQA--GPVVNTHMPKDRVTGQH--QGYGFVEFLSEEDADYAIKIMDMIKLYGK   79 (93)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTT--SCEEEEECCBCSSSCSB--CSCEEEEESSHHHHHHHHHHSSSCBCSSC
T ss_pred             CcCCCCCEEEEeCCCCcCCHHHHHHHHHHh--CCccccceeeccccccc--ccceEEEECCHHHHHHHHHHcCCCEECCE
Confidence            345566789999999999999999999875  24543333222111111  12499999999999999999999988542


Q ss_pred             CCCeeeeEEEec
Q 009860           82 KGAQFKAIVEYA   93 (523)
Q Consensus        82 KGne~~A~VEfA   93 (523)
                           .-.|++|
T Consensus        80 -----~l~V~~A   86 (93)
T d1x5ua1          80 -----PIRVNKA   86 (93)
T ss_dssp             -----BCEEEET
T ss_pred             -----EEEEEEc
Confidence                 4567766

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.10  E-value=0.002  Score=51.71  Aligned_cols=71  Identities=20%  Similarity=0.182  Sum_probs=55.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      ....+|.|.+||+.+|+++|.+.+...  +.|.+..-.     .    -.-|||.|.+.+++..-++.|+|..|....-.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~--G~v~~~~i~-----~----~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~   81 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREA--GDVCYADVQ-----K----DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGE   81 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTS--SCEEEEEEE-----T----TTEEEEEESSHHHHHHHHHHHSSEEEECTTSC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhh--ccccccccc-----c----cceEEEEECCHHHHHHHHHHhCCCEeCCeEEE
Confidence            345689999999999999999999764  345444321     1    14799999999999999999999999877654


Q ss_pred             ee
Q 009860           85 QF   86 (523)
Q Consensus        85 e~   86 (523)
                      ..
T Consensus        82 v~   83 (98)
T d1wg4a_          82 TS   83 (98)
T ss_dssp             EE
T ss_pred             EE
Confidence            33

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=97.07  E-value=0.00096  Score=55.98  Aligned_cols=79  Identities=16%  Similarity=0.197  Sum_probs=58.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCccee--EEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSR--AYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySR--AYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      ....+|.|.+||+.+||+++.+.+...  |.|.....+.-+.+.    .+|  |||.|.+.+++..-++.++|+.|-+  
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~--G~i~~v~i~~d~~t~----~~rg~afV~f~~~~~A~~Ai~~lng~~~~g--  111 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERY--GPIESVKIVCDRETR----QSRGYGFVKFQSGSSAQQAIAGLNGFNILN--  111 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHH--SCEEEEEEEEETTTT----EEEEEEEEEESSHHHHHHHHHHTTTEECSS--
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhh--ccccccccccccccc----cccceeeEEECCHHHHHHHHHHhCCCEECC--
Confidence            344689999999999999999998875  345444433222211    244  9999999999999999999998842  


Q ss_pred             CCeeeeEEEecc
Q 009860           83 GAQFKAIVEYAP   94 (523)
Q Consensus        83 Gne~~A~VEfAP   94 (523)
                         ..-.|+||-
T Consensus       112 ---r~l~V~~a~  120 (139)
T d1u6fa1         112 ---KRLKVALAA  120 (139)
T ss_dssp             ---CEEEEEESS
T ss_pred             ---EEEEEEEcC
Confidence               357788874

>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=97.06  E-value=0.0013  Score=51.37  Aligned_cols=79  Identities=19%  Similarity=0.175  Sum_probs=61.2

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeee
Q 009860            8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFK   87 (523)
Q Consensus         8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~   87 (523)
                      .||-|.+||+.+||+++.+.+...  |.|.-...+..+.+.+  .-.-|||.|.+++++...++.++|+.|.+.     .
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~--G~v~~v~i~~d~~tg~--~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~-----~   72 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSF--GPLKAFNLVKDSATGL--SKGYAFCEYVDINVTDQAIAGLNGMQLGDK-----K   72 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSS--SCEEEEEEECCCSSSC--CCCEEEEEESSSHHHHHHHHTSSSCCCSSS-----C
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhc--CccceEEeeccccccc--cceeEEEEECCHHHHHHHHHHhCCCEECCE-----E
Confidence            379999999999999999999874  3465555554333221  234799999999999999999999988653     4


Q ss_pred             eEEEeccC
Q 009860           88 AIVEYAPS   95 (523)
Q Consensus        88 A~VEfAPY   95 (523)
                      ..|++|..
T Consensus        73 l~V~~A~~   80 (85)
T d2u2fa_          73 LLVQRASV   80 (85)
T ss_dssp             CEEEECCC
T ss_pred             EEEEECCC
Confidence            78888864

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.02  E-value=0.00092  Score=52.31  Aligned_cols=65  Identities=23%  Similarity=0.266  Sum_probs=52.7

Q ss_pred             eEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      ||.|.+||+++|++++.+.+...  |.|.......         ..-|||.|.+.+++..-++.++|..|.+....
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~--G~v~~~~i~~---------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~   66 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREA--GDVCYADVYR---------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGE   66 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGG--SCEEEEEECT---------TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSC
T ss_pred             eEEEECCCCcCCHHHHHHHHhhh--cccccccccc---------cceeeEEeCCHHHHHHHHHHhCCCEECCcEeE
Confidence            79999999999999999999875  3465443221         13599999999999999999999999776543

>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=96.98  E-value=0.0024  Score=50.92  Aligned_cols=83  Identities=14%  Similarity=0.161  Sum_probs=57.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+.+.|.|++||+.+||+++.+.+...  + +.....+.-+... ...-.-|||.|.+.+++.... .++++.|.+   
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~--g-~~~~~~~~~~~~~-g~~~g~afV~f~~~e~a~~~~-~~~~~~~~g---   83 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGL--N-ISAVRLPREPSNP-ERLKGFGYAEFEDLDSLLSAL-SLNEESLGN---   83 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTS--C-EEEEECCBCSSCT-TSBCSCEEEEESSHHHHHHHH-GGGTCEETT---
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHh--c-cccceeeeeeccC-CCcceeeeEEECCHHHHHHHH-HcCCCEECC---
Confidence            3456899999999999999999999874  3 3333332211111 111236999999999998766 589998733   


Q ss_pred             CeeeeEEEeccCC
Q 009860           84 AQFKAIVEYAPSQ   96 (523)
Q Consensus        84 ne~~A~VEfAPYQ   96 (523)
                        ....|++|--+
T Consensus        84 --r~l~V~~a~~~   94 (104)
T d1wi8a_          84 --KRIRVDVADQA   94 (104)
T ss_dssp             --EECEEEECCCC
T ss_pred             --EEEEEEECCCC
Confidence              36688887543

>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=96.98  E-value=0.00041  Score=54.71  Aligned_cols=78  Identities=14%  Similarity=0.209  Sum_probs=57.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCC--CceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFN--DRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~--gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      |...|.|.+||+.+|++++.+.|...+.  |.|....+...     .....-|||.|.+.+++......++|+.|.+   
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~-----~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g---   73 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS-----LKMRGQAFVIFKEVSSATNALRSMQGFPFYD---   73 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHH-----HHHTTCEEEEESSHHHHHHHHHHHTTCEETT---
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeee-----ccCCCceEEEECCHHHHHHHHHHhCCCEECC---
Confidence            4578999999999999999887755442  45655443211     0112359999999999999999999988753   


Q ss_pred             CeeeeEEEec
Q 009860           84 AQFKAIVEYA   93 (523)
Q Consensus        84 ne~~A~VEfA   93 (523)
                        ..-.|+||
T Consensus        74 --~~l~v~~a   81 (91)
T d1nu4a_          74 --KPMRIQYA   81 (91)
T ss_dssp             --EECEEEEC
T ss_pred             --EEEEEEEe
Confidence              35677776

>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=96.94  E-value=0.0023  Score=48.92  Aligned_cols=72  Identities=17%  Similarity=0.228  Sum_probs=54.7

Q ss_pred             EEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeeeeE
Q 009860           10 VVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKAI   89 (523)
Q Consensus        10 VVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~A~   89 (523)
                      |.|++||+.+|++++.+.+.++-   +.... + ++      ...-|||.|.+.+++..-.+.++|+.|.+     ..-.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g---~~~~~-~-~~------~~g~afv~f~~~~~A~~Ai~~ln~~~~~g-----~~l~   64 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE---LKYCF-V-DK------YKGTAFVTLLNGEQAEAAINTFHQSRLRE-----RELS   64 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC---EEEEE-E-ET------TTTEEEEEESSHHHHHHHHHHHTTEESSS-----CEEE
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc---cccee-e-cc------cceeEEEEECCHHHHHHHHHHhCCccCCC-----CEEE
Confidence            68999999999999999998752   22111 1 11      12359999999999999999999998843     2577


Q ss_pred             EEeccCCC
Q 009860           90 VEYAPSQR   97 (523)
Q Consensus        90 VEfAPYQK   97 (523)
                      |+|||-.-
T Consensus        65 V~~a~~d~   72 (75)
T d1wi6a1          65 VQLQPTDA   72 (75)
T ss_dssp             EEECCSTT
T ss_pred             EEEeCCCC
Confidence            89887543

>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=96.93  E-value=0.0028  Score=49.32  Aligned_cols=82  Identities=15%  Similarity=0.245  Sum_probs=60.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..|...|.|++||+.+|++++++.+.+.  +.|....+.+.+        .-|||.|.+.++.....+.+.++.+.- .|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~--G~i~~v~~~~~~--------~~afV~f~~~e~A~~a~~~~~~~~~~~-~g   73 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPF--GKVTNILMLKGK--------NQAFLELATEEAAITMVNYYSAVTPHL-RN   73 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTT--SCEEEEEEETTT--------TEEEEEESSHHHHHHHHHHHHHSCCEE-TT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcc--cccccccccccc--------eEEEEEeCCHHHHHHHHHHHccCCCcc-CC
Confidence            3456678899999999999999999875  356666665432        249999999999999988876543221 22


Q ss_pred             CeeeeEEEeccCCCC
Q 009860           84 AQFKAIVEYAPSQRV   98 (523)
Q Consensus        84 ne~~A~VEfAPYQKv   98 (523)
                        .+..|+||-++.+
T Consensus        74 --~~l~v~~sk~~~l   86 (88)
T d2cq1a1          74 --QPIYIQYSNHKEL   86 (88)
T ss_dssp             --EECEEEECSCSSC
T ss_pred             --CEEEEEECCCCCC
Confidence              3678899977653

>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=96.90  E-value=0.002  Score=51.57  Aligned_cols=75  Identities=12%  Similarity=0.170  Sum_probs=56.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+.++|.|.+||+.+||+++.+.+...  |.|.....+...   ......-|||.|.+.++...-++.++|..|.+...
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~--G~i~~~~~~~~~---~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~   89 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPF--GQVISTRILRDS---SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPG   89 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTT--SCEEEEEEEECS---SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTT
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhc--ccccceeeeccc---ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCC
Confidence            3456899999999999999999999875  345443333221   12234569999999999999999999999876544

>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=96.90  E-value=0.0014  Score=52.99  Aligned_cols=87  Identities=10%  Similarity=0.094  Sum_probs=65.2

Q ss_pred             CCCCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            1 MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         1 mk~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      |-.+.+-+.|.|++||..+||+++.+.+..+-  .|.-...+..+      .-.-|||.|.+.+++..-++.++|+.|.+
T Consensus         1 ~~~~s~~~~v~V~NL~~~vte~~L~~~F~~~G--~i~~~~i~~~~------~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~   72 (108)
T d2adba1           1 MAGQSPVLRIIVENLFYPVTLDVLHQIFSKFG--TVLKIITFTKN------NQFQALLQYADPVSAQHAKLSLDGQNIYN   72 (108)
T ss_dssp             SCCCCCEEEEESCSCCSTTHHHHHHHHHTTTS--CEEEEEEEEET------TEEEEEEEESCHHHHHHHHHHHHSCCSST
T ss_pred             CCCCCCeEEEEEeCcCCCCCHHHHHHHHccCC--cEEEEEEEeeC------CCCeEEEEECCHHHHHHHHHHHCCCEecc
Confidence            77888999999999999999999999999853  34322222221      12359999999999999999999998854


Q ss_pred             CCCCeeeeEEEeccCCCC
Q 009860           81 EKGAQFKAIVEYAPSQRV   98 (523)
Q Consensus        81 sKGne~~A~VEfAPYQKv   98 (523)
                      .   .....|.|+-.+.+
T Consensus        73 ~---~~~l~v~~s~~~~~   87 (108)
T d2adba1          73 A---CCTLRIDFSKLTSL   87 (108)
T ss_dssp             T---CCCCEEEECSSCSC
T ss_pred             C---CcEEEEEecCCccc
Confidence            3   23566788755543

>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=96.90  E-value=0.0029  Score=49.10  Aligned_cols=75  Identities=17%  Similarity=0.154  Sum_probs=55.7

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF   86 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~   86 (523)
                      ...|.|.+||+..||+++.+.+...-  .+.....+.++-      ..-|||.|.+.++...-...++|+.+.|.    .
T Consensus        10 s~tL~V~NLp~~~te~~l~~~F~~~G--~v~~~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~~g----~   77 (88)
T d2adca2          10 SATLHLSNIPPSVSEEDLKVLFSSNG--GVVKGFKFFQKD------RKMALIQMGSVEEAVQALIDLHNHDLGEN----H   77 (88)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTS--CCEEEEEECSSS------TTCEEEEESSHHHHHHHHHHHTTCBSSSS----C
T ss_pred             CCEEEEECCCCCCCHHHHHHHhhccC--CEEEEEEeeecc------cceeEEEECCHHHHHHHHHhccCCEecCC----C
Confidence            45688999999999999999998753  333333444432      12499999999999999999999876543    2


Q ss_pred             eeEEEec
Q 009860           87 KAIVEYA   93 (523)
Q Consensus        87 ~A~VEfA   93 (523)
                      .-.|+||
T Consensus        78 ~l~v~~s   84 (88)
T d2adca2          78 HLRVSFS   84 (88)
T ss_dssp             BCEEEEC
T ss_pred             EEEEEeC
Confidence            4567776

>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=96.90  E-value=0.0031  Score=50.33  Aligned_cols=80  Identities=18%  Similarity=0.196  Sum_probs=62.7

Q ss_pred             CceEEEecCCCC-CCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            7 RTKVVIRHLPPS-LSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         7 r~KVVIRrLPP~-LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      ...|.|.+|||. +||+++.+.+..+  |.|.....+..+       -.-|||.|.+.+++...++.++|..|.+.    
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~f--G~I~~v~i~~~~-------kg~afV~f~~~~~A~~ai~~lng~~l~g~----   68 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVY--GDVQRVKILFNK-------KENALVQMADGNQAQLAMSHLNGHKLHGK----   68 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHH--TCEEEEEECCTT-------SCCEEEEESCHHHHHHHHHHHTTCBCSSS----
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhc--cccceEEEEecc-------cceEEEEECCHHHHHHHHHHhCCCEECCE----
Confidence            367999999885 9999999999875  467666665432       12599999999999999999999998653    


Q ss_pred             eeeEEEeccCCCCCC
Q 009860           86 FKAIVEYAPSQRVPK  100 (523)
Q Consensus        86 ~~A~VEfAPYQKvPk  100 (523)
                       ...|+||....+..
T Consensus        69 -~l~v~~s~~~~~~~   82 (109)
T d2adca1          69 -PIRITLSKHQNVQL   82 (109)
T ss_dssp             -BCEEECCSCCCCCC
T ss_pred             -EEEEEECCCCCCCC
Confidence             56899987665443

>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=96.88  E-value=0.00084  Score=50.31  Aligned_cols=67  Identities=16%  Similarity=0.189  Sum_probs=48.7

Q ss_pred             EEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860           10 VVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus        10 VVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      |-|.+||+.+||+++.+.+...  +.+.-.....-+...  ....-|||.|.+.+++....+.++|..|..
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~--G~v~~~~~~~~~~~~--~~~g~afV~f~~~~~A~~Ai~~lng~~~~G   67 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPY--GKIVSTKAILDKTTN--KCKGYGFVDFDSPSAAQKAVTALKASGVQA   67 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTT--SCEEEEEEECCSSSC--SCCSEEEEEESCHHHHHHHHHHHHHHTCCE
T ss_pred             CEEeCCCCcCCHHHHHHHHhhh--ccccccccccccccc--cccceeEEEECCHHHHHHHHHHhCCCEECC
Confidence            5799999999999999998864  234332222222211  223469999999999999999999988754

>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=96.84  E-value=0.0017  Score=51.00  Aligned_cols=78  Identities=15%  Similarity=0.272  Sum_probs=58.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      ....+|.|++||+..|++++.+.+.++- -.+....          ....-|||.|.+.++...-++.++++.|.+    
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~----------~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G----   67 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD----------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRG----   67 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE----------GGGTEEEECCSCHHHHHHHHHHHTTEEETT----
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee----------ccCCceEEEECCHHHHHHHHHHhCCCEECC----
Confidence            3457899999999999999999998752 1221111          012359999999999999999999998732    


Q ss_pred             eeeeEEEeccCCCC
Q 009860           85 QFKAIVEYAPSQRV   98 (523)
Q Consensus        85 e~~A~VEfAPYQKv   98 (523)
                       ..-.|+||+-...
T Consensus        68 -~~l~V~~a~~~~~   80 (88)
T d1wg1a_          68 -KDLIVQLQPTDAL   80 (88)
T ss_dssp             -EEEEEEECCCCCC
T ss_pred             -EEEEEEEcCCCCC
Confidence             3678899976543

>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=96.82  E-value=0.0011  Score=51.88  Aligned_cols=76  Identities=14%  Similarity=0.151  Sum_probs=56.5

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF   86 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~   86 (523)
                      ...|.|.+||+.+|++++.+.+...  +.|.....+..+..    ...-|||.|.+.+++..-++.++|..|.+     .
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 VGNIFIKNLDKSIDNKALYDTFSAF--GNILSCKVVCDENG----SKGYGFVHFETQEAAERAIEKMNGMLLND-----R   76 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTT--SCEEEEEECCBTTB----CCSCEEEEESCHHHHHHHTTSSSEEEETT-----E
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhc--CCceEEEEEeecCC----CcceeEEEECCHHHHHHHHHHcCCCEECC-----E
Confidence            3569999999999999999999875  34554443322211    12359999999999999999999988733     2


Q ss_pred             eeEEEec
Q 009860           87 KAIVEYA   93 (523)
Q Consensus        87 ~A~VEfA   93 (523)
                      .-.|++|
T Consensus        77 ~i~V~~a   83 (89)
T d1cvja2          77 KVFVGRF   83 (89)
T ss_dssp             EEEEEEC
T ss_pred             EEEEEEC
Confidence            5667776

>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=96.80  E-value=0.004  Score=50.04  Aligned_cols=85  Identities=19%  Similarity=0.171  Sum_probs=61.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      ..+||-|.+||+.+||+++.+.+...  +.|.....+..+.+.+.  -.-|||.|.+.+++...++.+++ .| +  |  
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~--G~i~~v~i~~d~~tg~~--kg~afV~f~~~~~A~~Ai~~~~~-~l-~--G--   78 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGF--GDIEEAVVITDRQTGKS--RGYGFVTMADRAAAERACKDPNP-II-D--G--   78 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTT--SCEEEEEESCCSSSCCC--CSEEEEEESSHHHHHHHHTCSSC-EE-T--T--
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhc--ccccceecccccccccc--CCeEEEEECCHHHHHHHHHHCCC-cC-C--C--
Confidence            45789999999999999999999864  35665555544433221  22499999999999999988875 43 3  3  


Q ss_pred             eeeEEEeccCCCCCC
Q 009860           86 FKAIVEYAPSQRVPK  100 (523)
Q Consensus        86 ~~A~VEfAPYQKvPk  100 (523)
                      ....|++|.....|+
T Consensus        79 r~l~V~~a~~~~~pr   93 (103)
T d2cqda1          79 RKANVNLAYLGAKPR   93 (103)
T ss_dssp             EECEEEESTTTCCCC
T ss_pred             EEEEEEEcCCCCCCC
Confidence            356788887655554

>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=96.78  E-value=0.0019  Score=50.61  Aligned_cols=86  Identities=9%  Similarity=0.019  Sum_probs=57.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+..+|.|.+||++.||+++.+.+..+  +.+........+...  ..-.-|||.|.+.+++...++.+++..+.+..-
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~--G~v~~~~~~~~~~~~--~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~   80 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQF--GDLKYVRVVLHPDTE--HSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLK   80 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTT--SCEEEEECCBCSSSC--CBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEE
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhcc--ccceeeeeccccccc--cccceEEEEEcCHHHHHHHHHHcccccccCCcE
Confidence            4456789999999999999999999875  344433333332221  112359999999999999999988655433210


Q ss_pred             -CeeeeEEEec
Q 009860           84 -AQFKAIVEYA   93 (523)
Q Consensus        84 -ne~~A~VEfA   93 (523)
                       +-....|++|
T Consensus        81 ~~gr~l~v~~a   91 (98)
T d1x4ha1          81 LDGRQLKVDLA   91 (98)
T ss_dssp             SSSCEEEEECC
T ss_pred             ECCEEEEEEEC
Confidence             0114667776

>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=96.77  E-value=0.0024  Score=50.30  Aligned_cols=82  Identities=18%  Similarity=0.160  Sum_probs=56.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEE-------EeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWF-------CFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGH   76 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwf-------yFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~   76 (523)
                      ..+...|.|.+||+.+||++|++.+...-  .|...       .+..-+... .....-|||.|.+.+++...++.++|+
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G--~i~~~~~~~~~~~~~~~d~~~-~~~~g~afV~f~~~~~a~~Ai~~l~g~   81 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCG--VVKMNKRTGQPMIHIYLDKET-GKPKGDATVSYEDPPTAKAAVEWFDGK   81 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTS--CBCBCSSSCCBSEECCBCTTT-CSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCc--eEEEeeecccceeEEeecccc-ccccceeeEEecCHHHHHHHHHHhCCC
Confidence            34678999999999999999999987642  12111       111111111 112235999999999999999999999


Q ss_pred             eeEeCCCCeeeeEEEec
Q 009860           77 VFVNEKGAQFKAIVEYA   93 (523)
Q Consensus        77 vFvDsKGne~~A~VEfA   93 (523)
                      .|.   |  ..-.|++|
T Consensus        82 ~~~---g--r~i~V~~a   93 (101)
T d2cpea1          82 DFQ---G--SKLKVSLA   93 (101)
T ss_dssp             EET---T--EECEEECS
T ss_pred             EEC---C--EEEEEEEc
Confidence            883   2  35667776

>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=96.76  E-value=0.0011  Score=52.22  Aligned_cols=72  Identities=17%  Similarity=0.206  Sum_probs=50.8

Q ss_pred             CCceEEEecCCCCCCHHHHHH---HhcccCCCceeEEEeeCCCCCCCC-CcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009860            6 QRTKVVIRHLPPSLSQNDLLA---LFRDHFNDRYNWFCFRPGKSSYKH-QRYSRAYVELKKPAGVFEFAELLNGHVFV   79 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~e---qL~p~~~gkvdwfyFVpGK~S~Kp-~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv   79 (523)
                      ++..|-|.+|||.+|+++++.   .++..  |.|.......-+..... ....-|||.|.+.++...-++.++|+.|.
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~--G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~   82 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKF--GKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD   82 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTT--SCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhccc--CCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEEC
Confidence            456788999999999999943   34432  45655444333222221 22346999999999999999999999874

>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=96.73  E-value=0.0021  Score=49.00  Aligned_cols=65  Identities=15%  Similarity=0.167  Sum_probs=47.3

Q ss_pred             eEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      ||-|.+||+++||+++.+.+...  |.|.......-+.+.+..  .-|||.|.+.+++..-.+ .+++.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~--G~i~~~~i~~d~~t~~~k--g~afV~f~~~~~a~~Al~-~~~~~l   65 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKF--GEVVDCTLKLDPITGRSR--GFGFVLFKESESVDKVMD-QKEHKL   65 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTT--SCEEEEECCCBTTTTBCC--SEEEEEESSHHHHHHHHH-TCCCCB
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhh--ccccccccccCCCCCCcC--ceEEEEECCHHHHHHHHh-cCCCEE
Confidence            78999999999999999999874  345544433222222222  349999999999998886 677765

>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=96.71  E-value=0.0032  Score=49.87  Aligned_cols=80  Identities=9%  Similarity=0.097  Sum_probs=53.9

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      +.....+|.|++||+++||+++.+.+...  |.|....-..-....  ..-.-|||.|.+.+++....+.  ++ ++|. 
T Consensus         4 ~~~~~~~lfV~nLp~~~te~~l~~~F~~~--G~i~~v~i~~d~~tg--~srG~aFV~f~~~~~a~~al~~--~~-~l~G-   75 (90)
T d2cqga1           4 AVQKTSDLIVLGLPWKTTEQDLKEYFSTF--GEVLMVQVKKDLKTG--HSKGFGFVRFTEYETQVKVMSQ--RH-MIDG-   75 (90)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGG--SCEEEEEEEECSSSC--SEEEEEEEEESSHHHHHHHHHS--CE-EETT-
T ss_pred             CCcCCCeEEEECCCCCCCHHHHHHHHHhh--cccceeeeccCCCCc--ccCCEEEEEECCHHHHHHHHhc--CC-ccCC-
Confidence            55677899999999999999999999975  345444333221111  1123599999999999888763  33 4443 


Q ss_pred             CCeeeeEEEec
Q 009860           83 GAQFKAIVEYA   93 (523)
Q Consensus        83 Gne~~A~VEfA   93 (523)
                         ....|.+|
T Consensus        76 ---r~i~v~~a   83 (90)
T d2cqga1          76 ---RWCDCKLP   83 (90)
T ss_dssp             ---EEEEEECC
T ss_pred             ---EEeEEEeC
Confidence               24566655

>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=96.61  E-value=0.0047  Score=49.88  Aligned_cols=67  Identities=19%  Similarity=0.216  Sum_probs=50.5

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009860            8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV   79 (523)
Q Consensus         8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv   79 (523)
                      ..|-|++||+.+||+++.+.+...  |.|.....+..+.+.+.-  .-|||.|.+.+++..-.+ ++|..|.
T Consensus        19 ~tifV~nL~~~~te~~l~~~F~~~--G~V~~v~i~~d~~tg~~k--G~afV~F~~~e~a~~A~~-l~g~~~~   85 (101)
T d2cq4a1          19 RTVFCMQLAARIRPRDLEDFFSAV--GKVRDVRIISDRNSRRSK--GIAYVEFCEIQSVPLAIG-LTGQRLL   85 (101)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTT--SCEEEEEECCSCCSSSCC--CCEEEEESCGGGHHHHHH-HTTEEET
T ss_pred             CEEEEECCCCCCCHHHHHHHHcCC--CeEEEEEeeecCCCcccc--ceEEEEECCHHHHHHHHH-HCCCEEC
Confidence            469999999999999999999874  456555554433322222  249999999999998874 9999873

>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=96.57  E-value=0.0035  Score=47.91  Aligned_cols=64  Identities=19%  Similarity=0.257  Sum_probs=48.7

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      +-|.|++||+++|++++.+.+...  |.|........+...    ..-|||.|.+.+++.... .++++.|
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~--G~I~~v~~~~~~~~~----~~~afV~F~~~~~a~~Al-~~~~~~i   64 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHC--GPIIHVDVADSLKKN----FRFARIEFARYDGALAAI-TKTHKVV   64 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGG--SCEEEEEEEECTTSS----SEEEEEEESSHHHHHHHH-TTTTCEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcC--CceEEEEEEeecccc----ceEEEEEEcchHHhHHHH-HhcCcEE
Confidence            468999999999999999999875  456555544333221    247999999999998876 5788876

>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=96.55  E-value=0.0061  Score=47.52  Aligned_cols=77  Identities=16%  Similarity=0.077  Sum_probs=55.4

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeee
Q 009860            8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFK   87 (523)
Q Consensus         8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~   87 (523)
                      ..|-|.+||+.+||+++.+.+...-  .|.....+.-..+.+ + -.-|||.|.+.+++....+.++|+.|-   |  ..
T Consensus         6 ~tlfV~nLp~~~te~~l~~~F~~~G--~i~~v~i~~d~~~~~-~-kg~afV~f~~~~~A~~ai~~l~~~~i~---g--~~   76 (89)
T d2cqba1           6 RVLYVGGLAEEVDDKVLHAAFIPFG--DITDIQIPLDYETEK-H-RGFAFVEFELAEDAAAAIDNMNESELF---G--RT   76 (89)
T ss_dssp             SCEEEESCCSSCCHHHHHHHHTTTS--CCCCEECCCCSSSCC-C-SSEEEECCSSHHHHHHHHHHHTTEEET---T--EE
T ss_pred             cEEEEeCCCCcCCHHHHHHHHhhCC--eEEeccccccccccc-c-cceeEEEECCHHHHHHHHHHcCCCEEC---C--EE
Confidence            5788999999999999999998642  343333322111111 1 124999999999999999999998773   2  25


Q ss_pred             eEEEec
Q 009860           88 AIVEYA   93 (523)
Q Consensus        88 A~VEfA   93 (523)
                      ..|+||
T Consensus        77 l~v~~a   82 (89)
T d2cqba1          77 IRVNLA   82 (89)
T ss_dssp             EEEEEC
T ss_pred             EEEEEe
Confidence            778888

>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=96.54  E-value=0.0037  Score=47.85  Aligned_cols=75  Identities=16%  Similarity=0.194  Sum_probs=53.8

Q ss_pred             EEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeeeeE
Q 009860           10 VVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKAI   89 (523)
Q Consensus        10 VVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~A~   89 (523)
                      |=|.+|||.+||+++.+.+... . .|.-...+.-..+.  ..-.-|||.|.+++++....+.++|+.|-   |  ..-.
T Consensus         3 lfV~nL~~~~te~~l~~~F~~~-G-~i~~v~i~~d~~tg--~~~g~aFV~f~~~~~a~~ai~~l~g~~~~---g--r~i~   73 (80)
T d1cvja1           3 LYVGDLHPDVTEAMLYEKFSPA-G-PILSIRVCRDMITR--RSLGYAYVNFQQPADAERALDTMNFDVIK---G--KPVR   73 (80)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGG-S-CEEEEEEEECTTTC--CEEEEEEEEESSHHHHHHHHTTSTTCEET---T--EECE
T ss_pred             EEEeCCCCcCCHHHHHHHHHHh-C-CEeEEEEEeccccc--CCCCceEEEECCHHHHHHHHHHcCCCEEC---C--EEEE
Confidence            6689999999999999999865 2 34333333222211  12347999999999999999999999873   2  2466


Q ss_pred             EEec
Q 009860           90 VEYA   93 (523)
Q Consensus        90 VEfA   93 (523)
                      |+||
T Consensus        74 v~~a   77 (80)
T d1cvja1          74 IMWS   77 (80)
T ss_dssp             EEEC
T ss_pred             EEEe
Confidence            7776

>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=96.54  E-value=0.0034  Score=48.80  Aligned_cols=72  Identities=17%  Similarity=0.117  Sum_probs=52.4

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            2 KEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         2 k~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      ++|-+..+|-|.+||+++||+++.+.+..+  |.+.......-..+.+  .-.-|||.|.+.+++....+ .+++.|
T Consensus         1 ~epe~~~~lfV~nlp~~~te~~l~~~F~~~--G~i~~v~i~~d~~tg~--~kG~afV~f~~~~~a~~ai~-~~~~~i   72 (84)
T d1l3ka1           1 KEPEQLRKLFIGGLSFETTDESLRSHFEQW--GTLTDCVVMRDPNTKR--SRGFGFVTYATVEEVDAAMN-ARPHKV   72 (84)
T ss_dssp             CCCGGGGEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTCC--EEEEEEEEESSHHHHHHHHH-TCSCEE
T ss_pred             CCCCCCcEEEEECCCCCCCHHHHHHHHHhh--ccccceeecccccCCC--cccEEEEEEcCHHHHHHHHH-hCCCEE
Confidence            355666799999999999999999999875  3565555432222111  12459999999999988876 488776

>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=96.53  E-value=0.0046  Score=49.27  Aligned_cols=74  Identities=11%  Similarity=0.096  Sum_probs=58.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA   84 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn   84 (523)
                      .+.+.|.|.+||+.+||+++.+.+.+.  |.|....+++.+        .-|||.|.+.++....++.++|..|.+    
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~f--G~i~~v~i~~~k--------g~afV~f~~~~~A~~Ai~~l~~~~i~g----   81 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPF--GQIMEIRVFPEK--------GYSFVRFSTHESAAHAIVSVNGTTIEG----   81 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHH--SCEEEEEEETTT--------TEEEEEESSHHHHHHHHHHHTTCEETT----
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHh--CCceEEEEEecc--------eEEEEEECCHHHHHHHHHHhCCCEECC----
Confidence            345789999999999999999999875  356666666542        359999999999999999999988732    


Q ss_pred             eeeeEEEec
Q 009860           85 QFKAIVEYA   93 (523)
Q Consensus        85 e~~A~VEfA   93 (523)
                       ....|+||
T Consensus        82 -~~l~v~~a   89 (96)
T d1x4ga1          82 -HVVKCYWG   89 (96)
T ss_dssp             -EECEEECC
T ss_pred             -EEEEEEEc
Confidence             34667775

>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=96.49  E-value=0.0051  Score=47.46  Aligned_cols=70  Identities=20%  Similarity=0.120  Sum_probs=52.3

Q ss_pred             eEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeeee
Q 009860            9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKA   88 (523)
Q Consensus         9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~A   88 (523)
                      .|-|++||+.+||+++.+.+...-.  +.......   +     -.-|||.|.+.++...-...++|+.|.+     ..-
T Consensus        10 ~l~V~nLp~~~te~~l~~~F~~~g~--i~~~~~~~---~-----rg~afV~f~~~~~A~~Ai~~l~~~~i~g-----~~i   74 (86)
T d2cpda1          10 ILYVRNLMLSTSEEMIEKEFNNIKP--GAVERVKK---I-----RDYAFVHFSNREDAVEAMKALNGKVLDG-----SPI   74 (86)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHTTST--TCEEEEEE---C-----SSEEEEEESSHHHHHHHHHHHSSEEETT-----EEE
T ss_pred             EEEEcCCCCCCCHHHHHHhhcccce--eeeEEEcc---c-----cEEEEEEeCCHHHHHHHHHHcCCCEECC-----EEE
Confidence            5779999999999999999887532  22222211   1     1269999999999999999999988743     256


Q ss_pred             EEEec
Q 009860           89 IVEYA   93 (523)
Q Consensus        89 ~VEfA   93 (523)
                      .|+||
T Consensus        75 ~V~~a   79 (86)
T d2cpda1          75 EVTLA   79 (86)
T ss_dssp             EEECC
T ss_pred             EEEec
Confidence            78877

>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=96.46  E-value=0.0054  Score=47.18  Aligned_cols=69  Identities=13%  Similarity=0.087  Sum_probs=51.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCCC-ceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFND-RYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~g-kvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      ...+.|.|++||++.||+++.+.+...-.- ...++.+.+.     .....-|||.|.+.+++..-++.++++.+
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~-----g~~~G~afV~f~~~e~a~~Ai~~l~~~~l   76 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEK-----GMPTGEAMVAFESRDEATAAVIDLNDRPI   76 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSS-----SCEEEEEEEEESCHHHHHHHHHHTTTCEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCC-----CCcceEEEEEEcCcHHHHHHHHHcCCCEE
Confidence            345779999999999999999999875321 1123333211     11234699999999999999999999987

>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=96.45  E-value=0.0062  Score=48.03  Aligned_cols=78  Identities=15%  Similarity=0.298  Sum_probs=55.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhcccCC-CceeEE-EeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            5 LQRTKVVIRHLPPSLSQNDLLALFRDHFN-DRYNWF-CFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~-gkvdwf-yFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      .+...|.|.+||+.+|++++.+.+...-. ..+.+. ....|+.      -.-|||.|.+.+++...++.++|+.|.+  
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~------~g~~fV~f~~~~~A~~Ai~~l~g~~~~g--   87 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRM------RGQAFITFPNKEIAWQALHLVNGYKLYG--   87 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSS------CSEEEEECSSHHHHHHHHHHSTTCBCSS--
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccc------cccceEEeccHHHHHHHHHHhCCCEECC--
Confidence            34578999999999999999998875421 111111 1222321      2358999999999999999999998832  


Q ss_pred             CCeeeeEEEec
Q 009860           83 GAQFKAIVEYA   93 (523)
Q Consensus        83 Gne~~A~VEfA   93 (523)
                         .+-.|+||
T Consensus        88 ---~~l~V~~a   95 (102)
T d2cpxa1          88 ---KILVIEFG   95 (102)
T ss_dssp             ---CBCEEEEC
T ss_pred             ---EEEEEEeC
Confidence               25678887

>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=96.45  E-value=0.005  Score=47.08  Aligned_cols=76  Identities=17%  Similarity=0.143  Sum_probs=51.6

Q ss_pred             EEEecCCCCCCHHHHHHHhcccCCCce-eEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeeee
Q 009860           10 VVIRHLPPSLSQNDLLALFRDHFNDRY-NWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKA   88 (523)
Q Consensus        10 VVIRrLPP~LTEEeF~eqL~p~~~gkv-dwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~A   88 (523)
                      |-|.+||+.+||+++.+.+...-  .+ .....+.-..+.+  ...-|||.|.+.+++...++.++|..|.+     .+.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G--~i~~~~~i~~~~~~g~--~~g~afV~f~~~~~a~~Ai~~~~g~~~~g-----r~l   71 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFG--VILQTPKIMRDPDTGN--SKGYAFINFASFDASDAAIEAMNGQYLCN-----RPI   71 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTS--CBSSCCEECCCTTTCS--CCSEEEEEBSSHHHHHHHHHTTTTCEETT-----EEC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhC--ceeeeEEEEeeccccc--cCceEEEEECCHHHHHHHHHhCCCcEECC-----EEE
Confidence            56899999999999999998742  22 2111111111111  12349999999999999999999998732     256


Q ss_pred             EEEecc
Q 009860           89 IVEYAP   94 (523)
Q Consensus        89 ~VEfAP   94 (523)
                      .|++|-
T Consensus        72 ~v~~a~   77 (83)
T d1x5ta1          72 TVSYAF   77 (83)
T ss_dssp             EEEESC
T ss_pred             EEEEec
Confidence            677763

>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=96.42  E-value=0.0037  Score=50.05  Aligned_cols=71  Identities=15%  Similarity=0.070  Sum_probs=50.3

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      .+.....|.||.||++.||+++.+.+...-...+.+.+-..      -....-|||.|.+.+++....+ ++++.|-+
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~~v~~~~~~~------g~~~G~afVeF~~~~~a~~Al~-~~~~~i~g   81 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPD------GRVTGEADVEFATHEDAVAAMA-KDKANMQH   81 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCSEEEEEESSS------SCEEEEEEEECSSSHHHHHHHT-TSSCCSSS
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccCcceeeeEEecC------CcceEEEEEEECCHHHHHHHHH-cCCCEECC
Confidence            34556789999999999999999988864222232222111      1234679999999999998765 78887654

>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=96.39  E-value=0.0046  Score=47.54  Aligned_cols=71  Identities=25%  Similarity=0.351  Sum_probs=52.0

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcccCCC-ceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCe-eEeCCCCe
Q 009860            8 TKVVIRHLPPSLSQNDLLALFRDHFND-RYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHV-FVNEKGAQ   85 (523)
Q Consensus         8 ~KVVIRrLPP~LTEEeF~eqL~p~~~g-kvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~v-FvDsKGne   85 (523)
                      -+|.|++||+.+||+++.+.+...-.- .+.+..           .-.-|||.|.+.++.....+.++|.. | +  |  
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~-----------~rg~aFV~f~~~~~A~~Ai~~lng~~~~-~--G--   65 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----------KSGYAFVDYPDQNWAIRAIETLSGKVEL-H--G--   65 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-----------ETTEEEECCSCHHHHHHHHHHHTTTCEE-T--T--
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec-----------ccceEEEEECCHHHHHHHHHHhCCCeEE-C--C--
Confidence            479999999999999999999874210 111111           01259999999999999999999964 4 2  2  


Q ss_pred             eeeEEEecc
Q 009860           86 FKAIVEYAP   94 (523)
Q Consensus        86 ~~A~VEfAP   94 (523)
                      .+-.|+||-
T Consensus        66 ~~i~V~~a~   74 (80)
T d2cqha1          66 KIMEVDYSV   74 (80)
T ss_dssp             EECEEEECC
T ss_pred             EEEEEEEcC
Confidence            267788875

>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=96.36  E-value=0.0034  Score=48.26  Aligned_cols=64  Identities=14%  Similarity=0.222  Sum_probs=45.8

Q ss_pred             eEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCe
Q 009860            9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHV   77 (523)
Q Consensus         9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~v   77 (523)
                      ||-|.+||+.+||+++.+.+...  |.|.......-+.+.++.  .-|||.|.+.+++....+. +++.
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~--G~I~~v~i~~d~~t~~~r--G~~FV~f~~~~~a~~al~~-~~~~   64 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGF--GEVESIELPMDNKTNKRR--GFCFITFKEEEPVKKIMEK-KYHN   64 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHH--SCEEEEECCCCTTTCCTT--CCEEEEESSSHHHHHHTTC-SSCC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHh--CCcccccccccccccccc--cEEEEEECCHHHHHHHHhh-CCCE
Confidence            78999999999999999999975  456554443332222222  2399999999999888764 4443

>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=96.28  E-value=0.0038  Score=47.98  Aligned_cols=66  Identities=17%  Similarity=0.134  Sum_probs=47.3

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      +||-|++||+.+||+++.+.+...  |.|.-..-..-+.+.++  -.-|||.|.+.+++..-.+ .+++.+
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~--G~i~~v~i~~d~~tg~~--kG~aFV~f~~~~~a~~al~-~~~~~i   66 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQF--GEVKECLVMRDPLTKRS--RGFGFVTFMDQAGVDKVLA-QSRHEL   66 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTT--SCCCCEEEECCCCSSSC--SSEEEECCCCTTHHHHHHH-TTTCCC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHh--CCcceeeeecccCCCCc--cceEEEEECCHHHHHHHHH-cCCCEE
Confidence            689999999999999999999875  23432233222222211  2459999999999998886 587766

>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=96.28  E-value=0.015  Score=45.73  Aligned_cols=82  Identities=13%  Similarity=0.087  Sum_probs=57.7

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF   86 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~   86 (523)
                      ++||-|.+||+.+||+++.+.+...-. .+.-...+.-... ....-.-|||.|.+.++....++.+++..|.-. |  .
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~-~i~~v~~~~~~~~-~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~-g--~   75 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTE-GVLDVIVYASAAD-KMKNRGFAFVEYESHRAAAMARRKLMPGRIQLW-G--H   75 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHST-TEEEEECCSSSCT-TTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBT-T--B
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCC-cceEEEEeeeccc-cccCCCeEEEEEcCHHHHHHHHHHHcCCCeEEC-C--E
Confidence            579999999999999999999987643 2443333322111 111223599999999999999999987655432 2  2


Q ss_pred             eeEEEec
Q 009860           87 KAIVEYA   93 (523)
Q Consensus        87 ~A~VEfA   93 (523)
                      ...|+||
T Consensus        76 ~i~V~~A   82 (96)
T d2disa1          76 QIAVDWA   82 (96)
T ss_dssp             CCEEEES
T ss_pred             EEEEEEc
Confidence            5779998

>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=96.19  E-value=0.01  Score=44.75  Aligned_cols=66  Identities=11%  Similarity=0.122  Sum_probs=46.0

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      -||-|.+||+.+||+++.+.+..+  +.+.-.....-  ......-.-|||.|.+.|+...... ++|+.|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~--G~i~~~~~~~~--~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l   68 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQY--GKIEVIEIMTD--RGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTV   68 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTT--SCEEEEEEEEC--TTTCCEEEEEEEEESSHHHHHHHHH-CSCCEE
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHh--ccccccccccC--CCCcccccEEEEEEcCHHHHHHHHH-hCCCEE
Confidence            489999999999999999999875  23332222111  1112223459999999988877774 799987

>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=96.10  E-value=0.0046  Score=48.90  Aligned_cols=77  Identities=17%  Similarity=0.229  Sum_probs=55.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ..+...|.|++||+++||+++.+.+...-  .+... ...|      ....-|||.|.+.+++..-++.++|+.|.+   
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g--~v~~~-~~~~------~~~~~afV~f~~~~~A~~A~~~l~~~~~~g---   80 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDAL--EIRLV-SQDG------KSKGIAYIEFKSEADAEKNLEEKQGAEIDG---   80 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEE--EECCE-EETT------EEEEEEEEEESSHHHHHHHHHHTTEEEETT---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcc--cceee-eecC------ccccEEEEEeCCHHHHHHHHHHcCCCEECC---
Confidence            34567899999999999999999988642  22111 1122      112359999999999999999999988743   


Q ss_pred             CeeeeEEEecc
Q 009860           84 AQFKAIVEYAP   94 (523)
Q Consensus        84 ne~~A~VEfAP   94 (523)
                        ....|+||-
T Consensus        81 --r~i~V~~a~   89 (96)
T d1fjca_          81 --RSVSLYYTG   89 (96)
T ss_dssp             --EEEEEEECS
T ss_pred             --EEEEEEEeC
Confidence              366777764

>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=96.04  E-value=0.0084  Score=46.50  Aligned_cols=78  Identities=19%  Similarity=0.275  Sum_probs=52.4

Q ss_pred             CCCceEEEecCCCCCCH-HHHHHHhcccCCCceeEEEeeCCCCCCCCCcce--eEEEEecCcccHHHHHHHhcCCeeEeC
Q 009860            5 LQRTKVVIRHLPPSLSQ-NDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYS--RAYVELKKPAGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         5 ~~r~KVVIRrLPP~LTE-EeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~yS--RAYI~Fkn~Edl~~F~d~fdG~vFvDs   81 (523)
                      .++.+|.|++||+.+|+ +++.+.+...  |.|........+   +....+  -|||.|.+.+++....+ ++|+.|-+ 
T Consensus         2 ~e~~~l~V~nLp~~~t~ed~l~~~F~~~--G~i~~v~i~~~~---~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~g-   74 (86)
T d2ghpa3           2 LEGREIMIRNLSTELLDENLLRESFEGF--GSIEKINIPAGQ---KEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGN-   74 (86)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGG--SCEEEEECCSCC---C---CCCEEEEEEESSHHHHHHHGG-GTTEEETT-
T ss_pred             CCCCEEEEECCCCCcccHHHHHHHHHhh--hhccceeeeccc---CCccccceeeeEEECCHHHHHHHHh-cCCCEECC-
Confidence            46789999999999975 5577777764  356554432211   122223  39999999999998885 89988732 


Q ss_pred             CCCeeeeEEEec
Q 009860           82 KGAQFKAIVEYA   93 (523)
Q Consensus        82 KGne~~A~VEfA   93 (523)
                          ..-.|++|
T Consensus        75 ----r~l~V~~a   82 (86)
T d2ghpa3          75 ----REISVSLA   82 (86)
T ss_dssp             ----EEEEEEEC
T ss_pred             ----EEEEEEEc
Confidence                24566665

>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=96.01  E-value=0.012  Score=47.02  Aligned_cols=71  Identities=13%  Similarity=0.076  Sum_probs=48.1

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      .......|-||+||.+.||+++.+.+...-. -+........  ... ....-|||.|.+++++....+ ++++.|
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~-v~~~v~~~~~--~~~-~~kG~afV~F~~~e~a~~a~~-~~~~~i   81 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEI-VPNGMTLPVD--FQG-RSTGEAFVQFASQEIAEKALK-KHKERI   81 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCE-EEEEEECCBC--SSS-CBCSEEEEEESSHHHHHHHHT-TTTCCS
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCC-ceEEEEEEeC--CCC-CcceEEEEEeCCHHHHHHHHh-hCCCEE
Confidence            3445567999999999999999999987531 1121221111  111 223469999999999987664 788766

>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=95.89  E-value=0.017  Score=43.93  Aligned_cols=74  Identities=16%  Similarity=0.132  Sum_probs=56.7

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      +|.....|.|.+||  +||+++.+.++..  |.|.-......        ...|||.|.+.++....++.++|..|.+. 
T Consensus         1 ap~~~~ti~V~~~~--~te~~L~~~F~~~--G~I~~v~~~~~--------~~~afV~f~~~~~A~~Ai~~lng~~~~g~-   67 (79)
T d2bz2a1           1 APRKGNTLYVYGED--MTPTLLRGAFSPF--GNIIDLSMDPP--------RNCAFVTYEKMESADQAVAELNGTQVESV-   67 (79)
T ss_dssp             CCCCCCEEEEECSS--CCHHHHHHHHSTT--CCCSCEEEETT--------TTEEEEECSSHHHHHHHHHHHTTCBCSSC-
T ss_pred             CCCCCCEEEEECCC--CCHHHHHHHHhcc--CccceeeeccC--------CCEEEEEEcccHHHHHHHHHhCCCEECCE-
Confidence            57788899999996  8999999999875  23433333221        23799999999999999999999998442 


Q ss_pred             CCeeeeEEEec
Q 009860           83 GAQFKAIVEYA   93 (523)
Q Consensus        83 Gne~~A~VEfA   93 (523)
                          .-.|+||
T Consensus        68 ----~l~V~~a   74 (79)
T d2bz2a1          68 ----QLKVNIA   74 (79)
T ss_dssp             ----BCEEEEC
T ss_pred             ----EEEEEEe
Confidence                4567777

>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=95.88  E-value=0.013  Score=49.62  Aligned_cols=80  Identities=15%  Similarity=0.162  Sum_probs=56.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      .....+|.|+.||+.+|++++.+.+...  +.|.+...+......  ..-.-|||.|.+.+++..... .+++.|.   |
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~--G~v~~~~i~~~~~~~--~~~g~~fV~f~~~e~A~~Al~-~~~~~~~---G  165 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQY--GKIEVIEIMTDRGSG--KKRGFAFVTFDDHDSVDKIVI-QKYHTVN---G  165 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTC--CEEEEEEEEESCHHHHHHHHT-SSCEEET---T
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccC--CceeeeeeecccccC--ccceeEEEEECCHHHHHHHHH-hCCCeEC---C
Confidence            3456789999999999999999999875  457666655432221  122359999999999998886 5776652   2


Q ss_pred             CeeeeEEEec
Q 009860           84 AQFKAIVEYA   93 (523)
Q Consensus        84 ne~~A~VEfA   93 (523)
                        ....|.+|
T Consensus       166 --~~i~V~~A  173 (183)
T d1u1qa_         166 --HNCEVRKA  173 (183)
T ss_dssp             --EEEEEEEC
T ss_pred             --EEEEEEec
Confidence              24556655

>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=95.77  E-value=0.02  Score=45.61  Aligned_cols=74  Identities=14%  Similarity=0.135  Sum_probs=55.0

Q ss_pred             CCCceEEEecCCCC-CCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCC
Q 009860            5 LQRTKVVIRHLPPS-LSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG   83 (523)
Q Consensus         5 ~~r~KVVIRrLPP~-LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG   83 (523)
                      ....+|.|.+|||. .+|+++.+.+..+  +.|.-.....          .-|||.|.+.+++...++.++|+.|.+   
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~--G~i~~~~i~r----------g~aFV~f~~~~~A~~Ai~~lng~~~~g---   77 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKY--GKIVGCSVHK----------GFAFVQYVNERNARAAVAGEDGRMIAG---   77 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTS--SCEEEEEEET----------EEEEEEESSHHHHHHHHHTTTTCEETT---
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhc--CCEEEEEEeC----------CeEEEEECCHHHHHHHHHHcCCCEECC---
Confidence            34578999999875 5677788877764  3444333222          369999999999999999999998832   


Q ss_pred             CeeeeEEEeccC
Q 009860           84 AQFKAIVEYAPS   95 (523)
Q Consensus        84 ne~~A~VEfAPY   95 (523)
                        ..-.|++|.-
T Consensus        78 --~~l~V~~a~~   87 (98)
T d1wf2a_          78 --QVLDINLAAE   87 (98)
T ss_dssp             --EECEEEETTS
T ss_pred             --EEEEEEECCC
Confidence              3678898853

>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=95.70  E-value=0.012  Score=47.58  Aligned_cols=67  Identities=13%  Similarity=0.084  Sum_probs=48.4

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      ..+|-|++||+.+||+++.+.+..+  |.|....-..-+.+.  ..-.-|||.|.+.+++....+ .+++.|
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~--G~i~~~~i~~d~~~~--~~kg~aFV~f~~~~~a~~al~-~~~~~l   86 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQW--GKLTDCVVMRDPASK--RSRGFGFVTFSSMAEVDAAMA-ARPHSI   86 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSS--CCCSEEEEECCTTTS--SCCSEEEEECSSHHHHHHHHT-SCSEEE
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhh--CcccceeecccccCC--CccCeEEEEECCHHHHHHHHH-hCCCeE
Confidence            3689999999999999999999875  344433332222222  123459999999999988775 588876

>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=95.51  E-value=0.0049  Score=48.68  Aligned_cols=79  Identities=19%  Similarity=0.235  Sum_probs=54.2

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCC-CceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFN-DRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~-gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs   81 (523)
                      .+.....|.|++||+.+||+++.+.+..+-. ..+...+-..|+      .-..|||.|.+.+++...++ ++|+.|.+ 
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~------~kg~afv~F~~~e~a~~Al~-~~g~~~~g-   80 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGT------NRKFGYVDFESAEDLEKALE-LTGLKVFG-   80 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEET------TTTEEEEEESSHHHHHHHHH-GGGEEETT-
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCC------ccEEeEEeeCCHHHHHHHHh-cCCcEECC-
Confidence            3556678999999999999999998876421 011111212222      12479999999999999986 89887653 


Q ss_pred             CCCeeeeEEEec
Q 009860           82 KGAQFKAIVEYA   93 (523)
Q Consensus        82 KGne~~A~VEfA   93 (523)
                          ....|++|
T Consensus        81 ----~~i~V~~a   88 (91)
T d1fjeb1          81 ----NEIKLEKP   88 (91)
T ss_dssp             ----EEEEEECC
T ss_pred             ----EEEEEEec
Confidence                24556655

>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=95.45  E-value=0.033  Score=45.30  Aligned_cols=68  Identities=18%  Similarity=0.216  Sum_probs=54.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCc-ccHHHHHHHhcCCeeEeC
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKP-AGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~-Edl~~F~d~fdG~vFvDs   81 (523)
                      |.--+.+.|.+||+.+||+++.+.+.++  +.|.+..+..++        .-|||.|.++ +++...+..+++..+...
T Consensus         8 ~~g~~~~fvgnL~~~~tee~Lk~~F~~f--G~V~~v~i~~~k--------g~gfV~F~~~~~~A~~a~~~~~~~~l~~~   76 (113)
T d1owxa_           8 KIGCLLKFSGDLDDQTCREDLHILFSNH--GEIKWIDFVRGA--------KEGIILFKEKAKEALGKAKDANNGNLQLR   76 (113)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSS--CCEEEEECCTTC--------SEEEEEESSCHHHHHHHHHHTTTSCBCTT
T ss_pred             CCCCeEEEECCCCCCCCHHHHHHHHHhc--CChheEEEecCC--------ceEEEEecCcHHHHHHHHHHhcCCceecC
Confidence            4445667899999999999999999985  568888887663        4599999997 678888888888765543

>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=95.41  E-value=0.016  Score=47.04  Aligned_cols=69  Identities=14%  Similarity=0.084  Sum_probs=47.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcccCC--CceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009860            4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFN--DRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV   79 (523)
Q Consensus         4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~--gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv   79 (523)
                      +.+..-|.||+||..+|++++.+.+...-.  ..+....-..|.      ...-|||.|.+.+++..-.+ ++|+.|-
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~------~~G~afVeF~~~e~a~~al~-~~~~~i~   85 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGK------ATGEGFVEFRNEADYKAALC-RHKQYMG   85 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSS------EEEEEEEEBSSSHHHHHHHT-SCSBCST
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccc------eeeEEEEEECCHHHHHHHHH-cCCCcCC
Confidence            455667999999999999999999976421  112111112221      24579999999999986664 7888753

>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=95.40  E-value=0.026  Score=44.99  Aligned_cols=74  Identities=15%  Similarity=0.218  Sum_probs=55.5

Q ss_pred             CCCceEEEecCCC-CCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHH--hcCCeeEeC
Q 009860            5 LQRTKVVIRHLPP-SLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAEL--LNGHVFVNE   81 (523)
Q Consensus         5 ~~r~KVVIRrLPP-~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~--fdG~vFvDs   81 (523)
                      .+...|.|++||. .+||+++.+.+.+.  |.|....+.+.+        .-|||.|.+.++.....+.  .++..|.+.
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~f--G~V~~v~~~~~k--------~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr   85 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPY--GKIKNYILMRMK--------SQAFIEMETREDAMAMVDHCLKKALWFQGR   85 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTT--SCCSEEEEETTT--------TEEEEECSSHHHHHHHHHHHHHSCCCSSSS
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccc--cceeEEEEeecC--------CcEEEEecchHHHHHHHHHHhcCCceECCE
Confidence            3456799999997 59999999999875  467777776543        3699999999999988875  455555332


Q ss_pred             CCCeeeeEEEec
Q 009860           82 KGAQFKAIVEYA   93 (523)
Q Consensus        82 KGne~~A~VEfA   93 (523)
                           ...|+||
T Consensus        86 -----~l~V~~s   92 (99)
T d1x4fa1          86 -----CVKVDLS   92 (99)
T ss_dssp             -----CCEEEEE
T ss_pred             -----EEEEEEc
Confidence                 4667777

>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=95.38  E-value=0.02  Score=44.41  Aligned_cols=68  Identities=16%  Similarity=0.218  Sum_probs=49.0

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      ...|.|++||+.+|++++.+.+...  |.+.-......+  .+. .-.-|||.|.+.+++....+ .++..|.+
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~--G~v~~v~l~~~~--~~~-~kG~afV~f~~~e~a~~al~-~~~~~~~g   73 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDK--GQVLNIQMRRTL--HKA-FKGSIFVVFDSIESAKKFVE-TPGQKYKE   73 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTS--CCEEEEEEEECT--TCC-EEEEEEEEESCHHHHHHHHT-CCCCEETT
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHh--cccccceeeeec--cCC-cceEEEEEEcCHHHHHHHHH-HCCCEECC
Confidence            4579999999999999999999875  234433332221  111 23469999999999999885 58888744

>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=94.93  E-value=0.014  Score=47.39  Aligned_cols=78  Identities=14%  Similarity=0.232  Sum_probs=54.2

Q ss_pred             CCceEEEecCCCCC-CHHHHHHHhcccC--CCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009860            6 QRTKVVIRHLPPSL-SQNDLLALFRDHF--NDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK   82 (523)
Q Consensus         6 ~r~KVVIRrLPP~L-TEEeF~eqL~p~~--~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK   82 (523)
                      ....|.|++|++.+ ++++..++|..++  -+.|.-+.+.++        ..+|+|.|.+.++....++.++|+.|.+. 
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            45789999999996 6654444333332  134444455432        34799999999999999999999988432 


Q ss_pred             CCeeeeEEEeccCC
Q 009860           83 GAQFKAIVEYAPSQ   96 (523)
Q Consensus        83 Gne~~A~VEfAPYQ   96 (523)
                          .-.|+||--+
T Consensus        75 ----~l~v~~a~~~   84 (104)
T d1weya_          75 ----EMKLYFAQTL   84 (104)
T ss_dssp             ----ECEEECCCCS
T ss_pred             ----EeEEeecccC
Confidence                5678888433

>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=94.77  E-value=0.039  Score=42.73  Aligned_cols=72  Identities=11%  Similarity=0.135  Sum_probs=48.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009860            6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ   85 (523)
Q Consensus         6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne   85 (523)
                      ...+|.|.+||+.+||+++.+.+..+-  .|.-.. +...    .  ..-|||.|.+.+++.....  +++.| +  |  
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G--~v~~v~-~~~~----~--~gfafV~f~~~~~a~~a~~--~~~~i-~--g--   67 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYG--DVMDVF-IPKP----F--RAFAFVTFADDQIAQSLCG--EDLII-K--G--   67 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTS--CCCEEE-CCSS----C--CSCCEEECSCHHHHHHTTT--CEEEE-T--T--
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcC--CceEEE-Eeec----c--CceEEEEECCHHHHHHHHh--CCCEE-C--C--
Confidence            457899999999999999999998752  332221 1211    1  1249999999988876653  44443 2  2  


Q ss_pred             eeeEEEec
Q 009860           86 FKAIVEYA   93 (523)
Q Consensus        86 ~~A~VEfA   93 (523)
                      ....|++|
T Consensus        68 ~~l~v~~a   75 (88)
T d1wf0a_          68 ISVHISNA   75 (88)
T ss_dssp             EEEEEECC
T ss_pred             EEeEEEeC
Confidence            25677776

>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=94.40  E-value=0.076  Score=41.45  Aligned_cols=73  Identities=12%  Similarity=0.058  Sum_probs=55.7

Q ss_pred             ceEEEecCCCC-CCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCe-eEeCCCCe
Q 009860            8 TKVVIRHLPPS-LSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHV-FVNEKGAQ   85 (523)
Q Consensus         8 ~KVVIRrLPP~-LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~v-FvDsKGne   85 (523)
                      -.|-|++||.. .|++++++.+.+.  |.|....+.+.+-        -|||.|.+.++.....+.+++.. .++.    
T Consensus         9 r~v~v~nl~~~~~t~~eL~~lF~~f--G~I~~i~i~~~k~--------~afV~f~~~~~A~~A~~~l~~~~~~~~g----   74 (89)
T d1x4da1           9 RVVHIMDFQRGKNLRYQLLQLVEPF--GVISNHLILNKIN--------EAFIEMATTEDAQAAVDYYTTTPALVFG----   74 (89)
T ss_dssp             CEEEEESCCCSSSHHHHHHTTTGGG--SCEEEEEECSSSS--------CEEEEESSHHHHHHHHHHHHHSCCEETT----
T ss_pred             cEEEEECCCCCcCCHHHHHHHHHhh--CCeEEEEeeccce--------EEEEEEcchhhHHHHHHHHhhCCCccCC----
Confidence            45889999997 8999999999985  4677777765432        49999999999999998875442 2233    


Q ss_pred             eeeEEEecc
Q 009860           86 FKAIVEYAP   94 (523)
Q Consensus        86 ~~A~VEfAP   94 (523)
                      .+..|+||.
T Consensus        75 r~l~V~~s~   83 (89)
T d1x4da1          75 KPVRVHLSQ   83 (89)
T ss_dssp             EECEEEEEC
T ss_pred             ceEEEEECC
Confidence            267888885

>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=93.93  E-value=0.049  Score=43.04  Aligned_cols=67  Identities=16%  Similarity=0.160  Sum_probs=46.4

Q ss_pred             CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      .+-|-|++||+..|++++++.+...-. ...+..++....   ...--.|||.|.+.+++....+ ++++.|
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~-i~~~~~~~~~~~---g~~~G~afV~F~s~~~a~~Al~-~n~~~i   74 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPV-DENAVHVLVDNN---GQGLGQALVQFKNEDDARKSER-LHRKKL   74 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCC-CSTTEEECCCTT---SSCSSCEEEECSSHHHHHHHGG-GCSEEE
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccce-EEEEEEEEeCCC---CCcCccEEEEECCHHHHHHHHh-cCCCeE
Confidence            455999999999999999999986531 111222222111   1124589999999999987775 788776

>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=93.31  E-value=0.057  Score=45.52  Aligned_cols=70  Identities=14%  Similarity=0.062  Sum_probs=47.9

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCC
Q 009860            3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGH   76 (523)
Q Consensus         3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~   76 (523)
                      +|.+..+|.|++|||.+||+++.+.+...  |.|....++.-.. . ...-..||+.|.+.+++........+.
T Consensus         2 ep~~~r~lfV~nLp~~~te~~L~~~F~~~--G~v~~~~~~~~~~-~-~~~~g~afv~f~~~~~a~~a~~~~~~~   71 (183)
T d1u1qa_           2 EPEQLRKLFIGGLSFETTDESLRSHFEQW--GTLTDCVVMRDPN-T-KRSRGFGFVTYATVEEVDAAMNARPHK   71 (183)
T ss_dssp             CCHHHHEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTT-T-CCEEEEEEEEESSHHHHHHHHHTCSCE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHc--CCEEEEEeeeccc-C-CCccCceecccCCHHHHHHHHHhcCCc
Confidence            44555689999999999999999999764  3343333321111 1 122357999999999998877765444

>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=92.14  E-value=0.0095  Score=46.24  Aligned_cols=67  Identities=9%  Similarity=0.240  Sum_probs=43.9

Q ss_pred             eEEEecCCCCCCHHHHHHHhcccCC---Ccee---EEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009860            9 KVVIRHLPPSLSQNDLLALFRDHFN---DRYN---WFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE   81 (523)
Q Consensus         9 KVVIRrLPP~LTEEeF~eqL~p~~~---gkvd---wfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs   81 (523)
                      +|-|.+||+.+||+++.+.+.....   -.+.   -..+..   ..+..  --|||.|.+.|++.... .++|+.|.+.
T Consensus         3 rlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~---~~~~k--g~afV~f~~~e~a~~a~-~l~g~~~~Gr   75 (90)
T d1u2fa_           3 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQ---INQDK--NFAFLEFRSVDETTQAM-AFDGIIFQGQ   75 (90)
T ss_dssp             EEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECC---EETTT--TEEEEEESSCTTTTTGG-GGSSCCSSSS
T ss_pred             EEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecc---cCCCc--eEEEEEeCCHHHHHHHH-hhCCcEECCE
Confidence            6899999999999999988876421   0110   001100   00111  23999999999987765 5999998554

>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=85.55  E-value=0.95  Score=35.75  Aligned_cols=79  Identities=15%  Similarity=0.228  Sum_probs=49.8

Q ss_pred             EEEecC--CCCCCHHHHHHHh----cccC--CCceeEEEeeCCCC-CCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009860           10 VVIRHL--PPSLSQNDLLALF----RDHF--NDRYNWFCFRPGKS-SYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN   80 (523)
Q Consensus        10 VVIRrL--PP~LTEEeF~eqL----~p~~--~gkvdwfyFVpGK~-S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD   80 (523)
                      |+|++|  |-.|..++.++.|    ...+  -|.|.-.. ++=+. ........+|||.|.+.++...-...++|..|-+
T Consensus         7 l~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~-I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f~g   85 (104)
T d1o0pa_           7 LCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIE-IPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFAN   85 (104)
T ss_dssp             EEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEE-CCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCSSS
T ss_pred             EEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEE-EeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            677999  8887655444332    2222  24555433 32111 1123445689999999999999999999999844


Q ss_pred             CCCCeeeeEEEecc
Q 009860           81 EKGAQFKAIVEYAP   94 (523)
Q Consensus        81 sKGne~~A~VEfAP   94 (523)
                      -     .-.|+|++
T Consensus        86 R-----~v~v~f~~   94 (104)
T d1o0pa_          86 R-----VVVTKYCD   94 (104)
T ss_dssp             S-----CCEEEEEC
T ss_pred             e-----EEEEEEcC
Confidence            2     44556654

>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=84.94  E-value=0.52  Score=37.19  Aligned_cols=75  Identities=15%  Similarity=0.185  Sum_probs=47.3

Q ss_pred             ceEEEecC--CCCCCH-----HHHHHHhcccCC--CceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009860            8 TKVVIRHL--PPSLSQ-----NDLLALFRDHFN--DRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF   78 (523)
Q Consensus         8 ~KVVIRrL--PP~LTE-----EeF~eqL~p~~~--gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF   78 (523)
                      --|+|++|  |..|.+     .+|.+-|...+.  +.|.-.....++      ....|||.|.++++...-...++|+.|
T Consensus         9 r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~------~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1           9 RVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH------PDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             CEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC------TTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             cEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC------CccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            34899999  776532     123333333221  345444433332      235899999999999999999999998


Q ss_pred             EeCCCCeeeeEEEec
Q 009860           79 VNEKGAQFKAIVEYA   93 (523)
Q Consensus        79 vDsKGne~~A~VEfA   93 (523)
                      -+-     .-.|+|+
T Consensus        83 ~gr-----~i~v~~~   92 (99)
T d2dita1          83 GGR-----QITAQAW   92 (99)
T ss_dssp             TTE-----ECEEEEC
T ss_pred             CCE-----EEEEEEe
Confidence            332     4556654

>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=84.88  E-value=0.24  Score=39.72  Aligned_cols=75  Identities=11%  Similarity=0.069  Sum_probs=52.0

Q ss_pred             EEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeeeeE
Q 009860           10 VVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKAI   89 (523)
Q Consensus        10 VVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~A~   89 (523)
                      +.|+.|+..++|+.|.+.+...  |.|.-. .++-+..  ...-..|||.|.+.++.....+.++|+.|-+.     +-.
T Consensus        30 ~~v~~~~~~~~ed~l~e~f~k~--G~I~~v-~I~~~~~--~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr-----~i~   99 (104)
T d1jmta_          30 VEMQEHYDEFFEEVFTEMEEKY--GEVEEM-NVCDNLG--DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ-----PIH   99 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHT--CCEEEE-EECCSSS--SSSEEEEEEEESCHHHHHHHHHHHTTCEETTE-----ECC
T ss_pred             HHhhhhhhhhhHHHHHHHhccC--CCEEEE-EeecCCC--CCEeeEEEEEEechhHHHHHHHHHCCCEECCE-----EEE
Confidence            4567788888888887777654  345443 2432221  12235699999999999999999999988221     556


Q ss_pred             EEecc
Q 009860           90 VEYAP   94 (523)
Q Consensus        90 VEfAP   94 (523)
                      |||+|
T Consensus       100 v~~sP  104 (104)
T d1jmta_         100 AELSP  104 (104)
T ss_dssp             EEECC
T ss_pred             EEECC
Confidence            78776