Psyllid ID: psy14139

---

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-------
Protein Sequence
MATSKTSSTYNRQSWEDATKEKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLEPVPGLPGALPPPPKDFFNLSNPVV
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccEEEEEccccccccccHHHHHHHHHcccccccccccccccccHHHHHHHHHcccccccccccHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEEccccEEEEEEccHHHHHHHHHHHccccEEccEEEEEEEccccccccccHHHHHcccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccHHHHHHHHcccccEEEcccEEEEEEcccccccEcEEEEHHHHHHHHHHHHHHHHHHHccccHEHHHHHHHHHcccccccHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHccccccccccccccccEEccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHccccccccccccEEEEEEEcccccccHHHHHHHHHHcccEEEEEEEccccEEEEEEccHHHHHHHHHHHcccEEEccEEEEEEEccccccccccHHHHccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
matsktsstynrqswedatkekygkeckicarpftvfrwcpgarmrfkktEVCQTCARLKNVCQTCLldleyglpiqVRDTALkikddipksdvnkeyyIQNMdheigkidsttpagalgkasgsSEMLMKLARttpyykrnrphicsfwvkgecrrgeecpyrhekptdpddpladqnikdryygvndpVAEKLMARastmpkldppedktitTLYVgnlgdklteqDLRDHFYQFGEIRSVTILSKQQCAFIQytsrpaaeaAVEHSFNKVILggrrlnikwgraqanrgedTAELKVrlepvpglpgalppppkdffnlsnpvv
Flexible Loop (DISEMBL)
matsktsstynrqswedatkekygkeckicarpftvfrwcpGARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTalkikddipksdvNKEYYIQNMDHEIGKIDSTTPAGALgkasgsseMLMKLARttpyykrnrphICSFWVKGecrrgeecpyrhekptdpddpladqNIKDRYYGVNDPVAEKLMARAstmpkldppedkTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLEPVpglpgalppppkdffnlsnpvv
Low Complexity Region (SEG)
MATSKTSSTYNRQSWEDATKEKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLEpvpglpgalppppKDFFNLSNPVV
Disordered region (IsUnstruct)
*********************KYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQNMDHEIG*********************MKLARTTPYYKRNRPHICSFWVKGECRRG*************************YYGV************************TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA****************************************
Disordered Region (DISOPRED)
***S**S**YNRQSWEDATKEKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTA****************YIQNMDHEIG***************************************************************************************************PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK****************************************NP**
Disordered Region (DISEMBL)
*********************KYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLEPVPGLPGALPPPPKDFFNLSNPVV
Disordered Region (DISPRO)
********TYNRQSWEDATKEKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQNMDHEIGKID*TTPA*ALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ************RLEPVPGLPGALPPPPKDFFNLS****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MATSKTSSTYNRQSWEDATKEKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLEPVPGLPGALPPPPKDFFNLSNPVV
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	327	2.2.26 [Sep-21-2011]
Q4V7D7	420	Pre-mRNA-splicing factor	yes	N/A	0.932	0.726	0.734	1e-145
Q8BHS3	420	Pre-mRNA-splicing factor	yes	N/A	0.932	0.726	0.731	1e-144
Q4R4J1	420	Pre-mRNA-splicing factor	N/A	N/A	0.932	0.726	0.731	1e-144
Q9NW64	420	Pre-mRNA-splicing factor	yes	N/A	0.932	0.726	0.731	1e-144
Q5RAY5	420	Pre-mRNA-splicing factor	yes	N/A	0.932	0.726	0.731	1e-144
Q5ZM16	420	Pre-mRNA-splicing factor	yes	N/A	0.932	0.726	0.728	1e-144
Q3B7L8	420	Pre-mRNA-splicing factor	yes	N/A	0.932	0.726	0.731	1e-144
Q6P616	417	Pre-mRNA-splicing factor	yes	N/A	0.932	0.731	0.716	1e-143
Q7ZXB5	417	Pre-mRNA-splicing factor	N/A	N/A	0.932	0.731	0.710	1e-143
Q6NZZ9	425	Pre-mRNA-splicing factor	yes	N/A	0.932	0.717	0.709	1e-141

>sp|Q4V7D7|RBM22_RAT Pre-mRNA-splicing factor RBM22 OS=Rattus norvegicus GN=Rbm22 PE=2 SV=1

 Score =  513 bits (1321), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 241/328 (73%), Positives = 273/328 (83%), Gaps = 23/328 (7%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           MATS  S+TYNRQ+WEDA                  TKEKYGKECKICARPFTVFRWCPG
Sbjct: 1   MATSLGSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEKYGKECKICARPFTVFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
            RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQVRD  L  KDD+PKSDVNKEYY QN
Sbjct: 61  VRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQVRDAGLSFKDDMPKSDVNKEYYTQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           M+ EI   D T P G LGKA+ +S+ML+KLARTTPYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 MEREISNSDGTRPVGMLGKATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDRYYG+NDPVA+KL+ RASTMP+LDPPEDKTITTLYVG LG
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKRASTMPRLDPPEDKTITTLYVGGLG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           D +TE DLR+HFYQFGEIR+VT++ +QQCAFIQ+ +R AAE A E SFNK+I+ GRRLN+
Sbjct: 241 DTITETDLRNHFYQFGEIRTVTVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV 300

Query: 283 KWGRAQANRGED-----TAELKVRLEPV 305
           KWGR+QA RG++     T +  ++LEPV
Sbjct: 301 KWGRSQAARGKEKEKDGTTDSGIKLEPV 328

Involved in the first step of pre-mRNA splicing. Binds directly to the internal stem-loop (ISL) domain of the U6 snRNA and to the pre-mRNA intron near the 5' splice site during the activation and catalytic phases of the spliceosome cycle. Involved in both translocations of the nuclear SLU7 to the cytoplasm and the cytosolic calcium-binding protein PDCD6 to the nucleus upon cellular stress responses.
Rattus norvegicus (taxid: 10116)

>sp|Q8BHS3|RBM22_MOUSE Pre-mRNA-splicing factor RBM22 OS=Mus musculus GN=Rbm22 PE=2 SV=1

 Score =  513 bits (1320), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 240/328 (73%), Positives = 273/328 (83%), Gaps = 23/328 (7%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           MATS  S+TYNRQ+WEDA                  TKEKYGKECKICARPFTVFRWCPG
Sbjct: 1   MATSLGSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEKYGKECKICARPFTVFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
            RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQVRD  L  KDD+PKSDVNKEYY QN
Sbjct: 61  VRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQVRDAGLSFKDDMPKSDVNKEYYTQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           M+ EI   D T P G LGKA+ +S+ML+KLARTTPYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 MEREISNSDGTRPVGMLGKATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDRYYG+NDPVA+KL+ RASTMP+LDPPEDKTITTLYVG LG
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKRASTMPRLDPPEDKTITTLYVGGLG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           D +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +R AAE A E SFNK+I+ GRRLN+
Sbjct: 241 DTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV 300

Query: 283 KWGRAQANRGED-----TAELKVRLEPV 305
           KWGR+QA RG++     T +  ++LEPV
Sbjct: 301 KWGRSQAARGKEKEKDGTTDSGIKLEPV 328

Involved in the first step of pre-mRNA splicing. Binds directly to the internal stem-loop (ISL) domain of the U6 snRNA and to the pre-mRNA intron near the 5' splice site during the activation and catalytic phases of the spliceosome cycle. Involved in both translocations of the nuclear SLU7 to the cytoplasm and the cytosolic calcium-binding protein PDCD6 to the nucleus upon cellular stress responses.

Mus musculus (taxid: 10090)

>sp|Q4R4J1|RBM22_MACFA Pre-mRNA-splicing factor RBM22 OS=Macaca fascicularis GN=RBM22 PE=2 SV=1

 Score =  513 bits (1320), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 240/328 (73%), Positives = 273/328 (83%), Gaps = 23/328 (7%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           MATS  S+TYNRQ+WEDA                  TKEKYGKECKICARPFTVFRWCPG
Sbjct: 1   MATSLGSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEKYGKECKICARPFTVFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
            RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQVRD  L  KDD+PKSDVNKEYY QN
Sbjct: 61  VRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQVRDAGLSFKDDMPKSDVNKEYYTQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           M+ EI   D T P G LGKA+ +S+ML+KLARTTPYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 MEREISNSDGTRPVGMLGKATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDRYYG+NDPVA+KL+ RASTMP+LDPPEDKTITTLYVG LG
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKRASTMPRLDPPEDKTITTLYVGGLG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           D +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +R AAE A E SFNK+I+ GRRLN+
Sbjct: 241 DTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV 300

Query: 283 KWGRAQANRGED-----TAELKVRLEPV 305
           KWGR+QA RG++     T +  ++LEPV
Sbjct: 301 KWGRSQAARGKEKEKDGTTDSGIKLEPV 328

Involved in the first step of pre-mRNA splicing. Binds directly to the internal stem-loop (ISL) domain of the U6 snRNA and to the pre-mRNA intron near the 5' splice site during the activation and catalytic phases of the spliceosome cycle. Involved in both translocations of the nuclear SLU7 to the cytoplasm and the cytosolic calcium-binding protein PDCD6 to the nucleus upon cellular stress responses.

Macaca fascicularis (taxid: 9541)

>sp|Q9NW64|RBM22_HUMAN Pre-mRNA-splicing factor RBM22 OS=Homo sapiens GN=RBM22 PE=1 SV=1

 Score =  513 bits (1320), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 240/328 (73%), Positives = 273/328 (83%), Gaps = 23/328 (7%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           MATS  S+TYNRQ+WEDA                  TKEKYGKECKICARPFTVFRWCPG
Sbjct: 1   MATSLGSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEKYGKECKICARPFTVFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
            RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQVRD  L  KDD+PKSDVNKEYY QN
Sbjct: 61  VRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQVRDAGLSFKDDMPKSDVNKEYYTQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           M+ EI   D T P G LGKA+ +S+ML+KLARTTPYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 MEREISNSDGTRPVGMLGKATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDRYYG+NDPVA+KL+ RASTMP+LDPPEDKTITTLYVG LG
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKRASTMPRLDPPEDKTITTLYVGGLG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           D +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +R AAE A E SFNK+I+ GRRLN+
Sbjct: 241 DTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV 300

Query: 283 KWGRAQANRGED-----TAELKVRLEPV 305
           KWGR+QA RG++     T +  ++LEPV
Sbjct: 301 KWGRSQAARGKEKEKDGTTDSGIKLEPV 328

Involved in the first step of pre-mRNA splicing. Binds directly to the internal stem-loop (ISL) domain of the U6 snRNA and to the pre-mRNA intron near the 5' splice site during the activation and catalytic phases of the spliceosome cycle. Involved in both translocations of the nuclear SLU7 to the cytoplasm and the cytosolic calcium-binding protein PDCD6 to the nucleus upon cellular stress responses.

Homo sapiens (taxid: 9606)

>sp|Q5RAY5|RBM22_PONAB Pre-mRNA-splicing factor RBM22 OS=Pongo abelii GN=RBM22 PE=2 SV=1

 Score =  513 bits (1320), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 240/328 (73%), Positives = 273/328 (83%), Gaps = 23/328 (7%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           MATS  S+TYNRQ+WEDA                  TKEKYGKECKICARPFTVFRWCPG
Sbjct: 1   MATSLGSNTYNRQNWEDADFPILCQTCLGENPYIRVTKEKYGKECKICARPFTVFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
            RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQVRD  L  KDD+PKSDVNKEYY QN
Sbjct: 61  VRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQVRDAGLSFKDDMPKSDVNKEYYTQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           M+ EI   D T P G LGKA+ +S+ML+KLARTTPYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 MEREISNSDGTRPVGMLGKATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDRYYG+NDPVA+KL+ RASTMP+LDPPEDKTITTLYVG LG
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKRASTMPRLDPPEDKTITTLYVGGLG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           D +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +R AAE A E SFNK+I+ GRRLN+
Sbjct: 241 DTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV 300

Query: 283 KWGRAQANRGED-----TAELKVRLEPV 305
           KWGR+QA RG++     T +  ++LEPV
Sbjct: 301 KWGRSQAARGKEKEKDGTTDSGIKLEPV 328

Involved in the first step of pre-mRNA splicing. Binds directly to the internal stem-loop (ISL) domain of the U6 snRNA and to the pre-mRNA intron near the 5' splice site during the activation and catalytic phases of the spliceosome cycle. Involved in both translocations of the nuclear SLU7 to the cytoplasm and the cytosolic calcium-binding protein PDCD6 to the nucleus upon cellular stress responses.

Pongo abelii (taxid: 9601)

>sp|Q5ZM16|RBM22_CHICK Pre-mRNA-splicing factor RBM22 OS=Gallus gallus GN=RBM22 PE=2 SV=1

 Score =  512 bits (1319), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 239/328 (72%), Positives = 274/328 (83%), Gaps = 23/328 (7%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           M+TS  S+TYNRQ+WEDA                  TKEKYGKECKICARPFTVFRWCPG
Sbjct: 1   MSTSLGSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEKYGKECKICARPFTVFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
            RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQVRD  L +KD++PKSDVNKEYY QN
Sbjct: 61  VRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQVRDAGLSLKDEMPKSDVNKEYYTQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           M+ EI   D T P GALGKA+ +S+ML+KLARTTPYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 MEREIANSDGTRPVGALGKATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQ+IKDRYYG+NDPVA+KL+ RASTMP+LDPP+DKTITTLYVG LG
Sbjct: 181 YRHEKPTDPDDPLADQDIKDRYYGINDPVADKLLKRASTMPRLDPPDDKTITTLYVGGLG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           D +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +R AAE A E SFNK+I+ GRRLN+
Sbjct: 241 DTITESDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV 300

Query: 283 KWGRAQANRG-----EDTAELKVRLEPV 305
           KWGR+QA RG     E T E  ++LEPV
Sbjct: 301 KWGRSQAARGKEKDKEGTTESGIKLEPV 328

Involved in the first step of pre-mRNA splicing. Binds directly to the internal stem-loop (ISL) domain of the U6 snRNA and to the pre-mRNA intron near the 5' splice site during the activation and catalytic phases of the spliceosome cycle.

Gallus gallus (taxid: 9031)

>sp|Q3B7L8|RBM22_BOVIN Pre-mRNA-splicing factor RBM22 OS=Bos taurus GN=RBM22 PE=2 SV=1

 Score =  512 bits (1318), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 240/328 (73%), Positives = 272/328 (82%), Gaps = 23/328 (7%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           MATS  S+TYNRQ+WEDA                  TKEKYGKECKICARPFTVFRWCPG
Sbjct: 1   MATSLGSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEKYGKECKICARPFTVFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
            RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQVRD  L  KDD+PKSDVNKEYY QN
Sbjct: 61  VRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQVRDAGLSFKDDMPKSDVNKEYYTQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           M+ EI   D T P G LGKA+ +S+ML+KLARTTPYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 MEREISNSDGTRPVGMLGKATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDRYYG+NDPVA+KL+ RASTMP+LDPPEDKTITTLYVG LG
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKRASTMPRLDPPEDKTITTLYVGGLG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           D +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +R AAE A E SFNK I+ GRRLN+
Sbjct: 241 DTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKFIVNGRRLNV 300

Query: 283 KWGRAQANRGED-----TAELKVRLEPV 305
           KWGR+QA RG++     T +  ++LEPV
Sbjct: 301 KWGRSQAARGKEKEKDGTTDSGIKLEPV 328

Involved in the first step of pre-mRNA splicing. Binds directly to the internal stem-loop (ISL) domain of the U6 snRNA and to the pre-mRNA intron near the 5' splice site during the activation and catalytic phases of the spliceosome cycle. Involved in both translocations of the nuclear SLU7 to the cytoplasm and the cytosolic calcium-binding protein PDCD6 to the nucleus upon cellular stress responses.

Bos taurus (taxid: 9913)

>sp|Q6P616|RBM22_XENTR Pre-mRNA-splicing factor RBM22 OS=Xenopus tropicalis GN=rbm22 PE=2 SV=1

 Score =  508 bits (1307), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 235/328 (71%), Positives = 275/328 (83%), Gaps = 23/328 (7%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           MATS  S+TYNRQ+WEDA                  TKEKYGKECKICARPFTVFRWCPG
Sbjct: 1   MATSLGSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEKYGKECKICARPFTVFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
            RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQVRD    +KD++P+SDVNKEYY QN
Sbjct: 61  VRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQVRDAGASLKDEMPRSDVNKEYYTQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           M+ EI   D T P GALGKA+ SS+ML+KLARTTPYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 MEREIANSDGTRPVGALGKATSSSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDRYYG+NDPVA+KL+ RASTMP+LDPPEDK+ITTLYVG LG
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKRASTMPRLDPPEDKSITTLYVGGLG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           D ++E +LR+HFYQFGEIR++T++ +QQCAFIQ+ +R AAE A E SFNK+I+ GRRLN+
Sbjct: 241 DTISESELRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEMAAEKSFNKLIVNGRRLNV 300

Query: 283 KWGRAQANRGED-----TAELKVRLEPV 305
           KWGR+QA RG++     +++  ++LEPV
Sbjct: 301 KWGRSQAARGKERERDGSSDPGMKLEPV 328

Involved in the first step of pre-mRNA splicing. Binds directly to the internal stem-loop (ISL) domain of the U6 snRNA and to the pre-mRNA intron near the 5' splice site during the activation and catalytic phases of the spliceosome cycle. May be involved in early embryogenesis.

Xenopus tropicalis (taxid: 8364)

>sp|Q7ZXB5|RBM22_XENLA Pre-mRNA-splicing factor RBM22 OS=Xenopus laevis GN=rbm22 PE=2 SV=1

 Score =  506 bits (1304), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 233/328 (71%), Positives = 275/328 (83%), Gaps = 23/328 (7%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           MATS  S+TYNRQ+WEDA                  TKEKYGKECKICARPFTVFRWCPG
Sbjct: 1   MATSLGSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEKYGKECKICARPFTVFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
            RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQVRDT + +KD++P+SDVNKEYY QN
Sbjct: 61  VRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQVRDTGVSLKDEMPRSDVNKEYYTQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           M+ EI   D T P GALGKA+ SS+ML+KLARTTPYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 MEREIANSDGTRPVGALGKATSSSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDR+YG+NDPVA+KL+ RASTMP+LDPPEDK+ITTLYVG LG
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRFYGINDPVADKLLKRASTMPRLDPPEDKSITTLYVGGLG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           D ++E +LR+HFYQFGEIR++T++ +QQCAFIQ+ +R +AE A E SFNK+I+ GRRLN+
Sbjct: 241 DTISESELRNHFYQFGEIRTITVVQRQQCAFIQFATRQSAETAAEKSFNKLIVNGRRLNV 300

Query: 283 KWGRAQANRGED-----TAELKVRLEPV 305
           KWGR+QA RG++     + +  ++ EPV
Sbjct: 301 KWGRSQAARGKEREHDGSGDPGMKFEPV 328

Involved in the first step of pre-mRNA splicing. Binds directly to the internal stem-loop (ISL) domain of the U6 snRNA and to the pre-mRNA intron near the 5' splice site during the activation and catalytic phases of the spliceosome cycle. May be involved in early embryogenesis.

Xenopus laevis (taxid: 8355)

>sp|Q6NZZ9|RBM22_DANRE Pre-mRNA-splicing factor RBM22 OS=Danio rerio GN=rbm22 PE=2 SV=1

 Score =  502 bits (1292), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 232/327 (70%), Positives = 270/327 (82%), Gaps = 22/327 (6%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           MATS  S+TYNRQ+WED+                  TKEK+GKECKICARPFTVFRWCPG
Sbjct: 1   MATSLGSNTYNRQNWEDSDFPILCQTCLGENPYIRMTKEKFGKECKICARPFTVFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
            RMRFKKTEVCQTC+++KNVCQTCLLDLEYGLPIQVRDT L +KD++P+SDVNKEYY QN
Sbjct: 61  VRMRFKKTEVCQTCSKMKNVCQTCLLDLEYGLPIQVRDTGLSVKDEVPRSDVNKEYYTQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           M+ EI   D T P G LGKA  SS+ML+KLARTTPYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 MEREIANSDGTRPVGLLGKAPSSSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDRYYG+NDPVA KL+ RASTMP+LD P+DK+ITTLY+G LG
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRYYGINDPVANKLLMRASTMPRLDVPDDKSITTLYIGGLG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           + +T+ +LR+HFYQFGEIR++TI+ +QQCAFIQ+ +R AAE A E SFNK+I+ GRRLN+
Sbjct: 241 ENVTDSELRNHFYQFGEIRTITIVQRQQCAFIQFATRQAAETAAEKSFNKLIINGRRLNV 300

Query: 283 KWGRAQANRG----EDTAELKVRLEPV 305
           KWGR+QA RG    +   E  +RLEPV
Sbjct: 301 KWGRSQAARGKGEKDGVTESGIRLEPV 327

Involved in the first step of pre-mRNA splicing. Binds directly to the internal stem-loop (ISL) domain of the U6 snRNA and to the pre-mRNA intron near the 5' splice site during the activation and catalytic phases of the spliceosome cycle (By similarity). Involved in early embryogenesis.

Danio rerio (taxid: 7955)

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	327
405971196	434	Pre-mRNA-splicing factor RBM22 [Crassost	0.993	0.748	0.714	1e-147
291243067	429	PREDICTED: RNA binding motif protein 22-	0.972	0.741	0.715	1e-146
338713130	421	PREDICTED: LOW QUALITY PROTEIN: pre-mRNA	0.951	0.738	0.730	1e-145
260830806	435	hypothetical protein BRAFLDRAFT_145268 [	0.981	0.737	0.698	1e-145
307181748	411	Pre-mRNA-splicing factor RBM22 [Camponot	0.932	0.742	0.771	1e-144
242011910	457	pre-mRNA-splicing factor SLT11, putative	0.972	0.695	0.729	1e-144
224067689	420	PREDICTED: pre-mRNA-splicing factor RBM2	0.932	0.726	0.734	1e-144
383857285	412	PREDICTED: pre-mRNA-splicing factor RBM2	0.932	0.740	0.768	1e-144
156546667	409	PREDICTED: pre-mRNA-splicing factor RBM2	0.932	0.745	0.746	1e-143
340722791	411	PREDICTED: pre-mRNA-splicing factor RBM2	0.932	0.742	0.768	1e-143

>gi|405971196|gb|EKC36046.1| Pre-mRNA-splicing factor RBM22 [Crassostrea gigas]

 Score =  526 bits (1355), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 250/350 (71%), Positives = 288/350 (82%), Gaps = 25/350 (7%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           MATSK ++TYNRQ+WEDA                   KEKYGKECKICARPFTVFRWCPG
Sbjct: 1   MATSKGANTYNRQNWEDAEFPILCQTCLGDNPYIRMMKEKYGKECKICARPFTVFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
           ARMRFKKTEVCQTC++LKNVCQTCLLDLEYGLP+QVRD ALK++D++PKSDVNKEYY QN
Sbjct: 61  ARMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPVQVRDAALKVQDNMPKSDVNKEYYTQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           M+ EI   D T P GALGKA   S+ML+KLARTTPYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 MEREIATNDGTAPGGALGKAMAPSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDR+YG NDPVA+KL+ R + MPKL  PEDKTITTLY+GNLG
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRFYGSNDPVADKLLQRYTDMPKLTLPEDKTITTLYIGNLG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           +K+ E++LRDHFYQFGEIR + +++KQQCAF+Q+TSR +AEAA E SFNK+I+GGRRL I
Sbjct: 241 EKIGEKELRDHFYQFGEIRMINVVAKQQCAFVQFTSRSSAEAAAEKSFNKLIVGGRRLTI 300

Query: 283 KWGRAQANR---GEDTAELKVRLEPVPGLPGALPPPPK----DFFNLSNP 325
           KWGR+Q  +    ++  E    LEPVPGLPGALP PP+    +FFNLSNP
Sbjct: 301 KWGRSQGQQLALKKEGEEDDKDLEPVPGLPGALPAPPEEIANNFFNLSNP 350

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|291243067|ref|XP_002741428.1| PREDICTED: RNA binding motif protein 22-like [Saccoglossus kowalevskii]

 Score =  525 bits (1353), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 244/341 (71%), Positives = 285/341 (83%), Gaps = 23/341 (6%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           MA SK+++TYNRQ+WEDA                  TKEKYGKECKICARPFT+FRWCPG
Sbjct: 1   MAASKSTNTYNRQNWEDAEFPILCQTCLGDNPYVRMTKEKYGKECKICARPFTIFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
           ARMRFKKTEVCQTC+++KN CQTCLLDLEYGLP+QVRD AL IKDD+PKSDVNKEYY QN
Sbjct: 61  ARMRFKKTEVCQTCSKVKNCCQTCLLDLEYGLPLQVRDAALSIKDDMPKSDVNKEYYTQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           M+ EI   D T   GA+GK+   S++L+KLARTTPYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 MEREIANSDGTQAVGAVGKSQSPSDLLLKLARTTPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDR+YGVNDPVA KL+ RA+TMPKL+ PED+TITTLYVG LG
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRFYGVNDPVAHKLLNRAATMPKLEAPEDRTITTLYVGGLG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           DK++E+DLRDHFYQFGEIRS+ ++++QQCAF+Q+T+R ++E A E SFNK+I+ GRRLNI
Sbjct: 241 DKISEKDLRDHFYQFGEIRSINVVARQQCAFVQFTTRQSSELAAERSFNKLIMNGRRLNI 300

Query: 283 KWGRAQANR---GEDTAELK--VRLEPVPGLPGALPPPPKD 318
           KWGR+QA +   G+   E K  V+LEPVPGLPGALP PP D
Sbjct: 301 KWGRSQAQQALMGKKDGEFKDIVQLEPVPGLPGALPLPPTD 341

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|338713130|ref|XP_001917686.2| PREDICTED: LOW QUALITY PROTEIN: pre-mRNA-splicing factor RBM22-like [Equus caballus]

 Score =  521 bits (1343), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 244/334 (73%), Positives = 277/334 (82%), Gaps = 23/334 (6%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           MATS  S+TYNRQ+WEDA                  TKEKYGKECKICARPFTVFRWCPG
Sbjct: 1   MATSLGSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEKYGKECKICARPFTVFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
            RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQVRD  L  KDD+PKSDVNKEYY QN
Sbjct: 61  VRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQVRDAGLSFKDDMPKSDVNKEYYTQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           M+ EI   D T P G LGKA+ +S+ML+KLARTTPYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 MEREISNSDGTRPVGMLGKATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDRYYG+NDPVA+KL+ RASTMP+LDPPEDKTITTLYVG LG
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKRASTMPRLDPPEDKTITTLYVGGLG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           D +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +R AAE A E SFNK+I+ GRRLN+
Sbjct: 241 DTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV 300

Query: 283 KWGRAQANRGED-----TAELKVRLEPVPGLPGA 311
           KWGR+QA R ++     T +  ++LEPVPGLPG 
Sbjct: 301 KWGRSQAARXKEKEKDGTTDSGIKLEPVPGLPGV 334

Source: Equus caballus

Species: Equus caballus

Genus: Equus

Family: Equidae

Order: Perissodactyla

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|260830806|ref|XP_002610351.1| hypothetical protein BRAFLDRAFT_145268 [Branchiostoma floridae] gi|229295716|gb|EEN66361.1| hypothetical protein BRAFLDRAFT_145268 [Branchiostoma floridae]

 Score =  520 bits (1338), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 245/351 (69%), Positives = 286/351 (81%), Gaps = 30/351 (8%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           MATS  ++TYNRQ+WED+                  TKEK+GKECKIC RPFTVFRWCPG
Sbjct: 1   MATSLGANTYNRQNWEDSEFPILCQTCLGDNPYIRMTKEKFGKECKICQRPFTVFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
           ARMRFKKTEVCQTC++LKNVCQTCLLDLEYGLP++VRD AL++KDD+PKSDVNKEYY QN
Sbjct: 61  ARMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPVEVRDRALQLKDDVPKSDVNKEYYTQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           M+ EI   D +   G LGKA   S+ML+KLARTTPYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 MEREIANTDGSKAVGTLGKAQAPSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDRYYGVNDPVA KL+ R   MP L PPED++ITTLY+G LG
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRYYGVNDPVANKLLKRYDNMPSLKPPEDRSITTLYIGGLG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           DK+TEQDLRDHFYQFGEIRS+T++++QQCAFIQ+TSRPAAE A E +FNK+I+ GRRL++
Sbjct: 241 DKITEQDLRDHFYQFGEIRSITMVARQQCAFIQFTSRPAAEMAAERTFNKLIINGRRLSV 300

Query: 283 KWGRAQANRGEDT----AELKVRLEPVPGLPGALPPPPK-------DFFNL 322
           +WGR+QA +G+D     +EL + L PVPGLPGALP PP        ++FNL
Sbjct: 301 RWGRSQA-QGKDKKLEHSELDMSLAPVPGLPGALPLPPGEMTGSTPNYFNL 350

Source: Branchiostoma floridae

Species: Branchiostoma floridae

Genus: Branchiostoma

Family: Branchiostomidae

Phylum: Chordata

Superkingdom: Eukaryota

>gi|307181748|gb|EFN69209.1| Pre-mRNA-splicing factor RBM22 [Camponotus floridanus]

 Score =  517 bits (1331), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 250/324 (77%), Positives = 282/324 (87%), Gaps = 19/324 (5%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           MATSKT++TYNRQ+WEDA                  TKEKYGKECKIC RPFTVFRWCPG
Sbjct: 1   MATSKTTNTYNRQNWEDAEFPILCQTCLGDNPYIRMTKEKYGKECKICMRPFTVFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
           ARMRFKKTEVCQTC+RLKNVCQTCLLDLEYGLPIQVRD ALKIKDD+P+SDVNKEYY+QN
Sbjct: 61  ARMRFKKTEVCQTCSRLKNVCQTCLLDLEYGLPIQVRDAALKIKDDLPRSDVNKEYYVQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           +D+EIGKID TTPAGA+GK++ +S++LMKLART+PYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 IDNEIGKIDPTTPAGAVGKSAAASDLLMKLARTSPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDRYYGVNDPVA+KLM RA+ MPKLDPPEDK+ITTLY+GNLG
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRYYGVNDPVADKLMRRAAAMPKLDPPEDKSITTLYIGNLG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           D LTE+ LRDHFYQ+GEIRSVT++ +QQCAFIQYT R AAEAA E +FNK+ILGGRRL I
Sbjct: 241 DILTEKQLRDHFYQYGEIRSVTMVPRQQCAFIQYTQRNAAEAAAERTFNKLILGGRRLTI 300

Query: 283 KWGRAQANRGEDTAE-LKVRLEPV 305
           KWGR+Q  +     E ++  LEPV
Sbjct: 301 KWGRSQGRQTISATEAMREILEPV 324

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242011910|ref|XP_002426686.1| pre-mRNA-splicing factor SLT11, putative [Pediculus humanus corporis] gi|212510857|gb|EEB13948.1| pre-mRNA-splicing factor SLT11, putative [Pediculus humanus corporis]

 Score =  516 bits (1330), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 245/336 (72%), Positives = 292/336 (86%), Gaps = 18/336 (5%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           MATSKTS+TYNRQ+WEDA                  TKEKYGKECKIC+RPFTVFRW PG
Sbjct: 1   MATSKTSNTYNRQNWEDAEFPILCQTCLGDNPYIRMTKEKYGKECKICSRPFTVFRWNPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
           A+MRFKKTEVCQTC+R+KNVCQTCLLDLEYGLPIQVRD ALKIKDDIP+S++NKEYY+QN
Sbjct: 61  AKMRFKKTEVCQTCSRMKNVCQTCLLDLEYGLPIQVRDAALKIKDDIPRSEINKEYYVQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           +D E+GKID+T+P GA+GK+  +S++L+KLART+PYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 IDRELGKIDATSPTGAVGKSQAASDLLLKLARTSPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLM RA TMPKL+ PEDK++TTLYVGN+ 
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMRRAETMPKLELPEDKSVTTLYVGNVS 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           D++TE++L+DHFYQ+GEIRS+T+L+KQQCAFIQ+T+R AAE+A E +FNK+IL GRR+ I
Sbjct: 241 DRITEKELQDHFYQYGEIRSITVLAKQQCAFIQFTTRAAAESAAERTFNKLILCGRRMTI 300

Query: 283 KWGRAQANRGEDTAELKVRLEPVPGLPGALPPPPKD 318
           +WGR+Q  +     E ++ LEPVPGLPGALP PP +
Sbjct: 301 RWGRSQGRQKTSLEEGEIDLEPVPGLPGALPLPPDE 336

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|224067689|ref|XP_002198708.1| PREDICTED: pre-mRNA-splicing factor RBM22 [Taeniopygia guttata]

 Score =  516 bits (1329), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 241/328 (73%), Positives = 274/328 (83%), Gaps = 23/328 (7%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           M+TS  S+TYNRQ+WEDA                  TKEKYGKECKICARPFTVFRWCPG
Sbjct: 1   MSTSLGSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEKYGKECKICARPFTVFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
            RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQVRD  L +KD++PKSDVNKEYY QN
Sbjct: 61  VRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQVRDAGLSLKDEMPKSDVNKEYYTQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           M+ EI   D T P GALGKA+ +S+ML+KLARTTPYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 MEREIANSDGTRPVGALGKATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDRYYG+NDPVA+KL+ RASTMP+LDPPEDKTITTLYVG LG
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKRASTMPRLDPPEDKTITTLYVGGLG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           D +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +R AAE A E SFNK+I+ GRRLN+
Sbjct: 241 DTITESDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV 300

Query: 283 KWGRAQANRG-----EDTAELKVRLEPV 305
           KWGR+QA RG     E T E  ++LEPV
Sbjct: 301 KWGRSQAARGKEKDKEGTTESGIKLEPV 328

Source: Taeniopygia guttata

Species: Taeniopygia guttata

Genus: Taeniopygia

Family: Estrildidae

Order: Passeriformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|383857285|ref|XP_003704135.1| PREDICTED: pre-mRNA-splicing factor RBM22-like [Megachile rotundata]

 Score =  516 bits (1328), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 249/324 (76%), Positives = 281/324 (86%), Gaps = 19/324 (5%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           MATSKT++TYNRQ+WEDA                  TKEKYGKECKIC RPFTVFRWCPG
Sbjct: 1   MATSKTTNTYNRQNWEDAEFPILCQTCLGDNPYIRMTKEKYGKECKICMRPFTVFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
           ARMRFKKTEVCQTC+RLKNVCQTCLLDLEYGLPIQVRD ALKIKDD+P+SDVNKEYY+QN
Sbjct: 61  ARMRFKKTEVCQTCSRLKNVCQTCLLDLEYGLPIQVRDAALKIKDDLPRSDVNKEYYVQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           +D EIGKID T+PAGA+GK++ +S++LMKLART+PYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 IDSEIGKIDPTSPAGAVGKSAAASDLLMKLARTSPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDRYYGVNDPVA+KLM RA+ MPKLDPPEDK+ITTLY+GNLG
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRYYGVNDPVADKLMRRAAAMPKLDPPEDKSITTLYIGNLG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           D LTE+ LRDHFYQ+GEIRS+T++ +QQCAFIQYT R AAEAA E +FNK+ILGGRRL I
Sbjct: 241 DVLTEKQLRDHFYQYGEIRSITMVPRQQCAFIQYTQRSAAEAAAERTFNKLILGGRRLTI 300

Query: 283 KWGRAQANRGEDTAE-LKVRLEPV 305
           KWGR+Q  +    AE  +  LEPV
Sbjct: 301 KWGRSQGRQTVSAAEATREILEPV 324

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156546667|ref|XP_001603806.1| PREDICTED: pre-mRNA-splicing factor RBM22-like [Nasonia vitripennis]

 Score =  515 bits (1327), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 242/324 (74%), Positives = 279/324 (86%), Gaps = 19/324 (5%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           M+ SKT++TYNRQ+WEDA                  TKEKYGKECKIC RPFTVFRWCPG
Sbjct: 1   MSMSKTTNTYNRQNWEDAEFPILCQTCLGDNPYIRMTKEKYGKECKICVRPFTVFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
           ARMRFKKTEVCQTC+RLKNVCQTCLLDLEYGLPIQVRD ALKIKDDIP+SDVNKEYY+QN
Sbjct: 61  ARMRFKKTEVCQTCSRLKNVCQTCLLDLEYGLPIQVRDAALKIKDDIPRSDVNKEYYVQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           +D+EI K D TTPAGA+GK++ +S++LMKLART+PYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 IDNEISKNDPTTPAGAVGKSAAASDLLMKLARTSPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDRYYG NDPVA+KLM RA+ MPKL+PPED +ITTLY+GN+G
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRYYGFNDPVADKLMRRAAAMPKLEPPEDTSITTLYIGNIG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           + LTE+ LRDHFYQ+GEIRSVT+++K QCAFI+YT+R AAE A E +FNK+ILGGRRLNI
Sbjct: 241 EVLTEKTLRDHFYQYGEIRSVTMVAKNQCAFIEYTNRSAAELAAERTFNKLILGGRRLNI 300

Query: 283 KWGRAQANRGEDTAE-LKVRLEPV 305
           KWGR+Q  +    AE ++  LEPV
Sbjct: 301 KWGRSQGRQTISAAEGVREILEPV 324

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340722791|ref|XP_003399785.1| PREDICTED: pre-mRNA-splicing factor RBM22-like [Bombus terrestris] gi|350424167|ref|XP_003493709.1| PREDICTED: pre-mRNA-splicing factor RBM22-like [Bombus impatiens]

 Score =  514 bits (1325), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 249/324 (76%), Positives = 280/324 (86%), Gaps = 19/324 (5%)

Query: 1   MATSKTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPG 42
           MATSKT++ YNRQ+WEDA                  TKE+YGKECKIC RPFTVFRWCPG
Sbjct: 1   MATSKTTNMYNRQNWEDAEFPILCQTCLGDNPYIRMTKERYGKECKICMRPFTVFRWCPG 60

Query: 43  ARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQN 102
           ARMRFKKTEVCQTC+RLKNVCQTCLLDLEYGLPIQVRD ALKIKDD+P+SDVNKEYY+QN
Sbjct: 61  ARMRFKKTEVCQTCSRLKNVCQTCLLDLEYGLPIQVRDAALKIKDDLPRSDVNKEYYVQN 120

Query: 103 MDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECP 162
           +D EIGKID T+PAGA+GK++ +S++LMKLART+PYYKRNRPHICSFWVKGEC+RGEECP
Sbjct: 121 IDSEIGKIDPTSPAGAVGKSAAASDLLMKLARTSPYYKRNRPHICSFWVKGECKRGEECP 180

Query: 163 YRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG 222
           YRHEKPTDPDDPLADQNIKDRYYGVNDPVA+KLM RA+ MPKLDPPEDK+ITTLYVGNLG
Sbjct: 181 YRHEKPTDPDDPLADQNIKDRYYGVNDPVADKLMRRAAAMPKLDPPEDKSITTLYVGNLG 240

Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           D LTE+ LRDHFYQ+GEIRSVT++ +QQCAFIQYT R AAEAA E +FNK+ILGGRRL I
Sbjct: 241 DVLTEKQLRDHFYQYGEIRSVTMVPRQQCAFIQYTQRSAAEAAAERTFNKLILGGRRLTI 300

Query: 283 KWGRAQANRGEDTAE-LKVRLEPV 305
           KWGR+Q  +    AE  +  LEPV
Sbjct: 301 KWGRSQGRQTVSAAEATREILEPV 324

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	327
UNIPROTKB|F1NMD7	420	RBM22 "Pre-mRNA-splicing facto	0.871	0.678	0.775	4e-129
RGD|1305770	420	Rbm22 "RNA binding motif prote	0.844	0.657	0.804	1.1e-128
UNIPROTKB|Q5ZM16	420	RBM22 "Pre-mRNA-splicing facto	0.871	0.678	0.772	1.4e-128
UNIPROTKB|F2Z4G3	420	RBM22 "Pre-mRNA-splicing facto	0.844	0.657	0.800	1.4e-128
UNIPROTKB|Q9NW64	420	RBM22 "Pre-mRNA-splicing facto	0.844	0.657	0.800	1.4e-128
UNIPROTKB|Q4R4J1	420	RBM22 "Pre-mRNA-splicing facto	0.844	0.657	0.800	1.4e-128
UNIPROTKB|Q5RAY5	420	RBM22 "Pre-mRNA-splicing facto	0.844	0.657	0.800	1.4e-128
MGI|MGI:1914060	420	Rbm22 "RNA binding motif prote	0.844	0.657	0.800	1.4e-128
UNIPROTKB|Q3B7L8	420	RBM22 "Pre-mRNA-splicing facto	0.844	0.657	0.800	2.2e-128
UNIPROTKB|E2RG35	422	RBM22 "Uncharacterized protein	0.844	0.654	0.794	2e-127

UNIPROTKB|F1NMD7 RBM22 "Pre-mRNA-splicing factor RBM22" [Gallus gallus (taxid:9031)]

 Score = 1267 (451.1 bits), Expect = 4.0e-129, P = 4.0e-129
 Identities = 225/290 (77%), Positives = 256/290 (88%)

Query:    19 TKEKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQV 78
             TKEKYGKECKICARPFTVFRWCPG RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQV
Sbjct:    37 TKEKYGKECKICARPFTVFRWCPGVRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQV 96

Query:    79 RDTALKIKDDIPKSDVNKEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPY 138
             RD  L +KD++PKSDVNKEYY QNM+ EI   D T P GALGKA+ +S+ML+KLARTTPY
Sbjct:    97 RDAGLSLKDEMPKSDVNKEYYTQNMEREIANSDGTRPVGALGKATSTSDMLLKLARTTPY 156

Query:   139 YKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMAR 198
             YKRNRPHICSFWVKGEC+RGEECPYRHEKPTDPDDPLADQNIKDRYYG+NDPVA+KL+ R
Sbjct:   157 YKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKR 216

Query:   199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTS 258
             ASTMP+LDPP+DKTITTLYVG LGD +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +
Sbjct:   217 ASTMPRLDPPDDKTITTLYVGGLGDTITESDLRNHFYQFGEIRTITVVQRQQCAFIQFAT 276

Query:   259 RPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRG-----EDTAELKVRLE 303
             R AAE A E SFNK+I+ GRRLN+KWGR+QA RG     E T E  ++LE
Sbjct:   277 RQAAEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKEKDKEGTTESGIKLE 326

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000060 "protein import into nucleus, translocation" evidence=IEA

GO:0005487 "nucleocytoplasmic transporter activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0017069 "snRNA binding" evidence=IEA

GO:0033120 "positive regulation of RNA splicing" evidence=IEA

GO:0033554 "cellular response to stress" evidence=IEA

GO:0036002 "pre-mRNA binding" evidence=IEA

GO:0045292 "mRNA cis splicing, via spliceosome" evidence=IEA

GO:0048306 "calcium-dependent protein binding" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0090316 "positive regulation of intracellular protein transport" evidence=IEA

RGD|1305770 Rbm22 "RNA binding motif protein 22" [Rattus norvegicus (taxid:10116)]

 Score = 1263 (449.7 bits), Expect = 1.1e-128, P = 1.1e-128
 Identities = 222/276 (80%), Positives = 249/276 (90%)

Query:    19 TKEKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQV 78
             TKEKYGKECKICARPFTVFRWCPG RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQV
Sbjct:    37 TKEKYGKECKICARPFTVFRWCPGVRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQV 96

Query:    79 RDTALKIKDDIPKSDVNKEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPY 138
             RD  L  KDD+PKSDVNKEYY QNM+ EI   D T P G LGKA+ +S+ML+KLARTTPY
Sbjct:    97 RDAGLSFKDDMPKSDVNKEYYTQNMEREISNSDGTRPVGMLGKATSTSDMLLKLARTTPY 156

Query:   139 YKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMAR 198
             YKRNRPHICSFWVKGEC+RGEECPYRHEKPTDPDDPLADQNIKDRYYG+NDPVA+KL+ R
Sbjct:   157 YKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKR 216

Query:   199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTS 258
             ASTMP+LDPPEDKTITTLYVG LGD +TE DLR+HFYQFGEIR+VT++ +QQCAFIQ+ +
Sbjct:   217 ASTMPRLDPPEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTVTVVQRQQCAFIQFAT 276

Query:   259 RPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGED 294
             R AAE A E SFNK+I+ GRRLN+KWGR+QA RG++
Sbjct:   277 RQAAEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKE 312

GO:0000060 "protein import into nucleus, translocation" evidence=IEA;ISO

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005487 "nucleocytoplasmic transporter activity" evidence=ISO;ISS

GO:0005634 "nucleus" evidence=ISO;ISS

GO:0005737 "cytoplasm" evidence=ISO;ISS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0017069 "snRNA binding" evidence=ISO;ISS

GO:0033120 "positive regulation of RNA splicing" evidence=ISO;ISS

GO:0033554 "cellular response to stress" evidence=ISO;ISS

GO:0036002 "pre-mRNA binding" evidence=ISO;ISS

GO:0045292 "mRNA cis splicing, via spliceosome" evidence=ISO;ISS

GO:0048306 "calcium-dependent protein binding" evidence=IEA;ISO

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA;ISO

GO:0090316 "positive regulation of intracellular protein transport" evidence=ISO;ISS

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|Q5ZM16 RBM22 "Pre-mRNA-splicing factor RBM22" [Gallus gallus (taxid:9031)]

 Score = 1262 (449.3 bits), Expect = 1.4e-128, P = 1.4e-128
 Identities = 224/290 (77%), Positives = 256/290 (88%)

Query:    19 TKEKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQV 78
             TKEKYGKECKICARPFTVFRWCPG RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQV
Sbjct:    37 TKEKYGKECKICARPFTVFRWCPGVRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQV 96

Query:    79 RDTALKIKDDIPKSDVNKEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPY 138
             RD  L +KD++PKSDVNKEYY QNM+ EI   D T P GALGKA+ +S+ML+KLARTTPY
Sbjct:    97 RDAGLSLKDEMPKSDVNKEYYTQNMEREIANSDGTRPVGALGKATSTSDMLLKLARTTPY 156

Query:   139 YKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMAR 198
             YKRNRPHICSFWVKGEC+RGEECPYRHEKPTDPDDPLADQ+IKDRYYG+NDPVA+KL+ R
Sbjct:   157 YKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQDIKDRYYGINDPVADKLLKR 216

Query:   199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTS 258
             ASTMP+LDPP+DKTITTLYVG LGD +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +
Sbjct:   217 ASTMPRLDPPDDKTITTLYVGGLGDTITESDLRNHFYQFGEIRTITVVQRQQCAFIQFAT 276

Query:   259 RPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRG-----EDTAELKVRLE 303
             R AAE A E SFNK+I+ GRRLN+KWGR+QA RG     E T E  ++LE
Sbjct:   277 RQAAEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKEKDKEGTTESGIKLE 326

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006913 "nucleocytoplasmic transport" evidence=ISS

GO:0033120 "positive regulation of RNA splicing" evidence=ISS

GO:0033554 "cellular response to stress" evidence=ISS

GO:0045292 "mRNA cis splicing, via spliceosome" evidence=ISS

GO:0090316 "positive regulation of intracellular protein transport" evidence=ISS

GO:0005487 "nucleocytoplasmic transporter activity" evidence=ISS

GO:0017069 "snRNA binding" evidence=ISS

GO:0036002 "pre-mRNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

UNIPROTKB|F2Z4G3 RBM22 "Pre-mRNA-splicing factor RBM22" [Bos taurus (taxid:9913)]

 Score = 1262 (449.3 bits), Expect = 1.4e-128, P = 1.4e-128
 Identities = 221/276 (80%), Positives = 249/276 (90%)

Query:    19 TKEKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQV 78
             TKEKYGKECKICARPFTVFRWCPG RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQV
Sbjct:    37 TKEKYGKECKICARPFTVFRWCPGVRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQV 96

Query:    79 RDTALKIKDDIPKSDVNKEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPY 138
             RD  L  KDD+PKSDVNKEYY QNM+ EI   D T P G LGKA+ +S+ML+KLARTTPY
Sbjct:    97 RDAGLSFKDDMPKSDVNKEYYTQNMEREISNSDGTRPVGMLGKATSTSDMLLKLARTTPY 156

Query:   139 YKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMAR 198
             YKRNRPHICSFWVKGEC+RGEECPYRHEKPTDPDDPLADQNIKDRYYG+NDPVA+KL+ R
Sbjct:   157 YKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKR 216

Query:   199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTS 258
             ASTMP+LDPPEDKTITTLYVG LGD +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +
Sbjct:   217 ASTMPRLDPPEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFAT 276

Query:   259 RPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGED 294
             R AAE A E SFNK+I+ GRRLN+KWGR+QA RG++
Sbjct:   277 RQAAEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKE 312

GO:0090316 "positive regulation of intracellular protein transport" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0048306 "calcium-dependent protein binding" evidence=IEA

GO:0045292 "mRNA cis splicing, via spliceosome" evidence=IEA

GO:0036002 "pre-mRNA binding" evidence=IEA

GO:0033554 "cellular response to stress" evidence=IEA

GO:0033120 "positive regulation of RNA splicing" evidence=IEA

GO:0017069 "snRNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005487 "nucleocytoplasmic transporter activity" evidence=IEA

GO:0000060 "protein import into nucleus, translocation" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q9NW64 RBM22 "Pre-mRNA-splicing factor RBM22" [Homo sapiens (taxid:9606)]

 Score = 1262 (449.3 bits), Expect = 1.4e-128, P = 1.4e-128
 Identities = 221/276 (80%), Positives = 249/276 (90%)

Query:    19 TKEKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQV 78
             TKEKYGKECKICARPFTVFRWCPG RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQV
Sbjct:    37 TKEKYGKECKICARPFTVFRWCPGVRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQV 96

Query:    79 RDTALKIKDDIPKSDVNKEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPY 138
             RD  L  KDD+PKSDVNKEYY QNM+ EI   D T P G LGKA+ +S+ML+KLARTTPY
Sbjct:    97 RDAGLSFKDDMPKSDVNKEYYTQNMEREISNSDGTRPVGMLGKATSTSDMLLKLARTTPY 156

Query:   139 YKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMAR 198
             YKRNRPHICSFWVKGEC+RGEECPYRHEKPTDPDDPLADQNIKDRYYG+NDPVA+KL+ R
Sbjct:   157 YKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKR 216

Query:   199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTS 258
             ASTMP+LDPPEDKTITTLYVG LGD +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +
Sbjct:   217 ASTMPRLDPPEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFAT 276

Query:   259 RPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGED 294
             R AAE A E SFNK+I+ GRRLN+KWGR+QA RG++
Sbjct:   277 RQAAEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKE 312

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0000060 "protein import into nucleus, translocation" evidence=IDA

GO:0048306 "calcium-dependent protein binding" evidence=IPI

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

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0005487 "nucleocytoplasmic transporter activity" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0033554 "cellular response to stress" evidence=IDA

GO:0090316 "positive regulation of intracellular protein transport" evidence=IDA

GO:0033120 "positive regulation of RNA splicing" evidence=IDA

GO:0045292 "mRNA cis splicing, via spliceosome" evidence=IDA

GO:0017069 "snRNA binding" evidence=IDA

GO:0036002 "pre-mRNA binding" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|Q4R4J1 RBM22 "Pre-mRNA-splicing factor RBM22" [Macaca fascicularis (taxid:9541)]

 Score = 1262 (449.3 bits), Expect = 1.4e-128, P = 1.4e-128
 Identities = 221/276 (80%), Positives = 249/276 (90%)

Query:    19 TKEKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQV 78
             TKEKYGKECKICARPFTVFRWCPG RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQV
Sbjct:    37 TKEKYGKECKICARPFTVFRWCPGVRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQV 96

Query:    79 RDTALKIKDDIPKSDVNKEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPY 138
             RD  L  KDD+PKSDVNKEYY QNM+ EI   D T P G LGKA+ +S+ML+KLARTTPY
Sbjct:    97 RDAGLSFKDDMPKSDVNKEYYTQNMEREISNSDGTRPVGMLGKATSTSDMLLKLARTTPY 156

Query:   139 YKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMAR 198
             YKRNRPHICSFWVKGEC+RGEECPYRHEKPTDPDDPLADQNIKDRYYG+NDPVA+KL+ R
Sbjct:   157 YKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKR 216

Query:   199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTS 258
             ASTMP+LDPPEDKTITTLYVG LGD +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +
Sbjct:   217 ASTMPRLDPPEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFAT 276

Query:   259 RPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGED 294
             R AAE A E SFNK+I+ GRRLN+KWGR+QA RG++
Sbjct:   277 RQAAEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKE 312

GO:0005487 "nucleocytoplasmic transporter activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0006913 "nucleocytoplasmic transport" evidence=ISS

GO:0017069 "snRNA binding" evidence=ISS

GO:0033120 "positive regulation of RNA splicing" evidence=ISS

GO:0033554 "cellular response to stress" evidence=ISS

GO:0036002 "pre-mRNA binding" evidence=ISS

GO:0045292 "mRNA cis splicing, via spliceosome" evidence=ISS

GO:0090316 "positive regulation of intracellular protein transport" evidence=ISS

UNIPROTKB|Q5RAY5 RBM22 "Pre-mRNA-splicing factor RBM22" [Pongo abelii (taxid:9601)]

 Score = 1262 (449.3 bits), Expect = 1.4e-128, P = 1.4e-128
 Identities = 221/276 (80%), Positives = 249/276 (90%)

Query:    19 TKEKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQV 78
             TKEKYGKECKICARPFTVFRWCPG RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQV
Sbjct:    37 TKEKYGKECKICARPFTVFRWCPGVRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQV 96

Query:    79 RDTALKIKDDIPKSDVNKEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPY 138
             RD  L  KDD+PKSDVNKEYY QNM+ EI   D T P G LGKA+ +S+ML+KLARTTPY
Sbjct:    97 RDAGLSFKDDMPKSDVNKEYYTQNMEREISNSDGTRPVGMLGKATSTSDMLLKLARTTPY 156

Query:   139 YKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMAR 198
             YKRNRPHICSFWVKGEC+RGEECPYRHEKPTDPDDPLADQNIKDRYYG+NDPVA+KL+ R
Sbjct:   157 YKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKR 216

Query:   199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTS 258
             ASTMP+LDPPEDKTITTLYVG LGD +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +
Sbjct:   217 ASTMPRLDPPEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFAT 276

Query:   259 RPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGED 294
             R AAE A E SFNK+I+ GRRLN+KWGR+QA RG++
Sbjct:   277 RQAAEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKE 312

GO:0005487 "nucleocytoplasmic transporter activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0006913 "nucleocytoplasmic transport" evidence=ISS

GO:0017069 "snRNA binding" evidence=ISS

GO:0033120 "positive regulation of RNA splicing" evidence=ISS

GO:0033554 "cellular response to stress" evidence=ISS

GO:0036002 "pre-mRNA binding" evidence=ISS

GO:0045292 "mRNA cis splicing, via spliceosome" evidence=ISS

GO:0090316 "positive regulation of intracellular protein transport" evidence=ISS

MGI|MGI:1914060 Rbm22 "RNA binding motif protein 22" [Mus musculus (taxid:10090)]

 Score = 1262 (449.3 bits), Expect = 1.4e-128, P = 1.4e-128
 Identities = 221/276 (80%), Positives = 249/276 (90%)

Query:    19 TKEKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQV 78
             TKEKYGKECKICARPFTVFRWCPG RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQV
Sbjct:    37 TKEKYGKECKICARPFTVFRWCPGVRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQV 96

Query:    79 RDTALKIKDDIPKSDVNKEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPY 138
             RD  L  KDD+PKSDVNKEYY QNM+ EI   D T P G LGKA+ +S+ML+KLARTTPY
Sbjct:    97 RDAGLSFKDDMPKSDVNKEYYTQNMEREISNSDGTRPVGMLGKATSTSDMLLKLARTTPY 156

Query:   139 YKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMAR 198
             YKRNRPHICSFWVKGEC+RGEECPYRHEKPTDPDDPLADQNIKDRYYG+NDPVA+KL+ R
Sbjct:   157 YKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKR 216

Query:   199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTS 258
             ASTMP+LDPPEDKTITTLYVG LGD +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +
Sbjct:   217 ASTMPRLDPPEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFAT 276

Query:   259 RPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGED 294
             R AAE A E SFNK+I+ GRRLN+KWGR+QA RG++
Sbjct:   277 RQAAEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKE 312

GO:0000060 "protein import into nucleus, translocation" evidence=ISO

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005487 "nucleocytoplasmic transporter activity" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0017069 "snRNA binding" evidence=ISO

GO:0033120 "positive regulation of RNA splicing" evidence=ISO

GO:0033554 "cellular response to stress" evidence=ISO

GO:0036002 "pre-mRNA binding" evidence=ISO

GO:0045292 "mRNA cis splicing, via spliceosome" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

GO:0048306 "calcium-dependent protein binding" evidence=ISO

GO:0071013 "catalytic step 2 spliceosome" evidence=ISO

GO:0090316 "positive regulation of intracellular protein transport" evidence=ISO

UNIPROTKB|Q3B7L8 RBM22 "Pre-mRNA-splicing factor RBM22" [Bos taurus (taxid:9913)]

 Score = 1260 (448.6 bits), Expect = 2.2e-128, P = 2.2e-128
 Identities = 221/276 (80%), Positives = 248/276 (89%)

Query:    19 TKEKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVCQTCLLDLEYGLPIQV 78
             TKEKYGKECKICARPFTVFRWCPG RMRFKKTEVCQTC++LKNVCQTCLLDLEYGLPIQV
Sbjct:    37 TKEKYGKECKICARPFTVFRWCPGVRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQV 96

Query:    79 RDTALKIKDDIPKSDVNKEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPY 138
             RD  L  KDD+PKSDVNKEYY QNM+ EI   D T P G LGKA+ +S+ML+KLARTTPY
Sbjct:    97 RDAGLSFKDDMPKSDVNKEYYTQNMEREISNSDGTRPVGMLGKATSTSDMLLKLARTTPY 156

Query:   139 YKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMAR 198
             YKRNRPHICSFWVKGEC+RGEECPYRHEKPTDPDDPLADQNIKDRYYG+NDPVA+KL+ R
Sbjct:   157 YKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKR 216

Query:   199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTS 258
             ASTMP+LDPPEDKTITTLYVG LGD +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +
Sbjct:   217 ASTMPRLDPPEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFAT 276

Query:   259 RPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGED 294
             R AAE A E SFNK I+ GRRLN+KWGR+QA RG++
Sbjct:   277 RQAAEVAAEKSFNKFIVNGRRLNVKWGRSQAARGKE 312

GO:0006913 "nucleocytoplasmic transport" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0036002 "pre-mRNA binding" evidence=ISS

GO:0017069 "snRNA binding" evidence=ISS

GO:0005487 "nucleocytoplasmic transporter activity" evidence=ISS

GO:0090316 "positive regulation of intracellular protein transport" evidence=ISS

GO:0045292 "mRNA cis splicing, via spliceosome" evidence=ISS

GO:0033554 "cellular response to stress" evidence=ISS

GO:0033120 "positive regulation of RNA splicing" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2RG35 RBM22 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 1251 (445.4 bits), Expect = 2.0e-127, P = 2.0e-127
 Identities = 221/278 (79%), Positives = 249/278 (89%)

Query:    19 TKEKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVCQTCLLDLEYGL--PI 76
             TKEKYGKECKICARPFTVFRWCPG RMRFKKTEVCQTC++LKNVCQTCLLDLEYGL  PI
Sbjct:    37 TKEKYGKECKICARPFTVFRWCPGVRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLGLPI 96

Query:    77 QVRDTALKIKDDIPKSDVNKEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLARTT 136
             QVRD  L  KDD+PKSDVNKEYY QNM+ EI   D T P G LGKA+ +S+ML+KLARTT
Sbjct:    97 QVRDAGLSFKDDMPKSDVNKEYYTQNMEREISNSDGTRPVGMLGKATSTSDMLLKLARTT 156

Query:   137 PYYKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLM 196
             PYYKRNRPHICSFWVKGEC+RGEECPYRHEKPTDPDDPLADQNIKDRYYG+NDPVA+KL+
Sbjct:   157 PYYKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDRYYGINDPVADKLL 216

Query:   197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQY 256
              RASTMP+LDPPEDKTITTLYVG LGD +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+
Sbjct:   217 KRASTMPRLDPPEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQF 276

Query:   257 TSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGED 294
              +R AAE A E SFNK+I+ GRRLN+KWGR+QA RG++
Sbjct:   277 ATRQAAEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKE 314

GO:0090316 "positive regulation of intracellular protein transport" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0048306 "calcium-dependent protein binding" evidence=IEA

GO:0045292 "mRNA cis splicing, via spliceosome" evidence=IEA

GO:0036002 "pre-mRNA binding" evidence=IEA

GO:0033554 "cellular response to stress" evidence=IEA

GO:0033120 "positive regulation of RNA splicing" evidence=IEA

GO:0017069 "snRNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005487 "nucleocytoplasmic transporter activity" evidence=IEA

GO:0000060 "protein import into nucleus, translocation" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q4V7D7	RBM22_RAT	No assigned EC number	0.7347	0.9327	0.7261	yes	N/A
Q6NZZ9	RBM22_DANRE	No assigned EC number	0.7094	0.9327	0.7176	yes	N/A
Q5ZM16	RBM22_CHICK	No assigned EC number	0.7286	0.9327	0.7261	yes	N/A
Q8I4V2	RBM22_PLAF7	No assigned EC number	0.3674	0.7645	0.7002	yes	N/A
Q8BHS3	RBM22_MOUSE	No assigned EC number	0.7317	0.9327	0.7261	yes	N/A
Q4R4J1	RBM22_MACFA	No assigned EC number	0.7317	0.9327	0.7261	N/A	N/A
Q6C3L4	SLT11_YARLI	No assigned EC number	0.3156	0.7798	0.7162	yes	N/A
Q9LNV5	C3H4_ARATH	No assigned EC number	0.5192	0.8990	0.6112	yes	N/A
Q5AX35	SLT11_EMENI	No assigned EC number	0.3529	0.7828	0.6790	yes	N/A
Q5SNN4	C3H40_ORYSJ	No assigned EC number	0.5755	0.8226	0.5580	yes	N/A
Q7ZXB5	RBM22_XENLA	No assigned EC number	0.7103	0.9327	0.7314	N/A	N/A
P0CR50	SLT11_CRYNJ	No assigned EC number	0.4676	0.8226	0.8251	yes	N/A
O59800	SLT11_SCHPO	No assigned EC number	0.3016	0.7920	0.7316	yes	N/A
Q6P616	RBM22_XENTR	No assigned EC number	0.7164	0.9327	0.7314	yes	N/A
Q3B7L8	RBM22_BOVIN	No assigned EC number	0.7317	0.9327	0.7261	yes	N/A
Q4W9V0	SLT11_ASPFU	No assigned EC number	0.3469	0.7645	0.6527	yes	N/A
Q9NW64	RBM22_HUMAN	No assigned EC number	0.7317	0.9327	0.7261	yes	N/A
Q5RAY5	RBM22_PONAB	No assigned EC number	0.7317	0.9327	0.7261	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	327
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	2e-46
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	3e-17
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	6e-17
smart00360	73	smart00360, RRM, RNA recognition motif	6e-17
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	4e-14
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	8e-14
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-13
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	3e-13
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	9e-13
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-12
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-12
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	4e-12
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	6e-12
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-11
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-10
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	1e-10
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-10
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-09
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-09
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-09
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	3e-09
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	3e-09
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-08
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-08
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-08
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	2e-08
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-08
cd12262	82	cd12262, RRM2_4_MRN1, RNA recognition motif 2 and	3e-08
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-08
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	5e-08
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	6e-08
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	6e-08
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	1e-07
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	1e-07
cd12462	79	cd12462, RRM_SCAF8, RNA recognition motif in SR-re	3e-07
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	4e-07
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	4e-07
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	4e-07
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	4e-07
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	5e-07
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	5e-07
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	8e-07
cd12520	74	cd12520, RRM1_MRN1, RNA recognition motif 1 of RNA	8e-07
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	8e-07
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-06
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	1e-06
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-06
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	2e-06
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	2e-06
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	2e-06
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	2e-06
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	2e-06
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	2e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-06
cd12348	75	cd12348, RRM1_SHARP, RNA recognition motif 1 in SM	3e-06
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	3e-06
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	4e-06
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	4e-06
cd12689	80	cd12689, RRM1_hnRNPL_like, RNA recognition motif 1	4e-06
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	4e-06
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	5e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	7e-06
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	8e-06
smart00356	27	smart00356, ZnF_C3H1, zinc finger	9e-06
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-05
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	1e-05
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	1e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-05
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	1e-05
cd12461	81	cd12461, RRM_SCAF4, RNA recognition motif found in	1e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-05
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-05
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	2e-05
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-05
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	2e-05
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-05
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	2e-05
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-05
cd12258	72	cd12258, RRM2_RBM26_like, RNA recognition motif 2	2e-05
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	2e-05
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	2e-05
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-05
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	3e-05
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-05
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	4e-05
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	4e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	4e-05
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	4e-05
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	5e-05
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	5e-05
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	5e-05
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	5e-05
cd12331	79	cd12331, RRM_NRD1_SEB1_like, RNA recognition motif	6e-05
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	6e-05
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	6e-05
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	6e-05
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	8e-05
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	9e-05
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	1e-04
cd12558	76	cd12558, RRM3_RBM15B, RNA recognition motif 3 in p	1e-04
cd12292	75	cd12292, RRM2_La_like, RNA recognition motif 2 in	1e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-04
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	1e-04
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	1e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	1e-04
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	1e-04
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-04
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-04
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	2e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	2e-04
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	2e-04
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-04
cd12716	76	cd12716, RRM1_2_NP220, RNA recognition motif 1 and	2e-04
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-04
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	2e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	2e-04
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	2e-04
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	2e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-04
cd12248	74	cd12248, RRM_RBM44, RNA recognition motif in RNA-b	3e-04
cd12299	71	cd12299, RRM4_Prp24, RNA recognition motif 4 in fu	3e-04
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	3e-04
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	3e-04
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	3e-04
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	3e-04
cd12557	73	cd12557, RRM3_RBM15, RNA recognition motif 3 in ve	3e-04
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	4e-04
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	4e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	4e-04
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	4e-04
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	4e-04
cd12261	73	cd12261, RRM1_3_MRN1, RNA recognition motif 1 and	5e-04
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	6e-04
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	6e-04
cd12269	69	cd12269, RRM_Vip1_like, RNA recognition motif in a	6e-04
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	6e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	6e-04
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	6e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	7e-04
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	7e-04
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	9e-04
PLN03120	260	PLN03120, PLN03120, nucleic acid binding protein;	9e-04
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	0.001
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	0.001
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	0.001
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.001
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	0.002
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	0.002
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	0.002
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	0.002
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	0.003
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	0.003
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	0.003
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	0.003
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	0.003
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	0.003
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	0.003
cd12625	77	cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in	0.003
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	0.003
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	0.003
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	0.003
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	0.003
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	0.004
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	0.004
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	0.004
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	0.004

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score =  151 bits (383), Expect = 2e-46
 Identities = 50/74 (67%), Positives = 64/74 (86%)

Query: 213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNK 272
           ITTLYVG LG+++TE+DLRDHFYQFGEIRS+T++ +QQCAF+ +T+R AAE A E  FNK
Sbjct: 1   ITTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFVTFTTREAAEKAAERLFNK 60

Query: 273 VILGGRRLNIKWGR 286
           +I+ GRRL +KWGR
Sbjct: 61  LIINGRRLKLKWGR 74

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 74.6 bits (184), Expect = 3e-17
 Identities = 31/72 (43%), Positives = 43/72 (59%), Gaps = 1/72 (1%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
           TT++VG L   +TE +LR  F  FGEI  V I   + C F+Q+  R AAEAA++      
Sbjct: 2   TTVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQ-QLQGT 60

Query: 274 ILGGRRLNIKWG 285
           I+GG R+ + WG
Sbjct: 61  IIGGSRIRLSWG 72

This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 72

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

 Score = 73.9 bits (182), Expect = 6e-17
 Identities = 30/73 (41%), Positives = 42/73 (57%), Gaps = 6/73 (8%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAEAAVEHSF 270
           L+VGNL    TE+DLR+ F +FGEI SV I+  +       AF+++ S   AE A+E   
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEA-L 59

Query: 271 NKVILGGRRLNIK 283
           N   L GR+L + 
Sbjct: 60  NGKELDGRKLKVS 72

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

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

 Score = 73.8 bits (182), Expect = 6e-17
 Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 7/74 (9%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVEH 268
           TL+VGNL    TE++LR+ F +FG++ SV ++  ++       AF+++ S   AE A+E 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 269 SFNKVILGGRRLNI 282
             N   L GR L +
Sbjct: 61  -LNGKELDGRPLKV 73

Length = 73

>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing factor SLT11 and similar proteins

 Score = 66.6 bits (163), Expect = 4e-14
 Identities = 23/86 (26%), Positives = 43/86 (50%), Gaps = 11/86 (12%)

Query: 212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFN 271
           +I + ++  + D L E  +RD+F QFG+ +SV +  + +C F+++ +R AAE        
Sbjct: 1   SIKSFFLFGVEDDLPEYKIRDYFEQFGKSKSVIVNHRAKCGFVRFETREAAEKFAAAISE 60

Query: 272 -----------KVILGGRRLNIKWGR 286
                       ++L G  L + WG+
Sbjct: 61  NGLNAGLSRGGLLVLEGCPLRVAWGK 86

This subfamily corresponds to the RRM of SLT11, also known as extracellular mutant protein 2, or synthetic lethality with U2 protein 11, and is a splicing factor required for spliceosome assembly in yeast. It contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). SLT11 can facilitate the cooperative formation of U2/U6 helix II in association with stem II in the yeast spliceosome by utilizing its RNA-annealing and -binding activities. . Length = 86

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

 Score = 65.3 bits (160), Expect = 8e-14
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
           TT+YVGNL   LTE++L+  F  FG I  V +   +  AF+++ +  AA  A+  + N  
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKGYAFVRFDTHEAAATAIV-AVNGT 59

Query: 274 ILGGRRLNIKWGR 286
            + G+ +   WG+
Sbjct: 60  SINGQTVKCSWGK 72

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

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

 Score = 64.9 bits (159), Expect = 1e-13
 Identities = 28/70 (40%), Positives = 40/70 (57%), Gaps = 6/70 (8%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAEAAVEHSF 270
           L+VGNL    TE+DL+D F +FG I S+ I+  +       AF+++     AE A+E + 
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALE-AL 59

Query: 271 NKVILGGRRL 280
           N   LGGR L
Sbjct: 60  NGKELGGREL 69

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

>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 63.8 bits (156), Expect = 3e-13
 Identities = 28/84 (33%), Positives = 43/84 (51%), Gaps = 10/84 (11%)

Query: 213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL---------SKQQCAFIQYTSRPAAE 263
            T LYVGNL  K+TE+ L   F +FG + SV I+           + C F+ + +R  AE
Sbjct: 1   TTNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAE 60

Query: 264 AAVEHSFNKVILGGRRLNIKWGRA 287
            A++   +   + G  L + WG+A
Sbjct: 61  RALD-ELDGKDVMGYELKLGWGKA 83

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

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

 Score = 62.7 bits (153), Expect = 9e-13
 Identities = 28/76 (36%), Positives = 41/76 (53%), Gaps = 11/76 (14%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ---------CAFIQYTSRPAAEAAV 266
           +YV NL  KL E DLR  F +FGE+ S+ I  KQ           AF+ +    +AE A+
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 267 EHSFNKVILGGRRLNI 282
           +   N   LGGR++++
Sbjct: 63  Q--LNGTELGGRKISV 76

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

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

 Score = 62.2 bits (152), Expect = 1e-12
 Identities = 25/68 (36%), Positives = 39/68 (57%), Gaps = 6/68 (8%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVEHS 269
           L+VG L    TE+D+R  F ++G I  VTI+  +       CAF++++SR  A+ A+E  
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 270 FNKVILGG 277
             KV + G
Sbjct: 62  HGKVTMPG 69

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

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

 Score = 60.6 bits (148), Expect = 4e-12
 Identities = 25/70 (35%), Positives = 41/70 (58%), Gaps = 5/70 (7%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC----AFIQYTSRPAAEAAVEHSFN 271
           LYV NL   +TE+DLR+ F  +G++  V ++  +      AF+++ S   AEAA++   N
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKK-LN 59

Query: 272 KVILGGRRLN 281
            ++L GR L 
Sbjct: 60  GLVLDGRTLR 69

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

>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 60.9 bits (148), Expect = 4e-12
 Identities = 23/53 (43%), Positives = 36/53 (67%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVE 267
            +Y+GN+ D LTE+ LR+ F Q+GEI SV  L ++ CAF+ +T+   A  A++
Sbjct: 5   NVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKNCAFVNFTNISNAIKAID 57

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins

 Score = 60.4 bits (147), Expect = 6e-12
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 4/74 (5%)

Query: 215 TLYVG----NLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSF 270
           TLYVG        K  E+ LR HF ++G+I  + +L  +  AF++Y  R +AE A E   
Sbjct: 3   TLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLPSKGIAFVRYKYRASAEFAKEAMA 62

Query: 271 NKVILGGRRLNIKW 284
           ++ + GG  LN++W
Sbjct: 63  DQSLDGGEVLNVRW 76

This subfamily corresponds to the RRM of yeast protein Cwc2, also termed Complexed with CEF1 protein 2, or PRP19-associated complex protein 40 (Ntc40), or synthetic lethal with CLF1 protein 3, one of the components of the Prp19-associated complex [nineteen complex (NTC)] that can bind to RNA. NTC is composed of the scaffold protein Prp19 and a number of associated splicing factors, and plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Cwc2 functions as an RNA-binding protein that can bind both small nuclear RNAs (snRNAs) and pre-mRNA in vitro. It interacts directly with the U6 snRNA to link the NTC to the spliceosome during pre-mRNA splicing. In the N-terminal half, Cwc2 contains a CCCH-type zinc finger (ZnF domain), a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an intervening loop, also termed RNA-binding loop or RB loop, between ZnF and RRM, all of which are necessary and sufficient for RNA binding. The ZnF is also responsible for mediating protein-protein interaction. The C-terminal flexible region of Cwc2 interacts with the WD40 domain of Prp19. Length = 78

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

 Score = 57.9 bits (141), Expect = 3e-11
 Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 2/56 (3%)

Query: 230 LRDHFYQFGEIRSVTIL-SKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW 284
           L   F  FG +  + +L  K   AF+++++  AAE AV++  N V+ GGR L + +
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQY-LNGVLFGGRPLRVDY 55

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

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

 Score = 61.5 bits (148), Expect = 1e-10
 Identities = 31/103 (30%), Positives = 54/103 (52%), Gaps = 7/103 (6%)

Query: 198 RASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------C 251
           R+S  PK      +   TL+VGNL   +TE+DLR+ F +FG ++ V ++  ++       
Sbjct: 100 RSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGF 159

Query: 252 AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGED 294
           AF+++ S  +AE A+E   N   L GR L ++  +  +    +
Sbjct: 160 AFVEFESEESAEKAIE-ELNGKELEGRPLRVQKAQPASQPRSE 201

Length = 306

>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 56.4 bits (137), Expect = 1e-10
 Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 214 TTLYVGNLGDKL-TEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNK 272
           TTL V N+  +L     L +HF +FG I ++ +    + A +Q+++   A+ A  +   +
Sbjct: 2   TTLEVRNIPPELNNITKLNEHFSKFGTIVNIQVNYNPESALVQFSTSEEAKKA--YRSPE 59

Query: 273 VILGGRRLNIKW 284
            +   R + + W
Sbjct: 60  AVFNNRFIKVFW 71

This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear. . Length = 72

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

 Score = 56.1 bits (136), Expect = 2e-10
 Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 10/81 (12%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL---------SKQQCAFIQYTSRPAAEAA 265
            L++GNL  +LTE  L   F ++G+I+    L           +   F+ + ++  AE A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 266 VEHSFNKVILGGRRLNIKWGR 286
           ++ S N     G++L ++W  
Sbjct: 61  LK-SLNGKTALGKKLVVRWAH 80

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

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

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 8/77 (10%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEI-RSVTILSKQQ-----CAFIQYTSRPAAEAAVE 267
           T ++VG L    T+  LR +F QFGEI  +V I  +Q        F+ +  + +AE A +
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 268 HSFNKVILGGRRLNIKW 284
                 I+ GR+ N+  
Sbjct: 61  DP--NPIIDGRKANVNL 75

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

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

 Score = 53.7 bits (130), Expect = 1e-09
 Identities = 25/80 (31%), Positives = 46/80 (57%), Gaps = 8/80 (10%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL----SKQQC-AFIQYTSRPAAEAAVEH 268
           T +YV NLG+ + ++ L++ F ++G+I S  ++     K +   F+ + +  AA+ AVE 
Sbjct: 2   TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEE 61

Query: 269 SFNKVILGGRRLNIKWGRAQ 288
             N   + G++L +  GRAQ
Sbjct: 62  -LNGKEVNGKKLYV--GRAQ 78

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

>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 53.4 bits (129), Expect = 1e-09
 Identities = 20/68 (29%), Positives = 41/68 (60%), Gaps = 1/68 (1%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL 275
           L+VGNL + +TE++ ++ F ++GE+  V +  ++   FI+  +R  AE A     + ++ 
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEKGFGFIRLDTRTNAEKAKA-ELDGIMR 62

Query: 276 GGRRLNIK 283
            GR+L ++
Sbjct: 63  KGRQLRVR 70

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 52.7 bits (127), Expect = 3e-09
 Identities = 26/79 (32%), Positives = 50/79 (63%), Gaps = 4/79 (5%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
           TTL++G+L  K+TE+DL++ F ++GEI+S+ ++  + CA++   +R  A  A++     V
Sbjct: 3   TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRGCAYVCMETRQDAHRALQ-KLRNV 61

Query: 274 ILGGRRLNIKWGRAQANRG 292
            L G+++ + W     N+G
Sbjct: 62  KLAGKKIKVAWAP---NKG 77

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

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

 Score = 52.7 bits (127), Expect = 3e-09
 Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 4/58 (6%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC----AFIQYTSRPAAEAAVEH 268
           +++VG L   +T+++L + F + G+I  V ++ +       AFI++    AA  AVE 
Sbjct: 5   SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVES 62

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

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

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 7/74 (9%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEH 268
            LYVGNL   +TE+DL+D F QFGE+ S  +++ ++        F++  +   A AA+E 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIE- 59

Query: 269 SFNKVILGGRRLNI 282
             N    GGR L +
Sbjct: 60  KLNGTDFGGRTLTV 73

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

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

 Score = 50.8 bits (122), Expect = 2e-08
 Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 7/73 (9%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
           +T+YV NL   LT  DL   F ++G++  VTI+  ++       AFI +  R  A   V 
Sbjct: 2   STVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCV- 60

Query: 268 HSFNKVILGGRRL 280
            + N   L GR L
Sbjct: 61  KALNNKELFGRTL 73

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

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

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 28/74 (37%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-----AFIQYTSRPAAEAAVEHSF 270
           L V NL  K TE DL+  F  FG +  VTI  K        AF+Q+TS+  AE A++   
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIK-GV 60

Query: 271 NKVILGGRRLNIKW 284
           N   + GR + + W
Sbjct: 61  NGKKIKGRPVAVDW 74

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

>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 50.5 bits (121), Expect = 2e-08
 Identities = 22/56 (39%), Positives = 33/56 (58%), Gaps = 5/56 (8%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----SKQQCAFIQYTSRPAAEAAV 266
           L+VG L  + TE D+R  F  FG I   TIL     + + CAF++++S   A+AA+
Sbjct: 4   LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAI 59

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

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

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
           LYVG L +++ E+ L   F  FG+I+ + I    +       AF+++     A AA++ +
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAID-N 59

Query: 270 FNKVILGGRRL 280
            N+  L GR +
Sbjct: 60  MNESELFGRTI 70

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

>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding protein MRN1 and similar proteins

 Score = 50.3 bits (120), Expect = 3e-08
 Identities = 22/57 (38%), Positives = 36/57 (63%), Gaps = 5/57 (8%)

Query: 216 LYVGNLGDK-----LTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVE 267
           +Y+GN+ D      L E++LR    ++GEI S+ IL ++ CAFI + + P A AA++
Sbjct: 5   VYIGNVSDVGDERNLPEKELRKECEKYGEIESIRILREKACAFINFMNIPNAIAALQ 61

This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 82

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

 Score = 49.9 bits (120), Expect = 3e-08
 Identities = 24/79 (30%), Positives = 44/79 (55%), Gaps = 12/79 (15%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSV-------TILSKQQCAFIQYTSRPAAEAAVE 267
           T+++ NL    TE++L++ F QFGE++         T  SK   AF+++ ++ +A+  +E
Sbjct: 2   TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSK-GTAFVKFKTKESAQKCLE 60

Query: 268 HSFN----KVILGGRRLNI 282
            + N     + L GRRL +
Sbjct: 61  AADNAEDSGLSLDGRRLIV 79

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

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

 Score = 48.8 bits (117), Expect = 5e-08
 Identities = 19/62 (30%), Positives = 37/62 (59%), Gaps = 3/62 (4%)

Query: 216 LYVGNLG-DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVI 274
           ++VGNL  DK++++DL + F ++G+I  +++   +   F+Q+ +   A AAV     + I
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGISLH--KGYGFVQFDNEEDARAAVAGENGREI 60

Query: 275 LG 276
            G
Sbjct: 61  AG 62

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

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

 Score = 48.8 bits (117), Expect = 6e-08
 Identities = 27/73 (36%), Positives = 35/73 (47%), Gaps = 7/73 (9%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
           LYVGNL   +TE DLR  F  FGEI  V +    +        FIQ+     A+ A+E  
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALE-Q 59

Query: 270 FNKVILGGRRLNI 282
            N   L GR + +
Sbjct: 60  LNGFELAGRPIKV 72

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

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

 Score = 49.1 bits (118), Expect = 6e-08
 Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 7/75 (9%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTI-LSKQQ---C--AFIQYTSRPAAEAAVEHS 269
           LYVGNL    TE+ + + F + G+I+ + + L +     C   F++Y +R  AE AV++ 
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKY- 59

Query: 270 FNKVILGGRRLNIKW 284
            N   L  R + + W
Sbjct: 60  LNGTKLDDRIIRVDW 74

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

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

 Score = 48.2 bits (115), Expect = 1e-07
 Identities = 30/77 (38%), Positives = 44/77 (57%), Gaps = 9/77 (11%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSV-----TILSKQQC-AFIQYTSRPAAEAAVEHS 269
           +YVG++  +L E  +R  F  FG I+S+      +  K +  AF++Y    AA+ A+E  
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ- 61

Query: 270 FNKVILGGRRLNIKWGR 286
            N V+LGGR  NIK GR
Sbjct: 62  MNGVMLGGR--NIKVGR 76

This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 76

>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 4/71 (5%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSV-TILSKQQCAFIQ-YTSRPAAEAAVEHSFNK 272
           TL V NL   +++Q+LR  F QFGE++ +     +    F++ Y  R AAEAA+  + N 
Sbjct: 3   TLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIR-AAEAAL-DALNG 60

Query: 273 VILGGRRLNIK 283
               G RL +K
Sbjct: 61  RPFLGGRLKVK 71

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|240908 cd12462, RRM_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 47.0 bits (111), Expect = 3e-07
 Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH-SFNK 272
           TTL+VG +  K T+QDL + F +FG+I S+ ++  + CA++    R  A  A++  S   
Sbjct: 3   TTLWVGQVDKKATQQDLTNLFEEFGQIESINMIPPRGCAYVCMVHRQDAYRALQKLSSGS 62

Query: 273 VILGGRRLNIKWG 285
             +G + + I W 
Sbjct: 63  YKIGSKVIKIAWA 75

This subgroup corresponds to the RRM of SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8), a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8, together with SCAF4, represents a new class of SCAFs (SR-like CTD-associated factors). They contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 79

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

 Score = 46.7 bits (111), Expect = 4e-07
 Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 5/67 (7%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAEAAVEHSF 270
           L+VG L  K  E D+R  F  FG I   T+L  Q      CAF+ + SR  A  A++   
Sbjct: 4   LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMH 63

Query: 271 NKVILGG 277
           +   + G
Sbjct: 64  HSQTMEG 70

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

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

 Score = 46.6 bits (111), Expect = 4e-07
 Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 8/74 (10%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVEH 268
            L+VGNL    T +DL  HF   G   SV +L+ ++      CAF+++ +  A   A+  
Sbjct: 2   ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKAL-- 59

Query: 269 SFNKVILGGRRLNI 282
             +  +L GR++N+
Sbjct: 60  KLHHTLLKGRKINV 73

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

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

 Score = 46.8 bits (112), Expect = 4e-07
 Identities = 29/81 (35%), Positives = 43/81 (53%), Gaps = 12/81 (14%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCA-----------FIQYTSRPAA 262
           TTL+V NL  K TE+ L+ HF + G +RSVTI  K+              F+++ S+ AA
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 263 EAAVEHSFNKVILGGRRLNIK 283
           + A++     V L G  L +K
Sbjct: 61  QKALKRLQGTV-LDGHALELK 80

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

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

 Score = 46.6 bits (111), Expect = 4e-07
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 7/75 (9%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
           ++VG+L  ++  + LR  F  FGEI    ++   Q        F+ +  +  AE A++ S
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQ-S 60

Query: 270 FNKVILGGRRLNIKW 284
            N   LGGR +   W
Sbjct: 61  MNGQWLGGRAIRTNW 75

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

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

 Score = 46.2 bits (110), Expect = 5e-07
 Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI-----LSKQQCAFIQYTSRPAAEAAVEHS 269
           TL+VGNL  ++TE+ L + F Q G +  V I        +  AF+ +    +   A++  
Sbjct: 3   TLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQ-L 61

Query: 270 FNKVILGGRRLNIK 283
            N + L GR L IK
Sbjct: 62  LNGIRLFGRELRIK 75

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

>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 46.2 bits (110), Expect = 5e-07
 Identities = 22/46 (47%), Positives = 27/46 (58%), Gaps = 5/46 (10%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ----QCAFIQY 256
           TL++GNL    T  DLR+ F +FGEI  + I  KQ      AFIQY
Sbjct: 4   TLFIGNLEKTTTYSDLREAFERFGEIIDIDI-KKQGGNPAYAFIQY 48

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 45.7 bits (109), Expect = 8e-07
 Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-CAFIQYTSRPAAEAAVEHSFNKVI 274
           +YVGNLG + T+++L D F ++G +RSV +       AF+++     AE AV     + I
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRRI 61

Query: 275 LGGR 278
            G R
Sbjct: 62  CGNR 65

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

>gnl|CDD|240964 cd12520, RRM1_MRN1, RNA recognition motif 1 of RNA-binding protein MRN1 and similar proteins

 Score = 45.9 bits (109), Expect = 8e-07
 Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEA-AVEHSFNKV 273
           T+Y+GNL    T ++L  H  + G I +V IL ++ CAFI +    AA A   +    ++
Sbjct: 3   TVYLGNLPPNTTVKELLSHV-RSGPIENVRILPEKNCAFISFLDPSAATAFHSDAILKRL 61

Query: 274 ILGGRRLNIKWGR 286
            + G  L I WG+
Sbjct: 62  SIKGVELKIGWGK 74

This subgroup corresponds to the RRM1 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa,which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 45.9 bits (109), Expect = 8e-07
 Identities = 16/51 (31%), Positives = 30/51 (58%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAV 266
           +Y+GNL +  +E++LR+   +FG I  + I+ ++  AF+ + S   A   V
Sbjct: 6   VYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKNIAFVHFLSIANAIKVV 56

This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 78

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 7/75 (9%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
             L+V  L  + TE++L   F +FG +  V ++   +        F+ + S   A+AA+ 
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 268 HSFNKVILGGRRLNI 282
              N   L GR + +
Sbjct: 62  D-LNGKELEGRVIKV 75

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

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

 Score = 45.5 bits (108), Expect = 1e-06
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAE 263
           D     L+VG +   L E+DLR  F QFG+I  +T+L  +       CAF+ Y +R +A 
Sbjct: 2   DDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESAL 61

Query: 264 AAVEHSFNKVILGG 277
            A      +  L G
Sbjct: 62  KAQSALHEQKTLPG 75

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

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

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 9/85 (10%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRS-------VTILSKQQCAFIQYTSRPAAEAAVE 267
           TL+VG L  + TE+ LR+ F ++G+IR        VT  SK   AF++Y     A  A  
Sbjct: 5   TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGY-AFVEYEHERDALRAYR 63

Query: 268 HSFNKVILGGRRLNIKWGRAQANRG 292
            + +K+++ G  + + + R +   G
Sbjct: 64  DA-HKLVIDGSEIFVDFERERTLPG 87

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

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

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 6/75 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAEAAVEH 268
           +TL+V N      + D+RD F Q+GEI S+   S +        ++Q+TS  +A AAV  
Sbjct: 1   STLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVA- 59

Query: 269 SFNKVILGGRRLNIK 283
             N  +  G +L +K
Sbjct: 60  LLNGKLGEGYKLVVK 74

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

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

 Score = 45.4 bits (108), Expect = 2e-06
 Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 10/74 (13%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ---CAFIQYTSRPAAEAAVEHSFN- 271
           +YVG +    T  +LR  F  FGEI  +T+  +       F+ Y     A  A+EH  + 
Sbjct: 5   IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFVTYRYACDAFRAIEHGNDD 64

Query: 272 ------KVILGGRR 279
                  +  GGRR
Sbjct: 65  PTEPKYDLCFGGRR 78

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

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 7/77 (9%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQF-GEIRSVTILSKQQ-----CAFIQYTSRPAAEAAVE 267
           + L V NL   LTE +L++HF +  GEI  V +L  +       AFI Y +   A+ A +
Sbjct: 1   SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKD 60

Query: 268 HSFNKVILGGRRLNIKW 284
           + FN   +   ++++++
Sbjct: 61  Y-FNNTYINTSKISVEF 76

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 44.6 bits (105), Expect = 2e-06
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVI 274
           T+Y G +   LTEQ +R  F  FG+I  + +  ++  +FI++++  +A  A+  S N   
Sbjct: 2   TVYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPEKGYSFIRFSTHESAAHAIV-SVNGTT 60

Query: 275 LGGRRLNIKWGR 286
           + G  +   WG+
Sbjct: 61  IEGHVVKCYWGK 72

This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 73

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

 Score = 44.3 bits (105), Expect = 2e-06
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 3/71 (4%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS--KQQCAFIQYTSRPAAEAAVEHSFNK 272
           T+Y G         D++  F   G +R VT+LS   Q  AFI + +  AA+ A+E + N 
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIE-TLNG 59

Query: 273 VILGGRRLNIK 283
             + G  + ++
Sbjct: 60  ASVDGNCIKVQ 70

This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 6/66 (9%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL 275
           L+VG LG   +  +L   F +FG IR +     +  A+I+Y S  AA+AA E       L
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRNYAYIEYESIEAAQAAKEA------L 54

Query: 276 GGRRLN 281
            G  L 
Sbjct: 55  RGFPLG 60

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

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

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL 275
           LYV NL    TE+ LR+ F ++GE+  V  +     AF+ +  R  A  A+E   N   L
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKDY--AFVHFEERDDAVKAME-EMNGKEL 60

Query: 276 GGRRLNIKWGRA 287
            G  + +   + 
Sbjct: 61  EGSPIEVSLAKP 72

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

>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 44.4 bits (105), Expect = 3e-06
 Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 8/72 (11%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAEAAVEHSF 270
           L+VGNL + + E+ + +HF ++G + SV IL K+       AF+ +    +A+ A  ++ 
Sbjct: 2   LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKA-HNAV 60

Query: 271 NKVILGGRRLNI 282
           NK+  G R L  
Sbjct: 61  NKM--GDRDLRT 70

This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 75

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

 Score = 44.3 bits (105), Expect = 3e-06
 Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 11/75 (14%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
           L+VGNL   +TE +L++ F +FG +  V I SK          F+ +    A +  +   
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILA-- 63

Query: 270 FNKVIL--GGRRLNI 282
            NK I   G  RLN+
Sbjct: 64  -NKPIYFRGDHRLNV 77

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

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

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 4/72 (5%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC---AFIQYTSRPAAEAAVEHSFNK 272
           LYVGNL   +TE  L + F Q G I+S  ++ +      AF++Y    +A AA++   N 
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQT-MNG 59

Query: 273 VILGGRRLNIKW 284
            ++ G+ + + W
Sbjct: 60  RLILGQEIKVNW 71

This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 72

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

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 8/72 (11%)

Query: 217 YVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVEHSF 270
           +VGN+    T ++L++HF   G I  +TIL  +        A+I++  + + E A+    
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL--LL 60

Query: 271 NKVILGGRRLNI 282
           N+    GR++ +
Sbjct: 61  NESEFRGRQIKV 72

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

>gnl|CDD|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 43.9 bits (104), Expect = 4e-06
 Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHS-FNKVI 274
           ++V  L D +TE DL +   +FG I  VT++ K++ A +++     A+A V H+  N V 
Sbjct: 5   VHVRGLPDGVTEADLVEALSEFGPISYVTMMPKKRQALVEFEDISDAKACVNHAQQNPVY 64

Query: 275 LGGRRLNIKWGRAQ 288
           + GR+    +  +Q
Sbjct: 65  IAGRQAYFNYSTSQ 78

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 80

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

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 9/77 (11%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEI------RS-VTILSKQQCAFIQYTSRPAAEAAVE 267
            L VGNL  + T++  R+    FG +       S  T  SK    F++Y S+ +A  A +
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGY-GFVEYASKASALKA-K 58

Query: 268 HSFNKVILGGRRLNIKW 284
           +  +   +GGR+L + W
Sbjct: 59  NQLDGKQIGGRKLQVDW 75

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

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

 Score = 43.4 bits (103), Expect = 5e-06
 Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 6/76 (7%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAEAAVEH 268
           T L V N+  + T+++LR+ F  FG+++SV +  K        AF+++ ++  A+ A+E 
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

Query: 269 SFNKVILGGRRLNIKW 284
                 L GR L +++
Sbjct: 61  -LKSTHLYGRHLVLEY 75

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

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

 Score = 47.1 bits (112), Expect = 7e-06
 Identities = 33/96 (34%), Positives = 43/96 (44%), Gaps = 7/96 (7%)

Query: 210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI--LSKQQC---AFIQYTSRPAAEA 264
            K  T LYV NL   + E  LR+ F +FGEI S  +      +    AF+ +     A  
Sbjct: 175 LKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAK 234

Query: 265 AVEHSFNKVILGGRRLNIKW-GRAQANRGEDTAELK 299
           AVE    K I   +     + GRAQ  R E  AEL+
Sbjct: 235 AVEEMNGKKIGLAKEGKKLYVGRAQK-RAEREAELR 269

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

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

 Score = 42.9 bits (102), Expect = 7e-06
 Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 12/72 (16%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSV-------TILSKQQCAFIQYTSRPAAEAAVE 267
           T+ V NL +   E DLR+ F  FG I  V       T  S+   AF+ + +R  AE A+E
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSR-GFAFVTFHTREDAERAIE 59

Query: 268 ----HSFNKVIL 275
                 ++ +IL
Sbjct: 60  KLNGFGYDNLIL 71

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

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 43.0 bits (101), Expect = 8e-06
 Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL 275
           L+VGNL   +TE+D +  F ++GE   V I   +   FI+  SR  AE A +   +  IL
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDRGFGFIRLESRTLAEIA-KAELDGTIL 62

Query: 276 GGRRLNIKW 284
             R L I++
Sbjct: 63  KNRPLRIRF 71

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|214632 smart00356, ZnF_C3H1, zinc finger

 Score = 41.5 bits (98), Expect = 9e-06
 Identities = 8/27 (29%), Positives = 15/27 (55%)

Query: 141 RNRPHICSFWVKGECRRGEECPYRHEK 167
           + +  +C F+ +G C RG+ C + H  
Sbjct: 1   KYKTELCKFFKRGYCPRGDRCKFAHPL 27

Length = 27

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 7/74 (9%)

Query: 217 YVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHSF 270
           +VGN+    TE+ L + F + G + S  +++ +         F ++     A +A+  + 
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIR-NL 60

Query: 271 NKVILGGRRLNIKW 284
           N     GR L + +
Sbjct: 61  NGYEFNGRALRVDF 74

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

>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 42.7 bits (100), Expect = 1e-05
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVI 274
           T+Y G +   LTEQ +R  F  FG+I  V +   +  +F+++ S  +A  A+  S N   
Sbjct: 2   TVYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDKGYSFVRFNSHESAAHAIV-SVNGTT 60

Query: 275 LGGRRLNIKWGR 286
           + G  +   WG+
Sbjct: 61  IEGHVVKCYWGK 72

This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 2/69 (2%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-CAFIQYTSRPAAEAAVEHSFNKV 273
           TL+V N+   + +++LR  F QFG+IR++    K +    + Y    AA  A   +    
Sbjct: 3   TLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAK-RALQGT 61

Query: 274 ILGGRRLNI 282
            LGGR+L+I
Sbjct: 62  ELGGRKLDI 70

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

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

 Score = 42.6 bits (100), Expect = 1e-05
 Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 8/74 (10%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
           L+VG L   + E DL +HF QFG +    +++ +Q        F+ + +  +A+ A    
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVK 61

Query: 270 FNKVILGGRRLNIK 283
           F+ +   G R+ +K
Sbjct: 62  FHPI--NGHRVEVK 73

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

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 6/73 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ--CAFIQYTSRPAAEAAVEHSFN 271
            TL+V NLG   TE++LR  F +    R + + +K      F+++     A  A+     
Sbjct: 3   NTLFVANLGPNTTEEELRQLFSRQPGFRRLKMHNKGGGPVCFVEFEDVSFATQALNSLQG 62

Query: 272 KVIL----GGRRL 280
            V+     GG R+
Sbjct: 63  AVLSSSDRGGIRI 75

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

>gnl|CDD|240907 cd12461, RRM_SCAF4, RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH-SFNK 272
           TTL+VG L  + T+QD+     +FG I S+ ++  + CA+I    R  A  A++  S   
Sbjct: 5   TTLWVGQLDKRTTQQDVTSLLEEFGPIESINMIPPRGCAYIVMVHRQDAYRALQKLSRGN 64

Query: 273 VILGGRRLNIKWG 285
           V +  + + I W 
Sbjct: 65  VKVNQKSIKIAWA 77

The CD corresponds to the RRM of SCAF4 (also termed splicing factor, arginine/serine-rich 15 or SFR15, or CTD-binding SR-like protein RA4) that belongs to a new class of SCAFs (SR-like CTD-associated factors). Although its biological function remains unclear, SCAF4 shows high sequence similarity to SCAF8 that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II) and may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF4 and SCAF8 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 81

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

 Score = 45.6 bits (108), Expect = 2e-05
 Identities = 26/84 (30%), Positives = 43/84 (51%), Gaps = 10/84 (11%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAEAAVEHSF 270
           LYV NL D +T++ LR+ F + GEI S  ++  ++       F+ +++   A  AV    
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVT-EM 346

Query: 271 NKVILGGRRLNIKWGRAQANRGED 294
           +  +LGG+ L +    A A R E 
Sbjct: 347 HGRMLGGKPLYV----ALAQRKEQ 366

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

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

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 10/76 (13%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSV-------TILSKQQCAFIQYTSRPAAEAAVE 267
            L+VGNL   +  ++L+++F QFG+++S        T LSK    F+ ++SR   E A  
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYG-FVSFSSRDGLENA-- 57

Query: 268 HSFNKVILGGRRLNIK 283
               K IL G +L ++
Sbjct: 58  LQKQKHILEGNKLQVQ 73

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

>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 21/69 (30%), Positives = 29/69 (42%), Gaps = 6/69 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAEAAVEH 268
           T LY+ NL   + EQDL      +G++ S  IL   +       F +  SR   E  +  
Sbjct: 1   TNLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISK 60

Query: 269 SFNKVILGG 277
            FN   L G
Sbjct: 61  -FNGKYLKG 68

This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 79

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

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 16/74 (21%), Positives = 34/74 (45%), Gaps = 8/74 (10%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
           L++G L    TE+ LR++F ++GE+    I+            F+ +    + +  +   
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 270 FNKVILGGRRLNIK 283
            +  +L GR ++ K
Sbjct: 61  PH--VLDGREIDPK 72

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

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

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 6/68 (8%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRPAAEAAVEHS 269
           L+VG++   +TEQ++R  F + G +  V I+       +Q C F++Y++R  A+ A+   
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 270 FNKVILGG 277
            N+  L G
Sbjct: 62  HNQRTLPG 69

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

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

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 11/79 (13%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-------AFIQYTSRPAAEAAVEH 268
           +YV ++   L+E D++  F  FG+I+S   L+            FI+Y +  +A+ A+  
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSC-SLAPDPETGKHKGYGFIEYENPQSAQDAIA- 60

Query: 269 SFNKVILGGRRLNIKWGRA 287
           S N   LGG++L +  G+A
Sbjct: 61  SMNLFDLGGQQLRV--GKA 77

This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 77

>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 42.4 bits (99), Expect = 2e-05
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 5/57 (8%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS-----KQQCAFIQYTSRPAAEAAVE 267
           L++G +  K  E D+R  F  FG+I    IL       + CAF+ +T+R  A+ A++
Sbjct: 4   LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK 60

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 42.2 bits (99), Expect = 2e-05
 Identities = 25/71 (35%), Positives = 34/71 (47%), Gaps = 7/71 (9%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
           T LYV NL  +LTE +LR  F  +G I    +L  +        AF++Y  R  A+AA+ 
Sbjct: 1   TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 268 HSFNKVILGGR 278
              N  I  G 
Sbjct: 61  S-LNGTIPPGS 70

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|240704 cd12258, RRM2_RBM26_like, RNA recognition motif 2 of vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 3/56 (5%)

Query: 229 DLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW 284
           +L  HF QFGEI  V +  +     I + +R  AE A           G+ L + W
Sbjct: 20  ELLAHFAQFGEIEDVEVDEEGLHLVITFKTRKEAEIAAVRG---RRFKGKSLILSW 72

This subfamily corresponds to the RRM2 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. RBM26 contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. Length = 72

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 41.8 bits (98), Expect = 2e-05
 Identities = 16/57 (28%), Positives = 35/57 (61%), Gaps = 5/57 (8%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAEAAVE 267
           L+VG L  + TE+++ + F  +G +  + ++  +      CAF++Y+S+  A+AA++
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIK 58

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 25/74 (33%), Positives = 33/74 (44%), Gaps = 3/74 (4%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQY-TSRPAAEAAVEHSFNK 272
           TT+YVGN+    T+ DL   F  FG I        +  AF++  T   AA A V      
Sbjct: 1   TTVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDRGFAFVKLDTHEQAAMAIV--QLQG 58

Query: 273 VILGGRRLNIKWGR 286
             + GR L   WG+
Sbjct: 59  FPVHGRPLRCGWGK 72

This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

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

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEH 268
           + + V NL   +TE  LR+HF   GE+  V ++       ++  F+ + S   A+ AV++
Sbjct: 1   SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKY 60

Query: 269 SFNKVILGGRRLNI 282
            FNK  +   ++++
Sbjct: 61  -FNKTFIDTSKISV 73

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

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

 Score = 45.3 bits (107), Expect = 3e-05
 Identities = 40/112 (35%), Positives = 51/112 (45%), Gaps = 13/112 (11%)

Query: 192 AEK-LMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL---S 247
           AEK   A+A+T    D P       LYVGNL   +TEQ+LR  F  FG+I  V +     
Sbjct: 167 AEKNRAAKAATHQPGDIPNFLK---LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPE 223

Query: 248 KQQC---AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTA 296
             +     FIQ+     A+ A+E   N   L GR   IK G AQ +     A
Sbjct: 224 TGRSKGFGFIQFHDAEEAKEALE-VMNGFELAGR--PIKVGYAQDSTYLLDA 272

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

>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 41.4 bits (98), Expect = 3e-05
 Identities = 18/66 (27%), Positives = 36/66 (54%), Gaps = 1/66 (1%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNK-VI 274
           L++ NL   +TE DL      FG++ +V +L  +  A ++  S  +A++ V++      +
Sbjct: 2   LHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALVEMDSVESAKSMVDYYLTVPAL 61

Query: 275 LGGRRL 280
           + GRR+
Sbjct: 62  IRGRRV 67

This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM. . Length = 74

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

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 11/79 (13%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRPAAEAAVEH 268
            ++VG +    TE++LRD F +FG ++ V I+      SK    F+ + ++  AE  +  
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGY-GFVTFETQEDAEKILAM 62

Query: 269 SFNKVILGGRRLNIKWGRA 287
               +   G++LNI  G A
Sbjct: 63  G--NLNFRGKKLNI--GPA 77

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

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

 Score = 41.2 bits (97), Expect = 4e-05
 Identities = 18/74 (24%), Positives = 39/74 (52%), Gaps = 7/74 (9%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEH 268
           TL+VGNL   + ++ L+  F +FG +    +++ ++        ++ + S   A+ A+E 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIE- 59

Query: 269 SFNKVILGGRRLNI 282
           + +   L GR +N+
Sbjct: 60  AMDGKELDGRPINV 73

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

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

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 8/74 (10%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-------QQCAFIQYTSRPAAEAAVEH 268
           L++GNL  ++ E+ L D F  FG I     + +       +  AFI Y S  A++AA+E 
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 269 SFNKVILGGRRLNI 282
             N   L  R + +
Sbjct: 64  -MNGQYLCNRPITV 76

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

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

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 7/71 (9%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----C-AFIQYTSRPAAEAAVEHS 269
           L++ +L ++ T+QDL   F  FG + S  +   +      C  F+ Y +  +A+AA++  
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKA- 59

Query: 270 FNKVILGGRRL 280
            N   +GG+RL
Sbjct: 60  MNGFQVGGKRL 70

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

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

 Score = 41.0 bits (97), Expect = 4e-05
 Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 8/75 (10%)

Query: 215 TLYVGNLGDKLTEQDLRDHFY----QFGEIRSVTILSKQQC---AFIQYTSRPAAEAAVE 267
           TLY+ NL +K+ + +L+   Y    QFG +  +      +    AF+ +    +A  A+ 
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALR 60

Query: 268 HSFNKVILGGRRLNI 282
            +        + + I
Sbjct: 61  -ALQGFPFYDKPMRI 74

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

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

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 21/74 (28%), Positives = 41/74 (55%), Gaps = 8/74 (10%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
           L+VG L + +TE+DLR++F Q+G + SV I++ ++       AF+ +      +  V   
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQK 61

Query: 270 FNKVILGGRRLNIK 283
           ++ +   G R+ +K
Sbjct: 62  YHTI--NGHRVEVK 73

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

>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 40.6 bits (95), Expect = 5e-05
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 8/74 (10%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEH 268
           ++YVGN+    T ++L  HF   G I  VTIL  +        A+I++ +R + EAAV  
Sbjct: 1   SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVA- 59

Query: 269 SFNKVILGGRRLNI 282
             ++    GR + +
Sbjct: 60  -LDESSFRGRVIKV 72

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

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

 Score = 41.0 bits (97), Expect = 5e-05
 Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 220 NLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ--CAFIQYTSRPAAEAAVEHSFNKVIL-- 275
           NL   +T   L   F  +G +  + I  K     A +Q+ S  +AE A + + N   +  
Sbjct: 8   NLLYPVTVDVLHQVFSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKK-ALNGRNIYD 66

Query: 276 GGRRLNIKWGRAQ 288
           G   L+I++ R +
Sbjct: 67  GCCTLDIQFSRLK 79

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

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

 Score = 40.6 bits (95), Expect = 5e-05
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 7/75 (9%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCA------FIQYTSRPAAEAAVEH 268
            +Y+G+L     E++L+ +F QFG +++V +   ++        FIQ+ +   A  A + 
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAK- 59

Query: 269 SFNKVILGGRRLNIK 283
           S N  +L G+ L + 
Sbjct: 60  SMNNYLLMGKVLQVH 74

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

>gnl|CDD|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in Saccharomyces cerevisiae protein Nrd1, Schizosaccharomyces pombe Rpb7-binding protein seb1 and similar proteins

 Score = 40.6 bits (95), Expect = 6e-05
 Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVI 274
           TL+ G +   + E DLR  F +FGE++S  + + ++ AF++  +R  AE A E +  +  
Sbjct: 5   TLFPGGVTFNMIEYDLRSGFGRFGEVQSCILNNDKRHAFVKMYNRRDAENARE-AMEQYK 63

Query: 275 LGGRRLNIKWG 285
            G  +L  +WG
Sbjct: 64  SGDMQLRTRWG 74

This subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1 is a novel heterogeneous nuclear ribonucleoprotein (hnRNP)-like RNA-binding protein encoded by gene NRD1 (for nuclear pre-mRNA down-regulation) from yeast S. cerevisiae. It is implicated in 3' end formation of small nucleolar and small nuclear RNAs transcribed by polymerase II, and plays a critical role in pre-mRNA metabolism. Nrd1 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a short arginine-, serine-, and glutamate-rich segment similar to the regions rich in RE and RS dipeptides (RE/RS domains) in many metazoan splicing factors, and a proline- and glutamine-rich C-terminal domain (P+Q domain) similar to domains found in several yeast hnRNPs. Disruption of NRD1 gene is lethal to yeast cells. Its N-terminal domain is sufficient for viability, which may facilitate interactions with RNA polymerase II where Nrd1 may function as an auxiliary factor. By contrast, the RRM, RE/RS domains, and P+Q domain are dispensable. Seb1 is an RNA-binding protein encoded by gene seb1 (for seven binding) from fission yeast S. pombe. It is essential for cell viability and bound directly to Rpb7 subunit of RNA polymerase II. Seb1 is involved in processing of polymerase II transcripts. It also contains one RRM motif and a region rich in arginine-serine dipeptides (RS domain). Length = 79

>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 40.6 bits (95), Expect = 6e-05
 Identities = 20/54 (37%), Positives = 33/54 (61%), Gaps = 3/54 (5%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC---AFIQYTSRPAAEAAV 266
           +YVGNL   + E+DL D FY++G IR + + +++     AF+++     AE AV
Sbjct: 2   IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAV 55

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

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

 Score = 40.3 bits (95), Expect = 6e-05
 Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 3/68 (4%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL 275
           L+VGNL D  T ++LR  F ++G +    ++  +   F+       AE A++ + N    
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVV--KNYGFVHMEEEEDAEDAIK-ALNGYEF 58

Query: 276 GGRRLNIK 283
            G+R+N++
Sbjct: 59  MGKRINVE 66

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

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

 Score = 40.3 bits (95), Expect = 6e-05
 Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 6/70 (8%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-----AFIQYTSRPAAEAAVEHSF 270
           LYV NL D + ++ LR+ F  FG I S  +++ ++       F+ ++S   A  AV    
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVT-EM 62

Query: 271 NKVILGGRRL 280
           N  I+GG+ L
Sbjct: 63  NGRIIGGKPL 72

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

>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 39.9 bits (94), Expect = 8e-05
 Identities = 17/53 (32%), Positives = 30/53 (56%), Gaps = 2/53 (3%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVE 267
           TLYV   G  LTE+ L+  F  FG I ++++  ++ C F+ +    +A+ A+ 
Sbjct: 6   TLYVH--GYGLTEEILKKAFSPFGNIINISMEKEKNCGFVTFEKMESADRAIA 56

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 39.8 bits (93), Expect = 9e-05
 Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 3/65 (4%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL 275
           ++VGN+ +  ++++LR  F  +G + S  ++  +Q AF+      AA+ A+E   N   L
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVM--RQFAFVHLRGEAAADRAIE-ELNGREL 59

Query: 276 GGRRL 280
            GR+L
Sbjct: 60  HGRKL 64

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

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

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 21/72 (29%), Positives = 41/72 (56%), Gaps = 4/72 (5%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC---AFIQYTSRPAAEAAVEHSFN 271
            +YVGNL   + E+D+ D FY++G I+++ + ++++    AF+++     AE AV    +
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAV-RGRD 59

Query: 272 KVILGGRRLNIK 283
                G RL ++
Sbjct: 60  GYDFDGYRLRVE 71

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

>gnl|CDD|241002 cd12558, RRM3_RBM15B, RNA recognition motif 3 in putative RNA-binding protein 15B (RBM15B) from vertebrate

 Score = 40.0 bits (93), Expect = 1e-04
 Identities = 27/75 (36%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
           T L+VG LG   +   L   F +FG IR++  +     A+IQY S  AA+AA        
Sbjct: 3   TRLWVGGLGPNTSLAALAREFDRFGSIRTIDYVKGDSFAYIQYESLDAAQAACAQ-MRGF 61

Query: 274 ILGG--RRLNIKWGR 286
            LGG  RRL + + +
Sbjct: 62  PLGGPDRRLRVDFAK 76

This subgroup corresponds to the RRM3 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 76

>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL 275
           L + ++G  +T +D++  F QFGE++ V         +I++ +  AA+ A E +F +   
Sbjct: 4   LKITSIGPGVTREDIKAVFAQFGEVKYVDFTEGADTGYIRFKTPEAAQKARE-AFVEKGE 62

Query: 276 GGRRLNIKW 284
           G     IK 
Sbjct: 63  GLLGKEIKL 71

This subfamily corresponds to the RRM2 of La and LARP7. La is a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. LARP7 is an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP), intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. LARP7 plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. Both La and LARP7 contain an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

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

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 7/73 (9%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAF-----IQYTSRPAAEAAVEHS 269
           TL+VGNL     + DL + F + GE+  V I             +++ +   A+ A+E S
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEKS 60

Query: 270 FNKVILGGRRLNI 282
             +  L GR + +
Sbjct: 61  GEE--LLGREIRV 71

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

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

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 15/70 (21%), Positives = 33/70 (47%), Gaps = 3/70 (4%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI-LSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
           +++V       +E+ L D+F  FG + +V +   K   A +++ S+   +  +     + 
Sbjct: 4   SVFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKDKGVYAIVEFDSKEGVDKVLSEP--QH 61

Query: 274 ILGGRRLNIK 283
            L G RL ++
Sbjct: 62  TLNGHRLRVR 71

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

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

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 12/76 (15%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
           ++VG L   +TE DLR +F QFG +  V ++   +        FI +     +E +V+  
Sbjct: 5   IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITF----ESEDSVDQV 60

Query: 270 FNK--VILGGRRLNIK 283
            N+    + G+++ +K
Sbjct: 61  VNEHFHDINGKKVEVK 76

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

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

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 6/73 (8%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
           L+VG L   +TE DL + F +FG +  V I+ K+        A+I   +  A     + +
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 270 FNKVILGGRRLNI 282
            N     G  L I
Sbjct: 62  LNGTKWKGSVLKI 74

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

>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
           T L V NL   +TE D+ + F   G ++   ++     A + Y  +  A  A++  +N  
Sbjct: 1   TRLVVSNLHPSVTEDDIVELFSAIGALKRARLVRPGV-AEVVYVRKDDALTAID-KYNNR 58

Query: 274 ILGGRRLNIK 283
            L G+ +  K
Sbjct: 59  ELDGQPMKCK 68

This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Length = 69

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

 Score = 39.4 bits (93), Expect = 2e-04
 Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 17/80 (21%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-----------AFIQYTSRPAAEA 264
           LYVG+L   +TE  L + F   G + S+ +     C           A++ + +   AE 
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRV-----CRDLITRRSLGYAYVNFQNPADAER 56

Query: 265 AVEHSFNKVILGGRRLNIKW 284
           A++ + N  ++ G+ + I W
Sbjct: 57  ALD-TLNFDVIKGKPIRIMW 75

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

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

 Score = 39.1 bits (91), Expect = 2e-04
 Identities = 20/68 (29%), Positives = 38/68 (55%), Gaps = 3/68 (4%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL 275
           L+VGNL  + TEQ++R  F Q+G++    I+  +   F+    + AA+ A+  + +   L
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDII--KNYGFVHMDDKTAADEAIR-NLHHYKL 59

Query: 276 GGRRLNIK 283
            G  +N++
Sbjct: 60  HGVAINVE 67

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

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

 Score = 42.7 bits (100), Expect = 2e-04
 Identities = 28/79 (35%), Positives = 42/79 (53%), Gaps = 9/79 (11%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTI------LSKQQCAFIQYTSRPAAEAAVEHS 269
           +YVG++  +L E  +R  F  FG I+S+ +         +  AF++Y    AA+ A+E  
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALE-Q 168

Query: 270 FNKVILGGRRLNIKWGRAQ 288
            N  +LGGR  NIK GR  
Sbjct: 169 MNGQMLGGR--NIKVGRPS 185

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 7/68 (10%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVEHS 269
           LYV  L   +T+Q+L   F  +G I +  IL            FI++  R  AE A++  
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA- 61

Query: 270 FNKVILGG 277
            N  I  G
Sbjct: 62  LNGTIPPG 69

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 3/73 (4%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ--QCAFIQYTSRPAAEAAVEHSFNKV 273
           +YVGNL   +  +D+ D FY++G IR + + +++    AF+++     AE AV +  +  
Sbjct: 2   IYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPPFAFVEFEDPRDAEDAV-YGRDGY 60

Query: 274 ILGGRRLNIKWGR 286
              G RL +++ R
Sbjct: 61  DYDGYRLRVEFPR 73

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

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

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 8/60 (13%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTI-------LSKQQCAFIQYTSRPAAEAAVEH 268
           L+VG L   + +  L++ F  +G ++ V +       L +   A++++ S   AE A++H
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGY-AYVEFESPEDAEKAIKH 59

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

>gnl|CDD|241160 cd12716, RRM1_2_NP220, RNA recognition motif 1 and 2 in vertebrate nuclear protein 220 (NP220)

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 18/72 (25%), Positives = 44/72 (61%), Gaps = 2/72 (2%)

Query: 214 TTLYVGNLGDK-LTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH-SFN 271
           + + + NL +K  +E+++ +    FG+++ + ILS  + A+++  ++ AAEA V++    
Sbjct: 1   SVVLISNLPEKGYSEEEIYNLAKPFGKLKDILILSSHKKAYLEMNNKEAAEAMVKYFETT 60

Query: 272 KVILGGRRLNIK 283
            V++ G+++ I 
Sbjct: 61  PVLVKGKQVKIS 72

This subgroup corresponds to RRM1 and RRM2 of NP220, also termed zinc finger protein 638 (ZN638), or cutaneous T-cell lymphoma-associated antigen se33-1, or zinc finger matrin-like protein, a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). NP220 contains multiple domains, including MH1, MH2, and MH3, domains homologous to the acidic nuclear protein matrin 3; RS, an arginine/serine-rich domain commonly found in pre-mRNA splicing factors; PstI-HindIII, a domain essential for DNA binding; acidic repeat, a domain with nine repeats of the sequence LVTVDEVIEEEDL; and a Cys2-His2 zinc finger-like motif that is also present in matrin 3. It may be involved in packaging, transferring, or processing transcripts. This subgroup corresponds to the domain of MH2 that contains two tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Length = 76

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

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 7/75 (9%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRS---VTILSKQQC---AFIQYTSRPAAEAAVEH 268
           TL+V NL    T++ L + F + G I+    V     ++C    ++ +     A+ A+E 
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 269 SFNKVILGGRRLNIK 283
              K   GGR+++++
Sbjct: 61  -KKKTKFGGRKIHVE 74

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

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 16/73 (21%), Positives = 33/73 (45%), Gaps = 7/73 (9%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----C-AFIQYTSRPAAEAAVEHS 269
           L+V  L       DL+  F ++G++    I++  +     C  F+   S   A   ++H 
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQH- 60

Query: 270 FNKVILGGRRLNI 282
            ++  L GR +++
Sbjct: 61  LHRTELHGRVISV 73

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 20/69 (28%), Positives = 40/69 (57%), Gaps = 1/69 (1%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL 275
           L+VGNL   +TE+++R  F ++G+   + I   +   FI+  +R  AE A +   + + L
Sbjct: 4   LFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDKGFGFIRLETRTLAEIA-KAELDNMPL 62

Query: 276 GGRRLNIKW 284
            G++L +++
Sbjct: 63  RGKQLRVRF 71

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 3/70 (4%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
             ++VGN+    T  +LR  F +FG +     +  +  AF+       A AA+E   N  
Sbjct: 1   WKIFVGNVSATCTSDELRGLFEEFGRVVECDKV--KDYAFVHMEREEEALAAIEA-LNGK 57

Query: 274 ILGGRRLNIK 283
            + GRR+N++
Sbjct: 58  EVKGRRINVE 67

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

>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 21/70 (30%), Positives = 40/70 (57%), Gaps = 2/70 (2%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSV-TILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
           TL V NL   ++  DL   F  +GEI+ +    +K+   FI++    +AEAA++ + N+ 
Sbjct: 3   TLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALK-ALNRS 61

Query: 274 ILGGRRLNIK 283
            + G+R+ ++
Sbjct: 62  EIAGKRIKLE 71

This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

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

 Score = 42.1 bits (99), Expect = 3e-04
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 7/76 (9%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSV-----TILSKQQC-AFIQYTSRPAAEAAVEH 268
           +LYVG+L   +TE  L D F  FG + SV     ++  +     ++ + +   AE A+E 
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALE- 60

Query: 269 SFNKVILGGRRLNIKW 284
           + N   LGG+ + I W
Sbjct: 61  TMNFKRLGGKPIRIMW 76

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

>gnl|CDD|240694 cd12248, RRM_RBM44, RNA recognition motif in RNA-binding protein 44 (RBM44) and similar proteins

 Score = 38.7 bits (90), Expect = 3e-04
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 4/74 (5%)

Query: 216 LYVGNLGDKLTEQDLRDHF--YQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
           ++VG L   ++E DLR HF  YQ   I S+  LS  + A + +     A  AV+     V
Sbjct: 2   VHVGGLSPSVSEGDLRSHFQKYQVSVI-SLCKLSNYRYASLHFDRASDALLAVKKMNGGV 60

Query: 274 ILGGRRLNIKWGRA 287
           +  G  + ++  +A
Sbjct: 61  L-SGLSIKVRMVKA 73

This subgroup corresponds to the RRM of RBM44, a novel germ cell intercellular bridge protein that is localized in the cytoplasm and intercellular bridges from pachytene to secondary spermatocyte stages. RBM44 interacts with itself and testis-expressed gene 14 (TEX14). Unlike TEX14, RBM44 does not function in the formation of stable intercellular bridges. It carries an RNA recognition motif (RRM) that could potentially bind a multitude of RNA sequences in the cytoplasm and help to shuttle them through the intercellular bridge, facilitating their dispersion into the interconnected neighboring cells. Length = 74

>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 15/70 (21%), Positives = 33/70 (47%), Gaps = 2/70 (2%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFG-EIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNK 272
            T+ + N+ D + E+ ++  F + G ++R + +    + A +++ S   A      S N 
Sbjct: 1   RTIGLFNVSDTVNEEQIKAFFEKIGPDVRKIELFPDHEGALVEFESPSDA-GKASLSLNG 59

Query: 273 VILGGRRLNI 282
              GG+ + I
Sbjct: 60  SQFGGKTIKI 69

This subfamily corresponds to the RRM4 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 71

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

 Score = 38.3 bits (90), Expect = 3e-04
 Identities = 18/75 (24%), Positives = 41/75 (54%), Gaps = 8/75 (10%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEH 268
           +++VGNL   + E++LR HF   G++ +V I+  ++        ++ + ++ +   A+  
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-- 58

Query: 269 SFNKVILGGRRLNIK 283
             N + L GR++ +K
Sbjct: 59  KLNGIKLKGRKIRVK 73

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

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

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 4/73 (5%)

Query: 215 TLYVGNLGDKLT-EQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
           TL+V       T E+D+   F  FG +    I  ++  AF+++     A  A+E + +  
Sbjct: 1   TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDI--RKTFAFVEFEDSEDATKALE-ALHGS 57

Query: 274 ILGGRRLNIKWGR 286
            + G  L +++ +
Sbjct: 58  RIDGSVLTVEFVK 70

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

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

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 6/64 (9%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
           L+VG L  K ++  LR HF ++G++    ++            FI ++S   A+ A+E  
Sbjct: 5   LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEAQ 64

Query: 270 FNKV 273
            + +
Sbjct: 65  PHSI 68

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

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

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 17/74 (22%), Positives = 36/74 (48%), Gaps = 8/74 (10%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCA------FIQYTSRPAAEAAVEHS 269
           ++VG L   +TE++ +++F QFG++    ++            F+ + S  A E      
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAG 61

Query: 270 FNKVILGGRRLNIK 283
             +  LGG+++ +K
Sbjct: 62  MLE--LGGKQVEVK 73

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

>gnl|CDD|241001 cd12557, RRM3_RBM15, RNA recognition motif 3 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 38.4 bits (89), Expect = 3e-04
 Identities = 27/72 (37%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL 275
           L+VG LG  +    L   F +FG IR++        A+IQY S  AA+AA  H      L
Sbjct: 2   LWVGGLGPWVPLAALAREFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTH-MRGFPL 60

Query: 276 GG--RRLNIKWG 285
           GG  RRL + + 
Sbjct: 61  GGPDRRLRVDFA 72

This subgroup corresponds to the RRM3 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contains three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralogue and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 73

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 22/91 (24%), Positives = 35/91 (38%), Gaps = 25/91 (27%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS----------------------KQQC- 251
           T++VGNL     ++DL+  F QFG I SV   S                      K    
Sbjct: 2   TVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVN 61

Query: 252 AFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           A++ +    +AE A++   N     G  + +
Sbjct: 62  AYVVFKEEESAEKALKL--NGTEFEGHHIRV 90

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 38.3 bits (89), Expect = 4e-04
 Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 11/70 (15%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ-----QCAFIQYTSRPAAEAAVEHSF 270
           LYVGNL  ++TE  L+  F   G +++V I+  +        F++Y     AE A++   
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQ--- 57

Query: 271 NKVILGGRRL 280
               L GR++
Sbjct: 58  ---TLNGRQI 64

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

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

 Score = 38.2 bits (89), Expect = 4e-04
 Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 10/76 (13%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSV---TILSKQQC---AFIQYTSRPAAEAAVEHS 269
           L+VGNL  + TE +LR HF + G IR V   T     +C   AF+ +     A  A++  
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60

Query: 270 FNKVILGGRRLNIKWG 285
                L GR L +++G
Sbjct: 61  ----HLNGRALRVEYG 72

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

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

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 15/30 (50%), Positives = 22/30 (73%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTI 245
           ++VG L + +TE+DLR +F QFGE+  V I
Sbjct: 3   VFVGRLTEDMTEEDLRQYFSQFGEVTDVYI 32

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

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

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 9/84 (10%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI-----LSKQQC-AFIQYTSRPAAEAAVE 267
           T+LYV N+ D     DLR  F ++G I  V I       + +  A++Q+     AE A+ 
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDAL- 59

Query: 268 HSFNKVILGGRRLNIKWGRAQANR 291
           +  ++    GR + I++  AQ +R
Sbjct: 60  YYLDRTRFLGREIEIQF--AQGDR 81

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

>gnl|CDD|240707 cd12261, RRM1_3_MRN1, RNA recognition motif 1 and 3 in RNA-binding protein MRN1 and similar proteins

 Score = 38.0 bits (89), Expect = 5e-04
 Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHS-FNKV 273
           T+Y+GNL +  T +D+       G + S+ +L  +  A + +    AAEA   ++  N  
Sbjct: 2   TVYLGNLPEDTTIRDILSAIRG-GPLESIKLLPTKNSATVSFLDEAAAEAFYAYARNNGF 60

Query: 274 ILGGRRLNIKWGR 286
            + G+R+ + WG+
Sbjct: 61  YINGKRIKVGWGK 73

This subfamily corresponds to the RRM1 and RRM3 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 73

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

 Score = 38.0 bits (89), Expect = 6e-04
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 10/65 (15%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ------QCAFIQYTSRP 260
           PPE      L+V  L    T++DL   F +FG+I+S  ++  +      Q AFI++ ++ 
Sbjct: 1   PPE----NVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKE 56

Query: 261 AAEAA 265
             E A
Sbjct: 57  DCEEA 61

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

>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 37.5 bits (88), Expect = 6e-04
 Identities = 16/68 (23%), Positives = 34/68 (50%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVI 274
            L++ NL ++ T++ L   F QF   + V ++ ++  AF+++ +   A  A++      I
Sbjct: 4   ILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPRRGIAFVEFETEEQATVALQALQGFKI 63

Query: 275 LGGRRLNI 282
             G  + I
Sbjct: 64  TPGHAMKI 71

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

>gnl|CDD|240715 cd12269, RRM_Vip1_like, RNA recognition motif in a group of uncharacterized plant proteins similar to fission yeast Vip1

 Score = 37.4 bits (87), Expect = 6e-04
 Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 3/52 (5%)

Query: 218 VGNLGDKLTEQDLRDHFYQFGEIRSVTILSK---QQCAFIQYTSRPAAEAAV 266
           V NL  K TE+D+ D F   G+I  V I       Q A++ +    A E A+
Sbjct: 3   VTNLSPKATERDIYDFFSFSGDIEYVEIQRSGEQSQTAYVTFKDPQAQETAL 54

This subfamily corresponds to the Vip1-like, uncharacterized proteins found in plants. Although their biological roles remain unclear, these proteins show high sequence similarity to the fission yeast Vip1. Like Vip1 protein, members in this family contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 69

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 37.8 bits (88), Expect = 6e-04
 Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 12/84 (14%)

Query: 216 LYVGNLGDKLTEQDL----RDHFYQFGEIRSVTILSKQQC----AFIQYTSRPAAEAAVE 267
           ++V +L    ++ +L     +HF ++G +  V +L +       AF+Q+T+   A+ A+ 
Sbjct: 5   VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVL-RDWRQRPYAFVQFTNDDDAKNALA 63

Query: 268 HSFNKVILGGRRLNIKWGRAQANR 291
                 IL GR +  +  RA+ NR
Sbjct: 64  KGQG-TILDGRHIRCE--RAKVNR 84

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

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

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 6/72 (8%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC----AFIQYTSRPAAEAAVEHSF 270
           T++VG +   L+E DL++ F   GE+  V +   +Q     AF+++    +A +A+  + 
Sbjct: 2   TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSAL--NL 59

Query: 271 NKVILGGRRLNI 282
           +  +LGG  L +
Sbjct: 60  SGTLLGGHPLRV 71

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

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 37.6 bits (88), Expect = 6e-04
 Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 8/75 (10%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI------LSKQQCAFIQYTSRPAAEAAVE 267
           T L V NL   +++ D+++ F +FG ++   +       S    A + +  R  A  A++
Sbjct: 1   TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGT-ADVVFERRADALKAMK 59

Query: 268 HSFNKVILGGRRLNI 282
             +N V L GR + I
Sbjct: 60  Q-YNGVPLDGRPMKI 73

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

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

 Score = 37.5 bits (87), Expect = 7e-04
 Identities = 21/76 (27%), Positives = 42/76 (55%), Gaps = 6/76 (7%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEH 268
           T + V NL  + T++D+R  F  +G+++SV +  K     +  AF+++++   A  A+  
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMN- 59

Query: 269 SFNKVILGGRRLNIKW 284
           +     L GRRL +++
Sbjct: 60  ALKDTHLLGRRLVLQY 75

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

>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 37.3 bits (87), Expect = 7e-04
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL 275
           +Y+G L  +  E+D+   F  +G IR + +  K    F+++     A+ AV +  N   L
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRIREINL--KNGFGFVEFEDPRDADDAV-YELNGKEL 58

Query: 276 GGRRLNIKWGRA 287
            G R+ ++  R 
Sbjct: 59  CGERVIVEHARG 70

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

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

 Score = 37.3 bits (87), Expect = 9e-04
 Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 7/71 (9%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTI----LSKQQ--CAFIQYTSRPAAEAAVEHS 269
           L V NL  + T  DLR  F ++GE+  V I     +++    AF+++  +  AE A++  
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 270 FNKVILGGRRL 280
             K  L GR L
Sbjct: 61  DGKE-LDGREL 70

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

>gnl|CDD|215588 PLN03120, PLN03120, nucleic acid binding protein; Provisional

 Score = 40.0 bits (94), Expect = 9e-04
 Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 5/59 (8%)

Query: 212 TITTLYVGNLGDKLTEQDLRDHFYQF-GEIRSVTILS---KQQCAFIQYTSRPAAEAAV 266
            + T+ V N+  K TE+D+++ F+ F G+I  V + S   + Q A++ +     AE A+
Sbjct: 3   QVRTVKVSNVSLKATERDIKE-FFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETAL 60

Length = 260

>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 19/52 (36%), Positives = 33/52 (63%), Gaps = 2/52 (3%)

Query: 219 GNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-AFIQYTSRPAAEAAVEHS 269
              GD  +E +LR  F ++G++  V + SK++  A +++ S+ AAEAAVE+ 
Sbjct: 11  KGNGD-YSEDELRKIFSKYGDVSDVVVSSKKKGSAIVEFASKKAAEAAVENE 61

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

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

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 20/75 (26%), Positives = 41/75 (54%), Gaps = 10/75 (13%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSV-----TILSKQQ--CAFIQYTSRPAAEAAVEH 268
           ++VG L  + TE+ +R++F +FG I  +        +K++  C FI + S    +  +E 
Sbjct: 2   IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFC-FITFDSEEPVKKILET 60

Query: 269 SFNKVILGGRRLNIK 283
            F+ +  GG+++ +K
Sbjct: 61  QFHVI--GGKKVEVK 73

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

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

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 19/76 (25%), Positives = 39/76 (51%), Gaps = 7/76 (9%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEI------RSVTILSKQQCAFIQYTSRPAAEAAVEHS 269
           ++VG+L  ++T +D++  F  FG+I      + +     +   F+ + ++  AE A+ H 
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 270 FNKVILGGRRLNIKWG 285
             +  LGGR++   W 
Sbjct: 64  GGQ-WLGGRQIRTNWA 78

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

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

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 9/73 (12%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSV-------TILSKQQCAFIQYTSRPAAEAAVE 267
            +Y+G+L     E +LR +F QFG +  +       T  SK   AF+++ S   A+   E
Sbjct: 1   VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGY-AFVEFESPEVAKIVAE 59

Query: 268 HSFNKVILGGRRL 280
            + N  +L  R L
Sbjct: 60  -TMNNYLLFERLL 71

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

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 8/72 (11%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC---AFIQYTSRPAAEAAVEH--SF 270
           LYV NL  K++ ++L D F ++G IR + I + ++    AF+ Y     A+ A +H   F
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHLSGF 64

Query: 271 NKVILGGRRLNI 282
           N   +  R L +
Sbjct: 65  N---VANRYLVV 73

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

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL 275
           L+VGNL   +TE + +  F ++GE   V I   +   FI+  SR  AE A +   +   +
Sbjct: 4   LFVGNLPADITEDEFKKLFAKYGEPGEVFINKGKGFGFIKLESRALAEIA-KAELDDTPM 62

Query: 276 GGRRLNIKW 284
            GR+L +++
Sbjct: 63  RGRQLRVRF 71

This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 71

>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL 275
           +++  L + +TEQ L  HF ++G +  V I  ++  A + +    AA+AAV     +  L
Sbjct: 10  VWLDGLDESVTEQYLTRHFSRYGPVVHVVIDRQRGQALVFFDKVEAAQAAVNEMKGR-KL 68

Query: 276 GGRRLNI 282
           GGR+L +
Sbjct: 69  GGRKLQV 75

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 77

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 14/81 (17%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ------------QCAFIQYTSRPAA 262
            +Y+ NL    +E+DL +    F  + SV I S+               A+ +++S   A
Sbjct: 1   RVYISNLSYSSSEEDLEEFLKDFEPV-SVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59

Query: 263 EAAVEHSFNKVILGGRRLNIK 283
           E  V+   N  +   R+L +K
Sbjct: 60  EKVVK-DLNGKVFKNRKLFVK 79

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC----AFIQYTSRPAAEAAVEHSF 270
           T+YVGNL    T   L + F Q GE++ V +   +      AF+++  + +   A++   
Sbjct: 6   TIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINALK--L 63

Query: 271 NKVILGGRRLNI 282
           N  + GGR L +
Sbjct: 64  NGAMFGGRPLKV 75

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI-LSK----QQCAFIQYTSRPAAEAAVEH 268
           + L V NL   + E  LR  F  FG I  V +  +K    ++  F+ Y +   A+ A++H
Sbjct: 1   SRLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKH 60

Query: 269 SFNKVILGGRRLNI 282
            FN   +   ++ +
Sbjct: 61  -FNNSFIDTSKITV 73

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

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

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 5/71 (7%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCA----FIQYTSRPAAEAAVEHSFN 271
           L+V N+  +  + DLR  F QFG I  V I+  ++ +    F+ + +   A+ A E   +
Sbjct: 3   LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRARE-KLH 61

Query: 272 KVILGGRRLNI 282
             ++ GR++ +
Sbjct: 62  GTVVEGRKIEV 72

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

>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 1/67 (1%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL 275
           LY+GNL   + E DLR  F +     S  ++ K   AF+    +  A+ A+E   N  IL
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKGGYAFVDCPDQSWADKAIE-KLNGKIL 59

Query: 276 GGRRLNI 282
            G+ + +
Sbjct: 60  QGKVIEV 66

Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. Length = 73

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNK 272
           +  L+V NL + +TE+ L   F QFG++  V  L  +  AFI +  R  A  A+E    K
Sbjct: 1   VKVLFVRNLANTVTEEILEKAFGQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGK 58

Query: 273 VILG 276
            + G
Sbjct: 59  ELEG 62

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 6/70 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
             LYV  L   +T+++L   F Q+G I +  IL  Q         FI++  R  AE A++
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 268 HSFNKVILGG 277
               +   G 
Sbjct: 61  GLNGQKPEGA 70

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 17/69 (24%), Positives = 37/69 (53%), Gaps = 7/69 (10%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL--SKQQC---AFIQYTSRPAAEAAVEHS 269
           T++V NL   + E +LR  F + GEI  V ++   K +    A++++ +  + + A+   
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEAL--K 58

Query: 270 FNKVILGGR 278
            ++ ++ GR
Sbjct: 59  LDRELIKGR 67

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

>gnl|CDD|241069 cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1)

 Score = 35.8 bits (82), Expect = 0.003
 Identities = 24/68 (35%), Positives = 31/68 (45%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL 275
           LY+GNL + +T  DL   F       S   L K   AF+       A  A+E    KV L
Sbjct: 4   LYIGNLNESVTPADLEKVFEDHKISYSGQFLVKSGYAFVDCPDEQWAMKAIETFSGKVEL 63

Query: 276 GGRRLNIK 283
            G+RL I+
Sbjct: 64  HGKRLEIE 71

This subgroup corresponds to the RRM1 of IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also termed coding region determinant-binding protein (CRD-BP), or VICKZ family member 1, or zipcode-binding protein 1 (ZBP-1). IGF2BP1 is a multi-functional regulator of RNA metabolism that has been implicated in the control of aspects of localization, stability, and translation for many mRNAs. It is predominantly located in cytoplasm and was initially identified as a trans-acting factor that interacts with the zipcode in the 3'- untranslated region (UTR) of the beta-actin mRNA, which is important for its localization and translational regulation. It inhibits IGF-II mRNA translation through binding to the 5'-UTR of the transcript. IGF2BP1 also acts as human immunodeficiency virus type 1 (HIV-1) Gag-binding factor that interacts with HIV-1 Gag protein and blocks the formation of infectious HIV-1 particles. IGF2BP1 promotes mRNA stabilization; it functions as a coding region determinant (CRD)-binding protein that binds to the coding region of betaTrCP1 mRNA and prevents miR-183-mediated degradation of betaTrCP1 mRNA. It also promotes c-myc mRNA stability by associating with the CRD and stabilizes CD44 mRNA via interaction with the 3'-UTR of the transcript. In addition, IGF2BP1 specifically interacts with both Hepatitis C virus (HCV) 5'-UTR and 3'-UTR, further recruiting eIF3 and enhancing HCV internal ribosome entry site (IRES)-mediated translation initiation via the 3'-UTR. IGF2BP1 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. It also contains two putative nuclear export signals (NESs) and a putative nuclear localization signal (NLS). . Length = 77

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

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 7/75 (9%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
           ++VG+L  ++T+  L   F  F       ++   +        F+ + S+  AE A+   
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAIN-E 60

Query: 270 FNKVILGGRRLNIKW 284
            N   LG R +   W
Sbjct: 61  MNGKWLGSRPIRCNW 75

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

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

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 7/72 (9%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEH 268
           TL+V  L    TE  LR  F ++G I+ + ++  ++       AFI++      +AA ++
Sbjct: 3   TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKY 62

Query: 269 SFNKVILGGRRL 280
           +  K I  GRR+
Sbjct: 63  ADGKKI-DGRRV 73

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

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

 Score = 36.9 bits (85), Expect = 0.003
 Identities = 24/86 (27%), Positives = 37/86 (43%), Gaps = 9/86 (10%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
           T L++G L     +  LRD F  FG++    ++  ++        F+ +    AA AA+ 
Sbjct: 35  TKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAIS 94

Query: 268 HSFNKVILGGR--RLNIKWGRAQANR 291
               K  L GR  R+N    R  A R
Sbjct: 95  EMDGKE-LNGRHIRVNPANDRPSAPR 119

Length = 144

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

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 8/74 (10%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
           +YVG +    TE ++R +F   GEI  + +++          AFI + +  AA+ A+   
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALA-- 58

Query: 270 FNKVILGGRRLNIK 283
            +   +GGR L ++
Sbjct: 59  LDGEDMGGRFLKVE 72

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 35.3 bits (81), Expect = 0.004
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----SKQQCAFIQYTSRPAAEAAVEHS 269
           TL+VGNL  K+TE+ + + F Q G +  V I        +Q AF+ +    +   A+ + 
Sbjct: 3   TLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAM-NL 61

Query: 270 FNKVILGGRRLNIK 283
            N + L GR LNI+
Sbjct: 62  LNGIKLYGRPLNIQ 75

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 7/75 (9%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI---LSKQQC---AFIQYTSRPAAEAAVE 267
             ++V NL     E  L   F  FG + +V +   L+  +C    F+  T+   A +A+ 
Sbjct: 2   WCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI- 60

Query: 268 HSFNKVILGGRRLNI 282
            S N   LGGR L +
Sbjct: 61  ASLNGYRLGGRVLQV 75

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

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

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 8/71 (11%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI------LSKQQCAFIQYTSRPAAEAAVE 267
           T L V NL   +TE+DL + F + GE++ V I       S+   A + +  R  AE A++
Sbjct: 1   TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSE-GTADVVFEKREDAERAIK 59

Query: 268 HSFNKVILGGR 278
             FN V+L G+
Sbjct: 60  -QFNGVLLDGQ 69

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

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 35.4 bits (81), Expect = 0.004
 Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 3/70 (4%)

Query: 213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNK 272
           +  L+V NL   +TE+ L   F +FG++  V  L  +  AF+ +  R AA  A++   N 
Sbjct: 1   VKVLFVRNLATTVTEEILEKSFSEFGKLERVKKL--KDYAFVHFEERDAAVRAMDE-MNG 57

Query: 273 VILGGRRLNI 282
             + G  + I
Sbjct: 58  KEIEGEEIEI 67

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	327
KOG0153|consensus	377		100.0
KOG0145|consensus	360		99.82
KOG0148|consensus	321		99.63
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.58
KOG0144|consensus	510		99.56
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.51
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.45
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.45
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.44
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.44
KOG0122|consensus	270		99.37
PLN03120	260	nucleic acid binding protein; Provisional	99.36
KOG0149|consensus	247		99.35
KOG0145|consensus	360		99.34
KOG0107|consensus	195		99.32
KOG0105|consensus	241		99.3
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.28
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.27
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.26
smart00362	72	RRM_2 RNA recognition motif.	99.26
KOG0125|consensus	376		99.26
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.25
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.24
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.24
KOG0121|consensus	153		99.23
KOG0117|consensus	506		99.23
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.22
KOG0144|consensus	510		99.21
PLN03121	243	nucleic acid binding protein; Provisional	99.21
PLN03213	759	repressor of silencing 3; Provisional	99.2
KOG0151|consensus	877		99.17
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.17
KOG4207|consensus	256		99.17
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.17
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.16
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.15
KOG0132|consensus	894		99.13
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.12
KOG0113|consensus	335		99.12
KOG0111|consensus	298		99.11
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.11
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.11
KOG0148|consensus	321		99.1
KOG0130|consensus	170		99.08
smart00360	71	RRM RNA recognition motif.	99.05
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.05
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.02
KOG0114|consensus	124		99.02
KOG0109|consensus	346		98.99
KOG0147|consensus	549		98.93
KOG0117|consensus	506		98.93
KOG0131|consensus	203		98.89
KOG0109|consensus	346		98.88
KOG0126|consensus	219		98.87
KOG0108|consensus	435		98.85
KOG4206|consensus	221		98.83
KOG0127|consensus	678		98.82
KOG0146|consensus	371		98.82
KOG0124|consensus	544		98.75
KOG0127|consensus	678		98.7
smart00361	70	RRM_1 RNA recognition motif.	98.68
KOG0146|consensus	371		98.66
KOG0131|consensus	203		98.65
KOG0123|consensus	369		98.52
KOG1457|consensus	284		98.51
KOG0415|consensus	479		98.5
KOG4205|consensus	311		98.47
KOG0123|consensus	369		98.44
KOG0110|consensus	725		98.41
KOG4212|consensus	608		98.4
KOG0110|consensus	725		98.37
KOG0116|consensus	419		98.36
KOG4660|consensus	549		98.3
KOG4208|consensus	214		98.3
KOG0124|consensus	544		98.27
KOG1190|consensus	492		98.22
KOG0106|consensus	216		98.21
KOG4205|consensus	311		98.15
KOG4212|consensus	608		98.13
KOG4661|consensus	940		98.12
KOG0533|consensus	243		98.1
KOG2202|consensus	260		98.07
KOG4454|consensus	267		98.01
KOG1548|consensus	382		98.01
KOG2135|consensus	526		97.99
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.86
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.7
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.68
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.65
KOG4209|consensus	231		97.58
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.52
KOG4206|consensus	221		97.5
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.37
KOG0106|consensus	216		97.3
KOG1457|consensus	284		97.29
KOG1190|consensus	492		97.27
KOG0112|consensus	975		97.22
KOG4211|consensus	510		97.07
smart00356	27	ZnF_C3H1 zinc finger.	97.05
KOG0120|consensus	500		96.97
KOG0147|consensus	549		96.88
KOG0226|consensus	290		96.86
PF00642	27	zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and si	96.59
KOG0129|consensus	520		96.42
KOG1855|consensus	484		96.34
KOG1456|consensus	494		96.17
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.02
KOG0120|consensus	500		95.91
KOG1456|consensus	494		95.9
KOG1995|consensus	351		95.84
KOG4676|consensus	479		95.71
KOG4210|consensus	285		95.7
KOG3152|consensus	278		95.68
KOG4211|consensus	510		95.68
KOG1548|consensus	382		95.67
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.57
KOG1365|consensus	508		95.0
KOG2193|consensus	584		94.87
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.79
KOG0129|consensus	520		94.52
KOG4285|consensus	350		94.41
KOG0112|consensus	975		94.3
PF14608	19	zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type	94.05
KOG2314|consensus	698		93.75
KOG0115|consensus	275		93.39
KOG2416|consensus	718		93.18
KOG0105|consensus	241		93.01
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	92.89
KOG4307|consensus	944		92.23
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	91.44
KOG1996|consensus	378		90.98
KOG4849|consensus	498		90.48
KOG2068|consensus	327		89.92
KOG0128|consensus	881		89.77
KOG4574|consensus	1007		88.14
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	87.34
KOG0128|consensus	881		87.33
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	85.71
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	85.08
KOG4307|consensus	944		84.96
PF10013	42	DUF2256: Uncharacterized protein conserved in bact	84.38
KOG1365|consensus	508		81.43
KOG4410|consensus	396		80.33
KOG0804|consensus	493		80.24

>KOG0153|consensus

Probab=100.00  E-value=2e-102  Score=714.21  Aligned_cols=281  Identities=67%  Similarity=1.224  Sum_probs=273.5

Q ss_pred             CCCCcccccchhhh------------------hccccCCcccccCCcceeEEecCCCCCcccchhhhhhhhcccCccccc
Q psy14139          5 KTSSTYNRQSWEDA------------------TKEKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVCQTC   66 (327)
Q Consensus         5 ~~~~~~~~~~~e~~------------------~k~~~g~eckic~rpft~f~w~~~~~~~~kkt~ic~~ca~~kn~cq~c   66 (327)
                      .+.+|||+++||++                  ||++||+||||||||||+|||+||+++|||||+||||||++|||||||
T Consensus         4 ~~~~~~n~~~wEd~dfPiiCe~CLGdnpyvRMtK~~~gkECKICtrPfT~Frw~pgr~~r~kKTeICqtCaklKNvCQ~C   83 (377)
T KOG0153|consen    4 GPKRDYNRQNWEDADFPIICETCLGDNPYVRMTKEPYGKECKICTRPFTIFRWCPGRGARFKKTEICQTCAKLKNVCQTC   83 (377)
T ss_pred             ccccccccccccccCccHHHHHhcCCCceeeeeccccCCccceecCcceEEEeccccccccccchHHHHHHHHHhHHHHh
Confidence            34569999999997                  999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCcHHHHHHHhhhcCCCCCccccHHHHHHHHHHhhhcCCCCCCccccCCCcChHHHHHHHhhcCCCccCCCccc
Q psy14139         67 LLDLEYGLPIQVRDTALKIKDDIPKSDVNKEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHI  146 (327)
Q Consensus        67 ~ldl~~~lp~~~rd~~l~~~~~~p~s~~n~ey~~~~~e~~l~~~~~~~~~~~~g~~~~~~~~l~kl~~~~p~y~r~~~~~  146 (327)
                      ||||+|||||||||++|++++.+|+|++|+|||+|++++++.++++++..++.++...++++|++|+++.|||+||++||
T Consensus        84 mLDle~glPiqvRD~~l~l~dn~p~~dvnre~f~qn~~r~l~~G~~~q~~~~~~~a~~~~d~l~~l~rt~p~ykrn~p~I  163 (377)
T KOG0153|consen   84 MLDLEYGLPIQVRDAALSLVDNVPTSDVNREYFAQNHDRKLSNGDDTQPASAKARALAPNDMLRKLQRTTPYYKRNRPHI  163 (377)
T ss_pred             hhhhccCCcceehhhhhhhhhccchhhhhHHHHHHHHHhhcccCCCcccccchhcccchHHHHHHHhccCccccCCCCcc
Confidence            99999999999999999999999999999999999999999999988777777888899999999999999999999999


Q ss_pred             cccccccccCCCCCCCCCCCCCCCCCCCCcccCccccCCCCCChhHHHHHHhhcCCCCCCCCCCCCccEEEEcCCCCCCC
Q psy14139        147 CSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLT  226 (327)
Q Consensus       147 C~ff~kG~C~rG~~Cpy~H~~p~~~~~~l~~qni~dr~~G~~~p~~~k~~~~~~~~p~~~~p~d~~~~tLfVgnLp~~it  226 (327)
                      ||||++|+|+||++|+|+|++|  ++++++.|||+|||+|.++|++.|++.++..++.++||+|.++++||||+|.+.++
T Consensus       164 csf~v~geckRG~ec~yrhEkp--~d~~L~~qni~dryyg~ndPva~kil~ra~~~~~lepPeD~~I~tLyIg~l~d~v~  241 (377)
T KOG0153|consen  164 CSFFVKGECKRGAECPYRHEKP--PDDPLSLQNIKDRYYGLNDPVALKILNRAGSAGTLEPPEDTSIKTLYIGGLNDEVL  241 (377)
T ss_pred             ccceeeccccccccccccccCC--CCcchhhcccccccccccChHHHHHHhhcccccccCCCcccceeEEEecccccchh
Confidence            9999999999999999999999  67889999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        227 EQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       227 e~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      |.+|+++|.+||+|++|++...++||||+|.++++||.|++..++.+.|+|++|+|.|+++
T Consensus       242 e~dIrdhFyqyGeirsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  242 EQDIRDHFYQYGEIRSIRILPRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             HHHHHHHHhhcCCeeeEEeecccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            9999999999999999999999999999999999999999999999999999999999999

>KOG0145|consensus

Probab=99.82  E-value=1.5e-21  Score=174.38  Aligned_cols=191  Identities=23%  Similarity=0.387  Sum_probs=147.2

Q ss_pred             CCCCccccHHHHHHHH-HHhhhcCCCCCCccccCCCcChHHHHHHHhhcCCCccCCCccccccccccccCCCCCCCCCCC
Q psy14139         88 DIPKSDVNKEYYIQNM-DHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECPYRHE  166 (327)
Q Consensus        88 ~~p~s~~n~ey~~~~~-e~~l~~~~~~~~~~~~g~~~~~~~~l~kl~~~~p~y~r~~~~~C~ff~kG~C~rG~~Cpy~H~  166 (327)
                      ++.++++.++|.+|+| ++++..     ||+++|++|+++.+++|++..+-+|+         |+            +..
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rS-----LF~SiGeiEScKLvRDKitGqSLGYG---------FV------------NYv   91 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRS-----LFGSIGEIESCKLVRDKITGQSLGYG---------FV------------NYV   91 (360)
T ss_pred             CcccceeeeeecccccCHHHHHH-----Hhhcccceeeeeeeeccccccccccc---------ee------------eec
Confidence            4567888999999999 788876     79999999999999999999999998         76            345


Q ss_pred             CCCCCCCCCcccCccccCCCCCChhHHHHHHhhcCCCCCCCCCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEe
Q psy14139        167 KPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL  246 (327)
Q Consensus       167 ~p~~~~~~l~~qni~dr~~G~~~p~~~k~~~~~~~~p~~~~p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~  246 (327)
                      .|.|++.+++..|      |.  .++.|..+.....|+.+...|   .+|||++||..++..+|+.+|++||.|..-+|+
T Consensus        92 ~p~DAe~AintlN------GL--rLQ~KTIKVSyARPSs~~Ik~---aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL  160 (360)
T KOG0145|consen   92 RPKDAEKAINTLN------GL--RLQNKTIKVSYARPSSDSIKD---ANLYVSGLPKTMTQKELEQIFSPFGRIITSRIL  160 (360)
T ss_pred             ChHHHHHHHhhhc------ce--eeccceEEEEeccCChhhhcc---cceEEecCCccchHHHHHHHHHHhhhhhhhhhh
Confidence            6666665554443      11  245677788888887654434   799999999999999999999999999888887


Q ss_pred             cC------CCeEEEEeCCHHHHHHHHHHhcCCeEECC--eeEEEEeccCCCCCCCCcccccccccCCCCCCCCCCCCC
Q psy14139        247 SK------QQCAFIQYTSRPAAEAAVEHSFNKVILGG--RRLNIKWGRAQANRGEDTAELKVRLEPVPGLPGALPPPP  316 (327)
Q Consensus       247 ~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G--~~L~V~~ak~~~~~~~~~~~~~~~~~pv~Glp~~~p~pp  316 (327)
                      .+      +|.+||.|+.+.+|+.|+.. +||..-.|  .+|.|+|+............+.....|..+.+|++..++
T Consensus       161 ~dqvtg~srGVgFiRFDKr~EAe~AIk~-lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~  237 (360)
T KOG0145|consen  161 VDQVTGLSRGVGFIRFDKRIEAEEAIKG-LNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQA  237 (360)
T ss_pred             hhcccceecceeEEEecchhHHHHHHHh-ccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchh
Confidence            64      89999999999999999998 79988888  689999998765443322222222233444445544443

>KOG0148|consensus

Probab=99.63  E-value=2.5e-16  Score=141.78  Aligned_cols=81  Identities=31%  Similarity=0.621  Sum_probs=76.2

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      .++++++||||++..++|++||+.|++||.|.+|+|..++|||||.|++.|+|.+||.+ .|+..+.|..+++.|++...
T Consensus       161 sp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~qGYaFVrF~tkEaAahAIv~-mNntei~G~~VkCsWGKe~~  239 (321)
T KOG0148|consen  161 SPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQGYAFVRFETKEAAAHAIVQ-MNNTEIGGQLVRCSWGKEGD  239 (321)
T ss_pred             CCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecccceEEEEecchhhHHHHHHH-hcCceeCceEEEEeccccCC
Confidence            45679999999999999999999999999999999999999999999999999999998 59999999999999999765


Q ss_pred             CC
Q psy14139        290 NR  291 (327)
Q Consensus       290 ~~  291 (327)
                      ..
T Consensus       240 ~~  241 (321)
T KOG0148|consen  240 DG  241 (321)
T ss_pred             CC
Confidence            43

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

Probab=99.58  E-value=1.9e-14  Score=121.88  Aligned_cols=79  Identities=23%  Similarity=0.463  Sum_probs=72.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.+++|++|+++|++||.|.++.|+.+      ++||||+|.+.++|+.|++. +++..|+|+.|+|.|+
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~-lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE-MDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHH-cCCCEECCEEEEEEeC
Confidence            3479999999999999999999999999999999853      79999999999999999997 6999999999999999


Q ss_pred             cCCCCC
Q psy14139        286 RAQANR  291 (327)
Q Consensus       286 k~~~~~  291 (327)
                      +++...
T Consensus       112 ~~~~~~  117 (144)
T PLN03134        112 NDRPSA  117 (144)
T ss_pred             CcCCCC
Confidence            876543

>KOG0144|consensus

Probab=99.56  E-value=2.2e-16  Score=149.91  Aligned_cols=176  Identities=22%  Similarity=0.354  Sum_probs=125.9

Q ss_pred             CCCCccccHHHHHHHHHHhhhcCCCCCCccccCCCcChHHHHHHHhhcCCCccCCCccccccccccccCCCCCCCCCCCC
Q psy14139         88 DIPKSDVNKEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECPYRHEK  167 (327)
Q Consensus        88 ~~p~s~~n~ey~~~~~e~~l~~~~~~~~~~~~g~~~~~~~~l~kl~~~~p~y~r~~~~~C~ff~kG~C~rG~~Cpy~H~~  167 (327)
                      +.|++++. ..|+..+.|...+.|...+|+.||.+.++..+.+|..+.+-++       |  |++.          .|.+
T Consensus        28 d~~d~~~v-KlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gc-------C--Fv~~----------~trk   87 (510)
T KOG0144|consen   28 DNPDGSAV-KLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGC-------C--FVKY----------YTRK   87 (510)
T ss_pred             CCCCchhh-hheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccce-------E--EEEe----------ccHH
Confidence            34444444 3567778777777777778999999999999999988854443       2  4422          2222


Q ss_pred             CCC-CCCCCcccCccccCCCCCChhHHHHHHhhcCCCCCCCCCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEe
Q psy14139        168 PTD-PDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL  246 (327)
Q Consensus       168 p~~-~~~~l~~qni~dr~~G~~~p~~~k~~~~~~~~p~~~~p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~  246 (327)
                      ..+ +-.++.++   --+.|...|+..|........-       ....+||||-|+...+|.+|+++|++||.|+++.|+
T Consensus        88 ~a~~a~~Alhn~---ktlpG~~~pvqvk~Ad~E~er~-------~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~il  157 (510)
T KOG0144|consen   88 EADEAINALHNQ---KTLPGMHHPVQVKYADGERERI-------VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYIL  157 (510)
T ss_pred             HHHHHHHHhhcc---cccCCCCcceeecccchhhhcc-------ccchhhhhhhccccccHHHHHHHHHhhCccchhhhe
Confidence            111 11122222   2345666777665543221110       234799999999999999999999999999999999


Q ss_pred             cC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECC--eeEEEEeccCCCCCCC
Q psy14139        247 SK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGG--RRLNIKWGRAQANRGE  293 (327)
Q Consensus       247 ~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G--~~L~V~~ak~~~~~~~  293 (327)
                      ++     ||||||+|.+++.|..|+++|.+-..+.|  .+|.|+|+++++.+..
T Consensus       158 rd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~~  211 (510)
T KOG0144|consen  158 RDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKDG  211 (510)
T ss_pred             ecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCchH
Confidence            84     89999999999999999999544467887  6999999999887644

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.51  E-value=3e-15  Score=143.85  Aligned_cols=78  Identities=29%  Similarity=0.524  Sum_probs=70.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECC--eeEEEE
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGG--RRLNIK  283 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G--~~L~V~  283 (327)
                      ..++|||+|||.+++|++|+++|++||+|.+++|+.+      +++|||+|.++++|++|++. +++..+.|  ++|+|+
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~-lng~~~~g~~~~l~V~  270 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISA-LNNVIPEGGSQPLTVR  270 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHH-hCCCccCCCceeEEEE
Confidence            4578999999999999999999999999999999875      48999999999999999998 79988876  799999


Q ss_pred             eccCCCC
Q psy14139        284 WGRAQAN  290 (327)
Q Consensus       284 ~ak~~~~  290 (327)
                      |++....
T Consensus       271 ~a~~~~~  277 (346)
T TIGR01659       271 LAEEHGK  277 (346)
T ss_pred             ECCcccc
Confidence            9987544

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.45  E-value=3.9e-13  Score=98.25  Aligned_cols=65  Identities=42%  Similarity=0.760  Sum_probs=61.5

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       216 LfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      |||+|||.++++++|+++|++||.|..+.+..+     +++|||+|.+.++|+.|++. ++|..++|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~-l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEE-LNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHH-HTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHH-cCCCEECccCcC
Confidence            799999999999999999999999999999884     79999999999999999998 699999999885

(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 ....

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.45  E-value=6.3e-13  Score=127.58  Aligned_cols=76  Identities=26%  Similarity=0.400  Sum_probs=71.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      .+|||+|||.++++++|+++|++||.|.+++|+.+      +|||||+|.+.++|..|+.+ +||..++|+.|+|.|..+
T Consensus       270 ~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~-lnG~~~~gr~i~V~~~~~  348 (352)
T TIGR01661       270 YCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILS-LNGYTLGNRVLQVSFKTN  348 (352)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHH-hCCCEECCeEEEEEEccC
Confidence            47999999999999999999999999999999864      79999999999999999998 799999999999999987


Q ss_pred             CCC
Q psy14139        288 QAN  290 (327)
Q Consensus       288 ~~~  290 (327)
                      +..
T Consensus       349 ~~~  351 (352)
T TIGR01661       349 KAY  351 (352)
T ss_pred             CCC
Confidence            754

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.44  E-value=6.4e-13  Score=127.53  Aligned_cols=77  Identities=26%  Similarity=0.484  Sum_probs=71.6

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      .++|||+|||.+++|++|+++|++||+|.+|+|+.+      +|||||+|.+.++|++|++. ++|..+.|+.|+|.|++
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~-l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNS-LNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhh-cccEEECCeeEEEEeec
Confidence            479999999999999999999999999999999864      58999999999999999997 79999999999999998


Q ss_pred             CCCC
Q psy14139        287 AQAN  290 (327)
Q Consensus       287 ~~~~  290 (327)
                      +...
T Consensus        82 ~~~~   85 (352)
T TIGR01661        82 PSSD   85 (352)
T ss_pred             cccc
Confidence            7654

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.44  E-value=5.6e-13  Score=128.19  Aligned_cols=95  Identities=22%  Similarity=0.395  Sum_probs=80.1

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      .+...++|||++||.+++|++|+++|+.||+|++|+|+.+      ++||||+|.+.++|++|++. +++..+.+++|+|
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~-LnG~~l~gr~i~V  181 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKN-LNGITVRNKRLKV  181 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHH-cCCCccCCceeee
Confidence            3456789999999999999999999999999999999764      58999999999999999997 7999999999999


Q ss_pred             EeccCCCCCCCCcccccccccCCCCCCC
Q psy14139        283 KWGRAQANRGEDTAELKVRLEPVPGLPG  310 (327)
Q Consensus       283 ~~ak~~~~~~~~~~~~~~~~~pv~Glp~  310 (327)
                      .|+++.....    ....+|  |.+||.
T Consensus       182 ~~a~p~~~~~----~~~~lf--V~nLp~  203 (346)
T TIGR01659       182 SYARPGGESI----KDTNLY--VTNLPR  203 (346)
T ss_pred             eccccccccc----ccceeE--EeCCCC
Confidence            9998754322    122345  777763

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).

>KOG0122|consensus

Probab=99.37  E-value=3.8e-12  Score=113.54  Aligned_cols=77  Identities=27%  Similarity=0.472  Sum_probs=72.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      .+..+|-|.||+.+++|++|+++|.+||.|..+.+..+      +|||||+|.+|+.|.+|++. |||.-++.-.|+|.|
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~-LnG~gyd~LILrvEw  265 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIAD-LNGYGYDNLILRVEW  265 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHH-ccCcccceEEEEEEe
Confidence            35678999999999999999999999999999999875      79999999999999999997 899999999999999


Q ss_pred             ccCC
Q psy14139        285 GRAQ  288 (327)
Q Consensus       285 ak~~  288 (327)
                      ++|+
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            9986

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.36  E-value=3.9e-12  Score=116.12  Aligned_cols=74  Identities=24%  Similarity=0.363  Sum_probs=68.8

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC---CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK---QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~---kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      .++|||+||+..++|++|+++|+.||+|.+|.|..+   ++||||+|.+.++|+.|+.  ++|..|.|+.|+|.++..-
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All--LnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL--LSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH--hcCCeeCCceEEEEeccCC
Confidence            479999999999999999999999999999999875   6999999999999999995  7999999999999997744

>KOG0149|consensus

Probab=99.35  E-value=5.5e-12  Score=112.10  Aligned_cols=78  Identities=28%  Similarity=0.470  Sum_probs=70.4

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      -.|...++||||||++++..++|+++|++||+|.+..|+.+      +|++||+|.+.++|++|.+.  ..-+|+||+-+
T Consensus         7 ~~DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d--p~piIdGR~aN   84 (247)
T KOG0149|consen    7 FGDTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD--PNPIIDGRKAN   84 (247)
T ss_pred             CCCceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC--CCCcccccccc
Confidence            36778899999999999999999999999999999988864      79999999999999999985  66799999998


Q ss_pred             EEeccC
Q psy14139        282 IKWGRA  287 (327)
Q Consensus       282 V~~ak~  287 (327)
                      +.+|.-
T Consensus        85 cnlA~l   90 (247)
T KOG0149|consen   85 CNLASL   90 (247)
T ss_pred             cchhhh
Confidence            888754

>KOG0145|consensus

Probab=99.34  E-value=3.8e-12  Score=114.47  Aligned_cols=98  Identities=27%  Similarity=0.485  Sum_probs=86.1

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCC------CeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ------QCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~k------g~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      .+.+.++|.|.-||..+++++++.+|+..|+|+++++++++      ||+||.|.+.++|++|+.. +||+.+..+.|+|
T Consensus        37 t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~Aint-lNGLrLQ~KTIKV  115 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINT-LNGLRLQNKTIKV  115 (360)
T ss_pred             cCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhh-hcceeeccceEEE
Confidence            45667899999999999999999999999999999999863      8999999999999999997 8999999999999


Q ss_pred             EeccCCCCCCCCcccccccccCCCCCCCCCC
Q psy14139        283 KWGRAQANRGEDTAELKVRLEPVPGLPGALP  313 (327)
Q Consensus       283 ~~ak~~~~~~~~~~~~~~~~~pv~Glp~~~p  313 (327)
                      .+++|....-++.    ..|  |+|||..+.
T Consensus       116 SyARPSs~~Ik~a----NLY--vSGlPktMt  140 (360)
T KOG0145|consen  116 SYARPSSDSIKDA----NLY--VSGLPKTMT  140 (360)
T ss_pred             EeccCChhhhccc----ceE--EecCCccch
Confidence            9999987665432    356  889875543

>KOG0107|consensus

Probab=99.32  E-value=5.4e-12  Score=107.51  Aligned_cols=78  Identities=28%  Similarity=0.515  Sum_probs=72.2

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCCC
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR  291 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~~  291 (327)
                      .+.||||||+..+++.||...|..||.|.+|.|..+ .|||||+|++..+|+.|+.. |+|..|.|..|+|+++.-....
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~-LDG~~~cG~r~rVE~S~G~~r~   88 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRY-LDGKDICGSRIRVELSTGRPRG   88 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhh-cCCccccCceEEEEeecCCccc
Confidence            589999999999999999999999999999999875 79999999999999999997 8999999999999998766553

>KOG0105|consensus

Probab=99.30  E-value=6.3e-12  Score=107.97  Aligned_cols=76  Identities=28%  Similarity=0.559  Sum_probs=69.7

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC---CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK---QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~---kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      ..++|||||||.++.|.+|.++|.+||.|..|.+...   -.||||+|++..+|+.|+.. -+|..++|..|+|++++.-
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiyg-RdGYdydg~rLRVEfprgg   83 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYG-RDGYDYDGCRLRVEFPRGG   83 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhc-ccccccCcceEEEEeccCC
Confidence            4579999999999999999999999999999988764   47999999999999999997 6999999999999998754

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.28  E-value=2.1e-11  Score=89.72  Aligned_cols=65  Identities=34%  Similarity=0.649  Sum_probs=59.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       216 LfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      |||+|||.++++++|+++|+.||.|..+.+..+     +++|||+|.+.++|++|++. +++..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~-~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALEL-LNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHH-HTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHH-CCCcEECCEEcC
Confidence            799999999999999999999999999999886     59999999999999999996 688999999875

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 ....

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

Probab=99.27  E-value=2.2e-11  Score=124.38  Aligned_cols=91  Identities=29%  Similarity=0.496  Sum_probs=75.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      .+|||||||.+++|++|+++|++||.|.+|+|..+      +|||||+|.+.++|++|++. +++..+.|+.|+|.|+..
T Consensus         1 ~sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~-ln~~~i~gk~i~i~~s~~   79 (562)
T TIGR01628         1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET-MNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             CeEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHH-hCCCEECCeeEEeecccc
Confidence            38999999999999999999999999999999864      57999999999999999997 799999999999999865


Q ss_pred             CCCCCCCcccccccccCCCCCC
Q psy14139        288 QANRGEDTAELKVRLEPVPGLP  309 (327)
Q Consensus       288 ~~~~~~~~~~~~~~~~pv~Glp  309 (327)
                      .......  ....+|  |.+||
T Consensus        80 ~~~~~~~--~~~~vf--V~nLp   97 (562)
T TIGR01628        80 DPSLRRS--GVGNIF--VKNLD   97 (562)
T ss_pred             ccccccc--CCCceE--EcCCC
Confidence            4332211  122344  66775

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=99.26  E-value=3e-11  Score=122.56  Aligned_cols=77  Identities=25%  Similarity=0.479  Sum_probs=71.1

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhc--CCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQF--GEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~f--G~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      ..++|||+||+.+++|++|+++|++|  |+|++|.++  ++||||+|.++++|++|++. +|+..|+|+.|+|.|+++..
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--rgfAFVeF~s~e~A~kAi~~-lnG~~i~Gr~I~V~~Akp~~  308 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--RDYAFVHFEDREDAVKAMDE-LNGKELEGSEIEVTLAKPVD  308 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--cCeEEEEeCCHHHHHHHHHH-hCCCEECCEEEEEEEccCCC
Confidence            45789999999999999999999999  999999877  67999999999999999998 79999999999999999865


Q ss_pred             CC
Q psy14139        290 NR  291 (327)
Q Consensus       290 ~~  291 (327)
                      ..
T Consensus       309 ~~  310 (578)
T TIGR01648       309 KK  310 (578)
T ss_pred             cc
Confidence            43

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.

>smart00362 RRM_2 RNA recognition motif

Probab=99.26  E-value=4.4e-11  Score=86.29  Aligned_cols=68  Identities=44%  Similarity=0.720  Sum_probs=63.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCC----CeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ----QCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       215 tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~k----g~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      +|||+|||..+++++|+++|.+||.|..+.+..+.    ++|||+|.+.++|+.|++. +++..+.|+.|+|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~-~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEA-LNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHH-hCCcEECCEEEeeC
Confidence            58999999999999999999999999999998875    9999999999999999997 79999999998873

>KOG0125|consensus

Probab=99.26  E-value=1.7e-11  Score=113.41  Aligned_cols=75  Identities=23%  Similarity=0.425  Sum_probs=70.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec----CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS----KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~----~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      -+.|+|+|||....|-||+.+|.+||.|.+|.|+-    +|||+||+|++.++|++|-++ |+|.++.||+|.|..+.++
T Consensus        96 pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~-LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen   96 PKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAE-LHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             CceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHH-hhcceeeceEEEEeccchh
Confidence            47999999999999999999999999999999986    389999999999999999998 7999999999999988765

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

Probab=99.25  E-value=3.2e-11  Score=121.20  Aligned_cols=77  Identities=21%  Similarity=0.369  Sum_probs=71.4

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHh-cCCeEECCeeEEEEeccCCC
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHS-FNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~-l~g~~i~G~~L~V~~ak~~~  289 (327)
                      .++|||+|||.+++|++|+++|++||.|.++.++.++++|||+|.+.++|+.|++.+ +++..+.|++|+|.|+..+.
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~   79 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQE   79 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCcc
Confidence            369999999999999999999999999999999999999999999999999999864 47899999999999997653

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).

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

Probab=99.24  E-value=3.9e-11  Score=122.08  Aligned_cols=75  Identities=31%  Similarity=0.563  Sum_probs=68.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++||||||+.+++|++|+++|++||.|.+|+|+.      ++|||||+|.+.++|++|++. +||..++|+.|+|.+.
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~-lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ-MNGQMLGGRNIKVGRP  184 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHh-cCCeEEecceeeeccc
Confidence            457999999999999999999999999999999975      389999999999999999998 6999999999999865


Q ss_pred             cC
Q psy14139        286 RA  287 (327)
Q Consensus       286 k~  287 (327)
                      ..
T Consensus       185 ~~  186 (612)
T TIGR01645       185 SN  186 (612)
T ss_pred             cc
Confidence            43

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.

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

Probab=99.24  E-value=3.7e-11  Score=122.22  Aligned_cols=78  Identities=24%  Similarity=0.445  Sum_probs=71.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+||+.++++++|+++|+.||.|.+++|..+      +|||||+|.+.++|.+|++. +|+..++|+.|+|.++
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~a-mNg~elgGr~LrV~kA  281 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS-MNLFDLGGQYLRVGKC  281 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHH-hCCCeeCCeEEEEEec
Confidence            4579999999999999999999999999999999863      79999999999999999998 6999999999999999


Q ss_pred             cCCCC
Q psy14139        286 RAQAN  290 (327)
Q Consensus       286 k~~~~  290 (327)
                      .+.+.
T Consensus       282 i~pP~  286 (612)
T TIGR01645       282 VTPPD  286 (612)
T ss_pred             CCCcc
Confidence            86543

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.

>KOG0121|consensus

Probab=99.23  E-value=1.7e-11  Score=99.46  Aligned_cols=75  Identities=31%  Similarity=0.497  Sum_probs=68.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      .+.+|||||||+..++|+.|.++|+..|+|+.|.|-.+      -||+||+|.++++|+.|+.- ++|..++.++|+|.|
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~Alry-isgtrLddr~ir~D~  112 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRY-ISGTRLDDRPIRIDW  112 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHH-hccCcccccceeeec
Confidence            34579999999999999999999999999999998765      48999999999999999996 899999999999998


Q ss_pred             cc
Q psy14139        285 GR  286 (327)
Q Consensus       285 ak  286 (327)
                      .-
T Consensus       113 D~  114 (153)
T KOG0121|consen  113 DA  114 (153)
T ss_pred             cc
Confidence            64

>KOG0117|consensus

Probab=99.23  E-value=5.2e-11  Score=114.07  Aligned_cols=80  Identities=25%  Similarity=0.456  Sum_probs=73.5

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQAN  290 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~  290 (327)
                      ...+-|||.||+.++||+.|++.|++||.|+.|+.+  +.||||.|.+|++|-+|++. +||..|+|..|.|.+|+|..+
T Consensus       257 s~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~--rDYaFVHf~eR~davkAm~~-~ngkeldG~~iEvtLAKP~~k  333 (506)
T KOG0117|consen  257 SKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKP--RDYAFVHFAEREDAVKAMKE-TNGKELDGSPIEVTLAKPVDK  333 (506)
T ss_pred             hheeeeeeeccchhhhHHHHHHHHHhccceEEeecc--cceeEEeecchHHHHHHHHH-hcCceecCceEEEEecCChhh
Confidence            446789999999999999999999999999999888  55999999999999999998 699999999999999999876


Q ss_pred             CCC
Q psy14139        291 RGE  293 (327)
Q Consensus       291 ~~~  293 (327)
                      +..
T Consensus       334 ~k~  336 (506)
T KOG0117|consen  334 KKK  336 (506)
T ss_pred             hcc
Confidence            544

>PF13893 RRM_5: RNA recognition motif

Probab=99.22  E-value=6.4e-11  Score=83.69  Aligned_cols=55  Identities=31%  Similarity=0.620  Sum_probs=51.2

Q ss_pred             HHHHHhhcCCeEEEEEecCC-CeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        230 LRDHFYQFGEIRSVTILSKQ-QCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       230 Lr~~F~~fG~I~~v~i~~~k-g~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      |+++|++||+|.++.+..++ ++|||+|.+.++|+.|++. ++|..++|++|+|.|+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~-l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQ-LNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHH-HTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHH-hCCCEECCcEEEEEEC
Confidence            67899999999999999987 9999999999999999998 7999999999999986

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>KOG0144|consensus

Probab=99.21  E-value=2.8e-11  Score=115.45  Aligned_cols=84  Identities=25%  Similarity=0.578  Sum_probs=76.7

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECC--eeE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGG--RRL  280 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G--~~L  280 (327)
                      .|.+.-+||||.+|..++|.||+++|++||.|.+|.|+++      +||+||.|.++++|.+|+.++.|.+.+.|  .+|
T Consensus        30 ~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pv  109 (510)
T KOG0144|consen   30 PDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPV  109 (510)
T ss_pred             CCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcce
Confidence            4577789999999999999999999999999999999985      69999999999999999999888889988  789


Q ss_pred             EEEeccCCCCCC
Q psy14139        281 NIKWGRAQANRG  292 (327)
Q Consensus       281 ~V~~ak~~~~~~  292 (327)
                      .|++++....+.
T Consensus       110 qvk~Ad~E~er~  121 (510)
T KOG0144|consen  110 QVKYADGERERI  121 (510)
T ss_pred             eecccchhhhcc
Confidence            999998876653

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.21  E-value=8.4e-11  Score=105.94  Aligned_cols=72  Identities=29%  Similarity=0.324  Sum_probs=66.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC---CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK---QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~---kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ...+|||+||++.++|++|+++|+.||+|.+|+|..+   +++|||+|.+.++|+.|+.  |+|..|.+++|.|...
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll--LnGa~l~d~~I~It~~   78 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL--LSGATIVDQRVCITRW   78 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh--cCCCeeCCceEEEEeC
Confidence            4479999999999999999999999999999999985   5899999999999999995  8999999999988753

>PLN03213 repressor of silencing 3; Provisional

Probab=99.20  E-value=6e-11  Score=114.82  Aligned_cols=76  Identities=21%  Similarity=0.410  Sum_probs=69.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC--CCeEEEEeCCH--HHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK--QQCAFIQYTSR--PAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~--kg~aFV~F~~~--~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      ....+||||||+.++++++|+.+|.+||.|.+|.|++.  +|||||+|.+.  .++.+|+.. |||..+.|+.|+|.-|+
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISa-LNGAEWKGR~LKVNKAK   86 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFST-YNGCVWKGGRLRLEKAK   86 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHH-hcCCeecCceeEEeecc
Confidence            34579999999999999999999999999999999974  89999999987  789999998 79999999999999987


Q ss_pred             C
Q psy14139        287 A  287 (327)
Q Consensus       287 ~  287 (327)
                      +
T Consensus        87 P   87 (759)
T PLN03213         87 E   87 (759)
T ss_pred             H
Confidence            4

>KOG0151|consensus

Probab=99.17  E-value=1.2e-10  Score=116.84  Aligned_cols=110  Identities=32%  Similarity=0.541  Sum_probs=91.9

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec---------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCee
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS---------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRR  279 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~---------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~  279 (327)
                      .|+..++|||+||++.++|+.|...|..||.|.+|+|+.         .+.|+||.|.++.+|++|++. ++|.++.+..
T Consensus       170 gDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~-lqg~iv~~~e  248 (877)
T KOG0151|consen  170 GDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKE-LQGIIVMEYE  248 (877)
T ss_pred             CCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHH-hcceeeeeee
Confidence            367889999999999999999999999999999999985         368999999999999999997 7999999999


Q ss_pred             EEEEeccCCCCCCCCcccccccccCCCCCCCCCCCCC-CCCCCCCCC
Q psy14139        280 LNIKWGRAQANRGEDTAELKVRLEPVPGLPGALPPPP-KDFFNLSNP  325 (327)
Q Consensus       280 L~V~~ak~~~~~~~~~~~~~~~~~pv~Glp~~~p~pp-~~~~~~~pp  325 (327)
                      +++-|+++-.-..      ..++.|.+++...+|+|| +..||..|+
T Consensus       249 ~K~gWgk~V~ip~------~p~~ipp~~h~~~lp~p~s~Lpfnaqp~  289 (877)
T KOG0151|consen  249 MKLGWGKAVPIPN------IPIYIPPPLHEATLPPPPSNLPFNAQPG  289 (877)
T ss_pred             eeeccccccccCC------ccccCCChhhhccCCCCccCCcccCCCC
Confidence            9999998765332      234455666666777666 667777665

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

Probab=99.17  E-value=1.1e-10  Score=119.18  Aligned_cols=78  Identities=28%  Similarity=0.511  Sum_probs=71.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ....+|||+||+.++++++|+++|++||.|.+++++.+     +|+|||+|.+.++|++|+.. ++|..++|++|.|.|+
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~-~~g~~~~gk~l~V~~a  361 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTE-MHGRMLGGKPLYVALA  361 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHH-hcCCeeCCceeEEEec
Confidence            34578999999999999999999999999999999864     69999999999999999998 6999999999999999


Q ss_pred             cCCC
Q psy14139        286 RAQA  289 (327)
Q Consensus       286 k~~~  289 (327)
                      ..+.
T Consensus       362 ~~k~  365 (562)
T TIGR01628       362 QRKE  365 (562)
T ss_pred             cCcH
Confidence            8653

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

>KOG4207|consensus

Probab=99.17  E-value=5.6e-11  Score=103.81  Aligned_cols=80  Identities=30%  Similarity=0.560  Sum_probs=72.9

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeE
Q psy14139        207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRL  280 (327)
Q Consensus       207 ~p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L  280 (327)
                      ||+-...++|-|-||...++-++|+.+|++||.|-+|.|..+      +|||||.|....+||.|+++ ++|.+|+|+.|
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~da-mDG~~ldgRel   85 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDA-MDGAVLDGREL   85 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHh-hcceeecccee
Confidence            444456789999999999999999999999999999999875      79999999999999999998 69999999999


Q ss_pred             EEEeccC
Q psy14139        281 NIKWGRA  287 (327)
Q Consensus       281 ~V~~ak~  287 (327)
                      +|++|+-
T Consensus        86 rVq~ary   92 (256)
T KOG4207|consen   86 RVQMARY   92 (256)
T ss_pred             eehhhhc
Confidence            9988763

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

Probab=99.17  E-value=1.8e-10  Score=115.79  Aligned_cols=77  Identities=25%  Similarity=0.355  Sum_probs=71.1

Q ss_pred             CCccEEEEcCCCC-CCCHHHHHHHHhhcCCeEEEEEecC-CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        211 KTITTLYVGNLGD-KLTEQDLRDHFYQFGEIRSVTILSK-QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       211 ~~~~tLfVgnLp~-~ite~~Lr~~F~~fG~I~~v~i~~~-kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      ...++|||+||+. .+++++|+++|++||.|.+|+++.+ +++|||+|.+.++|+.|+.. ++|..|.|+.|+|.+++..
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~-lng~~l~g~~l~v~~s~~~  351 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTH-LNGVKLFGKPLRVCPSKQQ  351 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHH-hCCCEECCceEEEEEcccc
Confidence            4567999999998 6999999999999999999999875 69999999999999999997 7999999999999998764

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

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

Probab=99.16  E-value=1.8e-10  Score=114.53  Aligned_cols=78  Identities=22%  Similarity=0.392  Sum_probs=70.7

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      ....++|||+|||..+++++|+++|++||.|.+|+|+.+      +|+|||+|.+.++|++|+.  ++|..+.|++|.|.
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~--l~g~~~~g~~i~v~  163 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA--LTGQMLLGRPIIVQ  163 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH--hCCCEECCeeeEEe
Confidence            455789999999999999999999999999999999864      7999999999999999997  69999999999999


Q ss_pred             eccCCC
Q psy14139        284 WGRAQA  289 (327)
Q Consensus       284 ~ak~~~  289 (327)
                      ++....
T Consensus       164 ~~~~~~  169 (457)
T TIGR01622       164 SSQAEK  169 (457)
T ss_pred             ecchhh
Confidence            876543

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.

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

Probab=99.15  E-value=1.8e-10  Score=114.59  Aligned_cols=73  Identities=36%  Similarity=0.600  Sum_probs=68.7

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      .++|||+|||..++|++|+++|++||.|.+|.+..      .+|||||+|.+.++|+.|++. ++|..|.|+.|+|.|+.
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~-l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEV-MNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHh-cCCcEECCEEEEEEEcc
Confidence            68999999999999999999999999999999985      368999999999999999997 79999999999999976

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.

>KOG0132|consensus

Probab=99.13  E-value=1.2e-10  Score=117.97  Aligned_cols=79  Identities=33%  Similarity=0.661  Sum_probs=74.2

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCCCC
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRG  292 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~~~  292 (327)
                      .+|||||+|+..++|.||..+|+.||+|.+|.++..++||||....|.+|++|+.+ ++...+.++.|+|.||....-+.
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R~cAfI~M~~RqdA~kalqk-l~n~kv~~k~Iki~Wa~g~G~ks  499 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPRGCAFIKMVRRQDAEKALQK-LSNVKVADKTIKIAWAVGKGPKS  499 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccCCceeEEEEeehhHHHHHHHH-HhcccccceeeEEeeeccCCcch
Confidence            47999999999999999999999999999999999999999999999999999998 58899999999999998766554

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

Probab=99.12  E-value=2.7e-10  Score=115.70  Aligned_cols=74  Identities=23%  Similarity=0.382  Sum_probs=66.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec-----CCCeEEEEeCCHHHHHHHHHHhcCCeEEC-CeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS-----KQQCAFIQYTSRPAAEAAVEHSFNKVILG-GRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~-----~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~-G~~L~V~~a  285 (327)
                      ..++|||+|||.+++|++|+++|++||.|.+++|+.     +++||||+|.+.++|++|++. +++..+. |+.|.|.++
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~-lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKL-LNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHH-cCCCeecCCcccccccc
Confidence            458999999999999999999999999999999975     479999999999999999997 6888774 788888776


Q ss_pred             c
Q psy14139        286 R  286 (327)
Q Consensus       286 k  286 (327)
                      .
T Consensus       136 ~  136 (578)
T TIGR01648       136 V  136 (578)
T ss_pred             c
Confidence            4

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.

>KOG0113|consensus

Probab=99.12  E-value=6.2e-10  Score=102.03  Aligned_cols=77  Identities=26%  Similarity=0.501  Sum_probs=70.7

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ..-+||||+-|+.+++|.+|+..|+.||.|+.|+|+.+      +|||||+|.+..+...|.+. .+|+.|+|+.|.|.+
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~-adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKD-ADGIKIDGRRILVDV  177 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHh-ccCceecCcEEEEEe
Confidence            45689999999999999999999999999999999985      79999999999999999998 799999999998887


Q ss_pred             ccCC
Q psy14139        285 GRAQ  288 (327)
Q Consensus       285 ak~~  288 (327)
                      -+.+
T Consensus       178 ERgR  181 (335)
T KOG0113|consen  178 ERGR  181 (335)
T ss_pred             cccc
Confidence            6643

>KOG0111|consensus

Probab=99.11  E-value=5.6e-11  Score=104.65  Aligned_cols=81  Identities=28%  Similarity=0.527  Sum_probs=74.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++||||+|.++++|.-|...|-+||.|..|.+..      +++||||+|..+++|..|+.. +|+.++.|+.|+|.++
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDN-MnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDN-MNESELFGRTIRVNLA   87 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhc-CchhhhcceeEEEeec
Confidence            347999999999999999999999999999999976      489999999999999999998 5999999999999999


Q ss_pred             cCCCCCCC
Q psy14139        286 RAQANRGE  293 (327)
Q Consensus       286 k~~~~~~~  293 (327)
                      +|.+-+.+
T Consensus        88 kP~kikeg   95 (298)
T KOG0111|consen   88 KPEKIKEG   95 (298)
T ss_pred             CCccccCC
Confidence            99775543

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

Probab=99.11  E-value=5.8e-10  Score=112.36  Aligned_cols=78  Identities=22%  Similarity=0.465  Sum_probs=71.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||..+++++|+++|+.||.|..+.++.      .+|||||+|.+.++|+.|++. ++|..+.|+.|.|.++
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~-l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAA-LNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            457999999999999999999999999999999875      379999999999999999997 7999999999999999


Q ss_pred             cCCCC
Q psy14139        286 RAQAN  290 (327)
Q Consensus       286 k~~~~  290 (327)
                      .....
T Consensus       373 ~~~~~  377 (509)
T TIGR01642       373 CVGAN  377 (509)
T ss_pred             ccCCC
Confidence            76543

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

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.11  E-value=7e-10  Score=80.34  Aligned_cols=69  Identities=42%  Similarity=0.739  Sum_probs=64.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       215 tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      +|+|+|||..+++++|+++|..||.|..+.+..+     +++|||+|.+.++|..|+.. +++..++|+.+.|.|
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~-~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEA-LNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHH-hCCCeECCeEEEEeC
Confidence            4899999999999999999999999999999875     68999999999999999997 799999999999875

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).

>KOG0148|consensus

Probab=99.10  E-value=1.8e-10  Score=104.29  Aligned_cols=77  Identities=23%  Similarity=0.586  Sum_probs=71.9

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      .-.+|||.|..+++-++|++.|.+||+|.+.+|+++      +||+||.|-++++||.|+.. +||.+|++|.|+..|+.
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~-MnGqWlG~R~IRTNWAT  140 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQ-MNGQWLGRRTIRTNWAT  140 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHH-hCCeeeccceeeccccc
Confidence            468999999999999999999999999999999985      89999999999999999999 59999999999999997


Q ss_pred             CCCC
Q psy14139        287 AQAN  290 (327)
Q Consensus       287 ~~~~  290 (327)
                      .++.
T Consensus       141 RKp~  144 (321)
T KOG0148|consen  141 RKPS  144 (321)
T ss_pred             cCcc
Confidence            6654

>KOG0130|consensus

Probab=99.08  E-value=2.3e-10  Score=93.79  Aligned_cols=78  Identities=23%  Similarity=0.479  Sum_probs=71.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..=-|||.++..+.+|++|.+.|..||+|+.|.+..+      +|||+|+|++.+.|++|+.+ +||..+-|+.|.|.|+
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~-~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDA-LNGAELLGQNVSVDWC  149 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHh-ccchhhhCCceeEEEE
Confidence            3457999999999999999999999999999999875      69999999999999999998 7999999999999999


Q ss_pred             cCCCC
Q psy14139        286 RAQAN  290 (327)
Q Consensus       286 k~~~~  290 (327)
                      ..+.+
T Consensus       150 Fv~gp  154 (170)
T KOG0130|consen  150 FVKGP  154 (170)
T ss_pred             EecCC
Confidence            87655

>smart00360 RRM RNA recognition motif

Probab=99.05  E-value=9.6e-10  Score=78.80  Aligned_cols=64  Identities=41%  Similarity=0.677  Sum_probs=58.9

Q ss_pred             EcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        218 VGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       218 VgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      |+|||..+++++|+++|.+||.|..+.+..+      +++|||+|.+.++|..|+.. +++..++|+.|+|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~-~~~~~~~~~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEA-LNGKELDGRPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHH-cCCCeeCCcEEEe
Confidence            5799999999999999999999999998875      46999999999999999996 7899999999887

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

Probab=99.05  E-value=1.3e-09  Score=109.77  Aligned_cols=77  Identities=22%  Similarity=0.412  Sum_probs=67.6

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhc------------CCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEE
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQF------------GEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL  275 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~f------------G~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i  275 (327)
                      ..+...++|||||||..+++++|+++|.++            +.|..+.+..+++||||+|.+.++|..|+.  ++|..+
T Consensus       170 ~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al~--l~g~~~  247 (509)
T TIGR01642       170 QATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAMA--LDSIIY  247 (509)
T ss_pred             cCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhhc--CCCeEe
Confidence            345667899999999999999999999975            467778888889999999999999999995  799999


Q ss_pred             CCeeEEEEecc
Q psy14139        276 GGRRLNIKWGR  286 (327)
Q Consensus       276 ~G~~L~V~~ak  286 (327)
                      .|+.|+|.+..
T Consensus       248 ~g~~l~v~r~~  258 (509)
T TIGR01642       248 SNVFLKIRRPH  258 (509)
T ss_pred             eCceeEecCcc
Confidence            99999997544

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

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

Probab=99.02  E-value=1.4e-09  Score=97.84  Aligned_cols=74  Identities=36%  Similarity=0.627  Sum_probs=69.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      ..+|||+|||.++++++|+++|.+||.|..+.+..+      +|+|||.|.+.+.|..|+.. +++..+.|++|.|.++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~-~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEE-LNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHH-cCCCeECCceeEeeccc
Confidence            589999999999999999999999999999988775      59999999999999999997 79999999999999965


Q ss_pred             C
Q psy14139        287 A  287 (327)
Q Consensus       287 ~  287 (327)
                      +
T Consensus       194 ~  194 (306)
T COG0724         194 P  194 (306)
T ss_pred             c
Confidence            3

>KOG0114|consensus

Probab=99.02  E-value=1.5e-09  Score=85.15  Aligned_cols=76  Identities=26%  Similarity=0.412  Sum_probs=69.4

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC---CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK---QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~---kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      ++-|||.|||.++|.+++.++|.+||.|..|+|...   +|-|||.|++..+|.+|+.+ ++|..+.++.|.|-+-.+..
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dh-lsg~n~~~ryl~vlyyq~~~   96 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDH-LSGYNVDNRYLVVLYYQPED   96 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHH-hcccccCCceEEEEecCHHH
Confidence            478999999999999999999999999999999764   79999999999999999999 79999999999998765543

>KOG0109|consensus

Probab=98.99  E-value=7.4e-10  Score=101.25  Aligned_cols=73  Identities=29%  Similarity=0.565  Sum_probs=68.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      .+|||||||.+.++.+|+.+|++||+|.++.|+  +.+|||..++...|+.|+.. |++..|+|..|+|+-++++.
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv--KNYgFVHiEdktaaedairN-LhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIV--KNYGFVHIEDKTAAEDAIRN-LHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeee--cccceEEeecccccHHHHhh-cccceecceEEEEEeccccC
Confidence            379999999999999999999999999999999  88999999999999999998 79999999999999888773

>KOG0147|consensus

Probab=98.93  E-value=7.5e-10  Score=108.70  Aligned_cols=170  Identities=24%  Similarity=0.267  Sum_probs=108.4

Q ss_pred             HHHHHHHHHHhhhcCCCCCCccccCCCcChHHHHHHHhhcCCCccCCCccccccccccccCCCCCCCCCCCCCCCCCCCC
Q psy14139         96 KEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPL  175 (327)
Q Consensus        96 ~ey~~~~~e~~l~~~~~~~~~~~~g~~~~~~~~l~kl~~~~p~y~r~~~~~C~ff~kG~C~rG~~Cpy~H~~p~~~~~~l  175 (327)
                      |--|..++-..+..-|.+..|+..|++-.+..|.++..+.+-+-.         |+  +|.        |+.-....-+|
T Consensus       180 Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~---------Yv--ef~--------D~~sVp~aiaL  240 (549)
T KOG0147|consen  180 RTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIA---------YV--EFC--------DEQSVPLAIAL  240 (549)
T ss_pred             HHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhccee---------EE--EEe--------cccchhhHhhh
Confidence            344555554444444555578888999889999998887644422         22  111        22222111123


Q ss_pred             cccCccccCCCCCChhHHHHHHhhcCCCCCCC-CCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------
Q psy14139        176 ADQNIKDRYYGVNDPVAEKLMARASTMPKLDP-PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------  248 (327)
Q Consensus       176 ~~qni~dr~~G~~~p~~~k~~~~~~~~p~~~~-p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------  248 (327)
                      +.|-+...+--.--+.++|... +...+.+.. ........||||||..+++|++|+.+|++||.|+.|.+..+      
T Consensus       241 sGqrllg~pv~vq~sEaeknr~-a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~s  319 (549)
T KOG0147|consen  241 SGQRLLGVPVIVQLSEAEKNRA-ANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRS  319 (549)
T ss_pred             cCCcccCceeEecccHHHHHHH-HhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccc
Confidence            3332211111111233444442 222222221 11122234999999999999999999999999999998764      


Q ss_pred             CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        249 QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       249 kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      +||+||+|.+.+.|.+|++. +||++|.|+.|+|....
T Consensus       320 kgfGfi~f~~~~~ar~a~e~-lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  320 KGFGFITFVNKEDARKALEQ-LNGFELAGRLIKVSVVT  356 (549)
T ss_pred             cCcceEEEecHHHHHHHHHH-hccceecCceEEEEEee
Confidence            79999999999999999998 79999999999987654

>KOG0117|consensus

Probab=98.93  E-value=4.3e-09  Score=101.11  Aligned_cols=76  Identities=20%  Similarity=0.390  Sum_probs=68.5

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEE-CCeeEEEE
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVIL-GGRRLNIK  283 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i-~G~~L~V~  283 (327)
                      ...+.+|||.||.++.|++|..+|++.|+|-+++++.+      +|||||+|.+.+.|+.|++. ||+.+| .|+.|.|.
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~-lnn~Eir~GK~igvc  159 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKE-LNNYEIRPGKLLGVC  159 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHH-hhCccccCCCEeEEE
Confidence            56689999999999999999999999999999999874      89999999999999999997 788877 57888887


Q ss_pred             eccC
Q psy14139        284 WGRA  287 (327)
Q Consensus       284 ~ak~  287 (327)
                      .+-.
T Consensus       160 ~Sva  163 (506)
T KOG0117|consen  160 VSVA  163 (506)
T ss_pred             Eeee
Confidence            6643

>KOG0131|consensus

Probab=98.89  E-value=3.4e-09  Score=91.07  Aligned_cols=74  Identities=31%  Similarity=0.469  Sum_probs=68.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ...|||||||+..++++-|.++|-+.|.|.++++.++      +||||++|.++++|+-|++- +|.+.+.|++|+|.-+
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAiki-ln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKI-LNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHH-HHHHHhcCceeEEEec
Confidence            3479999999999999999999999999999999874      79999999999999999996 7999999999999876


Q ss_pred             c
Q psy14139        286 R  286 (327)
Q Consensus       286 k  286 (327)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            6

>KOG0109|consensus

Probab=98.88  E-value=3.2e-10  Score=103.62  Aligned_cols=77  Identities=25%  Similarity=0.494  Sum_probs=71.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQAN  290 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~  290 (327)
                      +..++|+||||.+..+..+|+..|.+||.+.++.|+  ++++||.|.-.+.|..|+.. |++.++.|++++|..+.++-+
T Consensus        76 k~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv--kdy~fvh~d~~eda~~air~-l~~~~~~gk~m~vq~stsrlr  152 (346)
T KOG0109|consen   76 KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV--KDYAFVHFDRAEDAVEAIRG-LDNTEFQGKRMHVQLSTSRLR  152 (346)
T ss_pred             CCccccccCCCCccccCHHHhhhhcccCCceeeeee--cceeEEEEeeccchHHHHhc-ccccccccceeeeeeeccccc
Confidence            456899999999999999999999999999999999  88999999999999999998 799999999999999876543

>KOG0126|consensus

Probab=98.87  E-value=3.1e-10  Score=97.38  Aligned_cols=75  Identities=28%  Similarity=0.487  Sum_probs=69.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      .+..-|||||||.+++|.||.-.|++||+|..|.++++      +||||+.|++..+.--|+.. +||+.|.|+.|+|.-
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN-~NGiki~gRtirVDH  111 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDN-LNGIKILGRTIRVDH  111 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEec-cCCceecceeEEeee
Confidence            45579999999999999999999999999999999985      79999999999999999998 799999999999975


Q ss_pred             cc
Q psy14139        285 GR  286 (327)
Q Consensus       285 ak  286 (327)
                      ..
T Consensus       112 v~  113 (219)
T KOG0126|consen  112 VS  113 (219)
T ss_pred             cc
Confidence            44

>KOG0108|consensus

Probab=98.85  E-value=5.4e-09  Score=102.70  Aligned_cols=77  Identities=23%  Similarity=0.465  Sum_probs=72.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      .++||||+|.+++|++|.++|+..|.|.+++++.+      +||||++|.+.+.|+.|++. |||..+.|++|+|.|+..
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~-lNg~~~~gr~l~v~~~~~   97 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRN-LNGAEFNGRKLRVNYASN   97 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHh-cCCcccCCceEEeecccc
Confidence            79999999999999999999999999999999985      79999999999999999997 899999999999999987


Q ss_pred             CCCC
Q psy14139        288 QANR  291 (327)
Q Consensus       288 ~~~~  291 (327)
                      ...+
T Consensus        98 ~~~~  101 (435)
T KOG0108|consen   98 RKNA  101 (435)
T ss_pred             cchh
Confidence            6653

>KOG4206|consensus

Probab=98.83  E-value=1.3e-08  Score=90.36  Aligned_cols=76  Identities=26%  Similarity=0.545  Sum_probs=70.5

Q ss_pred             cEEEEcCCCCCCCHHHHHH----HHhhcCCeEEEEEec---CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        214 TTLYVGNLGDKLTEQDLRD----HFYQFGEIRSVTILS---KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~----~F~~fG~I~~v~i~~---~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      .||||.||++.+..++|+.    +|++||+|..|....   -+|-|||.|.+.++|-.|+.+ ++|..+-|++++|.+|+
T Consensus        10 ~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~-l~gfpFygK~mriqyA~   88 (221)
T KOG4206|consen   10 GTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRA-LQGFPFYGKPMRIQYAK   88 (221)
T ss_pred             ceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHH-hcCCcccCchhheeccc
Confidence            4999999999999999988    999999999999875   389999999999999999998 79999999999999999


Q ss_pred             CCCC
Q psy14139        287 AQAN  290 (327)
Q Consensus       287 ~~~~  290 (327)
                      .+..
T Consensus        89 s~sd   92 (221)
T KOG4206|consen   89 SDSD   92 (221)
T ss_pred             Cccc
Confidence            7764

>KOG0127|consensus

Probab=98.82  E-value=1.1e-08  Score=100.46  Aligned_cols=77  Identities=30%  Similarity=0.498  Sum_probs=71.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      .-.|.|.|||..+.+.+|+.+|+.||.|..|.|...     .|||||+|....+|+.|++. +|+..|+|++|-|.||-+
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~-~N~~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEF-FNGNKIDGRPVAVDWAVD  195 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHh-ccCceecCceeEEeeecc
Confidence            358999999999999999999999999999999864     59999999999999999997 799999999999999987


Q ss_pred             CCC
Q psy14139        288 QAN  290 (327)
Q Consensus       288 ~~~  290 (327)
                      +..
T Consensus       196 Kd~  198 (678)
T KOG0127|consen  196 KDT  198 (678)
T ss_pred             ccc
Confidence            654

>KOG0146|consensus

Probab=98.82  E-value=4.3e-09  Score=95.32  Aligned_cols=80  Identities=30%  Similarity=0.565  Sum_probs=70.8

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec-----CCCeEEEEeCCHHHHHHHHHHhcCCeEECC--eeEEEEec
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS-----KQQCAFIQYTSRPAAEAAVEHSFNKVILGG--RRLNIKWG  285 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~-----~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G--~~L~V~~a  285 (327)
                      .++||||-|...-+|+|++.+|..||.|.++.+++     .+|||||.|.+..+|..||.++.....+.|  ..|.|+++
T Consensus        19 drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~A   98 (371)
T KOG0146|consen   19 DRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKFA   98 (371)
T ss_pred             chhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEec
Confidence            37999999999999999999999999999999987     489999999999999999998544466777  68999999


Q ss_pred             cCCCCCC
Q psy14139        286 RAQANRG  292 (327)
Q Consensus       286 k~~~~~~  292 (327)
                      +..+.+.
T Consensus        99 DTdkER~  105 (371)
T KOG0146|consen   99 DTDKERT  105 (371)
T ss_pred             cchHHHH
Confidence            9877653

>KOG0124|consensus

Probab=98.75  E-value=6.6e-09  Score=97.61  Aligned_cols=69  Identities=33%  Similarity=0.620  Sum_probs=65.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      +.+|||.+..++.|+.||..|..||.|++|.+..      +++||||+|+-.+.|.-|++. +||..++|+.|+|.
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEq-MNg~mlGGRNiKVg  188 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ-MNGQMLGGRNIKVG  188 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHH-hccccccCcccccc
Confidence            7999999999999999999999999999999875      489999999999999999998 59999999999994

>KOG0127|consensus

Probab=98.70  E-value=6.4e-08  Score=95.16  Aligned_cols=79  Identities=29%  Similarity=0.529  Sum_probs=69.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHh----cCC-eEECCee
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHS----FNK-VILGGRR  279 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~----l~g-~~i~G~~  279 (327)
                      ....++||.|||.+++|++|.++|++||+|..+.++.+      +|+|||.|.+..+|..++++.    -.| +.+.|+.
T Consensus       290 ~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~  369 (678)
T KOG0127|consen  290 TEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRL  369 (678)
T ss_pred             cccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccE
Confidence            33489999999999999999999999999999988763      799999999999999999863    134 8899999


Q ss_pred             EEEEeccCCC
Q psy14139        280 LNIKWGRAQA  289 (327)
Q Consensus       280 L~V~~ak~~~  289 (327)
                      |+|..+-++.
T Consensus       370 Lkv~~Av~Rk  379 (678)
T KOG0127|consen  370 LKVTLAVTRK  379 (678)
T ss_pred             EeeeeccchH
Confidence            9999987654

>smart00361 RRM_1 RNA recognition motif

Probab=98.68  E-value=7.7e-08  Score=71.19  Aligned_cols=55  Identities=24%  Similarity=0.504  Sum_probs=48.2

Q ss_pred             HHHHHHHHh----hcCCeEEEE-E-ec-------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        227 EQDLRDHFY----QFGEIRSVT-I-LS-------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       227 e~~Lr~~F~----~fG~I~~v~-i-~~-------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      +++|+++|+    +||.|.++. | +.       .+|+|||+|.+.++|++|+.. ++|..+.|+.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~-l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVD-LNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHH-hCCCEECCEEEEe
Confidence            578899998    999999985 3 22       379999999999999999997 7999999999886

>KOG0146|consensus

Probab=98.66  E-value=2.4e-08  Score=90.48  Aligned_cols=81  Identities=22%  Similarity=0.443  Sum_probs=73.6

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      +.++.++|||-.||.+..+.+|..+|-.||.|.+.++..+      +.|+||.|++..+|+.||.+ +||..|+-++|+|
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqA-MNGFQIGMKRLKV  359 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQA-MNGFQIGMKRLKV  359 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHH-hcchhhhhhhhhh
Confidence            4567899999999999999999999999999999888653      78999999999999999998 5999999999999


Q ss_pred             EeccCCCC
Q psy14139        283 KWGRAQAN  290 (327)
Q Consensus       283 ~~ak~~~~  290 (327)
                      .+.+|+..
T Consensus       360 QLKRPkda  367 (371)
T KOG0146|consen  360 QLKRPKDA  367 (371)
T ss_pred             hhcCcccc
Confidence            99888753

>KOG0131|consensus

Probab=98.65  E-value=4.7e-08  Score=84.15  Aligned_cols=80  Identities=31%  Similarity=0.516  Sum_probs=70.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEE-EEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSV-TILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v-~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      .+|||+||.+++.|..|.+.|+.||.|.+. .+++      .++||||.|++.+++.+|+++ ++|..+.++++.|.++.
T Consensus        97 anlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s-~ngq~l~nr~itv~ya~  175 (203)
T KOG0131|consen   97 ANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGS-MNGQYLCNRPITVSYAF  175 (203)
T ss_pred             ccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHH-hccchhcCCceEEEEEE
Confidence            799999999999999999999999998663 3333      368999999999999999997 69999999999999998


Q ss_pred             CCCCCCCC
Q psy14139        287 AQANRGED  294 (327)
Q Consensus       287 ~~~~~~~~  294 (327)
                      .+..++..
T Consensus       176 k~~~kg~~  183 (203)
T KOG0131|consen  176 KKDTKGER  183 (203)
T ss_pred             ecCCCccc
Confidence            87776643

>KOG0123|consensus

Probab=98.52  E-value=2.6e-07  Score=89.72  Aligned_cols=77  Identities=25%  Similarity=0.533  Sum_probs=69.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCC
Q psy14139        215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQAN  290 (327)
Q Consensus       215 tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~  290 (327)
                      .+||-||+++++..+|.++|+.||+|.++++..+    +|+ ||+|++.++|.+|++. +||..+.|+.|.|.....+..
T Consensus        78 ~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~-~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen   78 LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEK-LNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHH-hcCcccCCCeeEEeeccchhh
Confidence            3999999999999999999999999999999874    788 9999999999999996 799999999999988777666


Q ss_pred             CCC
Q psy14139        291 RGE  293 (327)
Q Consensus       291 ~~~  293 (327)
                      +..
T Consensus       156 r~~  158 (369)
T KOG0123|consen  156 REA  158 (369)
T ss_pred             hcc
Confidence            543

>KOG1457|consensus

Probab=98.51  E-value=9.8e-07  Score=78.35  Aligned_cols=80  Identities=25%  Similarity=0.419  Sum_probs=66.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec--C-----CCeEEEEeCCHHHHHHHHHHhcCCeEEC---CeeE
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS--K-----QQCAFIQYTSRPAAEAAVEHSFNKVILG---GRRL  280 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~--~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~---G~~L  280 (327)
                      ..++||||.|||.++.-.+|..+|..|-.-+...+..  .     +.+|||+|.+...|+.|+.+ |||+.++   +..|
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamna-LNGvrFDpE~~stL  110 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNA-LNGVRFDPETGSTL  110 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHH-hcCeeeccccCcee
Confidence            4578999999999999999999999985555444332  2     36899999999999999996 8999997   5789


Q ss_pred             EEEeccCCCCC
Q psy14139        281 NIKWGRAQANR  291 (327)
Q Consensus       281 ~V~~ak~~~~~  291 (327)
                      ++.++++..++
T Consensus       111 hiElAKSNtK~  121 (284)
T KOG1457|consen  111 HIELAKSNTKR  121 (284)
T ss_pred             EeeehhcCccc
Confidence            99999976654

>KOG0415|consensus

Probab=98.50  E-value=3.2e-07  Score=86.14  Aligned_cols=78  Identities=26%  Similarity=0.497  Sum_probs=70.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ...-|||-.|.+-++.++|.-+|+.||.|.++.|+++      -.+|||+|.+.++.|+|.-. ++++.|+.++|.|.|+
T Consensus       238 PeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFK-MdNvLIDDrRIHVDFS  316 (479)
T KOG0415|consen  238 PENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFK-MDNVLIDDRRIHVDFS  316 (479)
T ss_pred             CcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhh-hcceeeccceEEeehh
Confidence            3458999999999999999999999999999999986      37999999999999999998 4889999999999998


Q ss_pred             cCCCC
Q psy14139        286 RAQAN  290 (327)
Q Consensus       286 k~~~~  290 (327)
                      .+-.+
T Consensus       317 QSVsk  321 (479)
T KOG0415|consen  317 QSVSK  321 (479)
T ss_pred             hhhhh
Confidence            76443

>KOG4205|consensus

Probab=98.47  E-value=1.7e-07  Score=88.60  Aligned_cols=94  Identities=24%  Similarity=0.444  Sum_probs=79.1

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      +..+||||+|+++++++.|+++|++||+|..+.++.+      ++|+||+|++.+...+++..  .-+.|+|+.|.++-+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~--~~h~~dgr~ve~k~a   82 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA--RTHKLDGRSVEPKRA   82 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc--cccccCCccccceec
Confidence            4589999999999999999999999999999999874      79999999999888888763  667899999999999


Q ss_pred             cCCCCCCCCcc--cccccccCCCCCC
Q psy14139        286 RAQANRGEDTA--ELKVRLEPVPGLP  309 (327)
Q Consensus       286 k~~~~~~~~~~--~~~~~~~pv~Glp  309 (327)
                      .++..+.....  .+.+++  |.|+|
T Consensus        83 v~r~~~~~~~~~~~tkkiF--vGG~~  106 (311)
T KOG4205|consen   83 VSREDQTKVGRHLRTKKIF--VGGLP  106 (311)
T ss_pred             cCcccccccccccceeEEE--ecCcC
Confidence            88876655433  244556  78885

>KOG0123|consensus

Probab=98.44  E-value=5.9e-07  Score=87.29  Aligned_cols=73  Identities=27%  Similarity=0.515  Sum_probs=67.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC---CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK---QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQAN  290 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~---kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~  290 (327)
                      .+||||   ++++|..|.+.|+++|.+.++++.++   -|||||+|.+.++|++|+.+ +|...+.|++|+|.|+...+.
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~-~n~~~~~~~~~rim~s~rd~~   77 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDT-MNFDVLKGKPIRIMWSQRDPS   77 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHH-cCCcccCCcEEEeehhccCCc
Confidence            479999   89999999999999999999999875   58999999999999999998 699999999999999876553

>KOG0110|consensus

Probab=98.41  E-value=2.5e-07  Score=93.53  Aligned_cols=81  Identities=26%  Similarity=0.498  Sum_probs=73.8

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      .+...+.|.|.|||...+-.+|+.+|..||.|.+|+|...      +|||||.|-+..+|.+|+.+ |....+.|+.|.+
T Consensus       609 ~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~a-l~STHlyGRrLVL  687 (725)
T KOG0110|consen  609 KKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDA-LGSTHLYGRRLVL  687 (725)
T ss_pred             cccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHh-hcccceechhhhe
Confidence            3455789999999999999999999999999999999864      89999999999999999998 5799999999999


Q ss_pred             EeccCCCC
Q psy14139        283 KWGRAQAN  290 (327)
Q Consensus       283 ~~ak~~~~  290 (327)
                      .|++....
T Consensus       688 EwA~~d~~  695 (725)
T KOG0110|consen  688 EWAKSDNT  695 (725)
T ss_pred             ehhccchH
Confidence            99987654

>KOG4212|consensus

Probab=98.40  E-value=8.4e-07  Score=85.38  Aligned_cols=76  Identities=25%  Similarity=0.426  Sum_probs=67.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHh-hcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFY-QFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~-~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ...+++||.|||.+....+|+++|. +-|+|+.|.++.+     ++||.|+|.+++.+++|++. +|...++|++|.|+-
T Consensus        42 ~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~-lnk~~~~GR~l~vKE  120 (608)
T KOG4212|consen   42 ARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEK-LNKYEVNGRELVVKE  120 (608)
T ss_pred             cccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHH-hhhccccCceEEEec
Confidence            3446799999999999999999996 4799999999874     89999999999999999998 799999999999986


Q ss_pred             ccC
Q psy14139        285 GRA  287 (327)
Q Consensus       285 ak~  287 (327)
                      ...
T Consensus       121 d~d  123 (608)
T KOG4212|consen  121 DHD  123 (608)
T ss_pred             cCc
Confidence            543

>KOG0110|consensus

Probab=98.37  E-value=1.1e-06  Score=89.12  Aligned_cols=72  Identities=31%  Similarity=0.495  Sum_probs=67.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC---------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK---------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~---------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ++|||.||+.+.+.+++..+|...|.|.++.|...         .|||||+|.+.++|+.|++. ++|..|+|+.|.|++
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~-lqgtvldGH~l~lk~  594 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKA-LQGTVLDGHKLELKI  594 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHH-hcCceecCceEEEEe
Confidence            34999999999999999999999999999988764         29999999999999999998 699999999999999


Q ss_pred             cc
Q psy14139        285 GR  286 (327)
Q Consensus       285 ak  286 (327)
                      +.
T Consensus       595 S~  596 (725)
T KOG0110|consen  595 SE  596 (725)
T ss_pred             cc
Confidence            88

>KOG0116|consensus

Probab=98.36  E-value=8.6e-07  Score=86.85  Aligned_cols=76  Identities=28%  Similarity=0.455  Sum_probs=67.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCC------CeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ------QCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~k------g~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      ..+|||.|||.++++.+|++.|.+||.|+...|....      .||||+|.+.++++.|+.+  +-..+++++|.|+--+
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A--sp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA--SPLEIGGRKLNVEEKR  365 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc--CccccCCeeEEEEecc
Confidence            4569999999999999999999999999998886633      8999999999999999996  6889999999999877


Q ss_pred             CCCC
Q psy14139        287 AQAN  290 (327)
Q Consensus       287 ~~~~  290 (327)
                      +...
T Consensus       366 ~~~~  369 (419)
T KOG0116|consen  366 PGFR  369 (419)
T ss_pred             cccc
Confidence            6443

>KOG4660|consensus

Probab=98.30  E-value=9.6e-07  Score=87.33  Aligned_cols=72  Identities=28%  Similarity=0.427  Sum_probs=66.6

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec-CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS-KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~-~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      .+....+|+|-|||..+++++|+.+|+.||+|+.|+.-+ .++..||+|-+...|++|+++ +++..+.|+.|+
T Consensus        71 ~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~-l~~~~~~~~~~k  143 (549)
T KOG4660|consen   71 KDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKA-LNRREIAGKRIK  143 (549)
T ss_pred             ccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHH-HHHHHhhhhhhc
Confidence            466678999999999999999999999999999998876 479999999999999999998 799999999888

>KOG4208|consensus

Probab=98.30  E-value=2.9e-06  Score=74.52  Aligned_cols=80  Identities=23%  Similarity=0.365  Sum_probs=69.8

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhc-CCeEEEEEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeE
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQF-GEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRL  280 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~f-G~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L  280 (327)
                      |.+....-+||+.+|..+.|..+..+|.+| |.+..+++.+      ++|||||+|++.+-|+-|++.| |+..+.|+.|
T Consensus        44 p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETM-NNYLl~e~lL  122 (214)
T KOG4208|consen   44 PEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETM-NNYLLMEHLL  122 (214)
T ss_pred             CccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHh-hhhhhhhhee
Confidence            445556789999999999999999999998 6777778755      3799999999999999999984 9999999999


Q ss_pred             EEEeccCC
Q psy14139        281 NIKWGRAQ  288 (327)
Q Consensus       281 ~V~~ak~~  288 (327)
                      .+.+-.|.
T Consensus       123 ~c~vmppe  130 (214)
T KOG4208|consen  123 ECHVMPPE  130 (214)
T ss_pred             eeEEeCch
Confidence            99887776

>KOG0124|consensus

Probab=98.27  E-value=1.6e-06  Score=81.73  Aligned_cols=74  Identities=27%  Similarity=0.483  Sum_probs=67.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      +....+||..+.++++|+||+..|+.||+|.++.+.+      ++||+||+|.+..+-..|+.. +|-+.++|+-|+|--
T Consensus       208 k~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAias-MNlFDLGGQyLRVGk  286 (544)
T KOG0124|consen  208 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS-MNLFDLGGQYLRVGK  286 (544)
T ss_pred             HhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhh-cchhhcccceEeccc
Confidence            4557999999999999999999999999999999976      489999999999999999998 599999999999954


Q ss_pred             c
Q psy14139        285 G  285 (327)
Q Consensus       285 a  285 (327)
                      +
T Consensus       287 ~  287 (544)
T KOG0124|consen  287 C  287 (544)
T ss_pred             c
Confidence            4

>KOG1190|consensus

Probab=98.22  E-value=1.3e-05  Score=76.89  Aligned_cols=78  Identities=27%  Similarity=0.400  Sum_probs=70.7

Q ss_pred             ccEEEEcCCCC-CCCHHHHHHHHhhcCCeEEEEEecC-CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCC
Q psy14139        213 ITTLYVGNLGD-KLTEQDLRDHFYQFGEIRSVTILSK-QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQAN  290 (327)
Q Consensus       213 ~~tLfVgnLp~-~ite~~Lr~~F~~fG~I~~v~i~~~-kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~  290 (327)
                      +..|.|.||.. .+|.+.|..+|+-||.|..|+|+.+ +.-|.|.|.+...|+-|+++ |+|..+.|++|+|.++|...-
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~h-L~g~~l~gk~lrvt~SKH~~v  375 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEH-LEGHKLYGKKLRVTLSKHTNV  375 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHH-hhcceecCceEEEeeccCccc
Confidence            57888999986 7999999999999999999999986 57899999999999999998 799999999999999987654


Q ss_pred             C
Q psy14139        291 R  291 (327)
Q Consensus       291 ~  291 (327)
                      .
T Consensus       376 q  376 (492)
T KOG1190|consen  376 Q  376 (492)
T ss_pred             c
Confidence            4

>KOG0106|consensus

Probab=98.21  E-value=1.8e-06  Score=77.24  Aligned_cols=72  Identities=24%  Similarity=0.481  Sum_probs=66.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      ..+|||+||....+.+|..+|..||.|..+.+.  .+|+||.|.+..+|+.|+.. +++.++.|..+.|.|++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--~gf~fv~fed~rda~Dav~~-l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--NGFGFVEFEDPRDADDAVHD-LDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--cccceeccCchhhhhcccch-hcCceecceeeeeeccccc
Confidence            468999999999999999999999999998877  78889999999999999997 7999999988999999864

>KOG4205|consensus

Probab=98.15  E-value=2.8e-06  Score=80.41  Aligned_cols=79  Identities=22%  Similarity=0.406  Sum_probs=69.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ....+|||+||.+++|++++++|.+||.|..+.++.+      ++|+||.|.++++++++..  ..-+.|+|+.+.|+-|
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~--~~f~~~~gk~vevkrA  173 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL--QKFHDFNGKKVEVKRA  173 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc--cceeeecCceeeEeec
Confidence            4569999999999999999999999999988877753      7999999999999999987  3778999999999999


Q ss_pred             cCCCCCC
Q psy14139        286 RAQANRG  292 (327)
Q Consensus       286 k~~~~~~  292 (327)
                      -|+....
T Consensus       174 ~pk~~~~  180 (311)
T KOG4205|consen  174 IPKEVMQ  180 (311)
T ss_pred             cchhhcc
Confidence            8876543

>KOG4212|consensus

Probab=98.13  E-value=5e-06  Score=80.18  Aligned_cols=75  Identities=24%  Similarity=0.376  Sum_probs=66.6

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ..+..++|||.|||.+.|...|++-|..||.+....|+.+ +.-+.|.|.+.+.||+|+.. +++..++|+.|+|.+
T Consensus       532 aarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~GkskGVVrF~s~edAEra~a~-Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  532 AARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMENGKSKGVVRFFSPEDAERACAL-MNGSRLDGRNIKVTY  607 (608)
T ss_pred             ccccccEEEEecCCccccHHHHHHHHHhccceehhhhhccCCccceEEecCHHHHHHHHHH-hccCcccCceeeeee
Confidence            3466789999999999999999999999999999888543 55569999999999999985 799999999999986

>KOG4661|consensus

Probab=98.12  E-value=5.6e-06  Score=82.03  Aligned_cols=76  Identities=18%  Similarity=0.456  Sum_probs=69.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      .++|||++|+..+.-.+|+.+|++||+|.-.+|+.+      +.|+||++.+.++|.+.|+. |+...|.|+.|.|.-++
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~h-LHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEH-LHRTELHGRMISVEKAK  483 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHH-hhhhhhcceeeeeeecc
Confidence            479999999999999999999999999999888864      68999999999999999998 79999999999998887


Q ss_pred             CCC
Q psy14139        287 AQA  289 (327)
Q Consensus       287 ~~~  289 (327)
                      ...
T Consensus       484 NEp  486 (940)
T KOG4661|consen  484 NEP  486 (940)
T ss_pred             cCc
Confidence            543

>KOG0533|consensus

Probab=98.10  E-value=1.2e-05  Score=73.41  Aligned_cols=79  Identities=29%  Similarity=0.457  Sum_probs=69.2

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      +...++|+|.||+..+.++||+++|..||.++.+-|..+     .|.|-|.|..+++|+.|++. ++++.++|+++++..
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~-~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKK-YNGVALDGRPMKIEI  158 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHH-hcCcccCCceeeeEE
Confidence            444579999999999999999999999998888877764     58999999999999999998 799999999988877


Q ss_pred             ccCCC
Q psy14139        285 GRAQA  289 (327)
Q Consensus       285 ak~~~  289 (327)
                      ..+..
T Consensus       159 i~~~~  163 (243)
T KOG0533|consen  159 ISSPS  163 (243)
T ss_pred             ecCcc
Confidence            65544

>KOG2202|consensus

Probab=98.07  E-value=1.8e-06  Score=78.18  Aligned_cols=117  Identities=26%  Similarity=0.448  Sum_probs=76.4

Q ss_pred             cccccc-cccccCCCCCCCCCCCCCCCCCCCCcccCccccCCCCCChhHHHHHHhhcCCCCCCCC-CCCCccEEEEcCCC
Q psy14139        145 HICSFW-VKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPP-EDKTITTLYVGNLG  222 (327)
Q Consensus       145 ~~C~ff-~kG~C~rG~~Cpy~H~~p~~~~~~l~~qni~dr~~G~~~p~~~k~~~~~~~~p~~~~p-~d~~~~tLfVgnLp  222 (327)
                      .-|+|+ ..|.|..|+.|.-.|++|+-..      .+              +++.....|...++ .|.     -...++
T Consensus        16 v~c~fy~k~gacR~gdrcsR~h~kpt~s~------t~--------------ll~nmyq~P~~~~~~~d~-----~~~~~~   70 (260)
T KOG2202|consen   16 VNCSFYFKIGACRHGDRCSRLHEKPTFSQ------TV--------------LLKNMYQNPENSWERRDA-----QGQFLT   70 (260)
T ss_pred             cccchHHhhcccccccHHHHhhcccccch------HH--------------HHHHHHhCCCCCchhhhh-----cccccc
Confidence            468888 6799999999999999887321      11              11112222322211 110     011111


Q ss_pred             CCC-------CHHHHHHHHh-hcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        223 DKL-------TEQDLRDHFY-QFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       223 ~~i-------te~~Lr~~F~-~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      +.-       .-++|...|+ +||+|++++|..+     .|-+||.|...++|++|++. ||+.+++|++|...+..-
T Consensus        71 de~~q~~~defyEd~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~-lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   71 DEELQRHEDEFYEDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALED-LNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHH-HcCccccCCcceeeecCc
Confidence            110       0123333344 8999999987664     68899999999999999997 899999999999888653

>KOG4454|consensus

Probab=98.01  E-value=2.7e-06  Score=75.41  Aligned_cols=71  Identities=24%  Similarity=0.214  Sum_probs=64.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      +||||+|+...++|+-|.++|-+-|.|..|.|...    ..||||.|.++.+..-|++ ++||..+.++.++|++-
T Consensus        10 rtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~-L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen   10 RTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQ-LENGDDLEEDEEQRTLR   84 (267)
T ss_pred             hHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhh-hcccchhccchhhcccc
Confidence            79999999999999999999999999999988763    4699999999999999998 58999999988887764

>KOG1548|consensus

Probab=98.01  E-value=2.3e-05  Score=73.69  Aligned_cols=84  Identities=24%  Similarity=0.343  Sum_probs=70.2

Q ss_pred             CCCCCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEE--------EEEecC-----CCeEEEEeCCHHHHHHHHHHhcC
Q psy14139        205 LDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRS--------VTILSK-----QQCAFIQYTSRPAAEAAVEHSFN  271 (327)
Q Consensus       205 ~~~p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~--------v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~  271 (327)
                      ...++...++++||+|||.++|-+++.++|+++|-|..        |++-.+     +|=|.+.|-.+++.+-|++. |+
T Consensus       126 ~~~~~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~i-lD  204 (382)
T KOG1548|consen  126 WFNPEPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKI-LD  204 (382)
T ss_pred             ccCcccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHH-hC
Confidence            33345667789999999999999999999999998754        333332     68899999999999999995 89


Q ss_pred             CeEECCeeEEEEeccCCC
Q psy14139        272 KVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       272 g~~i~G~~L~V~~ak~~~  289 (327)
                      +..+.|+.|+|..|+-+.
T Consensus       205 e~~~rg~~~rVerAkfq~  222 (382)
T KOG1548|consen  205 EDELRGKKLRVERAKFQM  222 (382)
T ss_pred             cccccCcEEEEehhhhhh
Confidence            999999999999987544

>KOG2135|consensus

Probab=97.99  E-value=7.7e-06  Score=79.59  Aligned_cols=78  Identities=23%  Similarity=0.339  Sum_probs=63.3

Q ss_pred             CccEEEEcCCCCCCC-HHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCC
Q psy14139        212 TITTLYVGNLGDKLT-EQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQAN  290 (327)
Q Consensus       212 ~~~tLfVgnLp~~it-e~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~  290 (327)
                      +.+.|-+.-.+..++ -.+|..+|.+||+|..|.+-.....|.|+|.++.+|-.|..  ..+..|+|+.|+|.|.++.+.
T Consensus       371 dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~~a~vTF~t~aeag~a~~--s~~avlnnr~iKl~whnps~~  448 (526)
T KOG2135|consen  371 DHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSLHAVVTFKTRAEAGEAYA--SHGAVLNNRFIKLFWHNPSPV  448 (526)
T ss_pred             ccchhhhhccCCCCchHhhhhhhhhhcCccccccccCchhhheeeeeccccccchhc--cccceecCceeEEEEecCCcc
Confidence            334555555555443 47899999999999999998888889999999999977775  599999999999999998664


Q ss_pred             C
Q psy14139        291 R  291 (327)
Q Consensus       291 ~  291 (327)
                      .
T Consensus       449 t  449 (526)
T KOG2135|consen  449 T  449 (526)
T ss_pred             c
Confidence            3

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

Probab=97.86  E-value=3.6e-05  Score=53.87  Aligned_cols=52  Identities=29%  Similarity=0.518  Sum_probs=45.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHH
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAV  266 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~  266 (327)
                      +.|-|.|.+.+.. +++..+|.+||+|..+.+.....+.+|.|.++.+|++|+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCCCCcEEEEEECCHHHHHhhC
Confidence            5678889998776 455669999999999999888999999999999999984

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

Probab=97.70  E-value=0.00012  Score=58.64  Aligned_cols=68  Identities=24%  Similarity=0.476  Sum_probs=43.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHh-cC---CeEECCeeEEE
Q psy14139        215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHS-FN---KVILGGRRLNI  282 (327)
Q Consensus       215 tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~-l~---g~~i~G~~L~V  282 (327)
                      -|.|.+++..++.++|++.|++||.|..|.+.....-|||.|.+.++|+.|++.+ ..   ++.+.+..+.+
T Consensus         3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~   74 (105)
T PF08777_consen    3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTL   74 (105)
T ss_dssp             EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEE
T ss_pred             EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEE
Confidence            5788889999999999999999999999999998899999999999999999874 12   35555655444

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

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

Probab=97.68  E-value=0.0002  Score=54.51  Aligned_cols=69  Identities=19%  Similarity=0.316  Sum_probs=46.6

Q ss_pred             cEEEEcCCCCCCCHHHHH----HHHhhcC-CeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        214 TTLYVGNLGDKLTEQDLR----DHFYQFG-EIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr----~~F~~fG-~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      +.|||.|||.+..-..|+    .++..+| .|.+|.    .+.|+|.|.+.+.|++|.+. ++|-.+-|..|.|.+..-
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----~~tAilrF~~~~~A~RA~KR-megEdVfG~kI~v~~~~~   76 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----GGTAILRFPNQEFAERAQKR-MEGEDVFGNKISVSFSPK   76 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------TT-EEEEESSHHHHHHHHHH-HTT--SSSS--EEESS--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----CCEEEEEeCCHHHHHHHHHh-hcccccccceEEEEEcCC
Confidence            579999999988876654    5555665 666663    78999999999999999998 599999999999988643

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

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.65  E-value=0.00025  Score=56.22  Aligned_cols=72  Identities=24%  Similarity=0.256  Sum_probs=54.7

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEE-------------EecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCe-
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVT-------------ILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGR-  278 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~-------------i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~-  278 (327)
                      .+.+.|.|.|+..+ ..|.++|++||+|.+..             +.....+-.|+|+++.+|.+|+..  ||..++|. 
T Consensus         6 ~~wVtVFGfp~~~~-~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~--NG~i~~g~~   82 (100)
T PF05172_consen    6 ETWVTVFGFPPSAS-NQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK--NGTIFSGSL   82 (100)
T ss_dssp             CCEEEEE---GGGH-HHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT--TTEEETTCE
T ss_pred             CeEEEEEccCHHHH-HHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh--CCeEEcCcE
Confidence            35788889999854 67778999999998875             455688999999999999999984  99999985 


Q ss_pred             eEEEEeccC
Q psy14139        279 RLNIKWGRA  287 (327)
Q Consensus       279 ~L~V~~ak~  287 (327)
                      .+-|.|.++
T Consensus        83 mvGV~~~~~   91 (100)
T PF05172_consen   83 MVGVKPCDP   91 (100)
T ss_dssp             EEEEEE-HH
T ss_pred             EEEEEEcHH
Confidence            566888754

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG4209|consensus

Probab=97.58  E-value=0.0002  Score=65.34  Aligned_cols=77  Identities=21%  Similarity=0.370  Sum_probs=68.4

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      +.+.+++||||+....+-+++..+|+.+|.|..+.|..+      +++|||.|.+.+.++.|+.  +++..+.|+.+.|.
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~--l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK--LDGSEIPGPAIEVT  175 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh--cCCcccccccceee
Confidence            345579999999999888889999999999988877653      7899999999999999998  69999999999999


Q ss_pred             eccCC
Q psy14139        284 WGRAQ  288 (327)
Q Consensus       284 ~ak~~  288 (327)
                      |-+-.
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            87765

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

Probab=97.52  E-value=0.00057  Score=53.88  Aligned_cols=75  Identities=24%  Similarity=0.277  Sum_probs=60.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhc--CCeEEEEEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECC----eeEE
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQF--GEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGG----RRLN  281 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~f--G~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G----~~L~  281 (327)
                      |||=|.|||...+.++|.+.+...  |...-+-+..      +.|||||.|.+.+.|.+..+. ++|..+..    +...
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~-f~g~~w~~~~s~Kvc~   80 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKA-FNGKKWPNFNSKKVCE   80 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHH-HcCCccccCCCCcEEE
Confidence            689999999999999999988753  5554444433      379999999999999999997 78887763    5678


Q ss_pred             EEeccCCC
Q psy14139        282 IKWGRAQA  289 (327)
Q Consensus       282 V~~ak~~~  289 (327)
                      |.||+-++
T Consensus        81 i~yAriQG   88 (97)
T PF04059_consen   81 ISYARIQG   88 (97)
T ss_pred             EehhHhhC
Confidence            88887654

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

>KOG4206|consensus

Probab=97.50  E-value=0.00045  Score=61.72  Aligned_cols=76  Identities=18%  Similarity=0.359  Sum_probs=66.7

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec-CCCeEEEEeCCHHHHHHHHHHhcCCeEEC-CeeEEEEecc
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS-KQQCAFIQYTSRPAAEAAVEHSFNKVILG-GRRLNIKWGR  286 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~-~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~-G~~L~V~~ak  286 (327)
                      .+....||+.|||.+.+.+.+..+|.+|+..+.|+++. ..+.|||+|.++..|..|..+ +++..+- ...++|.+++
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~~~iAfve~~~d~~a~~a~~~-lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQA-LQGFKITKKNTMQITFAK  220 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCCCceeEEecchhhhhHHHhhh-hccceeccCceEEecccC
Confidence            45678999999999999999999999999999999998 579999999999999999988 6776665 6778887764

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.37  E-value=0.00037  Score=65.55  Aligned_cols=72  Identities=24%  Similarity=0.536  Sum_probs=59.9

Q ss_pred             cEEEEcCCCCCCCHHH----H--HHHHhhcCCeEEEEEecC-------CCe--EEEEeCCHHHHHHHHHHhcCCeEECCe
Q psy14139        214 TTLYVGNLGDKLTEQD----L--RDHFYQFGEIRSVTILSK-------QQC--AFIQYTSRPAAEAAVEHSFNKVILGGR  278 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~----L--r~~F~~fG~I~~v~i~~~-------kg~--aFV~F~~~~~Ae~A~~~~l~g~~i~G~  278 (327)
                      .-+||-+|++.+..++    |  .++|.+||.|..|.|...       .+.  .||+|.+.++|.+++.+ .+|..++|+
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~-vDgs~~DGr  193 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAE-VDGSLLDGR  193 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHH-hccccccCc
Confidence            3678999998766555    2  478999999999998763       233  39999999999999998 799999999


Q ss_pred             eEEEEecc
Q psy14139        279 RLNIKWGR  286 (327)
Q Consensus       279 ~L~V~~ak  286 (327)
                      .|+..++.
T Consensus       194 ~lkatYGT  201 (480)
T COG5175         194 VLKATYGT  201 (480)
T ss_pred             eEeeecCc
Confidence            99999874

>KOG0106|consensus

Probab=97.30  E-value=0.00017  Score=64.61  Aligned_cols=72  Identities=32%  Similarity=0.535  Sum_probs=63.5

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ..+...+.|-+++..+++.+|.++|.++|++....+  ..+++||+|.+.++|..|+.. +++..+.|+.|.+..
T Consensus        96 ~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--~~~~~~v~Fs~~~da~ra~~~-l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen   96 SRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--RRNFAFVEFSEQEDAKRALEK-LDGKKLNGRRISVEK  167 (216)
T ss_pred             ccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--hccccceeehhhhhhhhcchh-ccchhhcCceeeecc
Confidence            345678999999999999999999999999955444  689999999999999999997 799999999999943

>KOG1457|consensus

Probab=97.29  E-value=0.0003  Score=62.84  Aligned_cols=64  Identities=23%  Similarity=0.442  Sum_probs=53.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec--CCCeEEEEeCCHHHHHHHHHHhcCCeEE
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS--KQQCAFIQYTSRPAAEAAVEHSFNKVIL  275 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~--~kg~aFV~F~~~~~Ae~A~~~~l~g~~i  275 (327)
                      ....||||.||..+++|++|+.+|+.|.....++|-.  ....||+.|++.+.|..|+.+ ++|..|
T Consensus       208 ~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~-lqg~~~  273 (284)
T KOG1457|consen  208 RACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNH-LQGNLL  273 (284)
T ss_pred             hhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHH-hhccee
Confidence            4457999999999999999999999997666665544  356799999999999999987 576554

>KOG1190|consensus

Probab=97.27  E-value=0.00027  Score=68.00  Aligned_cols=77  Identities=21%  Similarity=0.345  Sum_probs=62.7

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCe-EEEEEec-CCCeEEEEeCCHHHHHHHHHHhcCCeEECC-eeEEEEeccC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEI-RSVTILS-KQQCAFIQYTSRPAAEAAVEHSFNKVILGG-RRLNIKWGRA  287 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I-~~v~i~~-~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G-~~L~V~~ak~  287 (327)
                      +...+|...|+|.+++|++++.+|.+-|.. +..+... ++.+|++.+.+.++|-.|+.. ++...+++ ..|+|.|+++
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~kd~kmal~q~~sveeA~~ali~-~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQKDRKMALPQLESVEEAIQALID-LHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeeecCCCcceeecccCChhHhhhhccc-cccccCCCCceEEEEeecc
Confidence            445799999999999999999999998865 4444433 689999999999999999986 56666655 5899999876


Q ss_pred             C
Q psy14139        288 Q  288 (327)
Q Consensus       288 ~  288 (327)
                      .
T Consensus       491 ~  491 (492)
T KOG1190|consen  491 T  491 (492)
T ss_pred             c
Confidence            3

>KOG0112|consensus

Probab=97.22  E-value=0.00022  Score=74.38  Aligned_cols=85  Identities=35%  Similarity=0.520  Sum_probs=73.8

Q ss_pred             CCCCCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECC--eeEEE
Q psy14139        205 LDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGG--RRLNI  282 (327)
Q Consensus       205 ~~~p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G--~~L~V  282 (327)
                      +..+.....+.++|++|+.......|...|..||.|..|.+-+...||+|.|++...|..|+.. +-|.-++|  ++|+|
T Consensus       447 lG~~kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq~yayi~yes~~~aq~a~~~-~rgap~G~P~~r~rv  525 (975)
T KOG0112|consen  447 LGQPKSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQPYAYIQYESPPAAQAATHD-MRGAPLGGPPRRLRV  525 (975)
T ss_pred             ccccccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccCCcceeeecccCccchhhHHH-HhcCcCCCCCccccc
Confidence            3333445568999999999999999999999999999999999999999999999999999998 58888887  78999


Q ss_pred             EeccCCCC
Q psy14139        283 KWGRAQAN  290 (327)
Q Consensus       283 ~~ak~~~~  290 (327)
                      .++.+...
T Consensus       526 dla~~~~~  533 (975)
T KOG0112|consen  526 DLASPPGA  533 (975)
T ss_pred             ccccCCCC
Confidence            99876543

>KOG4211|consensus

Probab=97.07  E-value=0.0029  Score=62.34  Aligned_cols=72  Identities=22%  Similarity=0.343  Sum_probs=60.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      +..-|-+.+||++.|++||.++|+..+ |+++.+.+.    .|-|||+|.+.+++++|++.  +...+..+-|.|--+.
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alkk--dR~~mg~RYIEVf~~~   84 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALKK--DRESMGHRYIEVFTAG   84 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHHh--hHHHhCCceEEEEccC
Confidence            334566689999999999999999886 888777764    68999999999999999984  7788888888887663

>smart00356 ZnF_C3H1 zinc finger

Probab=97.05  E-value=0.00048  Score=40.81  Aligned_cols=24  Identities=29%  Similarity=1.006  Sum_probs=21.7

Q ss_pred             CccccccccccccCCCCCCCCCCC
Q psy14139        143 RPHICSFWVKGECRRGEECPYRHE  166 (327)
Q Consensus       143 ~~~~C~ff~kG~C~rG~~Cpy~H~  166 (327)
                      +..+|.+|..|.|.+|+.|+|.|.
T Consensus         3 k~~~C~~~~~g~C~~g~~C~~~H~   26 (27)
T smart00356        3 KTELCKFFKRGYCPYGDRCKFAHP   26 (27)
T ss_pred             CCCcCcCccCCCCCCCCCcCCCCc
Confidence            456899999999999999999996

>KOG0120|consensus

Probab=96.97  E-value=0.0008  Score=67.26  Aligned_cols=96  Identities=22%  Similarity=0.445  Sum_probs=78.6

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ....+|||+||..+++..++++...||.+....++.      +++|||.+|.+..-...|++. +||..+.+..|.|..+
T Consensus       288 ~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~ag-LnGm~lgd~~lvvq~A  366 (500)
T KOG0120|consen  288 SPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAG-LNGMQLGDKKLVVQRA  366 (500)
T ss_pred             ccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcc-cchhhhcCceeEeehh
Confidence            346899999999999999999999999999988775      389999999999999999998 7999999999999998


Q ss_pred             cCCCCCCCCcccccccccCCCCCCC
Q psy14139        286 RAQANRGEDTAELKVRLEPVPGLPG  310 (327)
Q Consensus       286 k~~~~~~~~~~~~~~~~~pv~Glp~  310 (327)
                      -...........  ..-.+++||+.
T Consensus       367 ~~g~~~~~~~~~--~~~~~~~~i~~  389 (500)
T KOG0120|consen  367 IVGASNANVNFN--ISQSQVPGIPL  389 (500)
T ss_pred             hccchhccccCC--ccccccccchh
Confidence            877665443222  01114677763

>KOG0147|consensus

Probab=96.88  E-value=0.00053  Score=68.16  Aligned_cols=82  Identities=22%  Similarity=0.437  Sum_probs=72.2

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      ++.+..+|+|+..|...+++.+|.++|+.+|.|..|+++.+      +|.|||+|.+.++...|+.  |.|..+.|.+|.
T Consensus       174 ~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia--LsGqrllg~pv~  251 (549)
T KOG0147|consen  174 PEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA--LSGQRLLGVPVI  251 (549)
T ss_pred             chHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh--hcCCcccCceeE
Confidence            45567789999999999999999999999999999999874      7999999999999999996  799999999999


Q ss_pred             EEeccCCCCC
Q psy14139        282 IKWGRAQANR  291 (327)
Q Consensus       282 V~~ak~~~~~  291 (327)
                      |......+.+
T Consensus       252 vq~sEaeknr  261 (549)
T KOG0147|consen  252 VQLSEAEKNR  261 (549)
T ss_pred             ecccHHHHHH
Confidence            9876554443

>KOG0226|consensus

Probab=96.86  E-value=0.0013  Score=59.79  Aligned_cols=75  Identities=16%  Similarity=0.411  Sum_probs=63.3

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      +.....||.|.|..+++.+.|-..|.+|-.-...++++      .+||+||.|.+..++..|+.. ++|..++.++|+++
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmre-m~gkyVgsrpiklR  265 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMRE-MNGKYVGSRPIKLR  265 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHh-hcccccccchhHhh
Confidence            34457999999999999999999999986555555554      479999999999999999998 59999999998875


Q ss_pred             ec
Q psy14139        284 WG  285 (327)
Q Consensus       284 ~a  285 (327)
                      =+
T Consensus       266 kS  267 (290)
T KOG0226|consen  266 KS  267 (290)
T ss_pred             hh
Confidence            33

>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=96.59  E-value=0.00056  Score=40.96  Aligned_cols=23  Identities=30%  Similarity=1.077  Sum_probs=17.4

Q ss_pred             ccccccccc-cccCCCCCCCCCCC
Q psy14139        144 PHICSFWVK-GECRRGEECPYRHE  166 (327)
Q Consensus       144 ~~~C~ff~k-G~C~rG~~Cpy~H~  166 (327)
                      ..+|.+|.+ |.|.+|+.|.|.|.
T Consensus         3 ~~~C~~f~~~g~C~~G~~C~f~H~   26 (27)
T PF00642_consen    3 TKLCRFFMRTGTCPFGDKCRFAHG   26 (27)
T ss_dssp             SSB-HHHHHTS--TTGGGSSSBSS
T ss_pred             cccChhhccCCccCCCCCcCccCC
Confidence            568999955 99999999999995

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....

>KOG0129|consensus

Probab=96.42  E-value=0.014  Score=57.99  Aligned_cols=56  Identities=20%  Similarity=0.401  Sum_probs=46.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec---------CCC---eEEEEeCCHHHHHHHHHHh
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS---------KQQ---CAFIQYTSRPAAEAAVEHS  269 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~---------~kg---~aFV~F~~~~~Ae~A~~~~  269 (327)
                      .+.+|||+||.+++|+.|...|..||.+. |....         .+|   |+|+.|+++.+...-+.++
T Consensus       259 S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  259 SRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             ccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            46899999999999999999999999753 33331         256   9999999998888877765

>KOG1855|consensus

Probab=96.34  E-value=0.0042  Score=60.32  Aligned_cols=58  Identities=28%  Similarity=0.375  Sum_probs=52.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-------------------CCeEEEEeCCHHHHHHHHHH
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-------------------QQCAFIQYTSRPAAEAAVEH  268 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-------------------kg~aFV~F~~~~~Ae~A~~~  268 (327)
                      -..++|.+-|||.+-.-+.|.++|+.+|.|++|+|+..                   +-||+|+|...++|.+|.+-
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~  305 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAREL  305 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHh
Confidence            46789999999999888999999999999999999862                   56999999999999999985

>KOG1456|consensus

Probab=96.17  E-value=0.025  Score=54.20  Aligned_cols=76  Identities=20%  Similarity=0.226  Sum_probs=62.2

Q ss_pred             ccEEEEcCCC--CCCCHHHHHHHHhhcCCeEEEEEecCCC-eEEEEeCCHHHHHHHHHHhcCCeEEC-C-eeEEEEeccC
Q psy14139        213 ITTLYVGNLG--DKLTEQDLRDHFYQFGEIRSVTILSKQQ-CAFIQYTSRPAAEAAVEHSFNKVILG-G-RRLNIKWGRA  287 (327)
Q Consensus       213 ~~tLfVgnLp--~~ite~~Lr~~F~~fG~I~~v~i~~~kg-~aFV~F~~~~~Ae~A~~~~l~g~~i~-G-~~L~V~~ak~  287 (327)
                      ++-|.+.=|.  ..|+-+.|..+-...|+|..|.|.+..+ .|.|+|++.+.|++|.++ +||..|. | ..|+|++|+|
T Consensus       120 N~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~a-lNGADIYsGCCTLKIeyAkP  198 (494)
T KOG1456|consen  120 NKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAA-LNGADIYSGCCTLKIEYAKP  198 (494)
T ss_pred             CeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhh-cccccccccceeEEEEecCc
Confidence            4455555444  3788899999999999999999987654 599999999999999998 7987664 4 7899999998


Q ss_pred             CC
Q psy14139        288 QA  289 (327)
Q Consensus       288 ~~  289 (327)
                      ..
T Consensus       199 ~r  200 (494)
T KOG1456|consen  199 TR  200 (494)
T ss_pred             ce
Confidence            65

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.02  E-value=0.03  Score=47.23  Aligned_cols=71  Identities=21%  Similarity=0.412  Sum_probs=51.4

Q ss_pred             cEEEEcCCCC------CCCH---HHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        214 TTLYVGNLGD------KLTE---QDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       214 ~tLfVgnLp~------~ite---~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      .|+.|.-+.+      ...+   .+|-+.|..||++.-++++.  +.-+|+|.+-++|-+|+.  ++|..++|+.|+|+.
T Consensus        28 aTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~--~~mwVTF~dg~sALaals--~dg~~v~g~~l~i~L  103 (146)
T PF08952_consen   28 ATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG--DTMWVTFRDGQSALAALS--LDGIQVNGRTLKIRL  103 (146)
T ss_dssp             -EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET--TCEEEEESSCHHHHHHHH--GCCSEETTEEEEEEE
T ss_pred             ceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC--CeEEEEECccHHHHHHHc--cCCcEECCEEEEEEe
Confidence            3666654441      2332   36777888999999888885  578999999999999998  699999999999987


Q ss_pred             ccCC
Q psy14139        285 GRAQ  288 (327)
Q Consensus       285 ak~~  288 (327)
                      ..|.
T Consensus       104 Ktpd  107 (146)
T PF08952_consen  104 KTPD  107 (146)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            5544

; PDB: 1UFW_A 2DNR_A.

>KOG0120|consensus

Probab=95.91  E-value=0.022  Score=57.18  Aligned_cols=60  Identities=20%  Similarity=0.376  Sum_probs=50.6

Q ss_pred             HHHHHHHhhcCCeEEEEEecC---------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        228 QDLRDHFYQFGEIRSVTILSK---------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       228 ~~Lr~~F~~fG~I~~v~i~~~---------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      ++++.-+++||.|.+|.+.+.         .|..||+|.+.+++++|.++ |+|..++|+.+...+-...
T Consensus       424 Edvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~-L~GrKF~nRtVvtsYydeD  492 (500)
T KOG0120|consen  424 EDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEE-LTGRKFANRTVVASYYDED  492 (500)
T ss_pred             HHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHH-ccCceeCCcEEEEEecCHH
Confidence            345666778999999998764         58899999999999999998 7999999999888775543

>KOG1456|consensus

Probab=95.90  E-value=0.051  Score=52.18  Aligned_cols=77  Identities=23%  Similarity=0.340  Sum_probs=67.8

Q ss_pred             CCccEEEEcCCCC-CCCHHHHHHHHhhcCCeEEEEEecC-CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        211 KTITTLYVGNLGD-KLTEQDLRDHFYQFGEIRSVTILSK-QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       211 ~~~~tLfVgnLp~-~ite~~Lr~~F~~fG~I~~v~i~~~-kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      .+..-+-|.+|.. .++-+.|..+|..||.|+.|+.++. .+-|.|+..+..+.++|+.. ||+..+-|.+|.|..++..
T Consensus       285 ~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~h-Lnn~~lfG~kl~v~~SkQ~  363 (494)
T KOG1456|consen  285 APGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTH-LNNIPLFGGKLNVCVSKQN  363 (494)
T ss_pred             CCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHH-hccCccccceEEEeecccc
Confidence            4456888999987 6778899999999999999999875 58999999999999999998 7998889999999988754

>KOG1995|consensus

Probab=95.84  E-value=0.0098  Score=56.62  Aligned_cols=80  Identities=26%  Similarity=0.375  Sum_probs=66.9

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEE--------EEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSV--------TILS------KQQCAFIQYTSRPAAEAAVEHSFNKVIL  275 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v--------~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i  275 (327)
                      .....++||-+|+..+++++|.++|.++|.|..=        .|-.      .++-|.|+|.+..+|+.|+. ++++..+
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~-~~agkdf  141 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIE-WFAGKDF  141 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhh-hhccccc
Confidence            3456799999999999999999999999987542        2211      27899999999999999998 5899999


Q ss_pred             CCeeEEEEeccCCCC
Q psy14139        276 GGRRLNIKWGRAQAN  290 (327)
Q Consensus       276 ~G~~L~V~~ak~~~~  290 (327)
                      .|..|+|..+..+..
T Consensus       142 ~gn~ikvs~a~~r~~  156 (351)
T KOG1995|consen  142 CGNTIKVSLAERRTG  156 (351)
T ss_pred             cCCCchhhhhhhccC
Confidence            999999988876653

>KOG4676|consensus

Probab=95.71  E-value=0.039  Score=53.21  Aligned_cols=67  Identities=13%  Similarity=0.372  Sum_probs=55.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC---------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK---------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       215 tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~---------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      -|-|.||.+.++.+.++.+|...|+|..+.+.+.         ...+||.|.+...+..|..  |-..++=++.|.|.
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh--Ltntvfvdraliv~   84 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH--LTNTVFVDRALIVR   84 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh--hccceeeeeeEEEE
Confidence            7889999999999999999999999999998773         5789999999999998864  45555555555443

>KOG4210|consensus

Probab=95.70  E-value=0.0076  Score=56.73  Aligned_cols=76  Identities=28%  Similarity=0.527  Sum_probs=66.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      +-++|++|+..+++++|+.+|..+|.|..+++...      +++|||.|.....+..++..  +...+.++++.+....+
T Consensus       186 ~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~  263 (285)
T KOG4210|consen  186 TIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND--QTRSIGGRPLRLEEDEP  263 (285)
T ss_pred             cceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc--ccCcccCcccccccCCC
Confidence            44559999999999999999999999999998763      69999999999999988863  67788999999998888


Q ss_pred             CCCC
Q psy14139        288 QANR  291 (327)
Q Consensus       288 ~~~~  291 (327)
                      .+..
T Consensus       264 ~~~~  267 (285)
T KOG4210|consen  264 RPKS  267 (285)
T ss_pred             Cccc
Confidence            7654

>KOG3152|consensus

Probab=95.68  E-value=0.0066  Score=55.35  Aligned_cols=66  Identities=21%  Similarity=0.449  Sum_probs=56.0

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCC------------------CeEEEEeCCHHHHHHHHHHhcCCe
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ------------------QCAFIQYTSRPAAEAAVEHSFNKV  273 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~k------------------g~aFV~F~~~~~Ae~A~~~~l~g~  273 (327)
                      ..--+|+++||+.+....|+++|+.||+|-.|-+.+..                  .-|.|+|.+...|...+.. ||+.
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~-Lnn~  151 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAEL-LNNT  151 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHH-hCCC
Confidence            34579999999999999999999999999999887621                  1267999999999988875 8999


Q ss_pred             EECCe
Q psy14139        274 ILGGR  278 (327)
Q Consensus       274 ~i~G~  278 (327)
                      .|+|+
T Consensus       152 ~Iggk  156 (278)
T KOG3152|consen  152 PIGGK  156 (278)
T ss_pred             ccCCC
Confidence            99885

>KOG4211|consensus

Probab=95.68  E-value=0.038  Score=54.72  Aligned_cols=70  Identities=20%  Similarity=0.287  Sum_probs=54.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEE-EEEec-----CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRS-VTILS-----KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~-v~i~~-----~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      -.+-+.+||..++++||.++|+-.--+.. |.++.     ..+-|||.|++.+.||.|+..  +...|+.+-|.|.-+
T Consensus       104 ~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r--hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  104 GVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR--HRENIGHRYIEVFRS  179 (510)
T ss_pred             ceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH--HHHhhccceEEeehh
Confidence            46777899999999999999986643333 22222     257899999999999999985  777788787777654

>KOG1548|consensus

Probab=95.67  E-value=0.048  Score=51.81  Aligned_cols=75  Identities=16%  Similarity=0.331  Sum_probs=60.0

Q ss_pred             CCccEEEEcCCCC----CCC-------HHHHHHHHhhcCCeEEEEEe--cCCCeEEEEeCCHHHHHHHHHHhcCCeEECC
Q psy14139        211 KTITTLYVGNLGD----KLT-------EQDLRDHFYQFGEIRSVTIL--SKQQCAFIQYTSRPAAEAAVEHSFNKVILGG  277 (327)
Q Consensus       211 ~~~~tLfVgnLp~----~it-------e~~Lr~~F~~fG~I~~v~i~--~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G  277 (327)
                      +..+++.+.|+=.    .-+       +++|++--++||.|.+|.|.  +..|.+-|.|.+.++|..+++. ++|..++|
T Consensus       263 r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~-m~GR~fdg  341 (382)
T KOG1548|consen  263 RADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQT-MDGRWFDG  341 (382)
T ss_pred             cCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHH-hcCeeecc
Confidence            4457888887742    222       34566667799999999998  5689999999999999999996 79999999


Q ss_pred             eeEEEEecc
Q psy14139        278 RRLNIKWGR  286 (327)
Q Consensus       278 ~~L~V~~ak  286 (327)
                      +.|....-.
T Consensus       342 Rql~A~i~D  350 (382)
T KOG1548|consen  342 RQLTASIWD  350 (382)
T ss_pred             eEEEEEEeC
Confidence            999876543

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=95.57  E-value=0.049  Score=48.00  Aligned_cols=64  Identities=16%  Similarity=0.264  Sum_probs=49.2

Q ss_pred             CHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcC--CeEECCeeEEEEeccCCCC
Q psy14139        226 TEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFN--KVILGGRRLNIKWGRAQAN  290 (327)
Q Consensus       226 te~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~--g~~i~G~~L~V~~ak~~~~  290 (327)
                      ....|+++|..|+.+..+..+++-+-..|.|.+.+.|..|... ++  +..+.|..++|.++.+...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sFrRi~v~f~~~~~A~~~r~~-l~~~~~~~~g~~l~~yf~~~~~~   73 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSFRRIRVVFESPESAQRARQL-LHWDGTSFNGKRLRVYFGQPTPI   73 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTTTEEEEE-SSTTHHHHHHHT-ST--TSEETTEE-EEE----SS-
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCCCEEEEEeCCHHHHHHHHHH-hcccccccCCCceEEEEcccccc
Confidence            3478999999999999999999888899999999999999986 68  8999999999999965543

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG1365|consensus

Probab=95.00  E-value=0.06  Score=51.85  Aligned_cols=73  Identities=23%  Similarity=0.261  Sum_probs=56.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCC-eEE--EEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGE-IRS--VTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~-I~~--v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ..-|-+.+||.+.+-++|.++|..|.. |..  |.|+.+     .|-|||+|.+.+.|..|+... +....+++-|.|.-
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~-hk~~mk~RYiEvfp  358 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKC-HKKLMKSRYIEVFP  358 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHH-HHhhcccceEEEee
Confidence            446778999999999999999999864 433  555543     688999999999999998875 44555778888865


Q ss_pred             cc
Q psy14139        285 GR  286 (327)
Q Consensus       285 ak  286 (327)
                      +.
T Consensus       359 ~S  360 (508)
T KOG1365|consen  359 CS  360 (508)
T ss_pred             cc
Confidence            43

>KOG2193|consensus

Probab=94.87  E-value=0.018  Score=55.89  Aligned_cols=79  Identities=29%  Similarity=0.378  Sum_probs=62.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCCCC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRG  292 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~~~  292 (327)
                      ..||+|||.+..+..+|+.+|...---.+-.++...+++||.+.+...|.+|++.+.....+.|.++.|..+-++..+.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkqrs   80 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQRS   80 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeeecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHHHh
Confidence            4789999999999999999997542112233455689999999999999999998444468999999998887776553

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.79  E-value=0.14  Score=42.97  Aligned_cols=75  Identities=23%  Similarity=0.384  Sum_probs=57.2

Q ss_pred             CCCCccEEEEcCCCCCCCH----HHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        209 EDKTITTLYVGNLGDKLTE----QDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite----~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      .++...||.|.=|..++.-    ..|...++.||+|.+|.+. .+.-|.|.|.+..+|=+|+.+ ++. ...|..++..|
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-GrqsavVvF~d~~SAC~Av~A-f~s-~~pgtm~qCsW  158 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-GRQSAVVVFKDITSACKAVSA-FQS-RAPGTMFQCSW  158 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-CCceEEEEehhhHHHHHHHHh-hcC-CCCCceEEeec
Confidence            4556679999877665442    3455567789999999766 456799999999999999998 454 56778888888


Q ss_pred             cc
Q psy14139        285 GR  286 (327)
Q Consensus       285 ak  286 (327)
                      ..
T Consensus       159 qq  160 (166)
T PF15023_consen  159 QQ  160 (166)
T ss_pred             cc
Confidence            54

>KOG0129|consensus

Probab=94.52  E-value=0.15  Score=50.91  Aligned_cols=56  Identities=23%  Similarity=0.319  Sum_probs=51.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHh-hcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHH
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFY-QFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEH  268 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~-~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~  268 (327)
                      .+|+|||+||.-++-++|-.+|. -||.|..+-|-.+      +|-|=|+|.+-.+--+|+.+
T Consensus       370 rrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  370 RRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            47999999999999999999998 6999999988765      78899999999999999986

>KOG4285|consensus

Probab=94.41  E-value=0.17  Score=47.42  Aligned_cols=68  Identities=24%  Similarity=0.259  Sum_probs=54.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCe-eEEEEe
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGR-RLNIKW  284 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~-~L~V~~  284 (327)
                      .=+-|.++++.-. ..|..+|++||+|.+.....+..+-+|.|.++.+|.+|+..  +|.+|+|. .|-|+-
T Consensus       198 ~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~~ngNwMhirYssr~~A~KALsk--ng~ii~g~vmiGVkp  266 (350)
T KOG4285|consen  198 TWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTPSNGNWMHIRYSSRTHAQKALSK--NGTIIDGDVMIGVKP  266 (350)
T ss_pred             ceEEEeccCccch-hHHHHHHHhhCeeeeeecCCCCceEEEEecchhHHHHhhhh--cCeeeccceEEeeee
Confidence            3455567777544 45677899999999888777788999999999999999984  99999984 455654

>KOG0112|consensus

Probab=94.30  E-value=0.015  Score=61.22  Aligned_cols=76  Identities=26%  Similarity=0.431  Sum_probs=62.3

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec-----CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS-----KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~-----~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ...+.|||+|||+..+++.+|+..|..+|.|.+|.|..     ...+|||.|.+...+-.|...+ .+..|..-.+++.+
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~-s~~~I~~g~~r~gl  447 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEE-SGPLIGNGTHRIGL  447 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhh-cCCccccCcccccc
Confidence            35678999999999999999999999999999998865     3579999999999999999874 55555444555555


Q ss_pred             cc
Q psy14139        285 GR  286 (327)
Q Consensus       285 ak  286 (327)
                      +.
T Consensus       448 G~  449 (975)
T KOG0112|consen  448 GQ  449 (975)
T ss_pred             cc
Confidence            53

>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type

Probab=94.05  E-value=0.035  Score=30.35  Aligned_cols=18  Identities=39%  Similarity=1.161  Sum_probs=15.5

Q ss_pred             ccccccccccCCCCCCCCCC
Q psy14139        146 ICSFWVKGECRRGEECPYRH  165 (327)
Q Consensus       146 ~C~ff~kG~C~rG~~Cpy~H  165 (327)
                      .|.||..  |..++.|+|.|
T Consensus         1 ~Ck~~~~--C~~~~~C~f~H   18 (19)
T PF14608_consen    1 PCKFGPN--CTNGDNCPFSH   18 (19)
T ss_pred             CCcCcCC--CCCCCcCccCC
Confidence            4888874  99999999998

>KOG2314|consensus

Probab=93.75  E-value=0.16  Score=51.30  Aligned_cols=70  Identities=19%  Similarity=0.208  Sum_probs=55.2

Q ss_pred             cEEEEcCCCCCCC------HHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECC-eeEE
Q psy14139        214 TTLYVGNLGDKLT------EQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGG-RRLN  281 (327)
Q Consensus       214 ~tLfVgnLp~~it------e~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G-~~L~  281 (327)
                      .-++|.|+|.--.      ...|..+|+++|+|..+-+..+     +|+.|++|.+...|+.|++. +||..++- +.+.
T Consensus        59 ~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~-l~G~~ldknHtf~  137 (698)
T KOG2314|consen   59 SVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKS-LNGKRLDKNHTFF  137 (698)
T ss_pred             eEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHh-cccceecccceEE
Confidence            5788899986322      2346788999999998887743     79999999999999999998 78877764 6666


Q ss_pred             EEe
Q psy14139        282 IKW  284 (327)
Q Consensus       282 V~~  284 (327)
                      |..
T Consensus       138 v~~  140 (698)
T KOG2314|consen  138 VRL  140 (698)
T ss_pred             eeh
Confidence            654

>KOG0115|consensus

Probab=93.39  E-value=0.16  Score=46.45  Aligned_cols=56  Identities=23%  Similarity=0.396  Sum_probs=49.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHh
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHS  269 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~  269 (327)
                      ..|||.||+..++-+.+...|+.||+|..-.+..+     .+-++|.|...-.|.+|+..+
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~   92 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRC   92 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHh
Confidence            68999999999999999999999999987655543     467899999999999999875

>KOG2416|consensus

Probab=93.18  E-value=0.085  Score=53.41  Aligned_cols=77  Identities=19%  Similarity=0.246  Sum_probs=63.1

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhh-cCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEE---CCeeEEEEec
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQ-FGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL---GGRRLNIKWG  285 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~-fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i---~G~~L~V~~a  285 (327)
                      ......|||.||-.-+|.-.|+.++.. .|.|.+..|-+-+..+||.|.+.++|-.-..+ |+|+.+   +++.|.+.|+
T Consensus       441 ~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkIKShCyV~yss~eEA~atr~A-lhnV~WP~sNPK~L~adf~  519 (718)
T KOG2416|consen  441 KEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKIKSHCYVSYSSVEEAAATREA-LHNVQWPPSNPKHLIADFV  519 (718)
T ss_pred             CCccceEeeecccccchHHHHHHHHhhccCchHHHHHHHhhcceeEecccHHHHHHHHHH-HhccccCCCCCceeEeeec
Confidence            344568999999999999999999995 56677776666689999999999999999988 577665   3478999888


Q ss_pred             cC
Q psy14139        286 RA  287 (327)
Q Consensus       286 k~  287 (327)
                      ..
T Consensus       520 ~~  521 (718)
T KOG2416|consen  520 RA  521 (718)
T ss_pred             ch
Confidence            64

>KOG0105|consensus

Probab=93.01  E-value=0.98  Score=39.67  Aligned_cols=69  Identities=19%  Similarity=0.320  Sum_probs=58.2

Q ss_pred             CCCCCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEE
Q psy14139        205 LDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL  275 (327)
Q Consensus       205 ~~~p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i  275 (327)
                      -.+|...+.-.+.|.+||.+-+.++|+++..+-|.+....+..+ +.+.|.|...++.+-|+.. |....+
T Consensus       107 rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-g~GvV~~~r~eDMkYAvr~-ld~~~~  175 (241)
T KOG0105|consen  107 RGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-GVGVVEYLRKEDMKYAVRK-LDDQKF  175 (241)
T ss_pred             cCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-cceeeeeeehhhHHHHHHh-hccccc
Confidence            34566777789999999999999999999999999988877755 5899999999999999997 454443

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=92.89  E-value=0.67  Score=33.42  Aligned_cols=53  Identities=11%  Similarity=0.308  Sum_probs=42.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhc---CCeEEEEEecCCCeEEEEeCCHHHHHHHHHH
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQF---GEIRSVTILSKQQCAFIQYTSRPAAEAAVEH  268 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~f---G~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~  268 (327)
                      .+|+|.|+. +++.++|+.+|..|   .....|.++.+..| =|.|.+.+.|.+|+.+
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDtSc-Nvvf~d~~~A~~AL~~   61 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDTSC-NVVFKDEETAARALVA   61 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCCcE-EEEECCHHHHHHHHHc
Confidence            489999985 58889999999998   23467888877664 5679999999999875

>KOG4307|consensus

Probab=92.23  E-value=0.45  Score=49.25  Aligned_cols=70  Identities=16%  Similarity=0.235  Sum_probs=58.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeE-EEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIR-SVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~-~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      +-|-+.|+|.+++-+||-++|+-|-.+- +|++-.+     .|-+-|.|+++++|.+|... +++..|..+.|.+..
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~d-l~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMD-LDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhc-cccCcccceeEEEEe
Confidence            4677899999999999999999996553 4444332     57899999999999999997 799999999887754

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=91.44  E-value=0.81  Score=35.04  Aligned_cols=52  Identities=19%  Similarity=0.382  Sum_probs=38.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHH
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH  268 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~  268 (327)
                      .-+||+ +|.++...||.++|+.||.|. |..+. -.-|||....++.|..|+..
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~-dTSAfV~l~~r~~~~~v~~~   61 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIN-DTSAFVALHNRDQAKVVMNT   61 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEE-EEEEC-TTEEEEEECCCHHHHHHHHH
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEc-CCcEEEEeecHHHHHHHHHH
Confidence            345555 999999999999999999974 44443 45699999999999999886

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>KOG1996|consensus

Probab=90.98  E-value=0.74  Score=43.10  Aligned_cols=60  Identities=20%  Similarity=0.359  Sum_probs=49.0

Q ss_pred             HHHHHHHHhhcCCeEEEEEecC-------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        227 EQDLRDHFYQFGEIRSVTILSK-------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       227 e~~Lr~~F~~fG~I~~v~i~~~-------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      |+++++-..+||.|..|.|...       .---||+|+..++|-+|+-. +||..|+|+.++..|-.-
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~Vd-lnGRyFGGr~v~A~Fyn~  366 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVD-LNGRYFGGRVVSACFYNL  366 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHh-cCCceecceeeeheeccH
Confidence            4566777789999998877642       34589999999999999985 899999999888776543

>KOG4849|consensus

Probab=90.48  E-value=1.1  Score=43.01  Aligned_cols=65  Identities=22%  Similarity=0.289  Sum_probs=51.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcC--CeEEEEEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCee
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFG--EIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRR  279 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG--~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~  279 (327)
                      --+|||||-+.++++||.+....-|  .|.++++..      ++|||+|...+..+.++-++- |....|.|+.
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~Mei-LP~k~iHGQ~  153 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEI-LPTKTIHGQS  153 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHh-cccceecCCC
Confidence            4799999999999999998887666  344444433      489999999999888888874 7888888854

>KOG2068|consensus

Probab=89.92  E-value=0.11  Score=49.25  Aligned_cols=72  Identities=22%  Similarity=0.421  Sum_probs=54.9

Q ss_pred             cEEEEcCCCCCCCHHH-HH--HHHhhcCCeEEEEEecCC---------CeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        214 TTLYVGNLGDKLTEQD-LR--DHFYQFGEIRSVTILSKQ---------QCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~-Lr--~~F~~fG~I~~v~i~~~k---------g~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      .-+||-+|+..+..+. |+  ++|.+||.|.+|.+..+.         .-++|+|...++|..|+.. .+|..++|+.|+
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~-v~g~~~dg~~lk  156 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDD-VDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHH-hhhHHhhhhhhH
Confidence            3567777876554443 33  679999999999887632         2389999999999999998 599999988776


Q ss_pred             EEecc
Q psy14139        282 IKWGR  286 (327)
Q Consensus       282 V~~ak  286 (327)
                      ..++.
T Consensus       157 a~~gt  161 (327)
T KOG2068|consen  157 ASLGT  161 (327)
T ss_pred             HhhCC
Confidence            66653

>KOG0128|consensus

Probab=89.77  E-value=0.23  Score=52.30  Aligned_cols=77  Identities=10%  Similarity=0.131  Sum_probs=64.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      ...+||.|.|..-|.++++.+++.+|.+.+++++..     +|.|||.|.+..+|.++... .....+.-..+.|..+.|
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s-~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVAS-VDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhccc-chhhhhhhcCccccccCC
Confidence            368999999999999999999999999999987653     68999999999999999876 466666666777777666


Q ss_pred             CCC
Q psy14139        288 QAN  290 (327)
Q Consensus       288 ~~~  290 (327)
                      ...
T Consensus       815 ~~~  817 (881)
T KOG0128|consen  815 ERD  817 (881)
T ss_pred             ccc
Confidence            433

>KOG4574|consensus

Probab=88.14  E-value=0.69  Score=48.91  Aligned_cols=75  Identities=16%  Similarity=0.211  Sum_probs=63.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEE--CCeeEEEEeccCCCC
Q psy14139        215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL--GGRRLNIKWGRAQAN  290 (327)
Q Consensus       215 tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i--~G~~L~V~~ak~~~~  290 (327)
                      +.++.|.+-..+...|..+++.||.+.+.+.+++-..|.|.|.+.+.|-.|..+ ++|..+  .|-+.+|.+++.-+-
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N~alvs~~s~~sai~a~dA-l~gkevs~~g~Ps~V~~ak~~~~  376 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLNMALVSFSSVESAILALDA-LQGKEVSVTGAPSRVSFAKTLPM  376 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheecccccchhhhhHHHHHHHHhhhh-hcCCcccccCCceeEEecccccc
Confidence            455566677788889999999999999999999999999999999999999998 687654  577899999986543

>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=87.34  E-value=4.6  Score=32.54  Aligned_cols=63  Identities=17%  Similarity=0.197  Sum_probs=45.7

Q ss_pred             cEEEEcCCCC-CCCHHHHHHHHhhc-CCeEEEEEecC----CCeEEEEeCCHHHHHHHHHHhcCCeEECC
Q psy14139        214 TTLYVGNLGD-KLTEQDLRDHFYQF-GEIRSVTILSK----QQCAFIQYTSRPAAEAAVEHSFNKVILGG  277 (327)
Q Consensus       214 ~tLfVgnLp~-~ite~~Lr~~F~~f-G~I~~v~i~~~----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G  277 (327)
                      +++.|--.|. -++-++|..+.+.+ ..|..++|+++    +-.+.+.|.+.+.|...... +||..++.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~-fNGk~Fns   81 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEE-FNGKPFNS   81 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHH-hCCCccCC
Confidence            4444444554 55555666555555 46788899875    44799999999999999997 89988876

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

>KOG0128|consensus

Probab=87.33  E-value=0.035  Score=58.17  Aligned_cols=60  Identities=30%  Similarity=0.479  Sum_probs=52.4

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHH
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEAAVEH  268 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~  268 (327)
                      +.+...++||.||+..+.+.+|...|+.+|.+..+++..      -+|.|||.|...+.+.+|+.-
T Consensus       663 ~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f  728 (881)
T KOG0128|consen  663 EIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAF  728 (881)
T ss_pred             HHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhh
Confidence            336667999999999999999999999999998887762      279999999999999999873

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=85.71  E-value=1.3  Score=32.88  Aligned_cols=67  Identities=19%  Similarity=0.389  Sum_probs=38.7

Q ss_pred             EEEEc-CCCCCCCHHHHHHHHhhcCCe-----EEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        215 TLYVG-NLGDKLTEQDLRDHFYQFGEI-----RSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       215 tLfVg-nLp~~ite~~Lr~~F~~fG~I-----~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      +|||. |--..++..+|..++..-+.|     -.|.|.  ..|+||+-... .|+.+++. +++..+.|++++|+.|
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~--~~~S~vev~~~-~a~~v~~~-l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIF--DNFSFVEVPEE-VAEKVLEA-LNGKKIKGKKVRVERA   74 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE---SS-EEEEE-TT--HHHHHHH-HTT--SSS----EEE-
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEe--eeEEEEEECHH-HHHHHHHH-hcCCCCCCeeEEEEEC
Confidence            56663 233478888999999876544     445554  67889888654 77888887 6999999999999764

; PDB: 2G0C_A 3MOJ_B.

>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=85.08  E-value=2  Score=37.56  Aligned_cols=74  Identities=11%  Similarity=0.118  Sum_probs=49.0

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhh-cCCe---EEEEEecC--------CCeEEEEeCCHHHHHHHHHHhcCCeEECC--
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQ-FGEI---RSVTILSK--------QQCAFIQYTSRPAAEAAVEHSFNKVILGG--  277 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~-fG~I---~~v~i~~~--------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G--  277 (327)
                      ....|.|.+||+.++|+++.+.++. ++..   ..+.-...        -.-|||.|.+.+.+...... ++|..+-+  
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~-~~g~~F~D~k   84 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDR-FDGHVFVDSK   84 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHH-CTTEEEE-TT
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHh-cCCcEEECCC
Confidence            3469999999999999999987776 6655   34431111        35699999999999888887 79977643  


Q ss_pred             ---eeEEEEecc
Q psy14139        278 ---RRLNIKWGR  286 (327)
Q Consensus       278 ---~~L~V~~ak  286 (327)
                         .+-.|.+|-
T Consensus        85 g~~~~~~VE~Ap   96 (176)
T PF03467_consen   85 GNEYPAVVEFAP   96 (176)
T ss_dssp             S-EEEEEEEE-S
T ss_pred             CCCcceeEEEcc
Confidence               345676664

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.

>KOG4307|consensus

Probab=84.96  E-value=0.51  Score=48.88  Aligned_cols=73  Identities=16%  Similarity=0.133  Sum_probs=57.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEE-EEEec-----CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRS-VTILS-----KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~-v~i~~-----~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..--|||.+||..+++.++-++|...-.|++ |.+..     .++.|||.|...+++..|+.. -....++.+.|+|.-.
T Consensus       433 ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~-~~k~y~G~r~irv~si  511 (944)
T KOG4307|consen  433 AGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSV-KTKFYPGHRIIRVDSI  511 (944)
T ss_pred             ccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhc-ccccccCceEEEeech
Confidence            3468999999999999999999998777766 55543     268999999998888888764 4556666788888643

>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function

Probab=84.38  E-value=0.43  Score=31.48  Aligned_cols=12  Identities=58%  Similarity=1.351  Sum_probs=10.7

Q ss_pred             CCcccccCCcce
Q psy14139         24 GKECKICARPFT   35 (327)
Q Consensus        24 g~eckic~rpft   35 (327)
                      .+.|.+|.||||
T Consensus         8 ~K~C~~C~rpf~   19 (42)
T PF10013_consen    8 SKICPVCGRPFT   19 (42)
T ss_pred             CCcCcccCCcch
Confidence            478999999996

>KOG1365|consensus

Probab=81.43  E-value=1.7  Score=42.14  Aligned_cols=67  Identities=18%  Similarity=0.281  Sum_probs=49.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhc----CCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQF----GEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~f----G~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      --+-..+||.+.++.++.++|.+-    |..+.|-.+..     .|=|||.|..++.|+.|+..  +...++.+-|.+
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k--hrq~iGqRYIEl  237 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK--HRQNIGQRYIEL  237 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH--HHHHHhHHHHHH
Confidence            345568999999999999999632    34445544442     58899999999999999986  555565555544

>KOG4410|consensus

Probab=80.33  E-value=5  Score=37.58  Aligned_cols=50  Identities=16%  Similarity=0.240  Sum_probs=42.4

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCe-EEEEEecCCCeEEEEeCCHHHH
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEI-RSVTILSKQQCAFIQYTSRPAA  262 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I-~~v~i~~~kg~aFV~F~~~~~A  262 (327)
                      .+-+|++||+.++.-.||+..+.+.|-+ .++.+....+-+|+.|.++..+
T Consensus       330 ~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~iswkg~~~k~flh~~~~~~~  380 (396)
T KOG4410|consen  330 KTDIKLTNLSRDIRVKDLKSELRKRECTPMSISWKGHFGKCFLHFGNRKGV  380 (396)
T ss_pred             ccceeeccCccccchHHHHHHHHhcCCCceeEeeecCCcceeEecCCccCC
Confidence            4679999999999999999999888754 6777777889999999987554

>KOG0804|consensus

Probab=80.24  E-value=4.7  Score=39.98  Aligned_cols=67  Identities=19%  Similarity=0.303  Sum_probs=57.7

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhc-CCeEEEEEecC----CCeEEEEeCCHHHHHHHHHHhcCCeEECC
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQF-GEIRSVTILSK----QQCAFIQYTSRPAAEAAVEHSFNKVILGG  277 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~f-G~I~~v~i~~~----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G  277 (327)
                      +.+.+.|+|-.+|..++-.||-.+...| -.|.+++++++    +-.+.|.|.+.++|....+. +||..++.
T Consensus        71 ~~~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~e-fNGk~Fn~  142 (493)
T KOG0804|consen   71 ASSSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEE-FNGKQFNS  142 (493)
T ss_pred             CCCCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHH-cCCCcCCC
Confidence            3347899999999999999999988776 56889999885    45689999999999999998 89988876

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	327
2ytc_A	85	Solution Structure Of Rna Binding Domain In Pre-Mrn		3e-31
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-05
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		2e-05
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-04
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		2e-04
1x4g_A	109	Solution Structure Of Rrm Domain In Nucleolysin Tia		2e-04
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		2e-04
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		3e-04
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		3e-04
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		3e-04
3tp2_A	229	Crystal Structure Of The Splicing Factor Cwc2 From		5e-04
2dno_A	102	Solution Structure Of Rna Binding Domain In Trinucl		5e-04
1why_A	97	Solution Structure Of The Rna Recognition Motif Fro		7e-04
2dgq_A	108	Solution Structure Of The N-Terminal Rna Binding Do		7e-04
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		8e-04
3u1l_A	240	Structure Of The Mrna Splicing Complex Component Cw		8e-04

>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna- Splicing Factor Rbm22 Length = 85

Iteration: 1
 Score =  132 bits (331), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 56/78 (71%), Positives = 68/78 (87%)
Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH 268
           EDKTITTLYVG LGD +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +R AAE A E 
Sbjct: 8   EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEK 67
Query: 269 SFNKVILGGRRLNIKWGR 286
           SFNK+I+ GRRLN+KWGR
Sbjct: 68  SFNKLIVNGRRLNVKWGR 85

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 46/80 (57%), Gaps = 9/80 (11%)
Query: 213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI------LSKQQCAFIQYTSRPAAEAAV 266
           ++ +YVG++  +L E  +R  F  FG I+S+ +      +  +  AF++Y    AA+ A+
Sbjct: 28  MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
Query: 267 EHSFNKVILGGRRLNIKWGR 286
           E   N V+LGGR  NIK GR
Sbjct: 88  EQ-MNSVMLGGR--NIKVGR 104

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 44/77 (57%), Gaps = 9/77 (11%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTI------LSKQQCAFIQYTSRPAAEAAVEHS 269
           +YVG++  +L E  +R  F  FG I+S+ +      +  +  AF++Y    AA+ A+E  
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ- 74
Query: 270 FNKVILGGRRLNIKWGR 286
            N V+LGGR  NIK GR
Sbjct: 75  MNSVMLGGR--NIKVGR 89

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/77 (38%), Positives = 44/77 (57%), Gaps = 9/77 (11%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSV-----TILSKQQ-CAFIQYTSRPAAEAAVEHS 269
           +YVG++  +L E  +R  F  FG I+S+     ++  K +  AF++Y    AA+ A+E  
Sbjct: 15  VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 270 FNKVILGGRRLNIKWGR 286
            N V LGGR  NIK GR
Sbjct: 75  -NSVXLGGR--NIKVGR 88

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/65 (36%), Positives = 36/65 (55%), Gaps = 8/65 (12%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----SKQQCAFIQYTSRPA 261
           PP  +    L+VG L  + +E D+R  F  FG I   TIL     + + CAF++Y+S   
Sbjct: 12  PPSHRK---LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAE 68
Query: 262 AEAAV 266
           A+AA+
Sbjct: 69  AQAAI 73

>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar Length = 109

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/72 (26%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVI 274
           T+Y G +   LT+Q +R  F  FG+I  + +  ++  +F+++++  +A  A+  S N   
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIV-SVNGTT 85
Query: 275 LGGRRLNIKWGR 286
           + G  +   WG+
Sbjct: 86  IEGHVVKCYWGK 97

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 5/57 (8%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS-----KQQCAFIQYTSRPAAEAAVE 267
           L++G +  K TE D+R  F  FG+I    IL       + CAF+ +T+R  A+ A++
Sbjct: 98  LFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIK 154

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 208 PEDKTITT---LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEA 264
           P +KT T    L+VGNL   +TE+D +  F ++GE   V I   +   FI+  SR  AE 
Sbjct: 14  PGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEI 73
Query: 265 AVEHSFNKVILGGRRLNIKWG 285
           A +   +  IL  R L I++ 
Sbjct: 74  A-KAELDGTILKSRPLRIRFA 93

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 5/57 (8%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS-----KQQCAFIQYTSRPAAEAAVE 267
           L++G +  K TE D+R  F  FG+I    IL       + CAF+ +T+R  A+ A++
Sbjct: 98  LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK 154

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 5/57 (8%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS-----KQQCAFIQYTSRPAAEAAVE 267
           L++G +  K TE D+R  F  FG+I    IL       + CAF+ +T+R  A+ A++
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK 166

>pdb|3TP2|A Chain A, Crystal Structure Of The Splicing Factor Cwc2 From Yeast Length = 229

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 37/140 (26%), Positives = 56/140 (40%), Gaps = 16/140 (11%)
Query: 146 ICSFWVKGECRRGEECPYRHEKPTDPD-DPLADQNIKDRYYGVNDPVAEKLMARASTMPK 204
            C F+ KG C  G +C Y H  P + D   LA +      +G      EK       M  
Sbjct: 74  FCLFFAKGMCCLGPKCEYLHHIPDEEDIGKLALRTEVLDCFG-----REKFADYREDMGG 128
Query: 205 LDPPEDKTITTLYVGNLGDKLT---------EQDLRDHFYQFGEIRSVTILSKQQCAFIQ 255
           +     K   TLYVG +   L          E  +R  F + G+I  +  +  + C F++
Sbjct: 129 IGSFRKKN-KTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVK 187
Query: 256 YTSRPAAEAAVEHSFNKVIL 275
           +  +  AE A E   N+ +L
Sbjct: 188 FKYQANAEFAKEAMSNQTLL 207

>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide Repeat Containing 4 Variant Length = 102

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 7/88 (7%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----SKQQCAFIQYTSRPAAEAAVE--H 268
           L+VG LG + T++D+R  F  FG I   T+L     + + CAF+++ +   A+AA+   H
Sbjct: 15  LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
Query: 269 SFNKVILGGRRLNIKWGRAQANRGEDTA 296
           S   +      L +K+   +   G  + 
Sbjct: 75  SSRTLPGASSSLVVKFADTEKESGPSSG 102

>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From Hypothetical Rna Binding Protein Bc052180 Length = 97

Iteration: 1
 Score = 41.6 bits (96), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 28/81 (34%), Positives = 41/81 (50%), Gaps = 3/81 (3%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
           T L+VG LG   +   L   F +FG IR++  +     A+IQY S  AA+AA        
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACA-KMRGF 76
Query: 274 ILGG--RRLNIKWGRAQANRG 292
            LGG  RRL + + ++  + G
Sbjct: 77  PLGGPDRRLRVDFAKSGPSSG 97

>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 6 Rna-Binding Protein Length = 108

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 31/95 (32%), Positives = 45/95 (47%), Gaps = 9/95 (9%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRP 260
           P +D     L+VG +   L EQDL+  F +FG I  +T+L        + CAF+ Y +R 
Sbjct: 9   PMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARD 68
Query: 261 AAEAAVEHSFNKVILGG--RRLNIKWGRAQANRGE 293
           +A  A      +  L G  R + +K   A   RGE
Sbjct: 69  SALKAQSALHEQKTLPGMNRPIQVKPA-ASEGRGE 102

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 45/81 (55%), Gaps = 4/81 (4%)
Query: 208 PEDKTITT---LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEA 264
           P +KT T    L+VGNL   +TE+++R  F ++G+   V I   +   FI+  +R  AE 
Sbjct: 14  PGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEI 73
Query: 265 AVEHSFNKVILGGRRLNIKWG 285
           A +   + + L G++L +++ 
Sbjct: 74  A-KVELDNMPLRGKQLRVRFA 93

>pdb|3U1L|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2 Length = 240

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 37/140 (26%), Positives = 56/140 (40%), Gaps = 16/140 (11%)
Query: 146 ICSFWVKGECRRGEECPYRHEKPTDPD-DPLADQNIKDRYYGVNDPVAEKLMARASTMPK 204
            C F+ KG C  G +C Y H  P + D   LA +      +G      EK       M  
Sbjct: 72  FCLFFAKGMCCLGPKCEYLHHIPDEEDIGKLALRTEVLDCFG-----REKFADYREDMGG 126
Query: 205 LDPPEDKTITTLYVGNLGDKLT---------EQDLRDHFYQFGEIRSVTILSKQQCAFIQ 255
           +     K   TLYVG +   L          E  +R  F + G+I  +  +  + C F++
Sbjct: 127 IGSFRKKN-KTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVK 185
Query: 256 YTSRPAAEAAVEHSFNKVIL 275
           +  +  AE A E   N+ +L
Sbjct: 186 FKYQANAEFAKEAMSNQTLL 205

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	327
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	4e-45
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-38
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-29
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-27
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	7e-27
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-23
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	4e-23
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-21
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-20
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-19
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	8e-19
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-18
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-18
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	5e-18
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	6e-18
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	9e-18
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-17
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-17
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-16
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-16
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-16
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-16
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	4e-16
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	4e-16
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	5e-16
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	6e-16
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	7e-16
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	8e-16
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	8e-16
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	9e-16
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-15
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-15
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	9e-14
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-15
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-15
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-14
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-15
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-15
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-15
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-11
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	4e-15
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-15
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-12
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	4e-15
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	6e-15
2dis_A	109	Unnamed protein product; structural genomics, RRM	7e-15
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-15
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-13
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-11
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	8e-15
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	9e-15
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	9e-15
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-14
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-14
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-14
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-14
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-14
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-14
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	8e-14
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-14
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-13
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-14
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-14
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-12
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-14
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-14
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-13
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-14
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-14
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-14
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	5e-14
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	7e-14
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	9e-14
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-13
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-13
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-11
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-13
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-13
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-13
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-13
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-13
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-13
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-13
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-13
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-13
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-13
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-13
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-13
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-13
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	4e-13
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	5e-13
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	5e-13
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	5e-13
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	7e-13
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	8e-13
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	9e-13
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	9e-13
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	9e-13
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	9e-13
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-12
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-12
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-12
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-09
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-12
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-12
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-12
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-12
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-12
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-12
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-12
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	3e-12
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-12
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-12
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-12
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	4e-12
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	6e-12
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	6e-12
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	6e-12
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-08
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	7e-12
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-12
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-11
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-11
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-11
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-11
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-11
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-08
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	3e-11
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	4e-11
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	4e-11
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-09
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-11
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-11
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	6e-11
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-11
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	9e-11
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-10
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-10
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-10
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-10
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-10
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	7e-10
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	7e-10
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	9e-10
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-09
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-09
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-09
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-09
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-09
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-09
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-09
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	3e-09
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	4e-09
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	5e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	5e-09
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	6e-09
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	6e-09
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	7e-09
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	7e-09
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	1e-08
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	2e-08
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-08
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	3e-08
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-08
2div_A	99	TRNA selenocysteine associated protein; structural	4e-08
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	6e-08
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	7e-08
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	8e-08
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-07
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-07
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-07
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	4e-07
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	8e-07
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-06
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	5e-06
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-05
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-05
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-05
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-05
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-05
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-05
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	7e-05
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	9e-05
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	1e-04
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	1e-04
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	2e-04
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	2e-04
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	6e-04
2rhk_C	72	Cleavage and polyadenylation specificity factor su	3e-04
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	4e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-04
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	6e-04

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score =  153 bits (386), Expect = 4e-45
 Identities = 40/198 (20%), Positives = 66/198 (33%), Gaps = 28/198 (14%)

Query: 117 GALGKASGSSEMLMKLARTTPYYK---RNRPHICSFWVKGECRRGEECPYRHEKPTDPDD 173
           G  G     S   ++    +   +     +   C F+ KG C  G +C Y H  P + D 
Sbjct: 40  GFAGNTRFVSPFALQPQLHSGKTRGDNDGQLFFCLFFAKGMCCLGPKCEYLHHIPDEEDI 99

Query: 174 PLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLT------- 226
                 ++       D    +  A             K   TLYVG +   L        
Sbjct: 100 G--KLALRTEVL---DCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPA 154

Query: 227 --EQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILG-------- 276
             E  +R  F + G+I  +  +  + C F+++  +  AE A E   N+ +L         
Sbjct: 155 QIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDD 214

Query: 277 ---GRRLNIKWGRAQANR 291
              G  L +KW     + 
Sbjct: 215 RREGTGLLVKWANEDPDP 232

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score =  130 bits (328), Expect = 2e-38
 Identities = 56/80 (70%), Positives = 68/80 (85%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAV 266
             EDKTITTLYVG LGD +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +R AAE A 
Sbjct: 6   SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAA 65

Query: 267 EHSFNKVILGGRRLNIKWGR 286
           E SFNK+I+ GRRLN+KWGR
Sbjct: 66  EKSFNKLIVNGRRLNVKWGR 85

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score =  108 bits (271), Expect = 1e-29
 Identities = 23/89 (25%), Positives = 36/89 (40%), Gaps = 1/89 (1%)

Query: 200 STMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSR 259
             +  +       +TT Y+GN+    TE DL   F  FG I       ++ C FI+Y + 
Sbjct: 14  QAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTH 73

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQ 288
             A   +  +       GR L   WG+ +
Sbjct: 74  EQAAVCIV-ALANFPFQGRNLRTGWGKER 101

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score =  103 bits (258), Expect = 1e-27
 Identities = 19/90 (21%), Positives = 41/90 (45%), Gaps = 1/90 (1%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAV 266
                   T+Y G +   LT+Q +R  F  FG+I  + +  ++  +F+++++  +A  A+
Sbjct: 19  NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAI 78

Query: 267 EHSFNKVILGGRRLNIKWGRAQANRGEDTA 296
             S N   + G  +   WG+   +     +
Sbjct: 79  V-SVNGTTIEGHVVKCYWGKESPDMTSGPS 107

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 92.4 bits (230), Expect = 1e-23
 Identities = 23/93 (24%), Positives = 37/93 (39%), Gaps = 3/93 (3%)

Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTS 258
            S+    +    +   TLYV      +T   LR  F  FG I  +++   + CAF+ Y  
Sbjct: 1   GSSGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEK 58

Query: 259 RPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
             +A+ AV    N   +   +L +   R Q   
Sbjct: 59  MESADQAVA-ELNGTQVESVQLKVNIARKQPML 90

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 90.8 bits (226), Expect = 4e-23
 Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 1/80 (1%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
           T L+VG LG   +   L   F +FG IR++  +     A+IQY S  AA+AA        
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFP 77

Query: 274 ILGG-RRLNIKWGRAQANRG 292
           + G  RRL + + ++  + G
Sbjct: 78  LGGPDRRLRVDFAKSGPSSG 97

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 85.8 bits (213), Expect = 3e-21
 Identities = 23/93 (24%), Positives = 44/93 (47%), Gaps = 1/93 (1%)

Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTS 258
            S+            + L+VGNL   +TE+++R  F ++G+   V I   +   FI+  +
Sbjct: 1   GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLET 60

Query: 259 RPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
           R  AE A     + + L G++L +++    A+ 
Sbjct: 61  RTLAEIAKV-ELDNMPLRGKQLRVRFACHSASL 92

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 83.9 bits (208), Expect = 2e-20
 Identities = 23/99 (23%), Positives = 40/99 (40%), Gaps = 4/99 (4%)

Query: 193 EKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCA 252
             L+ R S M      E    T L+V      + E +L + F  FG ++ V I      A
Sbjct: 12  SGLVPRGSHMHHRQEGELSN-TRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--LNGFA 68

Query: 253 FIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
           F+++    +A  A+E   +      + L + + +  A R
Sbjct: 69  FVEFEEAESAAKAIEE-VHGKSFANQPLEVVYSKLPAKR 106

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 81.2 bits (201), Expect = 1e-19
 Identities = 17/92 (18%), Positives = 36/92 (39%), Gaps = 1/92 (1%)

Query: 200 STMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSR 259
           S+    D     ++  LYV NL    +E+ +   F          +   +  AF+ +++R
Sbjct: 2   SSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNR 61

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
             A  A++ + N  +L G  + +   +     
Sbjct: 62  EDAVEAMK-ALNGKVLDGSPIEVTLAKPVDKD 92

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 79.3 bits (196), Expect = 8e-19
 Identities = 21/100 (21%), Positives = 47/100 (47%), Gaps = 7/100 (7%)

Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-------C 251
            S+      P+ +T + + V N+  +  ++++R+ F  FGE+++V +  K          
Sbjct: 1   GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60

Query: 252 AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
            F+ + ++  A+ A     +   L GRRL ++W  ++   
Sbjct: 61  GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTV 100

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 78.6 bits (194), Expect = 2e-18
 Identities = 24/107 (22%), Positives = 48/107 (44%), Gaps = 5/107 (4%)

Query: 186 GVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG-DKLTEQDLRDHFYQFGEIRSVT 244
           G +      L  +AS +   + P+    + +++GNL    + + D+   F ++G +   +
Sbjct: 1   GSSGSSGMSLKLQASNVTNKNDPKSIN-SRVFIGNLNTALVKKSDVETIFSKYGRVAGCS 59

Query: 245 ILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
           +   +  AF+QY++   A AAV    N  +L G+ L+I         
Sbjct: 60  V--HKGYAFVQYSNERHARAAVL-GENGRVLAGQTLDINMAGEPKPD 103

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 78.1 bits (193), Expect = 2e-18
 Identities = 22/92 (23%), Positives = 40/92 (43%), Gaps = 5/92 (5%)

Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI----LSKQQCAFIQYTSRPAAEA 264
           +D    TLYVGNL   +TE  +   F Q G  +S  +     S     F+++     A A
Sbjct: 11  DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAA 70

Query: 265 AVEHSFNKVILGGRRLNIKWGRAQANRGEDTA 296
           A+  + N   + G+ + + W    +++    +
Sbjct: 71  ALA-AMNGRKILGKEVKVNWATTPSSQKSGPS 101

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 77.1 bits (190), Expect = 5e-18
 Identities = 14/75 (18%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH-SFNKV 273
            ++V  L + + E DL +   +FG I  V ++  ++ A +++ +  +A+  V   +   V
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPV 76

Query: 274 ILGGRRLNIKWGRAQ 288
            + G++    +  ++
Sbjct: 77  YIAGQQAFFNYSTSK 91

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 76.5 bits (189), Expect = 6e-18
 Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 2/80 (2%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFN-K 272
             LY+GNL   +T  DLR  F       +  +L K   AF+ Y  +  A  A+E + + K
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIE-TLSGK 67

Query: 273 VILGGRRLNIKWGRAQANRG 292
           V L G+ + + +  ++  R 
Sbjct: 68  VELHGKIMEVDYSVSKKLRS 87

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 76.6 bits (189), Expect = 9e-18
 Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 3/84 (3%)

Query: 211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSF 270
             +  L+V NL + +TE+ L   F QFG++  V  L  +  AFI +  R  A  A+E   
Sbjct: 9   AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAME-EM 65

Query: 271 NKVILGGRRLNIKWGRAQANRGED 294
           N   L G  + I + +    + ++
Sbjct: 66  NGKDLEGENIEIVFAKPPDQKRKE 89

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 76.2 bits (188), Expect = 1e-17
 Identities = 25/96 (26%), Positives = 46/96 (47%), Gaps = 4/96 (4%)

Query: 200 STMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ---CAFIQY 256
           S    +  P       +YVGNL   +  +D+ D FY++G IR + + +++     AF+++
Sbjct: 9   SGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEF 68

Query: 257 TSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRG 292
                AE AV +  +     G RL +++ R+    G
Sbjct: 69  EDPRDAEDAV-YGRDGYDYDGYRLRVEFPRSGRGTG 103

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 76.2 bits (188), Expect = 1e-17
 Identities = 23/101 (22%), Positives = 39/101 (38%), Gaps = 7/101 (6%)

Query: 200 STMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFI 254
           S+              L+VG L  + +E+D+   F  FG I   T+L         CAF+
Sbjct: 2   SSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFV 61

Query: 255 QYTSRPAAEAAVEHSFNKVIL--GGRRLNIKWGRAQANRGE 293
           +++S   A+AA+        +      L +K+       G 
Sbjct: 62  KFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKESGP 102

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 73.3 bits (180), Expect = 1e-16
 Identities = 17/75 (22%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH-SFNKV 273
            +++  L D + E DL +   +FG I  V ++ K++ A +++     A  AV + + N++
Sbjct: 23  VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQI 82

Query: 274 ILGGRRLNIKWGRAQ 288
            + G    + +  +Q
Sbjct: 83  YIAGHPAFVNYSTSQ 97

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 72.6 bits (179), Expect = 2e-16
 Identities = 18/100 (18%), Positives = 45/100 (45%), Gaps = 11/100 (11%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFY----QFGEIRSVTILSKQQ---CAFIQYTSR 259
            PE +   T+Y+ NL +K+ + +L+   +    +FG+I  + +    +    AF+ +   
Sbjct: 2   VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 61

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELK 299
            +A  A+           + + I++ +  ++     A++K
Sbjct: 62  SSATNALRS-MQGFPFYDKPMRIQYAKTDSDI---IAKMK 97

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 73.1 bits (180), Expect = 2e-16
 Identities = 19/86 (22%), Positives = 37/86 (43%), Gaps = 8/86 (9%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRPAAEAAVE 267
           +T++V NL  K+  + L++ F   G +    IL      S+     + +     A  A+ 
Sbjct: 16  STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSR-GIGTVTFEQSIEAVQAIS 74

Query: 268 HSFNKVILGGRRLNIKWGRAQANRGE 293
             FN  +L  R +++K       +G+
Sbjct: 75  -MFNGQLLFDRPMHVKMDERALPKGD 99

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 72.3 bits (178), Expect = 2e-16
 Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 5/87 (5%)

Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVE 267
              K  T L+VGN+    T Q+LR  F ++G +    I   +  AF+       A  A+ 
Sbjct: 5   SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDI--VKDYAFVHMERAEDAVEAIR 62

Query: 268 HSFNKVILGGRRLNIKW--GRAQANRG 292
              +     G+R++++    R +   G
Sbjct: 63  -GLDNTEFQGKRMHVQLSTSRLRTASG 88

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 72.3 bits (178), Expect = 4e-16
 Identities = 27/101 (26%), Positives = 44/101 (43%), Gaps = 8/101 (7%)

Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------ 250
            R   M     P +     LY+ NL  ++TE+DL   F +F E +   I  +        
Sbjct: 10  IRKIPMFSSYNPGEPN-KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRG 68

Query: 251 CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
            AFI + ++  A  A+    N   L G+ L I++G+ +  R
Sbjct: 69  QAFITFPNKEIAWQALH-LVNGYKLYGKILVIEFGKNKKQR 108

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 71.9 bits (177), Expect = 4e-16
 Identities = 20/82 (24%), Positives = 41/82 (50%), Gaps = 4/82 (4%)

Query: 214 TTLYVGNL-GDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNK 272
           + L++GNL    ++++DL   F  +G I  + I  K    FIQ+ +  +   A+E   ++
Sbjct: 11  SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--KNAFGFIQFDNPQSVRDAIE-CESQ 67

Query: 273 VILGGRRLNIKWGRAQANRGED 294
            +  G++L ++   + A    D
Sbjct: 68  EMNFGKKLILEVSSSNARPQFD 89

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 72.0 bits (177), Expect = 5e-16
 Identities = 27/100 (27%), Positives = 47/100 (47%), Gaps = 8/100 (8%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ---CAFIQYTSRPAAE 263
           PPE      LY+ NL  K+T +++ D F ++G IR + + +  +    A++ Y     A+
Sbjct: 4   PPEVNR--ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAK 61

Query: 264 AAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLE 303
            AV+H  +   +  R L +      ANR     + K + E
Sbjct: 62  NAVDH-LSGFNVSNRYLVV--LYYNANRAFQKMDTKKKEE 98

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 71.7 bits (176), Expect = 6e-16
 Identities = 19/106 (17%), Positives = 41/106 (38%), Gaps = 11/106 (10%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
             +    L D + E  L+D   ++GE+  V IL   +       A + +TS   A+  V+
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 268 HSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLEPVPGLPGALP 313
           +  +   + G  ++ +       +G+   +    +      P  +P
Sbjct: 67  N-LHLTSVMGNIIHAQL----DIKGQQRMKYYELIVNGSYTPQTVP 107

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 70.7 bits (174), Expect = 7e-16
 Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 3/79 (3%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
             L++GNL  + TEQ++R  F Q+G++    I   +   F+    + AAE A+ +  +  
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQYGKVLECDI--IKNYGFVHIEDKTAAEDAIRN-LHHY 65

Query: 274 ILGGRRLNIKWGRAQANRG 292
            L G  +N++  + ++   
Sbjct: 66  KLHGVNINVEASKNKSKAS 84

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 71.2 bits (175), Expect = 8e-16
 Identities = 22/98 (22%), Positives = 43/98 (43%), Gaps = 5/98 (5%)

Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC----AFI 254
            S+    +     T   L+V N+  +  + DLR  F QFG+I  V I+  ++      F+
Sbjct: 1   GSSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFV 60

Query: 255 QYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRG 292
            + +   A+ A E   +  ++ GR++ +    A+    
Sbjct: 61  TFENSADADRARE-KLHGTVVEGRKIEVNNATARVMTN 97

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 71.0 bits (174), Expect = 8e-16
 Identities = 15/75 (20%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH-SFNKV 273
            +++  L   +TE ++      FG++ ++ +L  +  AFI+  +  AA   V + +    
Sbjct: 18  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTP 77

Query: 274 ILGGRRLNIKWGRAQ 288
           +L G+ + I++   +
Sbjct: 78  VLRGQPIYIQFSNHK 92

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 70.7 bits (174), Expect = 9e-16
 Identities = 23/91 (25%), Positives = 43/91 (47%), Gaps = 6/91 (6%)

Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS----KQQC-AF 253
           +S    + P +++   T++VGNL  ++ E+ L + F Q G +  VTI      K +   F
Sbjct: 2   SSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGF 61

Query: 254 IQYTSRPAAEAAVEHSFNKVILGGRRLNIKW 284
           + +    +   A+    N + L GR +N+  
Sbjct: 62  VCFKHPESVSYAIA-LLNGIRLYGRPINVSG 91

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 70.3 bits (173), Expect = 1e-15
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 3/78 (3%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
             ++VGN+    T Q+LR  F + G +    +   +  AF+       A+AA+    N  
Sbjct: 10  WKIFVGNVSAACTSQELRSLFERRGRVIECDV--VKDYAFVHMEKEADAKAAIA-QLNGK 66

Query: 274 ILGGRRLNIKWGRAQANR 291
            + G+R+N++       +
Sbjct: 67  EVKGKRINVELSTKGQKK 84

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 72.6 bits (179), Expect = 1e-15
 Identities = 21/88 (23%), Positives = 40/88 (45%), Gaps = 7/88 (7%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
           T L V  L   +T+++L   F   G I +  I+   +       AF+ +TS   ++ A++
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63

Query: 268 HSFNKVILGGRRLNIKWGRAQANRGEDT 295
              N + +  +RL + + R      +DT
Sbjct: 64  -VLNGITVRNKRLKVSYARPGGESIKDT 90

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 67.2 bits (165), Expect = 9e-14
 Identities = 25/84 (29%), Positives = 38/84 (45%), Gaps = 9/84 (10%)

Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAA 262
           E    T LYV NL   +T+  L   F ++G I    IL  +        AF++Y  R  A
Sbjct: 85  ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 144

Query: 263 EAAVEHSFNKVILGG--RRLNIKW 284
           + A+    N VI  G  + L+++ 
Sbjct: 145 QEAISA-LNNVIPEGGSQPLSVRL 167

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 70.0 bits (172), Expect = 2e-15
 Identities = 18/77 (23%), Positives = 39/77 (50%), Gaps = 4/77 (5%)

Query: 214 TTLYVGNL-GDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNK 272
           + L++GNL    ++++DL   F  +G I  + I  K    FIQ+ +  +   A+    ++
Sbjct: 23  SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--KNAFGFIQFDNPQSVRDAI-EXESQ 79

Query: 273 VILGGRRLNIKWGRAQA 289
            +  G++L ++   + A
Sbjct: 80  EMNFGKKLILEVSSSNA 96

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 72.3 bits (178), Expect = 2e-15
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 7/76 (9%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAEAAVEHSF 270
           L++G +  K TE D+R  F  FG+I    IL         CAF+ +T+R  A+ A++   
Sbjct: 98  LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157

Query: 271 NKVIL--GGRRLNIKW 284
               +      + +K+
Sbjct: 158 QAQTMEGCSSPMVVKF 173

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 68.8 bits (169), Expect = 3e-14
 Identities = 24/96 (25%), Positives = 43/96 (44%), Gaps = 10/96 (10%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL---------SKQQCAFIQYTSRPAAEA 264
             ++VG +    +E+DLR+ F Q+G +  + +L         SK  C F+ + +R AA  
Sbjct: 4   IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSK-GCCFVTFYTRKAALE 62

Query: 265 AVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKV 300
           A     N  +L G    I+   A + +     + K+
Sbjct: 63  AQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKL 98

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 70.7 bits (173), Expect = 2e-15
 Identities = 19/95 (20%), Positives = 43/95 (45%), Gaps = 2/95 (2%)

Query: 195 LMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFI 254
           L+ R S M         +   +++  L   +TE ++      FG++ ++ +L  +  AFI
Sbjct: 14  LVPRGSHMGDSRSAGVPS-RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFI 72

Query: 255 QYTSRPAAEAAVEH-SFNKVILGGRRLNIKWGRAQ 288
           +  +  AA   V + +    +L G+ + I++   +
Sbjct: 73  EMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK 107

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 69.8 bits (171), Expect = 2e-15
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 4/80 (5%)

Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL---SKQQCAFIQYTSRPAAEA 264
           P+ + I  L + N+   L  + L     Q+G + S   +   S+     + Y+S+  A  
Sbjct: 10  PKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQ 69

Query: 265 AVEHSFNKVILGGRRLNIKW 284
           A++   N   L    L + +
Sbjct: 70  ALDK-LNGFQLENFTLKVAY 88

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 72.2 bits (177), Expect = 2e-15
 Identities = 30/117 (25%), Positives = 50/117 (42%), Gaps = 6/117 (5%)

Query: 214 TTLYVGNLG-DKLTEQDLRDHFYQFGEIRSVTILSKQQC-AFIQYTSRPAAEAAVEHSFN 271
           + L V NL  +++T Q L   F  +G+++ V IL  ++  A +Q      A+ A+ H  N
Sbjct: 4   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSH-LN 62

Query: 272 KVILGGRRLNIKWGRAQANRGEDTAELKVRLEPVPG---LPGALPPPPKDFFNLSNP 325
              L G+ + I   + Q  +     +    L    G   L     P  K+F N+  P
Sbjct: 63  GHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPP 119

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 60.3 bits (146), Expect = 5e-11
 Identities = 24/125 (19%), Positives = 46/125 (36%), Gaps = 8/125 (6%)

Query: 164 RHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGD 223
           +H+    P +   DQ +   Y        +K    +     + PP      TL++ N+  
Sbjct: 77  KHQNVQLPREGQEDQGLTKDYGNSPLHRFKK--PGSKNFQNIFPPS----ATLHLSNIPP 130

Query: 224 KLTEQDLRDHFYQFGEIRSVTILSKQQ--CAFIQYTSRPAAEAAVEHSFNKVILGGRRLN 281
            ++E+DL+  F   G +       ++    A IQ  S   A  A+    N  +     L 
Sbjct: 131 SVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLR 190

Query: 282 IKWGR 286
           + + +
Sbjct: 191 VSFSK 195

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 69.2 bits (170), Expect = 4e-15
 Identities = 21/92 (22%), Positives = 39/92 (42%), Gaps = 14/92 (15%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ---------CAFIQYTSRPAAEA 264
           + L++ NL    TE+ L+  F + G I+S TI  K+            F++Y     A+ 
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 265 AVEHSFNKVILGGRRLNIKWGRAQANRGEDTA 296
           A++       + G +L ++     + R    A
Sbjct: 66  ALK-QLQGHTVDGHKLEVR----ISERATKPA 92

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 73.2 bits (180), Expect = 4e-15
 Identities = 29/91 (31%), Positives = 40/91 (43%), Gaps = 3/91 (3%)

Query: 202 MPKLDPPEDKT--ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSR 259
              L P E        L+VGNL   +TE+D +  F ++GE   V I   +   FI+  SR
Sbjct: 9   KSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESR 68

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQAN 290
             AE A     +  IL  R L I++    A 
Sbjct: 69  TLAEIAKA-ELDGTILKSRPLRIRFATHGAA 98

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 65.9 bits (161), Expect = 1e-12
 Identities = 17/108 (15%), Positives = 36/108 (33%), Gaps = 5/108 (4%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAEAAVEH 268
             L V NL   ++ + L   F QFG +    ++   +       F+++ ++P A  A+E 
Sbjct: 97  AALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALER 156

Query: 269 SFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLEPVPGLPGALPPPP 316
             +   L                 ++    +  ++           PP
Sbjct: 157 CGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPP 204

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 69.1 bits (169), Expect = 4e-15
 Identities = 15/71 (21%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH-SFNKV 273
            L++  L  ++TE ++      FG++ ++ +L  +  AF++  +  AA   V + S    
Sbjct: 17  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTP 76

Query: 274 ILGGRRLNIKW 284
            L  + + I++
Sbjct: 77  HLRNQPIYIQY 87

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 69.5 bits (170), Expect = 6e-15
 Identities = 19/115 (16%), Positives = 43/115 (37%), Gaps = 8/115 (6%)

Query: 192 AEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFY----QFGEIRSVTIL- 246
             +     S      PP  +    + + N+  ++ ++ L+   Y      G+I  + +  
Sbjct: 8   KFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL 67

Query: 247 --SKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELK 299
                  A+I + ++ +A+A VE  F      G  L I +     ++  +   L+
Sbjct: 68  SDDNSGKAYIVFATQESAQAFVEA-FQGYPFQGNPLVITFSETPQSQVAEDGSLE 121

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 68.7 bits (168), Expect = 7e-15
 Identities = 17/93 (18%), Positives = 37/93 (39%), Gaps = 9/93 (9%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGE-IRSVTIL-------SKQQCAFIQYTSRPAAEAA 265
             L++G +      +++ +   +  E +  V +          +  AF++Y S  AA  A
Sbjct: 9   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68

Query: 266 VEH-SFNKVILGGRRLNIKWGRAQANRGEDTAE 297
                  ++ L G ++ + W   + +  ED  E
Sbjct: 69  RRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVME 101

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 72.3 bits (178), Expect = 8e-15
 Identities = 16/95 (16%), Positives = 26/95 (27%), Gaps = 7/95 (7%)

Query: 203 PKLDPPEDKTITTLYVGNLGDKLTEQD-LRDHFYQFGEIRSVTILSKQQ-----CAFIQY 256
                P       L V  L     + D L              +   Q       A ++Y
Sbjct: 174 AGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEY 233

Query: 257 TSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
            +   AE A +   + + LGG  L + +       
Sbjct: 234 ETAEMAEEAQQ-QADGLSLGGSHLRVSFCAPGPPG 267

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 69.2 bits (170), Expect = 1e-13
 Identities = 21/94 (22%), Positives = 32/94 (34%), Gaps = 10/94 (10%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
             L V NL   LT+Q   +    FG +    ++  ++        F +Y  + +A  A  
Sbjct: 96  ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKS 155

Query: 268 HSFNKVILGGRRLNIKWGRAQANRGEDTAELKVR 301
                  LG R L + W           A L  R
Sbjct: 156 D-LLGKPLGPRTLYVHW--TD-AGQLTPALLHSR 185

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 62.3 bits (152), Expect = 3e-11
 Identities = 15/77 (19%), Positives = 33/77 (42%), Gaps = 2/77 (2%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
             + +  L   +T Q++ D    +  ++   +   +  AF+   +   AEAA+   F++ 
Sbjct: 23  RKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINA-FHQS 80

Query: 274 ILGGRRLNIKWGRAQAN 290
            L  R L+++     A 
Sbjct: 81  RLRERELSVQLQPTDAL 97

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 68.9 bits (169), Expect = 8e-15
 Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 8/92 (8%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSR 259
                +T   L V NL   +++ D+++ F +FG ++   +       S    A + +  R
Sbjct: 28  GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL-GTADVHFERR 86

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
             A  A++  +  V L GR ++I+   +Q + 
Sbjct: 87  ADALKAMK-QYKGVPLDGRPMDIQLVASQIDL 117

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 68.0 bits (167), Expect = 9e-15
 Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 7/84 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----SKQQCAFIQYTSRPAAEAAVEH 268
             ++V NL    T + L+D F + G +    I      SK  C  +++ S   AE A   
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSK-GCGVVKFESPEVAERACRM 67

Query: 269 SFNKVILGGRRLNIKWGRAQANRG 292
             N + L GR ++++  R  +   
Sbjct: 68  -MNGMKLSGREIDVRIDRNASGPS 90

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 68.3 bits (167), Expect = 9e-15
 Identities = 13/79 (16%), Positives = 28/79 (35%), Gaps = 1/79 (1%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAV 266
               ++ T +   NL       ++++ F +FG +  V +      A +++     A  A 
Sbjct: 4   GSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAF 63

Query: 267 EHSFNKVILGGRRLNIKWG 285
            H           L ++W 
Sbjct: 64  RH-LAYSKFHHVPLYLEWA 81

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 68.4 bits (168), Expect = 1e-14
 Identities = 21/97 (21%), Positives = 38/97 (39%), Gaps = 8/97 (8%)

Query: 192 AEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL----- 246
               +  +    ++   +++  T LY+ NL   + EQ+L +    FG++ S  IL     
Sbjct: 4   GSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSG 63

Query: 247 -SKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
            S+    F +  S    EA + H FN   +       
Sbjct: 64  TSR-GVGFARMESTEKCEAVIGH-FNGKFIKTPPGVS 98

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 68.0 bits (167), Expect = 1e-14
 Identities = 23/100 (23%), Positives = 37/100 (37%), Gaps = 7/100 (7%)

Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------A 252
            S+             T+ V NL +   E DL++ F  FG I  + +   +        A
Sbjct: 1   GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60

Query: 253 FIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRG 292
           FI +  R  A  A+    +        LN++W +   N G
Sbjct: 61  FISFHRREDAARAIA-GVSGFGYDHLILNVEWAKPSTNSG 99

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 68.1 bits (167), Expect = 1e-14
 Identities = 24/107 (22%), Positives = 45/107 (42%), Gaps = 13/107 (12%)

Query: 200 STMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAF 253
           S+     P +     T+++ NL     E+ L +   QFG+++ V ++          CAF
Sbjct: 2   SSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAF 61

Query: 254 IQYTSRPAAEAAVE-----HSFNKVILGGRRLNIKW--GRAQANRGE 293
            Q+ ++ AA+  +           + L GR+L +     R +A  G 
Sbjct: 62  AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGP 108

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 67.5 bits (165), Expect = 1e-14
 Identities = 21/84 (25%), Positives = 34/84 (40%), Gaps = 2/84 (2%)

Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEI-RSVTILSKQQCAFIQYTSRPAAEAAVE 267
                  +YVGNL       DL+    + G +   +T    ++ AF+ Y    AA+ AV 
Sbjct: 15  GAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVS 74

Query: 268 HSFNKVILGGRRLNIKWGRAQANR 291
                + LG   L +   R Q ++
Sbjct: 75  -CLQGLRLGTDTLRVALARQQRDK 97

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 67.7 bits (166), Expect = 1e-14
 Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 8/86 (9%)

Query: 203 PKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQY 256
                   +T   L V NL   +++ D+++ F +FG ++   +       S    A + +
Sbjct: 19  GFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSL-GTADVHF 77

Query: 257 TSRPAAEAAVEHSFNKVILGGRRLNI 282
             +  A  A++  +N V L GR +NI
Sbjct: 78  ERKADALKAMK-QYNGVPLDGRPMNI 102

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 70.1 bits (172), Expect = 2e-14
 Identities = 23/130 (17%), Positives = 48/130 (36%), Gaps = 14/130 (10%)

Query: 175 LADQNIK-DRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDH 233
              Q++K  R +                   +      +   L++G L + L +  +++ 
Sbjct: 75  FQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKEL 134

Query: 234 FYQFGEIRSVTI-------LSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR 286
              FG +++  +       LSK   AF +Y      + A+    N + LG ++L ++   
Sbjct: 135 LTSFGPLKAFNLVKDSATGLSK-GYAFCEYVDINVTDQAIA-GLNGMQLGDKKLLVQR-- 190

Query: 287 AQANRGEDTA 296
             A+ G   A
Sbjct: 191 --ASVGAKNA 198

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 68.1 bits (167), Expect = 8e-14
 Identities = 25/122 (20%), Positives = 40/122 (32%), Gaps = 15/122 (12%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-----------AFIQYTSRPAAE 263
            LYVGN+   +TE+ + D F     +  +T                  AF+++ S     
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 264 AAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLEPVPGLPGALPPPPKDFF-NL 322
            A+   F+ +I  G+ L I+            +E      P            K F   L
Sbjct: 66  QAMA--FDGIIFQGQSLKIRRPHDYQPL-PGMSENPSVYVPGVVSTVVPDSAHKLFIGGL 122

Query: 323 SN 324
            N
Sbjct: 123 PN 124

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 69.2 bits (170), Expect = 2e-14
 Identities = 13/93 (13%), Positives = 36/93 (38%), Gaps = 7/93 (7%)

Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAE 263
           E  T   L++GNL    +  +L+    +      + ++  +        ++ + S    E
Sbjct: 9   ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLE 68

Query: 264 AAVEHSFNKVILGGRRLNIKWGRAQANRGEDTA 296
            A+E     + + G  + ++  + + ++    A
Sbjct: 69  KALE--LTGLKVFGNEIKLEKPKGRDSKKVRAA 99

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 66.5 bits (163), Expect = 2e-13
 Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 2/80 (2%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-AFIQYTSRPAAEA 264
           D  + +   TL   NL   +TE +L++ F    EIR V+   K +  A+I++ S   AE 
Sbjct: 92  DSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEK 151

Query: 265 AVEHSFNKVILGGRRLNIKW 284
            +E       + GR +++ +
Sbjct: 152 NLE-EKQGAEIDGRSVSLYY 170

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 67.3 bits (165), Expect = 2e-14
 Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-AFIQYTSRPAAEAAVEHSFNKVI 274
           +YVGNLG    + +L   F  +G +R+V I       AF+++     AE AV    +  +
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAV-RGLDGKV 61

Query: 275 LGGRRLNIKWGRAQANRG 292
           + G R+ ++       R 
Sbjct: 62  ICGSRVRVELSTGMPRRS 79

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 68.8 bits (169), Expect = 2e-14
 Identities = 20/88 (22%), Positives = 36/88 (40%), Gaps = 7/88 (7%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
           T L V  L   +T+++ R  F   GEI S  ++  +         F+ Y     AE A+ 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 268 HSFNKVILGGRRLNIKWGRAQANRGEDT 295
            + N + L  + + + + R  +    D 
Sbjct: 63  -TLNGLRLQTKTIKVSYARPSSASIRDA 89

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 64.1 bits (157), Expect = 1e-12
 Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 8/87 (9%)

Query: 206 DPPEDKTITT-LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTS 258
            P         LYV  L   +T+++L   F Q+G I +  IL  Q         FI++  
Sbjct: 80  RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDK 139

Query: 259 RPAAEAAVEHSFNKVILGGRR-LNIKW 284
           R  AE A++    +   G    + +K+
Sbjct: 140 RIEAEEAIKGLNGQKPSGATEPITVKF 166

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 67.4 bits (165), Expect = 2e-14
 Identities = 24/95 (25%), Positives = 43/95 (45%), Gaps = 8/95 (8%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSR 259
              +D     L++G +   L E+DL+  F +FG+I  +T+L  +       CAF+ Y  R
Sbjct: 6   SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCER 65

Query: 260 PAAEAAVEHSFNKVIL--GGRRLNIKWGRAQANRG 292
            +A  A      +  L    R + +K   +++  G
Sbjct: 66  ESALKAQSALHEQKTLPGMNRPIQVKPADSESRGG 100

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 69.6 bits (171), Expect = 3e-14
 Identities = 28/117 (23%), Positives = 48/117 (41%), Gaps = 9/117 (7%)

Query: 194 KLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-- 251
           + M R S   +        ++ +YVG++  +L E  +R  F  FG I+S+ +        
Sbjct: 11  QQMGRGSAAQR--QGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMK 68

Query: 252 ----AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLEP 304
               AF++Y    AA+ A+E   N V+LGGR + +              +L      
Sbjct: 69  HKGFAFVEYEVPEAAQLALEQ-MNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA 124

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 66.2 bits (162), Expect = 5e-13
 Identities = 28/130 (21%), Positives = 46/130 (35%), Gaps = 21/130 (16%)

Query: 187 VNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL 246
           V  P           + +L          +YV ++   L++ D++  F  FG+I+S T+ 
Sbjct: 102 VGRPSNIG--QAQPIIDQLAEEARAF-NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLA 158

Query: 247 SKQQC------AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKV 300
                       FI+Y    +++ AV  S N   LGG+ L +             A    
Sbjct: 159 RDPTTGKHKGYGFIEYEKAQSSQDAVS-SMNLFDLGGQYLRVGK-----------AVTPP 206

Query: 301 RLEPVPGLPG 310
                P  PG
Sbjct: 207 MPLLTPATPG 216

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 66.3 bits (162), Expect = 3e-14
 Identities = 13/76 (17%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
           + + V NL      Q++ D    +  ++   +   ++ AF+   +   A+ A++  F++ 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQ-MFHQY 63

Query: 274 ILGGRRLNIKWGRAQA 289
              G+ L ++     A
Sbjct: 64  SFRGKDLIVQLQPTDA 79

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 66.9 bits (164), Expect = 3e-14
 Identities = 22/92 (23%), Positives = 37/92 (40%), Gaps = 7/92 (7%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRP 260
            P+   + TL V NL  + +   LR  F ++G +  V I  +         AF+++  R 
Sbjct: 7   GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRR 66

Query: 261 AAEAAVEHSFNKVILGGRRLNIKWGRAQANRG 292
            A+ A     +   L GR L ++  R      
Sbjct: 67  DAQDAEAA-MDGAELDGRELRVQVARYGRRDL 97

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 68.3 bits (167), Expect = 4e-14
 Identities = 22/112 (19%), Positives = 46/112 (41%), Gaps = 6/112 (5%)

Query: 185 YGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVT 244
           Y    P+ +K                +T   L V NL   +++ D+++ F +FG ++   
Sbjct: 60  YSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAA 119

Query: 245 ILSKQQ-----CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
           +   +       A + +  R  A  A++  +  V L GR ++I+   +Q + 
Sbjct: 120 VDYDRSGRSLGTADVHFERRADALKAMK-QYKGVPLDGRPMDIQLVASQIDL 170

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 66.7 bits (163), Expect = 5e-14
 Identities = 28/110 (25%), Positives = 41/110 (37%), Gaps = 15/110 (13%)

Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------- 251
            S+    DP ED   + +YV  L D +T  DL D F Q G ++      +          
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60

Query: 252 -------AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGED 294
                  A + Y   P A+AAVE  F+     G +L +   R +      
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVE-WFDGKDFQGSKLKVSLARKKPPMNSG 109

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 66.2 bits (162), Expect = 7e-14
 Identities = 20/96 (20%), Positives = 43/96 (44%), Gaps = 8/96 (8%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRP 260
            PE++   T++   L  ++  +DL D F   G++R V I+S +        A++++    
Sbjct: 19  SPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQ 78

Query: 261 AAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTA 296
           +   A+        L G  + ++  +A+ NR    +
Sbjct: 79  SVPLAIG--LTGQRLLGVPIIVQASQAEKNRLSGPS 112

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 68.5 bits (167), Expect = 9e-14
 Identities = 32/147 (21%), Positives = 59/147 (40%), Gaps = 9/147 (6%)

Query: 184 YYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG-DKLTEQDLRDHFYQFGEIRS 242
           ++  +  V          +P L    +   + L V NL  +++T Q L   F  +G+++ 
Sbjct: 8   HHHSSGLVPRGSHMGRIAIPGLAGAGN---SVLLVSNLNPERVTPQSLFILFGVYGDVQR 64

Query: 243 VTIL-SKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAEL--- 298
           V IL +K++ A +Q      A+ A+ H  N   L G+ + I   + Q  +     +    
Sbjct: 65  VKILFNKKENALVQMADGNQAQLAMSH-LNGHKLHGKPIRITLSKHQNVQLPREGQEDQG 123

Query: 299 KVRLEPVPGLPGALPPPPKDFFNLSNP 325
             +      L     P  K+F N+  P
Sbjct: 124 LTKDYGNSPLHRFKKPGSKNFQNIFPP 150

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 63.1 bits (153), Expect = 7e-12
 Identities = 22/129 (17%), Positives = 43/129 (33%), Gaps = 7/129 (5%)

Query: 160 ECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVG 219
                  +         +     + YG N P+       +     + PP      TL++ 
Sbjct: 103 RITLSKHQNVQLPREGQEDQGLTKDYG-NSPLHRFKKPGSKNFQNIFPPS----ATLHLS 157

Query: 220 NLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ--CAFIQYTSRPAAEAAVEHSFNKVILGG 277
           N+   ++E+DL+  F   G +       ++    A IQ  S   A  A+    N  +   
Sbjct: 158 NIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGEN 217

Query: 278 RRLNIKWGR 286
             L + + +
Sbjct: 218 HHLRVSFSK 226

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 69.6 bits (171), Expect = 1e-13
 Identities = 18/90 (20%), Positives = 31/90 (34%), Gaps = 7/90 (7%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
            TL++ N     T++++RD       +     L   +       A+I  TS+  A   VE
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177

Query: 268 HSFNKVILGGRRLNIKWGRAQANRGEDTAE 297
              N + + G  L  K            + 
Sbjct: 178 -KLNGLKIEGYTLVTKVSNPLEKSKRTDSA 206

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 67.7 bits (166), Expect = 4e-13
 Identities = 23/96 (23%), Positives = 43/96 (44%), Gaps = 10/96 (10%)

Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLT-EQDLRDHFYQFGEIRSVTILSKQQ----- 250
           +      K           + + NL  +L  E  LR+ F  FG I  + I + Q+     
Sbjct: 194 SNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFN 253

Query: 251 --CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW 284
             CAF+ + ++ +AE A++   N+ +LG R +++  
Sbjct: 254 NCCAFMVFENKDSAERALQ--MNRSLLGNREISVSL 287

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 61.5 bits (150), Expect = 5e-11
 Identities = 16/86 (18%), Positives = 33/86 (38%), Gaps = 6/86 (6%)

Query: 203 PKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ----CAFIQYTS 258
                  ++ +TT+ V NL     +  +  +F   G I  V +    +     A I++  
Sbjct: 31  ANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFAR 90

Query: 259 RPAAEAAVEHSFNKVILGGRRLNIKW 284
              A AA+    +K ++G   + +  
Sbjct: 91  YDGALAAITK-THK-VVGQNEIIVSH 114

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 65.4 bits (160), Expect = 1e-13
 Identities = 11/101 (10%), Positives = 37/101 (36%), Gaps = 6/101 (5%)

Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----C 251
             + +              L++  L    T+++L +     G ++ + +++ +       
Sbjct: 1   GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGL 60

Query: 252 AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRG 292
           A+++Y +   A  AV    + + +    + +    +  + G
Sbjct: 61  AYVEYENESQASQAVM-KMDGMTIKENIIKVAISNSGPSSG 100

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 65.0 bits (159), Expect = 1e-13
 Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 3/70 (4%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-AFIQYTSRPAAEAAVEHSFNKV 273
           +++V      +    L ++F  FG + SV +   +   A ++     A EA +  S +  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLSQSQHS- 68

Query: 274 ILGGRRLNIK 283
            LGG RL ++
Sbjct: 69  -LGGHRLRVR 77

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 66.9 bits (164), Expect = 1e-13
 Identities = 15/85 (17%), Positives = 35/85 (41%), Gaps = 7/85 (8%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSR 259
           D         L++G L + L +  +++    FG +++  ++           AF +Y   
Sbjct: 87  DYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDI 146

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKW 284
              + A+    N + LG ++L ++ 
Sbjct: 147 NVTDQAIA-GLNGMQLGDKKLLVQR 170

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 65.3 bits (160), Expect = 4e-13
 Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 13/81 (16%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-----------AFIQYTSRPAAE 263
            LYVGN+   +TE+ + D F     +  +T                  AF+++ S     
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 264 AAVEHSFNKVILGGRRLNIKW 284
            A+   F+ +I  G+ L I+ 
Sbjct: 66  QAMA--FDGIIFQGQSLKIRR 84

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 65.3 bits (159), Expect = 1e-13
 Identities = 10/72 (13%), Positives = 27/72 (37%)

Query: 213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNK 272
              +  G LG+ ++   L     + G + ++ +   +  +F +Y +   ++ A      K
Sbjct: 27  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGK 86

Query: 273 VILGGRRLNIKW 284
            ++      I  
Sbjct: 87  EVVDDLGQKITL 98

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 65.1 bits (159), Expect = 2e-13
 Identities = 26/102 (25%), Positives = 46/102 (45%), Gaps = 7/102 (6%)

Query: 196 MARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC---- 251
           M R S      PP+ + +T+L V NL  + +   LR  F ++G +  V I   +      
Sbjct: 30  MGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESR 89

Query: 252 --AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
             AF+++  +  AE A++   +  +L GR L ++  R     
Sbjct: 90  GFAFVRFHDKRDAEDAMDA-MDGAVLDGRELRVQMARYGRPP 130

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 64.7 bits (158), Expect = 2e-13
 Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 6/84 (7%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL----SKQQC-AFIQYTSRPAAEAAVEH 268
             L++G L  +  E+ L+  F + G I  V ++    SK +  AFI + +   A+ A + 
Sbjct: 8   GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAK- 66

Query: 269 SFNKVILGGRRLNIKWGRAQANRG 292
             N   L G+ + ++  +  + + 
Sbjct: 67  DMNGKSLHGKAIKVEQAKKPSFQS 90

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 64.1 bits (157), Expect = 3e-13
 Identities = 26/94 (27%), Positives = 42/94 (44%), Gaps = 7/94 (7%)

Query: 200 STMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AF 253
           S+    +         L V  L    TE+DLR+ F ++G I  V+I+  QQ       AF
Sbjct: 2   SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61

Query: 254 IQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA 287
           + + +   A+ A E   N + L GRR+ +    +
Sbjct: 62  VYFENVDDAKEAKE-RANGMELDGRRIRVSGPSS 94

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 63.7 bits (156), Expect = 3e-13
 Identities = 15/85 (17%), Positives = 40/85 (47%), Gaps = 8/85 (9%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-------AFIQYTSRPAAEAAV 266
           T +++G L   +T+  + + F  +G+I+ + +  ++         A++++ +   AE A+
Sbjct: 5   TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64

Query: 267 EHSFNKVILGGRRLNIKWGRAQANR 291
           +H  +   + G+ +      A   R
Sbjct: 65  KH-MDGGQIDGQEITATAVLAPWPR 88

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 64.3 bits (157), Expect = 3e-13
 Identities = 26/99 (26%), Positives = 47/99 (47%), Gaps = 10/99 (10%)

Query: 195 LMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ---- 250
           L+ R S M   +  + K    L+V N+  +  + DLR  F QFG+I  V I+  ++    
Sbjct: 14  LVPRGSHMNTENKSQPKR---LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG 70

Query: 251 CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA 289
             F+ + +   A+ A E   +  ++ GR++ +    A A
Sbjct: 71  FGFVTFENSADADRARE-KLHGTVVEGRKIEV--NNATA 106

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 64.2 bits (157), Expect = 3e-13
 Identities = 23/95 (24%), Positives = 48/95 (50%), Gaps = 7/95 (7%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSR 259
           DP  D+++ +++VGN+  + TE+ L+D F + G + S  ++  ++        F +Y  +
Sbjct: 1   DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGED 294
             A +A+  + N     GR L +    ++ N+ E 
Sbjct: 61  ETALSAMR-NLNGREFSGRALRVDNAASEKNKEEL 94

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 63.8 bits (156), Expect = 3e-13
 Identities = 23/91 (25%), Positives = 37/91 (40%), Gaps = 5/91 (5%)

Query: 203 PKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSV--TILSKQQCAFIQYTSRP 260
           P           TL   NL   +TE +L++ F    EIR V     SK   A+I++ S  
Sbjct: 7   PCTSKKVRAA-RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGI-AYIEFKSEA 64

Query: 261 AAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
            AE  +E       + GR +++ +   +   
Sbjct: 65  DAEKNLEE-KQGAEIDGRSVSLYYTGEKGGT 94

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 63.8 bits (156), Expect = 4e-13
 Identities = 16/87 (18%), Positives = 30/87 (34%), Gaps = 7/87 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
             L+V NL    +E+DL   F  +G +  +              AF+ +     A  A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 268 HSFNKVILGGRRLNIKWGRAQANRGED 294
              +  +  GR L++     +    + 
Sbjct: 69  -EVDGQVFQGRMLHVLPSTIKKEASQS 94

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 63.4 bits (155), Expect = 4e-13
 Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 7/86 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
             LYVG L +++ ++ L   F  FG+I  + I    +       AF+++     A AA++
Sbjct: 13  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72

Query: 268 HSFNKVILGGRRLNIKWGRAQANRGE 293
            + N+  L GR + +   +    +  
Sbjct: 73  -NMNESELFGRTIRVNLAKPMRIKES 97

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 64.8 bits (158), Expect = 4e-13
 Identities = 25/126 (19%), Positives = 45/126 (35%), Gaps = 11/126 (8%)

Query: 182 DRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIR 241
           D Y         +   +    P    PE   +  L V  +   + E  LR  F ++G I 
Sbjct: 11  DPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIE 70

Query: 242 SVTIL-------SKQQC-AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGE 293
           SV I+       S+     F+++ S  +A+ A+    N   +  +RL +    +   R  
Sbjct: 71  SVKIVCDRETRQSR--GYGFVKFQSGSSAQQAIA-GLNGFNILNKRLKVALAASGHQRPG 127

Query: 294 DTAELK 299
               + 
Sbjct: 128 IAGAVG 133

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 63.4 bits (155), Expect = 5e-13
 Identities = 17/87 (19%), Positives = 42/87 (48%), Gaps = 11/87 (12%)

Query: 208 PEDKTITT-LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-----AFIQYTSRPA 261
           PE K +   ++VG +  ++ E ++R  F ++G ++ V I++ +        F+ + +   
Sbjct: 3   PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVD 62

Query: 262 AEAAVEHSFNKVILGGRRLNIKWGRAQ 288
            +  VE   +++   G++L +    A 
Sbjct: 63  VQKIVE---SQINFHGKKLKLG--PAI 84

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 65.2 bits (159), Expect = 5e-13
 Identities = 23/143 (16%), Positives = 58/143 (40%), Gaps = 13/143 (9%)

Query: 171 PDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTI------TTLYVGNLGDK 224
                  ++ K R +G +    E + +      + D   +           L+V ++ ++
Sbjct: 24  VRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEE 83

Query: 225 LTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHSFNKVILGGR 278
             E ++++ F  +GEI+++ +   ++       A ++Y +   A AA E   N   + G+
Sbjct: 84  AQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA-LNGAEIMGQ 142

Query: 279 RLNIKWGRAQANRGEDTAELKVR 301
            + + W   +  +    +E + R
Sbjct: 143 TIQVDWCFVKGPKRVKKSEKRRR 165

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 63.4 bits (155), Expect = 5e-13
 Identities = 22/103 (21%), Positives = 45/103 (43%), Gaps = 10/103 (9%)

Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQ 250
           +  S+ P  +  +D T+   YVG L +K++E  L + F Q G + +  +         Q 
Sbjct: 2   SSGSSGPISERNQDATV---YVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQG 58

Query: 251 CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGE 293
             F+++ S   A+ A++   + + L G+ + +    A      
Sbjct: 59  YGFVEFLSEEDADYAIK-IMDMIKLYGKPIRVNKASAHNKNLS 100

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 64.5 bits (157), Expect = 7e-13
 Identities = 25/137 (18%), Positives = 50/137 (36%), Gaps = 12/137 (8%)

Query: 167 KPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKL-----DPPEDKTITTLYVGNL 221
           +  D               GV+         +  T+ +         + + +T+L V NL
Sbjct: 19  EAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNL 78

Query: 222 GDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHSFNKVIL 275
             + +   LR  F ++G +  V I   +        AF+++  +  AE A++   +  +L
Sbjct: 79  TYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA-MDGAVL 137

Query: 276 GGRRLNIKWGRAQANRG 292
            GR L ++  R      
Sbjct: 138 DGRELRVQMARYGRPPD 154

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 63.1 bits (154), Expect = 8e-13
 Identities = 25/99 (25%), Positives = 40/99 (40%), Gaps = 7/99 (7%)

Query: 198 RASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------ 251
            A+ M             LYVG+L   +TE  LR  F  FG I S+ ++   +       
Sbjct: 11  MAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGY 70

Query: 252 AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQAN 290
            FI ++    A+ A+E   N   L GR + +     + +
Sbjct: 71  GFITFSDSECAKKALE-QLNGFELAGRPMKVGHVTERTD 108

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 64.1 bits (156), Expect = 9e-13
 Identities = 20/85 (23%), Positives = 35/85 (41%), Gaps = 2/85 (2%)

Query: 203 PKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-AFIQYTSRPA 261
             +          +YVGNLG+   + +L   F  +G +RSV +       AF+++     
Sbjct: 63  HHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRD 122

Query: 262 AEAAVEHSFNKVILGGRRLNIKWGR 286
           A  AV    +   L G R+ ++   
Sbjct: 123 AADAVRE-LDGRTLCGCRVRVELSN 146

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 63.2 bits (154), Expect = 9e-13
 Identities = 26/110 (23%), Positives = 44/110 (40%), Gaps = 8/110 (7%)

Query: 192 AEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ- 250
           A             +  ++    ++YVGN+    T QDL  HF   G I  +TIL  +  
Sbjct: 15  AGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFS 74

Query: 251 -----CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDT 295
                 A+I++  R + +AAV    ++ +  GR + +   R        T
Sbjct: 75  GHPKGYAYIEFAERNSVDAAVA--MDETVFRGRTIKVLPKRTNMPGISST 122

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 64.1 bits (156), Expect = 9e-13
 Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 7/77 (9%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI----LSKQQC--AFIQYTSRPAAEAAVE 267
            TLYVGNL    TE+ + + F + G+I+ + +    + K  C   F++Y SR  AE A+ 
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99

Query: 268 HSFNKVILGGRRLNIKW 284
              N   L  R +   W
Sbjct: 100 -YINGTRLDDRIIRTDW 115

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 65.4 bits (160), Expect = 9e-13
 Identities = 27/117 (23%), Positives = 50/117 (42%), Gaps = 10/117 (8%)

Query: 206 DPPEDKTI-TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----SKQQCAFIQYTSR 259
           DP   K+    +++ NL   +  + L D F  FG I S  ++     SK    F+ + ++
Sbjct: 95  DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK-GYGFVHFETQ 153

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRL--EPVPGLPGALPP 314
            AAE A+E   N ++L  R++ +   +++  R  +            VP   G+   
Sbjct: 154 EAAERAIE-KMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPDYAGSSGR 209

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 63.8 bits (156), Expect = 3e-12
 Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 10/96 (10%)

Query: 206 DPPEDK-TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----SKQQC-AFIQYTS 258
           +P      + +LYVG+L   +TE  L + F   G I S+ +       +    A++ +  
Sbjct: 7   NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66

Query: 259 RPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGED 294
              AE A++ + N  ++ G+ + I W  +Q +    
Sbjct: 67  PADAERALD-TMNFDVIKGKPVRIMW--SQRDPSLR 99

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 62.8 bits (153), Expect = 1e-12
 Identities = 23/106 (21%), Positives = 45/106 (42%), Gaps = 9/106 (8%)

Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-------SKQQC 251
            S+       +      ++VG+L  ++T +D++  F  FG I    ++       SK   
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGY- 59

Query: 252 AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAE 297
            F+ + ++  AE A++       LGGR++   W   +    + T E
Sbjct: 60  GFVSFFNKWDAENAIQ-QMGGQWLGGRQIRTNWATRKPPAPKSTYE 104

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 62.2 bits (152), Expect = 1e-12
 Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 7/86 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
           + LYVG+L   +TE  LR  F  FG+I ++ ++            FI ++    A  A+E
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65

Query: 268 HSFNKVILGGRRLNIKWGRAQANRGE 293
              N   L GR + +     + + G 
Sbjct: 66  -QLNGFELAGRPMRVGHVTERLDGGS 90

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 62.8 bits (153), Expect = 1e-12
 Identities = 21/103 (20%), Positives = 46/103 (44%), Gaps = 7/103 (6%)

Query: 190 PVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ 249
           P+A   ++ A+        E      L++ +L  + T+ DL   F  FG + S  +   +
Sbjct: 17  PLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDK 76

Query: 250 QC------AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR 286
           Q        F+ + +  +A+ A++ + N   +G +RL ++  +
Sbjct: 77  QTSLSKCFGFVSFDNPDSAQVAIK-AMNGFQVGTKRLKVQLKK 118

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 66.4 bits (161), Expect = 1e-12
 Identities = 19/92 (20%), Positives = 42/92 (45%), Gaps = 8/92 (8%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFY----QFGEIRSVTILSKQQ---CAFIQYTSR 259
            PE +   T+Y+ NL +K+ + +L+   Y    QFG+I  + +    +    AF+ +   
Sbjct: 3   VPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEV 62

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
            +A  A+  S        + + I++ +  ++ 
Sbjct: 63  SSATNALR-SMQGFPFYDKPMRIQYAKTDSDI 93

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 56.4 bits (135), Expect = 3e-09
 Identities = 30/210 (14%), Positives = 64/210 (30%), Gaps = 10/210 (4%)

Query: 80  DTALKIKDDIPKSDVNKEYYIQNMDHEIGKID--STTPAGALGKASGSSEMLMKLARTTP 137
           D  ++I+     SD+  +     ++ +  +      +      K +        +     
Sbjct: 79  DKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQ 138

Query: 138 YYKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMA 197
                 P + +   +       + PY       P   LA   I               + 
Sbjct: 139 GPVPGMPPM-TQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQ------LM 191

Query: 198 RASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-CAFIQY 256
                P     E+     L++ NL ++  E  L   F QF   + V ++  +   AF+++
Sbjct: 192 PGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEF 251

Query: 257 TSRPAAEAAVEHSFNKVILGGRRLNIKWGR 286
            +   A AA +      I     + I + +
Sbjct: 252 DNEVQAGAARDALQGFKITQNNAMKISFAK 281

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 62.3 bits (152), Expect = 2e-12
 Identities = 24/112 (21%), Positives = 50/112 (44%), Gaps = 10/112 (8%)

Query: 186 GVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI 245
           G +        +  +   + + PE      L++ +L  +  +QDL   F  FG + S  +
Sbjct: 1   GSSGSSGLTQQSIGAAGSQKEGPEG---ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKV 57

Query: 246 LSKQQC------AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
              +Q        F+ Y +  +A+AA++ S N   +G +RL ++  R++ + 
Sbjct: 58  FIDKQTNLSKCFGFVSYDNPVSAQAAIQ-SMNGFQIGMKRLKVQLKRSKNDS 108

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 62.1 bits (151), Expect = 2e-12
 Identities = 12/81 (14%), Positives = 28/81 (34%), Gaps = 7/81 (8%)

Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAE 263
            D    ++Y+       T  D+++     G++ ++ +            F+ + S  +A+
Sbjct: 7   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 66

Query: 264 AAVEHSFNKVILGGRRLNIKW 284
             VE            L I +
Sbjct: 67  KFVET--PGQKYKETDLLILF 85

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 61.4 bits (150), Expect = 2e-12
 Identities = 18/83 (21%), Positives = 41/83 (49%), Gaps = 8/83 (9%)

Query: 210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAE 263
           +    ++YVGN+    T ++L  HF+  G +  VTIL  +        A+I+++ + +  
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 264 AAVEHSFNKVILGGRRLNIKWGR 286
            ++    ++ +  GR++ +   R
Sbjct: 63  TSLA--LDESLFRGRQIKVIPKR 83

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 62.9 bits (153), Expect = 2e-12
 Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 7/92 (7%)

Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------A 252
            S           T   LYVG L +++ ++ L   F  FG+I  + I    +       A
Sbjct: 49  GSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA 108

Query: 253 FIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW 284
           F+++     A AA++ + N+  L GR + +  
Sbjct: 109 FVEFELAEDAAAAID-NMNESELFGRTIRVNL 139

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 61.5 bits (150), Expect = 2e-12
 Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPA 261
               + +T+YV NL   LT  DL   F ++G++  VTI+  +        AFI +  + +
Sbjct: 11  GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDS 70

Query: 262 AEAAVEHSFNKVILGGRRL 280
           A+     + N   L GR +
Sbjct: 71  AQNCTR-AINNKQLFGRVI 88

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 61.9 bits (151), Expect = 2e-12
 Identities = 19/88 (21%), Positives = 41/88 (46%), Gaps = 5/88 (5%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC----AFIQYTSRPAAEAAVEHS 269
             +++ NL   +  + L D F  FG I S  ++  +       F+ + ++ AAE A+E  
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIE-K 64

Query: 270 FNKVILGGRRLNIKWGRAQANRGEDTAE 297
            N ++L  R++ +   +++  R  +   
Sbjct: 65  MNGMLLNDRKVFVGRFKSRKEREAELGA 92

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 61.5 bits (150), Expect = 3e-12
 Identities = 17/92 (18%), Positives = 37/92 (40%), Gaps = 7/92 (7%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSR 259
                     L+VG L     EQ L   F ++G+I  V ++  ++        F+ + + 
Sbjct: 5   SSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENI 64

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
             A+ A+  + N   + GR++ +      ++ 
Sbjct: 65  DDAKDAMM-AMNGKSVDGRQIRVDQAGKSSDN 95

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 64.4 bits (156), Expect = 3e-12
 Identities = 27/159 (16%), Positives = 49/159 (30%), Gaps = 12/159 (7%)

Query: 177 DQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQ 236
               +DR Y    P            P +          LY+GNL    T++DL +  + 
Sbjct: 32  GDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHS 91

Query: 237 FG--EIRSVTIL-------SKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA 287
            G  +I  +          SK     +   S  +++  ++    K  L G+   +     
Sbjct: 92  LGVNDILEIKFFENRANGQSKGFA-LVGVGSEASSKKLMD-LLPKRELHGQNPVVTPVNK 149

Query: 288 QA-NRGEDTAELKVRLEPVPGLPGALPPPPKDFFNLSNP 325
           Q  ++ E  +    +   + G   A PP           
Sbjct: 150 QFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQG 188

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 60.6 bits (148), Expect = 3e-12
 Identities = 17/76 (22%), Positives = 27/76 (35%), Gaps = 11/76 (14%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI-------LSKQQC-AFIQYTSRPAAEAA 265
           + LY+  L    T+QDL      +G+I S            K     F+ + S  AA+ A
Sbjct: 6   SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCK--GYGFVDFDSPSAAQKA 63

Query: 266 VEHSFNKVILGGRRLN 281
           V        +  +   
Sbjct: 64  VTA-LKASGVQAQMAK 78

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 62.2 bits (151), Expect = 3e-12
 Identities = 21/90 (23%), Positives = 39/90 (43%), Gaps = 14/90 (15%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSV------------TILSKQQCAFIQYTSRPA 261
             +YV NL   + E+DL+  F ++ +  S                 K Q AFI   +  A
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQ-AFIGLPNEKA 104

Query: 262 AEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
           A  A++   N  +L G+ + +++ R+   +
Sbjct: 105 AAKALK-EANGYVLFGKPMVVQFARSARPK 133

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 61.1 bits (149), Expect = 3e-12
 Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 7/81 (8%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----SKQQCAFIQYTSRPAAEAAVEHSF 270
           LYV NL D + ++ LR  F  FG I S  ++     SK    F+ ++S   A  AV    
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSK-GFGFVCFSSPEEATKAVT-EM 75

Query: 271 NKVILGGRRLNIKWGRAQANR 291
           N  I+  + L +   + +  R
Sbjct: 76  NGRIVATKPLYVALAQRKEER 96

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 60.7 bits (148), Expect = 4e-12
 Identities = 18/87 (20%), Positives = 36/87 (41%), Gaps = 7/87 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
             +Y+G++    TE+ + D     G + ++ ++   Q       AFI++    ++ +AV 
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 268 HSFNKVILGGRRLNIKWGRAQANRGED 294
            + N   LG R L   +       G  
Sbjct: 63  -NLNGYQLGSRFLKCGYSSNSDISGVS 88

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 60.4 bits (147), Expect = 6e-12
 Identities = 23/98 (23%), Positives = 43/98 (43%), Gaps = 6/98 (6%)

Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ--CAFI 254
           +  S+       E KT   L + NL    TE+ L++ F +   I+     + +    AFI
Sbjct: 2   SSGSSGNSTWSGESKT---LVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFI 58

Query: 255 QYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRG 292
           ++ S   A+ A+  S NK  + GR + ++    + +  
Sbjct: 59  EFASFEDAKEALN-SCNKREIEGRAIRLELQGPRGSPN 95

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 60.3 bits (147), Expect = 6e-12
 Identities = 12/90 (13%), Positives = 33/90 (36%), Gaps = 7/90 (7%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-----AFIQYTSRPA 261
             E  T   L++GNL    +  +L+    +      + ++  +        ++ + S   
Sbjct: 11  GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAED 70

Query: 262 AEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
            E A+E     + + G  + ++  + +   
Sbjct: 71  LEKALE--LTGLKVFGNEIKLEKPKGRDGT 98

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 62.8 bits (152), Expect = 6e-12
 Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 3/77 (3%)

Query: 214 TTLYVGNLG-DKLTEQDLRDHFYQFGEIRSVTIL-SKQQCAFIQYTSRPAAEAAVEHSFN 271
             L V  L   K+    + + F  +G +  V  + SK   A ++     A + A+ H  N
Sbjct: 5   PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITH-LN 63

Query: 272 KVILGGRRLNIKWGRAQ 288
              + G+++N+   +  
Sbjct: 64  NNFMFGQKMNVCVSKQP 80

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 52.4 bits (125), Expect = 3e-08
 Identities = 12/119 (10%), Positives = 33/119 (27%), Gaps = 7/119 (5%)

Query: 170 DPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQD 229
               P     ++D      D    +    ++               L+  N   ++TE++
Sbjct: 80  PAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEEN 139

Query: 230 LRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
             +   + G  R  ++        +     +++ S+  A   +    N   +       
Sbjct: 140 FFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLG-FLNHYQMKNPNGPY 197

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 59.9 bits (146), Expect = 7e-12
 Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 7/79 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
             LYVG L +++ ++ L   F  FG+I  + I    +       AF+++     A AA++
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67

Query: 268 HSFNKVILGGRRLNIKWGR 286
            + N+  L GR + +   +
Sbjct: 68  -NMNESELFGRTIRVNLAK 85

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 61.8 bits (151), Expect = 7e-12
 Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 8/86 (9%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL----SKQQC-AFIQYTSRPAAEAAVEHS 269
            LYVGNL   +TE  L+ +F   G I ++ I+    +K    AF++Y     A  A++ +
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQ-T 60

Query: 270 FNKVILGGRRLNIKWGRAQANRGEDT 295
            N   +    + I W  A  ++   +
Sbjct: 61  LNGKQIENNIVKINW--AFQSQQSSS 84

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 59.1 bits (144), Expect = 7e-11
 Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 8/86 (9%)

Query: 206 DPPEDKTIT-TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTS 258
                   T  L+VG+L   + ++ LR+ F  F    S  ++   Q        F+ +TS
Sbjct: 79  SQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTS 138

Query: 259 RPAAEAAVEHSFNKVILGGRRLNIKW 284
           +  A+ A++ S     L GR L I W
Sbjct: 139 QDDAQNAMD-SMQGQDLNGRPLRINW 163

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 60.5 bits (147), Expect = 1e-11
 Identities = 33/136 (24%), Positives = 52/136 (38%), Gaps = 18/136 (13%)

Query: 162 PYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNL 221
            + H   +    P        R   +      + M R S         D     L V  L
Sbjct: 4   SHHHHHHSSGLVP--------RGSHMASMTGGQQMGRGSRHVGNRANPDPN-CCLGVFGL 54

Query: 222 GDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHSFNKVIL 275
               TE+DLR+ F ++G I  V+I+  QQ       AF+ + +   A+ A E   N + L
Sbjct: 55  SLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE-RANGMEL 113

Query: 276 GGRRLNIKWGRAQANR 291
            GRR+ + +  +   R
Sbjct: 114 DGRRIRVDF--SITKR 127

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 60.0 bits (146), Expect = 1e-11
 Identities = 27/119 (22%), Positives = 46/119 (38%), Gaps = 11/119 (9%)

Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC----- 251
             + +       +D T T ++VG L    T+  LR +F  FG+I    +++ +Q      
Sbjct: 1   GSSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG 60

Query: 252 -AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLEPVPGLP 309
             F+    R AAE A +      I+ GR+ N+    A     +  +        V G  
Sbjct: 61  YGFVTMADRAAAERACKDPNP--IIDGRKANVN--LAYL-GAKPRSLQTGFAIGVSGPS 114

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 59.0 bits (143), Expect = 1e-11
 Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 13/79 (16%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-----------AFIQYTSRPAAEA 264
           LYVGN+   +TE+ + D F     +  +T                  AF+++ S      
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 265 AVEHSFNKVILGGRRLNIK 283
           A+   F+ +I  G+ L I+
Sbjct: 69  AMA--FDGIIFQGQSLKIR 85

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 60.6 bits (148), Expect = 2e-11
 Identities = 18/93 (19%), Positives = 40/93 (43%), Gaps = 13/93 (13%)

Query: 202 MPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQ 255
           +P+ +  +   I   +VG +G  +  ++  + F Q+G I    ++  +         F+ 
Sbjct: 79  IPRDEQDKTGKI---FVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVT 135

Query: 256 YTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ 288
           Y S  A +   ++    +    R++ IK  RA+
Sbjct: 136 YDSADAVDRVCQN--KFIDFKDRKIEIK--RAE 164

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 51.8 bits (125), Expect = 2e-08
 Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 12/92 (13%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEH 268
            +++G L    TE +LR++F ++G +  + I+            F+ +    + +  V+ 
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK- 63

Query: 269 SFNKVILGGRRLNIKWGRAQANRGEDTAELKV 300
              + IL G+ ++ K  RA   R E     K+
Sbjct: 64  --TQHILDGKVIDPK--RAIP-RDEQDKTGKI 90

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 58.8 bits (143), Expect = 3e-11
 Identities = 18/106 (16%), Positives = 47/106 (44%), Gaps = 7/106 (6%)

Query: 192 AEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC 251
            E++        +  P        L+V ++ ++  E ++++ F  +GEI+++ +   ++ 
Sbjct: 5   YERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRT 64

Query: 252 ------AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
                 A ++Y +   A AA E + N   + G+ + + W   +  +
Sbjct: 65  GFSKGYALVEYETHKQALAAKE-ALNGAEIMGQTIQVDWCFVKGPK 109

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 58.3 bits (141), Expect = 4e-11
 Identities = 13/80 (16%), Positives = 28/80 (35%), Gaps = 2/80 (2%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAV 266
           PP  ++   + V  L    + QDL+DH  + G++    +        +++  +     AV
Sbjct: 9   PPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAV 67

Query: 267 EHSFNKVILGGRRLNIKWGR 286
               +            + R
Sbjct: 68  R-KLDNTKFRSHEGETAYIR 86

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 60.4 bits (147), Expect = 4e-11
 Identities = 20/98 (20%), Positives = 42/98 (42%), Gaps = 11/98 (11%)

Query: 198 RASTMPKLDPPE-DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC----- 251
           RA +      P    T+  ++VG + +   E  LRD+F Q+G+I  + I++ +       
Sbjct: 88  RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRG 147

Query: 252 -AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ 288
            AF+ +    + +  V   +    + G    ++  +A 
Sbjct: 148 FAFVTFDDHDSVDKIVIQKY--HTVNGHNCEVR--KAL 181

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 56.1 bits (136), Expect = 1e-09
 Identities = 24/107 (22%), Positives = 46/107 (42%), Gaps = 9/107 (8%)

Query: 202 MPKLDPP-EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFI 254
           M K + P E + +  L++G L  + T++ LR HF Q+G +    ++            F+
Sbjct: 1   MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60

Query: 255 QYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVR 301
            Y +    +AA+        + GR +  K   ++ +     A L V+
Sbjct: 61  TYATVEEVDAAMNA--RPHKVDGRVVEPKRAVSREDSQRPGAHLTVK 105

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 58.5 bits (142), Expect = 4e-11
 Identities = 20/93 (21%), Positives = 44/93 (47%), Gaps = 7/93 (7%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRP 260
           P        L+V  + ++ TE+D+ D F ++GEI+++ +   ++         ++Y +  
Sbjct: 16  PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 75

Query: 261 AAEAAVEHSFNKVILGGRRLNIKWGRAQANRGE 293
            A+AA+E   N   L G+ +++ W   +     
Sbjct: 76  EAQAAME-GLNGQDLMGQPISVDWCFVRGPPKG 107

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 58.0 bits (141), Expect = 4e-11
 Identities = 17/89 (19%), Positives = 38/89 (42%), Gaps = 10/89 (11%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRP 260
                    ++VG +     E +LR++F +FG +  V ++   +        FI +    
Sbjct: 4   GSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQ 63

Query: 261 AAEAAVEHSFNKVILGGRRLNIKWGRAQA 289
           + + AV    +   + G+++ +K  RA+ 
Sbjct: 64  SVDQAVNM--HFHDIMGKKVEVK--RAEP 88

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 57.3 bits (139), Expect = 6e-11
 Identities = 17/92 (18%), Positives = 35/92 (38%), Gaps = 15/92 (16%)

Query: 203 PKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC----------- 251
                       T++V  LG+ +T + + D+F Q G I++     +              
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 252 ---AFIQYTSRPAAEAAVEHSFNKVILGGRRL 280
              A + +   P+A+AA++  F+     G  +
Sbjct: 63  KGEATVSFDDPPSAKAAID-WFDGKEFSGNPI 93

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 56.7 bits (138), Expect = 7e-11
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 7/75 (9%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
           L+VG+L   + ++ LR+ F  F    S  ++   Q        F+ +TS+  A+ A++ S
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD-S 62

Query: 270 FNKVILGGRRLNIKW 284
                L GR L I W
Sbjct: 63  MQGQDLNGRPLRINW 77

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 57.3 bits (139), Expect = 9e-11
 Identities = 19/79 (24%), Positives = 42/79 (53%), Gaps = 7/79 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
             L+V  + ++ TE+D+ D F ++GEI+++ +   ++         ++Y +   A+AA+E
Sbjct: 24  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83

Query: 268 HSFNKVILGGRRLNIKWGR 286
              N   L G+ +++ W  
Sbjct: 84  -GLNGQDLMGQPISVDWCF 101

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 58.0 bits (140), Expect = 1e-10
 Identities = 16/118 (13%), Positives = 35/118 (29%), Gaps = 9/118 (7%)

Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFG--EIRSVTILSKQQC--- 251
            +   +             +YVG+     T+Q L       G  ++  +     +     
Sbjct: 39  NKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQS 98

Query: 252 ---AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLEPVP 306
              A +   S  +    +E      +L G +++++    Q     +    K     VP
Sbjct: 99  KGYAEVVVASENSVHKLLE-LLPGKVLNGEKVDVRPATRQNLSQFEAQARKRECVRVP 155

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 56.4 bits (136), Expect = 2e-10
 Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 13/83 (15%)

Query: 215 TLYVGNLGDKLTEQDL---RDHFYQFGEIRSVTILSKQQ---------CAFIQYTSRPAA 262
            ++V  L  +L + ++    ++F +FG+I  V I +             A++ Y     A
Sbjct: 17  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76

Query: 263 EAAVEHSFNKVILGGRRLNIKWG 285
             A++   N V++ GR L    G
Sbjct: 77  LRAIQ-CVNNVVVDGRTLKASLG 98

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 55.7 bits (135), Expect = 2e-10
 Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-AFIQYTSRPAAEAAVEHSFNKVI 274
           ++VG     +TE +LR+ F Q+G++  V I    +  AF+ +     A++        +I
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG---EDLI 64

Query: 275 LGGRRLNIKWGRAQ 288
           + G  ++I    A+
Sbjct: 65  IKGISVHIS--NAE 76

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 56.3 bits (136), Expect = 3e-10
 Identities = 18/92 (19%), Positives = 40/92 (43%), Gaps = 15/92 (16%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC--------------AFIQYTSR 259
            T++V  LG+ +T + + D+F Q G I++     +                 A + +   
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
           P+A+AA++  F+     G  + + +   +A+ 
Sbjct: 68  PSAKAAID-WFDGKEFSGNPIKVSFATRRADF 98

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 55.3 bits (134), Expect = 3e-10
 Identities = 17/86 (19%), Positives = 38/86 (44%), Gaps = 6/86 (6%)

Query: 204 KLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-AFIQYTSRPAA 262
           +         + ++VG   + +T ++L+  F Q+GE+  V I    +  AF+ +     A
Sbjct: 2   RGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVA 61

Query: 263 EAAVEHSFNKVILGGRRLNIKWGRAQ 288
           ++        +I+ G  ++I    A+
Sbjct: 62  QSLCG---EDLIIKGISVHIS--NAE 82

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 54.1 bits (131), Expect = 7e-10
 Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 10/87 (11%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRP 260
              ++    ++VG L    +++DL+D+F +FGE+   TI             FI +    
Sbjct: 5   SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAA 64

Query: 261 AAEAAVEHSFNKVILGGRRLNIKWGRA 287
           + E  ++   ++  L GR ++ K  +A
Sbjct: 65  SVEKVLDQKEHR--LDGRVIDPK--KA 87

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 54.6 bits (132), Expect = 7e-10
 Identities = 21/102 (20%), Positives = 42/102 (41%), Gaps = 13/102 (12%)

Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC----- 251
           +  S+ P       KT   L+V  L +  TE+ L++    F       I++ ++      
Sbjct: 2   SSGSSGPNARSQPSKT---LFVKGLSEDTTEETLKES---FDGSVRARIVTDRETGSSKG 55

Query: 252 -AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRG 292
             F+ + S   A+AA E +     + G ++ + W + +   G
Sbjct: 56  FGFVDFNSEEDAKAAKE-AMEDGEIDGNKVTLDWAKPKGEGG 96

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 54.2 bits (131), Expect = 9e-10
 Identities = 20/97 (20%), Positives = 40/97 (41%), Gaps = 11/97 (11%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSR 259
                +  + L V  L  K TEQDL+++F  FGE+  V +    +        F+++T  
Sbjct: 8   VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEY 67

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTA 296
                 +     + ++ GR  + K     + + +D+ 
Sbjct: 68  ETQVKVMS---QRHMIDGRWCDCK--LPNSKQSQDSG 99

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 7/75 (9%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
           T + V N+   ++  ++ D FY +  I     L   +       A + + SR  A AAV 
Sbjct: 16  TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

Query: 268 HSFNKVILGGRRLNI 282
              N   +G R++ +
Sbjct: 76  -DLNDRPIGSRKVKL 89

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 53.7 bits (130), Expect = 1e-09
 Identities = 15/84 (17%), Positives = 32/84 (38%), Gaps = 9/84 (10%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFG--EIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
           LY+GNL    T++DL +  +  G  +I  +     +        A +   S  +++  ++
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 268 HSFNKVILGGRRLNIKWGRAQANR 291
               K  L G+   +       + 
Sbjct: 64  -LLPKRELHGQNPVVTPSNKLEHH 86

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 54.4 bits (131), Expect = 1e-09
 Identities = 13/80 (16%), Positives = 28/80 (35%), Gaps = 2/80 (2%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAV 266
           PP  ++   + V  L    + QDL+DH  + G++    +        +++  +     AV
Sbjct: 10  PPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAV 68

Query: 267 EHSFNKVILGGRRLNIKWGR 286
               +            + R
Sbjct: 69  R-KLDNTKFRSHEGETAYIR 87

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 52.5 bits (127), Expect = 2e-09
 Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 8/74 (10%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
           ++VG L     E+ +R++F  FGE+ S+ +    +        FI +      +  +E  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 270 FNKVILGGRRLNIK 283
           ++   +G  +  IK
Sbjct: 62  YH--NVGLSKCEIK 73

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 8/85 (9%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-------AFIQYTSRPAAEAAVE 267
            +++GNL  ++ E+ L D F  FG I     + +          AFI + S  A++AA+E
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 268 HSFNKVILGGRRLNIKWGRAQANRG 292
            + N   L  R + + +   + ++G
Sbjct: 67  -AMNGQYLCNRPITVSYAFKKDSKG 90

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 52.9 bits (128), Expect = 2e-09
 Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 9/76 (11%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-------SKQQCAFIQYTSRPAAEAAVEH 268
           ++VG+L  ++T   +   F  FG I    ++       SK    F+ + ++  AE A++ 
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGY-GFVSFFNKWDAENAIQ- 66

Query: 269 SFNKVILGGRRLNIKW 284
                 LGGR++   W
Sbjct: 67  QMGGQWLGGRQIRTNW 82

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 53.1 bits (128), Expect = 2e-09
 Identities = 9/93 (9%), Positives = 32/93 (34%), Gaps = 12/93 (12%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFG--EIRSVTILSKQQC------AFIQYT 257
                    T+ + N+        +      +    + ++ ++  +Q       AF+Q +
Sbjct: 3   HHHHHHM-DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLS 61

Query: 258 SRPAAEAAVEH---SFNKVILGGRRLNIKWGRA 287
           S   A   ++        + + G+ + + + ++
Sbjct: 62  SAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 53.4 bits (129), Expect = 3e-09
 Identities = 22/96 (22%), Positives = 44/96 (45%), Gaps = 11/96 (11%)

Query: 201 TMPKLD-PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAF 253
           T+P      E +    L++G L  + TE+ LR+++ Q+G++    ++            F
Sbjct: 14  TVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 73

Query: 254 IQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA 289
           + ++S    +AA+    +   + GR +  K  RA A
Sbjct: 74  VTFSSMAEVDAAMAARPHS--IDGRVVEPK--RAVA 105

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 52.6 bits (126), Expect = 4e-09
 Identities = 16/88 (18%), Positives = 37/88 (42%), Gaps = 3/88 (3%)

Query: 197 ARASTMPKLDPPEDKTITTLYVGNL-GDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQ 255
                  K D  ++     +++ NL     ++  +      +G+I++  ++  +  AFI+
Sbjct: 10  PEGKPDQKFDQKQELG-RVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIE 68

Query: 256 YTSRPAAEAAVEH-SFNKVILGGRRLNI 282
             +R  A A V+H     +   GR + +
Sbjct: 69  METREDAMAMVDHCLKKALWFQGRCVKV 96

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 54.0 bits (129), Expect = 5e-09
 Identities = 19/95 (20%), Positives = 35/95 (36%), Gaps = 3/95 (3%)

Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK--QQCAFI 254
           + A+    +       +  + V NL   +T   L   F +FG +  +   +K  Q  A +
Sbjct: 30  SAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALL 89

Query: 255 QYTSRPAAEAAVEHSFNKVIL-GGRRLNIKWGRAQ 288
           QY    +A+ A      + I      L I + +  
Sbjct: 90  QYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT 124

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 51.9 bits (125), Expect = 5e-09
 Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 7/76 (9%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
           T + V N+   ++  ++ D FY +  I     L   +       A + + SR  A AAV 
Sbjct: 16  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

Query: 268 HSFNKVILGGRRLNIK 283
              N   +G R++ + 
Sbjct: 76  -DLNDRPIGSRKVKLV 90

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 51.3 bits (124), Expect = 6e-09
 Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 10/78 (12%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
           ++VG L    T +D++ +F QFG++    ++  +         F+ + S    E   E  
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI- 60

Query: 270 FNKVILGGRRLNIKWGRA 287
            +   +  + +  K  +A
Sbjct: 61  -HFHEINNKMVECK--KA 75

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 51.4 bits (124), Expect = 6e-09
 Identities = 15/85 (17%), Positives = 37/85 (43%), Gaps = 8/85 (9%)

Query: 213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAV 266
           +  +YVGNL    T + +++ F QFG++ +V ++  ++        F++     +   A+
Sbjct: 1   MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAI 59

Query: 267 EHSFNKVILGGRRLNIKWGRAQANR 291
               +     GR + +     + + 
Sbjct: 60  A-KLDNTDFMGRTIRVTEANPKKSL 83

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 51.9 bits (125), Expect = 7e-09
 Identities = 14/87 (16%), Positives = 36/87 (41%), Gaps = 10/87 (11%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-------CAFIQYTSRPAAEAAVE 267
           T ++GNL   +TE+ +++ F     I +V +  +           + ++    +  +A+ 
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 268 HSFNKVILGGRRLNIKWGRAQANRGED 294
              N+  LG +R+ +       ++   
Sbjct: 76  --LNEESLGNKRIRVDVADQAQDKDSG 100

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 51.9 bits (125), Expect = 7e-09
 Identities = 19/97 (19%), Positives = 37/97 (38%), Gaps = 10/97 (10%)

Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CA 252
           +S    ++      I  L+VG L    T++ LR +F Q+GE+    I+  +         
Sbjct: 2   SSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFG 61

Query: 253 FIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA 289
           F+++         +    +   L GR ++ K      
Sbjct: 62  FVKFKDPNCVGTVLASRPHT--LDGRNIDPK--PCTP 94

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 52.3 bits (125), Expect = 1e-08
 Identities = 19/95 (20%), Positives = 35/95 (36%), Gaps = 3/95 (3%)

Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK--QQCAFI 254
           + A+    +       +  + V NL   +T   L   F +FG +  +   +K  Q  A +
Sbjct: 12  SAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALL 71

Query: 255 QYTSRPAAEAAVEHSFNKVIL-GGRRLNIKWGRAQ 288
           QY    +A+ A      + I      L I + +  
Sbjct: 72  QYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT 106

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 51.2 bits (122), Expect = 2e-08
 Identities = 17/85 (20%), Positives = 31/85 (36%), Gaps = 2/85 (2%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-CAFIQYTSRPAAEA 264
           DP     +  L + N    +T   L       G+++ + I  +    A +++ S   A+ 
Sbjct: 18  DPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQK 77

Query: 265 AVEHSFNKVILGGR-RLNIKWGRAQ 288
           A        I  G   L I++ R  
Sbjct: 78  AKAALNGADIYAGCCTLKIEYARPT 102

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 14/90 (15%), Positives = 37/90 (41%), Gaps = 10/90 (11%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSR 259
                 +   +++G L  + T++ LR++F QFGE++   ++            F+ +  +
Sbjct: 18  GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQA 289
              +  +    ++  L  + ++ K   A  
Sbjct: 78  AGVDKVLAQ--SRHELDSKTIDPK--VAFP 103

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 50.6 bits (121), Expect = 3e-08
 Identities = 15/109 (13%), Positives = 38/109 (34%), Gaps = 9/109 (8%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIR-SVTILSKQQ-----CAFIQYTSR 259
                +    +Y+  L  +   + + D F +   +  S+ I            F+++ + 
Sbjct: 18  SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNE 77

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWG-RAQANRGEDTAELKVRLEPVPG 307
              +AA+    +K  +G R + +    +       D    +++  P  G
Sbjct: 78  ADYKAALC--RHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQSGPSSG 124

>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 Length = 102

 Score = 50.2 bits (120), Expect = 3e-08
 Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 2/70 (2%)

Query: 215 TLYVGNLG-DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH-SFNK 272
            +++ +    K     L      FG I +  IL+K   AFI+  +   A+AAV++ +   
Sbjct: 17  VVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTP 76

Query: 273 VILGGRRLNI 282
            ++ G+ + +
Sbjct: 77  ALVFGKPVRV 86

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 49.6 bits (119), Expect = 4e-08
 Identities = 19/95 (20%), Positives = 36/95 (37%), Gaps = 18/95 (18%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGE-IRSVTI-------LSKQQCAFIQYTSRPAAEAA 265
            +L++G+L   + E  +   F   GE + SV I       +    C F+++     AE  
Sbjct: 10  ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYC-FVEFADLATAEKC 68

Query: 266 VEHSFNKVILGG----RRLNIKWGRAQANRGEDTA 296
           +    N   L G    +R  + +    A     ++
Sbjct: 69  LH-KINGKPLPGATPAKRFKLNY----ATYSGPSS 98

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 49.4 bits (118), Expect = 6e-08
 Identities = 11/76 (14%), Positives = 26/76 (34%), Gaps = 8/76 (10%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEI-RSVTILSKQQ-----CAFIQYTSRPAAEAAVE 267
              ++ N+   +T+ D+            +V +L          A +Q+ +   A  +  
Sbjct: 16  VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER 75

Query: 268 HSFNKVILGGRRLNIK 283
              ++  L GR   + 
Sbjct: 76  --LHRKKLNGREAFVH 89

>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 Length = 96

 Score = 48.8 bits (116), Expect = 7e-08
 Identities = 15/86 (17%), Positives = 38/86 (44%), Gaps = 8/86 (9%)

Query: 214 TTLYVGNLGDKLTEQDLR----DHFYQFGEIRSVTIL---SKQQCAFIQYTSRPAAEAAV 266
             + V N+  +L+ ++L+    + F + G+++SV +      Q  A +Q  +   A  AV
Sbjct: 10  ADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAV 69

Query: 267 EHSFNKVILGGRRLNIKWGRAQANRG 292
               ++  +G +++ +      +   
Sbjct: 70  NS-LHRYKIGSKKILVSLATGASGPS 94

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 48.8 bits (117), Expect = 8e-08
 Identities = 16/87 (18%), Positives = 37/87 (42%), Gaps = 6/87 (6%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQ-FGEIRSVTILSKQQC-----AFIQYTSRPAAEAAVEH 268
           +L+VG+L   + +  L + F + +   R   ++  Q        F+++T     + A+  
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70

Query: 269 SFNKVILGGRRLNIKWGRAQANRGEDT 295
               V LG + + +     +A+R +  
Sbjct: 71  CQGAVGLGSKPVRLSVAIPKASRVKPV 97

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 15/75 (20%), Positives = 34/75 (45%), Gaps = 10/75 (13%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-------CAFIQYTSRPAAEAAVE 267
           T ++GNL   +TE+ +++ F     I +V +  +           + ++    +  +A+ 
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79

Query: 268 HSFNKVILGGRRLNI 282
              N+  LG RR+ +
Sbjct: 80  --LNEESLGNRRIRV 92

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 47.5 bits (114), Expect = 1e-07
 Identities = 14/78 (17%), Positives = 36/78 (46%), Gaps = 10/78 (12%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVEHS 269
           +++G L  + T++ LR++F QFGE++   ++            F+ +  +   +  +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 61

Query: 270 FNKVILGGRRLNIKWGRA 287
            ++  L  + ++ K   A
Sbjct: 62  -SRHELDSKTIDPK--VA 76

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 17/86 (19%), Positives = 34/86 (39%), Gaps = 9/86 (10%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEH 268
           T YVGNL     + D+   F     IRSV ++  +         ++++    + + A+  
Sbjct: 17  TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT- 74

Query: 269 SFNKVILGGRRLNIKWGRAQANRGED 294
            ++  +LG R L +     +      
Sbjct: 75  -YDGALLGDRSLRVDIAEGRKQDKSG 99

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 47.6 bits (113), Expect = 3e-07
 Identities = 14/105 (13%), Positives = 33/105 (31%), Gaps = 8/105 (7%)

Query: 185 YGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVT 244
                     +          +  +      + +  L    T++++   F     + +  
Sbjct: 14  LVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGI 73

Query: 245 ILSKQQ------CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK 283
            L           AF+Q+ S+  AE A+    +K  +G R + + 
Sbjct: 74  TLPVDPEGKITGEAFVQFASQELAEKALG--KHKERIGHRYIEVF 116

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 47.1 bits (112), Expect = 4e-07
 Identities = 11/71 (15%), Positives = 30/71 (42%), Gaps = 4/71 (5%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ---CAFIQYTSRPAAEAAVEHSFNK 272
           + + NL +  + QDL+D   +     + + ++ +       +++ S      A+E   N 
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALER-LNN 89

Query: 273 VILGGRRLNIK 283
           +   G  + ++
Sbjct: 90  IEFRGSVITVE 100

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 46.3 bits (110), Expect = 8e-07
 Identities = 14/90 (15%), Positives = 34/90 (37%), Gaps = 8/90 (8%)

Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAF 253
           +S       P +     + V  +     E D+RD F+    + +V +L            
Sbjct: 2   SSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGL 60

Query: 254 IQYTSRPAAEAAVEHSFNKVILGGRRLNIK 283
           +++ S      A++   N++++  R + + 
Sbjct: 61  VKFLSPQDTFEALK--RNRMLMIQRYVEVS 88

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 19/105 (18%), Positives = 39/105 (37%), Gaps = 9/105 (8%)

Query: 183 RYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRS 242
           R   +      + M R S   +    +  T   +++  L  K TE D+ + F     +R 
Sbjct: 17  RGSHMASMTGGQQMGRGSGDSE-FTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR- 74

Query: 243 VTILSKQQ-----CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
           V I           A +++ +   A AA+    ++  +  R + +
Sbjct: 75  VHIEIGPDGRVTGEADVEFATHEEAVAAMSK--DRANMQHRYIEL 117

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 44.7 bits (106), Expect = 2e-06
 Identities = 15/84 (17%), Positives = 34/84 (40%), Gaps = 8/84 (9%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSR 259
           + P+      + +  L    +++++   F     + +   L           AF+Q+ S+
Sbjct: 8   NSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQ 67

Query: 260 PAAEAAVEHSFNKVILGGRRLNIK 283
             AE A++   +K  +G R + I 
Sbjct: 68  EIAEKALK--KHKERIGHRYIEIF 89

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 45.6 bits (107), Expect = 5e-06
 Identities = 12/88 (13%), Positives = 29/88 (32%), Gaps = 7/88 (7%)

Query: 202 MPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQY 256
               +   D    ++Y+       T  D+++     G++ ++ +            F+ +
Sbjct: 98  EVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVF 157

Query: 257 TSRPAAEAAVEHSFNKVILGGRRLNIKW 284
            S  +A+  VE            L I +
Sbjct: 158 DSIESAKKFVET--PGQKYKETDLLILF 183

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 9/69 (13%), Positives = 27/69 (39%), Gaps = 9/69 (13%)

Query: 217 YVGNLGDKLTEQDLRDHFYQFGEIRSVTI-------LSKQQCAFIQYTSRPAAEAAVEHS 269
            + +    + ++ L   F + G++ ++          +K    F++  S   A+  ++  
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTK-GFLFVECGSMNDAKKIIKS- 73

Query: 270 FNKVILGGR 278
           F+   L  +
Sbjct: 74  FHGKRLDLK 82

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 12/89 (13%), Positives = 36/89 (40%), Gaps = 8/89 (8%)

Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAE 263
              T  T+ +      +TE+++ +         ++ I+           F+ +++    +
Sbjct: 6   SGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVK 64

Query: 264 AAVEHSFNKVILGGRRLNIKWGRAQANRG 292
            A++   N+  +GGR + +   ++  + G
Sbjct: 65  QALK--CNREYMGGRYIEVFREKSGPSSG 91

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 45.2 bits (106), Expect = 1e-05
 Identities = 32/142 (22%), Positives = 55/142 (38%), Gaps = 13/142 (9%)

Query: 164 RHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKL-DPPEDKTIT-----TLY 217
             E P D   P   +  ++R         E+      T  K+ DP  D         TL+
Sbjct: 47  EFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLF 106

Query: 218 VGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRPAAEAAVEHSFN 271
           V  +    TE  LR  F  +G I+ + ++        +  AFI+Y       +A +H+ +
Sbjct: 107 VARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA-D 165

Query: 272 KVILGGRRLNIKWGRAQANRGE 293
              + GRR+ +   R +  +G 
Sbjct: 166 GKKIDGRRVLVDVERGRTVKGW 187

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 42.6 bits (100), Expect = 2e-05
 Identities = 11/83 (13%), Positives = 32/83 (38%), Gaps = 10/83 (12%)

Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQF---GEIRSVTILSKQQ-----CAFIQYTSR 259
           PE      + +  L    + +D+++          +  V  +  ++      AF++  S 
Sbjct: 12  PEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESE 71

Query: 260 PAAEAAVEHSFNKVILGGRRLNI 282
              + A++   ++  +G R + +
Sbjct: 72  DDVKLALKK--DRESMGHRYIEV 92

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 11/81 (13%), Positives = 28/81 (34%), Gaps = 13/81 (16%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ--------CAFIQYTSRPAAEAAVE 267
           ++VG L   + E ++   F +FG +        +          AF+ +    + +A ++
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70

Query: 268 HSF-----NKVILGGRRLNIK 283
                     + +    +  K
Sbjct: 71  ACLEEDGKLYLCVSSPTIKDK 91

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 19/89 (21%), Positives = 34/89 (38%), Gaps = 18/89 (20%)

Query: 203 PKLDPPEDKTITTLYVGNL-------GDKLTEQDLRDHFYQFGEIRSVTI-----LSKQQ 250
           P+     D  I    V N+        +KL +  +   F +FG+I +         +K  
Sbjct: 8   PQEADGIDSVI---VVDNVPQVGPDRLEKL-KNVIHKIFSKFGKITNDFYPEEDGKTKG- 62

Query: 251 CAFIQYTSRPAAEAAVEHSFNKVILGGRR 279
             F++Y S   A  AV++  +   L  + 
Sbjct: 63  YIFLEYASPAHAVDAVKN-ADGYKLDKQH 90

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 42.2 bits (99), Expect = 3e-05
 Identities = 13/95 (13%), Positives = 32/95 (33%), Gaps = 11/95 (11%)

Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIR----SVTILSKQQ-- 250
              ++         +    + +  L    T +++   F Q   I      +  ++     
Sbjct: 7   GGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGR 66

Query: 251 ---CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
               AF+ +     A+ A+    +K +LG R + +
Sbjct: 67  PTGDAFVLFACEEYAQNALRK--HKDLLGKRYIEL 99

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 40.5 bits (95), Expect = 7e-05
 Identities = 14/74 (18%), Positives = 27/74 (36%), Gaps = 8/74 (10%)

Query: 211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAEAA 265
            T   +++  L  + TE D+ + F        V I           A +++ +   A AA
Sbjct: 13  TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAA 71

Query: 266 VEHSFNKVILGGRR 279
           +    +K  +  R 
Sbjct: 72  MA--KDKANMQHRY 83

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 39.3 bits (92), Expect = 9e-05
 Identities = 16/78 (20%), Positives = 32/78 (41%), Gaps = 15/78 (19%)

Query: 214 TTLYVGNL-------GDKLTEQDLRDHFYQFGEIRSVTI-----LSKQQCAFIQYTSRPA 261
           + + V N+        +KL +  +   F +FG+I +         +K    F++Y S   
Sbjct: 2   SVIVVDNVPQVGPDRLEKL-KNVIHKIFSKFGKITNDFYPEEDGKTK-GYIFLEYASPAH 59

Query: 262 AEAAVEHSFNKVILGGRR 279
           A  AV++  +   L  + 
Sbjct: 60  AVDAVKN-ADGYKLDKQH 76

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 16/100 (16%), Positives = 35/100 (35%), Gaps = 14/100 (14%)

Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQF---GEIRSVTILSKQQ-----CAFIQYTSR 259
            E   +  +    L    T +D+ + F           +  L  +       A I+  S 
Sbjct: 6   EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESE 65

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELK 299
              + A+E   +++ +G R + +     + N  +  A +K
Sbjct: 66  QDVQKALEK--HRMYMGQRYVEVY----EINNEDVDALMK 99

>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1 Length = 98

 Score = 39.3 bits (91), Expect = 1e-04
 Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 1/40 (2%)

Query: 144 PHIC-SFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKD 182
              C  +   G C  G++C + H+  T+    L D+ + D
Sbjct: 36  DFPCKLYHTTGNCINGDDCMFSHDPLTEETRELLDKMLAD 75

>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1 Length = 98

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 10/35 (28%), Positives = 16/35 (45%)

Query: 133 ARTTPYYKRNRPHICSFWVKGECRRGEECPYRHEK 167
           +  +      +  +C F++ G C R E CPY H  
Sbjct: 2   SSGSSGELPKKRELCKFYITGFCARAENCPYMHGD 36

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 77

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 8/27 (29%), Positives = 17/27 (62%)

Query: 140 KRNRPHICSFWVKGECRRGEECPYRHE 166
              +  +C  W++G C++G++C + HE
Sbjct: 6   SGEKTVVCKHWLRGLCKKGDQCEFLHE 32

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 77

 Score = 37.2 bits (86), Expect = 6e-04
 Identities = 9/32 (28%), Positives = 13/32 (40%)

Query: 139 YKRNRPHICSFWVKGECRRGEECPYRHEKPTD 170
           Y   +   C F+ K      +ECP+ H  P  
Sbjct: 33  YDMTKMPECYFYSKFGECSNKECPFLHIDPES 64

>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens} Length = 72

 Score = 37.9 bits (88), Expect = 3e-04
 Identities = 8/27 (29%), Positives = 17/27 (62%)

Query: 140 KRNRPHICSFWVKGECRRGEECPYRHE 166
              +  +C  W++G C++G++C + HE
Sbjct: 12  SGEKTVVCKHWLRGLCKKGDQCEFLHE 38

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 37.7 bits (87), Expect = 4e-04
 Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 1/69 (1%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
           + L + NL  ++    LR    Q G + S      Q  A  +YT+R  A  A   + N  
Sbjct: 8   SWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQM-ALNNC 66

Query: 274 ILGGRRLNI 282
           +L    +  
Sbjct: 67  VLANTTIFA 75

>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 = 41.0 bits (95), Expect = 5e-04
 Identities = 50/426 (11%), Positives = 104/426 (24%), Gaps = 131/426 (30%)

Query: 4   SKTSSTYNRQSWEDATKEKYG-------KECKICARPFTVFRWCPGARMR-------FKK 49
           SK      +   E+  +  Y         E +  +    ++      R R       F K
Sbjct: 73  SKQEEMVQK-FVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQ---RDRLYNDNQVFAK 128

Query: 50  TEVCQTCARLKNVCQ--TCLLDLE-------YG--------LPIQV-RDTALKIK----- 86
             V     RL+   +    LL+L         G        + + V     ++ K     
Sbjct: 129 YNVS----RLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKI 184

Query: 87  -------DDIPKSDVNKEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLAR--TTP 137
                   + P++ +     +Q + ++I    ++    +         +  +L R   + 
Sbjct: 185 FWLNLKNCNSPETVLEM---LQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK 241

Query: 138 YYKR---------NRPHICSFWVKGECR-----RGEECPYRHEKPTDPDDPLADQNI--K 181
            Y+          N     +F     C+     R ++        TD        +I   
Sbjct: 242 PYENCLLVLLNVQNAKAWNAF--NLSCKILLTTRFKQV-------TDFLSAATTTHISLD 292

Query: 182 DRYYGVNDPVAEKLMARASTMPKLD-PPEDKTITTLYVGNLG------------------ 222
                +     + L+ +       D P E  T     +  +                   
Sbjct: 293 HHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNC 352

Query: 223 -----------DKLTEQDLRDHFYQFGEIR-SVTILSKQQCAFIQYTSRPAAEAAVEHSF 270
                      + L   + R  F +      S  I +           +      V    
Sbjct: 353 DKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLH 412

Query: 271 NKVILGGRRLNIKWG--------RAQANRGEDTAELKVRL-----EPVPGLPGALPPPPK 317
              ++  +               + +    E+   L   +      P       L PP  
Sbjct: 413 KYSLVEKQPKESTISIPSIYLELKVKL---ENEYALHRSIVDHYNIPKTFDSDDLIPPYL 469

Query: 318 D--FFN 321
           D  F++
Sbjct: 470 DQYFYS 475

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 38.4 bits (89), Expect = 6e-04
 Identities = 11/94 (11%), Positives = 33/94 (35%), Gaps = 10/94 (10%)

Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQF---GEIRSVTILSKQQ--- 250
            +      +  PE      + +  L    + +D+++             V  +  ++   
Sbjct: 28  QQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQ 87

Query: 251 --CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
              AF++  S    + A++   ++  +G R + +
Sbjct: 88  SGEAFVELGSEDDVKMALKK--DRESMGHRYIEV 119

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	327
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.95
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.74
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.74
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.73
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.73
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.72
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.71
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.71
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.7
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.7
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.7
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.7
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.69
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.69
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.69
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.69
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.69
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.69
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.69
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.69
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.69
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.69
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.69
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.68
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.68
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.68
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.68
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.68
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.68
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.68
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.67
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.67
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.67
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.67
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.67
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.67
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.67
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.67
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.67
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.67
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.67
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.66
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.66
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.66
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.66
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.66
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.66
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.66
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.66
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.66
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.66
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.66
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.66
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.66
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.66
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.66
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.66
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.66
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.65
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.65
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.65
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.65
1x5p_A	97	Negative elongation factor E; structure genomics,	99.65
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.65
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.65
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.65
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.65
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.65
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.64
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.64
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.64
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.64
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.64
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.64
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.64
2div_A	99	TRNA selenocysteine associated protein; structural	99.64
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.63
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.63
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.63
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.63
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.63
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.63
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.63
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.62
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.62
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.62
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.62
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.62
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.62
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.61
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.61
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.61
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.61
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.61
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.6
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.6
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.6
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.6
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.6
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.6
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.6
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.6
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.59
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.59
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.59
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.59
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.59
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.59
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.59
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.59
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.58
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.58
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.58
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.58
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.58
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.58
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.58
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.58
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.57
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.57
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.57
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.57
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.56
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.56
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.56
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.56
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.56
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.56
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.55
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.55
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.55
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.55
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.54
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.54
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.54
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.53
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.53
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.52
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.52
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.51
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.27
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.51
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.51
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.51
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.51
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.5
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.5
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.5
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.5
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.49
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.49
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.48
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.47
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.47
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.47
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.47
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.47
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.47
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.46
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.46
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.46
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.46
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.46
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.44
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.43
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.43
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.43
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.43
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.43
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.41
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.41
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.41
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.4
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.4
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.38
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.38
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.38
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.38
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.38
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.37
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.37
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.37
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.37
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.36
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.36
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.36
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.35
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.33
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.33
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.33
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.33
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.31
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.31
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.3
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.3
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.29
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.27
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.25
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.21
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.19
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.18
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.13
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.04
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.01
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.96
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.91
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.69
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.4
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.36
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.8
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.77
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.57
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.75
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	96.44
2rhk_C	72	Cleavage and polyadenylation specificity factor su	95.85
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	95.72
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	95.68
3d2q_A	70	Muscleblind-like protein 1; tandem zinc finger dom	95.67
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	95.51
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	95.41
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.34
3d2n_A	83	Muscleblind-like protein 1; tandem zinc finger dom	95.02
3d2q_A	70	Muscleblind-like protein 1; tandem zinc finger dom	94.55
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	94.36
2rhk_C	72	Cleavage and polyadenylation specificity factor su	94.12
2e5s_A	98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	94.01
2rpp_A	89	Muscleblind-like protein 2; zinc finger domain, C3	94.0
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	93.99
2e5s_A	98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	93.42
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	93.02
3d2n_A	83	Muscleblind-like protein 1; tandem zinc finger dom	92.43
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	92.34
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	90.78
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	90.09
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	89.79
2rpp_A	89	Muscleblind-like protein 2; zinc finger domain, C3	88.83
1z2q_A	84	LM5-1; membrane protein, FYVE domain, zinc-finger;	88.72
2d9m_A	69	Zinc finger CCCH-type domain containing protein 7A	88.21
2yw8_A	82	RUN and FYVE domain-containing protein 1; structur	87.83
2fc6_A	50	Nuclear, target of EGR1, member 1; structure genom	87.32
1y02_A	120	CARP2, FYVE-ring finger protein sakura; zinc-bindi	86.48
1vfy_A	73	Phosphatidylinositol-3-phosphate binding FYVE doma	85.79
3t7l_A	90	Zinc finger FYVE domain-containing protein 16; str	84.89
1joc_A	125	EEA1, early endosomal autoantigen 1; FYVE domain,	82.82
1wfk_A	88	Zinc finger, FYVE domain containing 19; riken stru	80.99
1x4u_A	84	Zinc finger, FYVE domain containing 27 isoform B;	80.74
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	80.37

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.95  E-value=1.6e-29  Score=229.41  Aligned_cols=149  Identities=28%  Similarity=0.498  Sum_probs=114.9

Q ss_pred             hcCCCccCCCccccccccccccCCCCCCCCCCCCCCCCCCCC-c-ccCccccCCCCCChhHHHHHHhhcCCCCCCCCCCC
Q psy14139        134 RTTPYYKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPL-A-DQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDK  211 (327)
Q Consensus       134 ~~~p~y~r~~~~~C~ff~kG~C~rG~~Cpy~H~~p~~~~~~l-~-~qni~dr~~G~~~p~~~k~~~~~~~~p~~~~p~d~  211 (327)
                      +.....+++++++|+||+||+|.+|++|+|+|++|++.+... + .+++.|.| |+     .++...+..+.+..+ .+.
T Consensus        60 g~t~~~~~~~~~~C~ffakG~C~~G~~C~y~H~lPt~~d~~~~~~~~~~~D~f-Gr-----~k~~~~~d~~~g~gs-~~~  132 (240)
T 3u1l_A           60 GKTRGDNDGQLFFCLFFAKGMCCLGPKCEYLHHIPDEEDIGKLALRTEVLDCF-GR-----EKFADYREDMGGIGS-FRK  132 (240)
T ss_dssp             BBCHHHHTTCCSBCHHHHTTCCSCGGGCSSBBSCCCHHHHHHHHHHCSSBCTT-SS-----BCGGGTC----------CC
T ss_pred             ccccCCcCCCCeEcCccccCCCCCCCCCCccCCCCCccchhhhcccccCcccc-cc-----hhcccchhcccCcCc-ccc
Confidence            333345678999999999999999999999999998765321 1 13455665 44     245555566665544 477


Q ss_pred             CccEEEEcCCCCCC---------CHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEE-------
Q psy14139        212 TITTLYVGNLGDKL---------TEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL-------  275 (327)
Q Consensus       212 ~~~tLfVgnLp~~i---------te~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i-------  275 (327)
                      ..++||||||+..+         +|++|+++|++||+|.+|+|+.++|||||+|.++++|+.|+++ ++|..|       
T Consensus       133 ~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~kG~AFV~F~~~~~Ae~A~~a-m~g~~l~~~~~~e  211 (240)
T 3u1l_A          133 KNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEA-MSNQTLLLPSDKE  211 (240)
T ss_dssp             CCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHH-HTTCCCCCTTSTT
T ss_pred             CCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECCCCEEEEEeCCHHHHHHHHHH-hCCCEEecccccc
Confidence            88999999999988         7999999999999999999999999999999999999999998 588888       


Q ss_pred             -----CCeeEEEEeccCCCC
Q psy14139        276 -----GGRRLNIKWGRAQAN  290 (327)
Q Consensus       276 -----~G~~L~V~~ak~~~~  290 (327)
                           .|+.|+|+||++.+.
T Consensus       212 ~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          212 WDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             GGGGGGSCCCEEEECC----
T ss_pred             ccccCCCCEEEEEEccCCCC
Confidence                 899999999997654

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.74  E-value=7.7e-18  Score=132.30  Aligned_cols=75  Identities=25%  Similarity=0.483  Sum_probs=70.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.+++|++|+++|++||+|.+++++.+      +|||||+|.+.++|++|++. ++|..++|+.|+|.||
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~-lng~~~~gr~l~V~~A   96 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT-LNGLRLQSKTIKVSYA   96 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHH-HTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHH-hCCCEECCEEEEEEEe
Confidence            3579999999999999999999999999999999864      57999999999999999997 6999999999999999


Q ss_pred             cC
Q psy14139        286 RA  287 (327)
Q Consensus       286 k~  287 (327)
                      +|
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            86

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=9.2e-18  Score=133.43  Aligned_cols=82  Identities=18%  Similarity=0.269  Sum_probs=74.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhc-CCeEECCeeEEEEeccCCC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSF-NKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l-~g~~i~G~~L~V~~ak~~~  289 (327)
                      ...++|||+|||.+++|++|+++|++||+|.+++|+.++|||||+|.+.++|+.|++.+. ++..+.|++|+|.|++++.
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~   93 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE   93 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCC
Confidence            345899999999999999999999999999999999999999999999999999999742 3589999999999998876


Q ss_pred             CCC
Q psy14139        290 NRG  292 (327)
Q Consensus       290 ~~~  292 (327)
                      ...
T Consensus        94 ~~~   96 (105)
T 1sjq_A           94 LKT   96 (105)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            543

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.8e-17  Score=125.50  Aligned_cols=80  Identities=70%  Similarity=1.198  Sum_probs=74.6

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       207 ~p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      ++.+...++|||+|||.++++++|+++|++||.|.++.+..++++|||+|.+.++|++|++.+.++..++|+.|+|.|++
T Consensus         6 ~~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            6 SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             CCSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            35567779999999999999999999999999999999999999999999999999999998449999999999999985

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

Probab=99.73  E-value=1.8e-17  Score=133.49  Aligned_cols=79  Identities=24%  Similarity=0.497  Sum_probs=72.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      .++|||+|||.+++|++|+++|++||.|.+++|+.+    +|||||+|.+.++|++|++. ++|..++|+.|+|.|++++
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~-l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK-MNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHH-HTTCEETTEECEEEESSCC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHH-cCCCEECCEEEEEEECCCc
Confidence            468999999999999999999999999999999875    68999999999999999997 6999999999999999887


Q ss_pred             CCCC
Q psy14139        289 ANRG  292 (327)
Q Consensus       289 ~~~~  292 (327)
                      ..+.
T Consensus        84 ~~~~   87 (115)
T 4f25_A           84 KERE   87 (115)
T ss_dssp             CC--
T ss_pred             cccc
Confidence            6543

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

Probab=99.72  E-value=5.2e-17  Score=126.36  Aligned_cols=81  Identities=32%  Similarity=0.539  Sum_probs=75.4

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEEC--CeeEEEEeccC
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILG--GRRLNIKWGRA  287 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~--G~~L~V~~ak~  287 (327)
                      ....++|||+|||.++++++|+++|++||.|.++.+..+++||||+|.+.++|++|++. +++..+.  |+.|+|.|+++
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~~g~afV~f~~~~~A~~A~~~-l~g~~~~~~g~~l~V~~a~~   92 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAK-MRGFPLGGPDRRLRVDFAKS   92 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHH-HTTCBCSSSSCBCEEEECCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCCCCEEEEEECCHHHHHHHHHH-HCCCEeCCCCcEEEEEECCC
Confidence            34558999999999999999999999999999999999999999999999999999997 6999999  99999999998


Q ss_pred             CCCC
Q psy14139        288 QANR  291 (327)
Q Consensus       288 ~~~~  291 (327)
                      ++.+
T Consensus        93 ~~~~   96 (97)
T 1why_A           93 GPSS   96 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8654

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.2e-16  Score=126.15  Aligned_cols=82  Identities=17%  Similarity=0.241  Sum_probs=74.7

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHh-cCCeEECCeeEEEEeccCCC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHS-FNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~-l~g~~i~G~~L~V~~ak~~~  289 (327)
                      ...++|||+|||.+++|++|+++|++||.|.++.++.++|||||+|.+.++|+.|++.+ .++..+.|++|+|.|++++.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~   92 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE   92 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCccc
Confidence            45589999999999999999999999999999999999999999999999999999974 26789999999999999876


Q ss_pred             CCC
Q psy14139        290 NRG  292 (327)
Q Consensus       290 ~~~  292 (327)
                      ...
T Consensus        93 ~~~   95 (101)
T 2cq1_A           93 LKT   95 (101)
T ss_dssp             CCC
T ss_pred             CcC
Confidence            543

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

Probab=99.71  E-value=2.1e-17  Score=127.65  Aligned_cols=79  Identities=16%  Similarity=0.353  Sum_probs=71.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcC-CeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFG-EIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG-~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      .+|||+|||.+++|++|+++|++|| +|.+|+|+.+      +|||||+|.+.++|++|++.+.++..++|++|+|.|++
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            5899999999999999999999999 8999998763      69999999999999999997557788999999999999


Q ss_pred             CCCCCC
Q psy14139        287 AQANRG  292 (327)
Q Consensus       287 ~~~~~~  292 (327)
                      +++...
T Consensus        82 ~~~~~~   87 (91)
T 2lxi_A           82 PKPKIN   87 (91)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            877653

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

Probab=99.70  E-value=3e-16  Score=123.27  Aligned_cols=83  Identities=25%  Similarity=0.485  Sum_probs=76.0

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      .+...++|||+|||.++++++|+++|++||.|.+|.|..+    ++||||+|.+.++|++|++. +++..+.|+.|+|.|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~V~~   89 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAA-MNGRKILGKEVKVNW   89 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHH-HTTEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHH-hCCCCcCCCeEEEEE
Confidence            4456689999999999999999999999999999999873    68999999999999999997 699999999999999


Q ss_pred             ccCCCCCC
Q psy14139        285 GRAQANRG  292 (327)
Q Consensus       285 ak~~~~~~  292 (327)
                      ++++..+.
T Consensus        90 a~~~~~~~   97 (103)
T 2cqi_A           90 ATTPSSQK   97 (103)
T ss_dssp             CCCTTCCC
T ss_pred             CCCCcccc
Confidence            99876554

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1.4e-16  Score=126.66  Aligned_cols=81  Identities=22%  Similarity=0.517  Sum_probs=75.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQAN  290 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~  290 (327)
                      ...++|||+|||.++++++|+++|++||.|.+|.+..+++||||+|.+.++|++|++. ++|..+.|+.|+|.|++++..
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~v~~a~~~~~  101 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVS-VNGTTIEGHVVKCYWGKESPD  101 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHH-HTTCEETTEECEEECCCCCCS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHH-cCCCEECCcEEEEEecCCCCC
Confidence            3458999999999999999999999999999999999999999999999999999997 699999999999999998765


Q ss_pred             CC
Q psy14139        291 RG  292 (327)
Q Consensus       291 ~~  292 (327)
                      ..
T Consensus       102 ~~  103 (109)
T 1x4g_A          102 MT  103 (109)
T ss_dssp             SC
T ss_pred             CC
Confidence            43

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

Probab=99.70  E-value=1.4e-16  Score=122.15  Aligned_cols=80  Identities=25%  Similarity=0.521  Sum_probs=74.1

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      +...++|||+|||.++++++|+++|++||.|.++.+.  ++||||+|.+.++|++|++. +++..++|+.|+|.|++++.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~v~~a~~~~   81 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAIRN-LHHYKLHGVNINVEASKNKS   81 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--TTEEEEEESSHHHHHHHHHH-HTTCBCSSCBCEEECSSCCC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--CCEEEEEECCHHHHHHHHHH-hcCCccCCcEEEEEECCCCC
Confidence            4456899999999999999999999999999999998  89999999999999999997 69999999999999999877


Q ss_pred             CCC
Q psy14139        290 NRG  292 (327)
Q Consensus       290 ~~~  292 (327)
                      ...
T Consensus        82 ~~~   84 (90)
T 2dnq_A           82 KAS   84 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

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

Probab=99.70  E-value=3.2e-16  Score=123.11  Aligned_cols=83  Identities=25%  Similarity=0.440  Sum_probs=76.2

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      .+...++|||+|||.++++++|+++|++||.|.+|.|..+    +++|||+|.+.++|++|++. +++..++|+.|+|.|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~v~~   89 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREK-LHGTVVEGRKIEVNN   89 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHH-HTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHH-hCCCEECCEEEEEEE
Confidence            3456689999999999999999999999999999999876    78999999999999999997 699999999999999


Q ss_pred             ccCCCCCC
Q psy14139        285 GRAQANRG  292 (327)
Q Consensus       285 ak~~~~~~  292 (327)
                      ++++....
T Consensus        90 a~~~~~~~   97 (103)
T 2cq3_A           90 ATARVMTN   97 (103)
T ss_dssp             CCSSCCCC
T ss_pred             cccCCCCC
Confidence            99887554

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

Probab=99.69  E-value=2.2e-16  Score=122.97  Aligned_cols=82  Identities=20%  Similarity=0.291  Sum_probs=74.8

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      ....++|||+|||.++++++|+++|++||.|.++.+..+      ++||||+|.+.++|++|++. +++..+.|+.|+|.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~V~   83 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE-VDGQVFQGRMLHVL   83 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHH-TTTEESSSCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHH-hCCCEECCcEEEEE
Confidence            345689999999999999999999999999999999864      59999999999999999987 79999999999999


Q ss_pred             eccCCCCCC
Q psy14139        284 WGRAQANRG  292 (327)
Q Consensus       284 ~ak~~~~~~  292 (327)
                      |++++..+.
T Consensus        84 ~a~~~~~~~   92 (99)
T 1whw_A           84 PSTIKKEAS   92 (99)
T ss_dssp             ECCCCSTTC
T ss_pred             EcCCCcccc
Confidence            999887653

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

Probab=99.69  E-value=6.5e-17  Score=126.62  Aligned_cols=77  Identities=30%  Similarity=0.561  Sum_probs=72.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      ...++|||+|||.++++++|+++|++||.|.++++...++||||+|.+.++|++|+.. ++|..++|+.|+|.|++++
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~-l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVA-LANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHH-HTTCEETTEECCCCBCCCC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEecCCCEEEEEECCHHHHHHHHHH-hCCCeECCeEEEEEeccCC
Confidence            3458999999999999999999999999999999999999999999999999999997 7999999999999999874

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

Probab=99.69  E-value=2.3e-16  Score=123.29  Aligned_cols=82  Identities=12%  Similarity=0.297  Sum_probs=75.0

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      .....++|||+|||.++++++|+++|++||.|.++++..+     +++|||+|.+.++|++|++. +++..++|+.|+|.
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~v~   91 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMK-MDGMTIKENIIKVA   91 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHH-HTTEESSSCEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHH-hCCCEECCEEEEEE
Confidence            3455689999999999999999999999999999999875     48999999999999999997 69999999999999


Q ss_pred             eccCCCCC
Q psy14139        284 WGRAQANR  291 (327)
Q Consensus       284 ~ak~~~~~  291 (327)
                      |++++..+
T Consensus        92 ~a~~~~~~   99 (100)
T 2do4_A           92 ISNSGPSS   99 (100)
T ss_dssp             ECCCCSCC
T ss_pred             ECCCCCCC
Confidence            99988754

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=2.7e-16  Score=122.33  Aligned_cols=79  Identities=19%  Similarity=0.357  Sum_probs=73.5

Q ss_pred             CccEEEEcCCCCCCCHHHHH----HHHhhcCCeEEEEEecC---CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        212 TITTLYVGNLGDKLTEQDLR----DHFYQFGEIRSVTILSK---QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr----~~F~~fG~I~~v~i~~~---kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ..++|||+|||.++++++|+    ++|++||.|.+++|+.+   ++||||+|.+.++|++|++. ++|..++|+.|+|.|
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~-l~g~~~~gr~l~V~~   86 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNS-LHRYKIGSKKILVSL   86 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHH-HTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHH-hCCCEECCeEEEEEE
Confidence            45799999999999999999    99999999999999876   89999999999999999998 699999999999999


Q ss_pred             ccCCCCC
Q psy14139        285 GRAQANR  291 (327)
Q Consensus       285 ak~~~~~  291 (327)
                      +++....
T Consensus        87 a~~~~~~   93 (96)
T 2dgx_A           87 ATGASGP   93 (96)
T ss_dssp             CCCSSCC
T ss_pred             cCCCCCC
Confidence            9887644

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

Probab=99.69  E-value=1.8e-16  Score=125.13  Aligned_cols=84  Identities=24%  Similarity=0.533  Sum_probs=76.9

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-------CCeEEEEeCCHHHHHHHHHHhc-CCeEECCee
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-------QQCAFIQYTSRPAAEAAVEHSF-NKVILGGRR  279 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-------kg~aFV~F~~~~~Ae~A~~~~l-~g~~i~G~~  279 (327)
                      +.+...++|||+|||..+++++|+++|++||.|.+|.|..+       ++||||+|.+.++|++|++. + ++..+.|+.
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~~~~~~~g~~   88 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA-LCHSTHLYGRR   88 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHH-HHTCCBSSSCB
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHH-hccCCeECCCE
Confidence            45566789999999999999999999999999999999876       79999999999999999997 7 899999999


Q ss_pred             EEEEeccCCCCCC
Q psy14139        280 LNIKWGRAQANRG  292 (327)
Q Consensus       280 L~V~~ak~~~~~~  292 (327)
                      |+|.|++++....
T Consensus        89 l~v~~a~~~~~~~  101 (107)
T 2cph_A           89 LVLEWADSEVTVQ  101 (107)
T ss_dssp             CEEEECCCCCCCC
T ss_pred             EEEEeCCCCCCCC
Confidence            9999999876553

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.69  E-value=4e-16  Score=122.71  Aligned_cols=81  Identities=30%  Similarity=0.506  Sum_probs=74.3

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      ....++|||+|||.++++++|+++|++||.|.++.+.  ++||||+|.+.++|++|++. +++..++|+.|+|.|++++.
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--~~~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~v~~a~~~~   84 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAMEE-MNGKDLEGENIEIVFAKPPD   84 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--SSCEEEEESSHHHHHHHHHH-HTTEEETTEEEEEEECCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--CCEEEEEeCCHHHHHHHHHH-HCCCccCCCEEEEEEcCCCc
Confidence            3456899999999999999999999999999999988  67999999999999999997 69999999999999999877


Q ss_pred             CCCC
Q psy14139        290 NRGE  293 (327)
Q Consensus       290 ~~~~  293 (327)
                      .+..
T Consensus        85 ~~~~   88 (103)
T 2dgu_A           85 QKRK   88 (103)
T ss_dssp             CCCC
T ss_pred             ccch
Confidence            6543

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

Probab=99.69  E-value=8.3e-17  Score=126.00  Aligned_cols=77  Identities=27%  Similarity=0.505  Sum_probs=72.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCCC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR  291 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~~  291 (327)
                      ++|||+|||.++++++|+++|++||+|.++.+..+ +++|||+|.+.++|++|++. +++..++|+.|+|.|++++..+
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~V~~a~~~~~~   78 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRG-LDGKVICGSRVRVELSTGMPRR   78 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHH-HHHSCSSSCCCEEEESSSCCCS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHH-HCCCeECCcEEEEEEccCCCCc
Confidence            58999999999999999999999999999999986 99999999999999999997 6999999999999999987654

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=1.7e-16  Score=125.98  Aligned_cols=82  Identities=17%  Similarity=0.283  Sum_probs=73.3

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhc-CCeEECCeeEEEEeccCC
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSF-NKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l-~g~~i~G~~L~V~~ak~~  288 (327)
                      ....++|||+|||.+++|++|+++|++||.|.+|.|+.+++||||+|.+.++|++|++.+. ++..+.|++|+|.|++++
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~   91 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCc
Confidence            3456899999999999999999999999999999999999999999999999999999741 346799999999999987


Q ss_pred             CCC
Q psy14139        289 ANR  291 (327)
Q Consensus       289 ~~~  291 (327)
                      ...
T Consensus        92 ~~~   94 (104)
T 1wex_A           92 RIT   94 (104)
T ss_dssp             SCC
T ss_pred             ccc
Confidence            644

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.69  E-value=1.4e-16  Score=125.50  Aligned_cols=78  Identities=21%  Similarity=0.341  Sum_probs=71.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCC--eEECCeeEEEEeccCC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNK--VILGGRRLNIKWGRAQ  288 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g--~~i~G~~L~V~~ak~~  288 (327)
                      +..++|||+|||.+++|++|+++|++||.|.++++++.+|+|||+|.+.++|+.|++. +++  ..+.|++|+|.|++++
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~kg~AFVef~~~~~A~~Av~~-ln~~~~~i~Gr~i~V~~S~~k   97 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNY-AADNQIYIAGHPAFVNYSTSQ   97 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETTTTEEEEEESSHHHHHHHHHH-HHHSCEEETTEEEEEEECSCS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcCCCEEEEEECCHHHHHHHHHH-hcCCCceeCCcEEEEEecccc
Confidence            3457999999999999999999999999999999999999999999999999999997 455  4589999999999876


Q ss_pred             C
Q psy14139        289 A  289 (327)
Q Consensus       289 ~  289 (327)
                      .
T Consensus        98 ~   98 (100)
T 3r27_A           98 K   98 (100)
T ss_dssp             C
T ss_pred             c
Confidence            4

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

Probab=99.69  E-value=3.7e-16  Score=120.30  Aligned_cols=80  Identities=24%  Similarity=0.455  Sum_probs=73.7

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      .....++|||+|||.++++++|+++|++||.|.++.+.  +++|||+|.+.++|++|++. +++..+.|+.|+|.|++++
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--~~~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~V~~a~~~   82 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAVEAIRG-LDNTEFQGKRMHVQLSTSR   82 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--SSEEEEEESCHHHHHHHHHH-HTTEEETTEEEEEEESSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--CCEEEEEECCHHHHHHHHHH-hCCCeeCCcEEEEEEccCC
Confidence            44567899999999999999999999999999999998  56999999999999999997 6999999999999999987


Q ss_pred             CCC
Q psy14139        289 ANR  291 (327)
Q Consensus       289 ~~~  291 (327)
                      ...
T Consensus        83 ~~~   85 (92)
T 2dgt_A           83 LRT   85 (92)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            654

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

Probab=99.69  E-value=5e-16  Score=124.39  Aligned_cols=84  Identities=21%  Similarity=0.521  Sum_probs=76.3

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      +....++|||+|||.++++++|+++|++||.|.+|.|..+      ++||||+|.+.++|++|++. +++..++|+.|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~V   89 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ-MGGQWLGGRQIRT   89 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-TTTCEETTEECEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHH-hCCCEECCEEEEE
Confidence            4456789999999999999999999999999999999875      58999999999999999997 7999999999999


Q ss_pred             EeccCCCCCCC
Q psy14139        283 KWGRAQANRGE  293 (327)
Q Consensus       283 ~~ak~~~~~~~  293 (327)
                      .|++++.....
T Consensus        90 ~~a~~~~~~~~  100 (115)
T 2dgo_A           90 NWATRKPPAPK  100 (115)
T ss_dssp             EESSCCCCCSC
T ss_pred             EEccCCCCCCc
Confidence            99998876543

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

Probab=99.68  E-value=1.6e-16  Score=119.50  Aligned_cols=75  Identities=27%  Similarity=0.497  Sum_probs=70.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      .+|||+|||.++++++|+++|++||.|.++.+..+      +++|||+|.+.++|++|++. ++|..++|+.|+|.|+++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~-l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS-MQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHH-HTTCEETTEECEEEECCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHH-hcCCeeCCcEEEEEecCc
Confidence            58999999999999999999999999999999865      78999999999999999997 699999999999999998


Q ss_pred             CC
Q psy14139        288 QA  289 (327)
Q Consensus       288 ~~  289 (327)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

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

Probab=99.68  E-value=4.6e-16  Score=123.62  Aligned_cols=83  Identities=14%  Similarity=0.262  Sum_probs=76.0

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECC-----eeEEE
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGG-----RRLNI  282 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G-----~~L~V  282 (327)
                      +.....++|||+|||.++++++|+++|++||+|.++.|+.+ +||||+|.+.++|++|++. +++..+.|     +.|+|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-g~afV~f~~~~~a~~Ai~~-l~g~~~~g~~~~~~~i~V   87 (108)
T 1x4c_A           10 PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRK-LDNTKFRSHEGETAYIRV   87 (108)
T ss_dssp             CCCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-TEEEEEESSHHHHHHHHHH-SSSEEEECTTSCEEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-CEEEEEECCHHHHHHHHHH-HCcCCccCCcCcceEEEE
Confidence            34456789999999999999999999999999999999988 9999999999999999997 79999999     99999


Q ss_pred             EeccCCCCCC
Q psy14139        283 KWGRAQANRG  292 (327)
Q Consensus       283 ~~ak~~~~~~  292 (327)
                      .|++++....
T Consensus        88 ~~a~~~~~~~   97 (108)
T 1x4c_A           88 KVDGPRSPSY   97 (108)
T ss_dssp             EESSCCSCCC
T ss_pred             EeCCCCCCCC
Confidence            9999876543

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

Probab=99.68  E-value=2.1e-16  Score=123.30  Aligned_cols=80  Identities=28%  Similarity=0.488  Sum_probs=75.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQAN  290 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~  290 (327)
                      ...++|||+|||.++++++|+++|++||.|.++.+..+++||||+|.+.++|++|++. +++..++|+.|+|.|++++..
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~kg~afV~f~~~~~a~~a~~~-l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVE-LDNMPLRGKQLRVRFACHSAS   91 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHH-HTTCCBTTBCCEEEESSCCSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCEEEEEECCHHHHHHHHHH-hCCCEeCCceEEEEEcCCCCC
Confidence            4558999999999999999999999999999999999999999999999999999997 699999999999999998765


Q ss_pred             C
Q psy14139        291 R  291 (327)
Q Consensus       291 ~  291 (327)
                      .
T Consensus        92 ~   92 (99)
T 2cpj_A           92 L   92 (99)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.68  E-value=2.2e-16  Score=120.94  Aligned_cols=74  Identities=23%  Similarity=0.247  Sum_probs=70.7

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      ....|||+||+..++|++|+++|.+||+|.++++..++|||||+|.++++|++|+++ +|+..+.|+.|+|++|.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~~kGfaFVey~~~~eA~~Ai~~-Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMA-LNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHH-HTTEEETTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCCCcEEEEEECCHHHHHHHHHH-hcCCEECCcEEEEEECC
Confidence            347999999999999999999999999999999999999999999999999999998 69999999999999983

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.3e-16  Score=129.57  Aligned_cols=81  Identities=19%  Similarity=0.322  Sum_probs=73.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcC--CeEECCeeEEEEeccCC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFN--KVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~--g~~i~G~~L~V~~ak~~  288 (327)
                      ...++|||+|||.+++|++|+++|++||.|.+|+|+.++|||||+|.+.++|++|++. ++  +..+.|++|+|.|++++
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~kG~AFVeF~~~e~A~~Ai~~-l~~~~~~l~Gr~l~V~~a~~k  107 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNY-YTSVTPVLRGQPIYIQFSNHK  107 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGGGTEEEEECSCHHHHHHHHHH-HHHHCCCBTTBCCEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEECCHHHHHHHHHH-hccCCceECCeEEEEEEccCC
Confidence            3457999999999999999999999999999999999999999999999999999997 45  57899999999999987


Q ss_pred             CCCC
Q psy14139        289 ANRG  292 (327)
Q Consensus       289 ~~~~  292 (327)
                      ..+.
T Consensus       108 ~~~~  111 (119)
T 2ad9_A          108 ELKT  111 (119)
T ss_dssp             SCCC
T ss_pred             CCCc
Confidence            6553

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.68  E-value=1.4e-16  Score=126.04  Aligned_cols=78  Identities=22%  Similarity=0.254  Sum_probs=71.6

Q ss_pred             CccEEEEcCCCC-CCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcC--CeEECCeeEEEEeccCC
Q psy14139        212 TITTLYVGNLGD-KLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFN--KVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       212 ~~~tLfVgnLp~-~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~--g~~i~G~~L~V~~ak~~  288 (327)
                      ..++|||+|||. +++|++|+++|++||.|.++.|+.++++|||+|.+.++|+.|++.+ +  +..+.|++|+|.|++..
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l-~~~~~~~~Gr~l~V~~a~~~   92 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYY-TTTPALVFGKPVRVHLSQKY   92 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHH-HHSCCEETTEECEEEEECCC
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHH-cCCCceECCcEEEEEECCCC
Confidence            457999999999 9999999999999999999999999999999999999999999974 5  46799999999999865


Q ss_pred             CC
Q psy14139        289 AN  290 (327)
Q Consensus       289 ~~  290 (327)
                      ..
T Consensus        93 ~~   94 (102)
T 1x4d_A           93 KR   94 (102)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

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

Probab=99.68  E-value=3.2e-16  Score=123.38  Aligned_cols=81  Identities=27%  Similarity=0.471  Sum_probs=74.5

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECC---eeEEE
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGG---RRLNI  282 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G---~~L~V  282 (327)
                      ...++|||+|||.++++++|+++|++||.|.++.|..+     ++||||+|.+.++|++|++. +++..+.|   +.|+|
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~-l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHA-LHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHH-HSSCCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHH-HcCCccCCCCCccEEE
Confidence            45689999999999999999999999999999999876     79999999999999999997 69998888   99999


Q ss_pred             EeccCCCCCC
Q psy14139        283 KWGRAQANRG  292 (327)
Q Consensus       283 ~~ak~~~~~~  292 (327)
                      .|++++..+.
T Consensus        92 ~~a~~~~~~~  101 (105)
T 2dnh_A           92 KFADTDKESG  101 (105)
T ss_dssp             EESCSSCCCS
T ss_pred             EECccCcccC
Confidence            9999887654

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

Probab=99.67  E-value=2.1e-16  Score=119.95  Aligned_cols=77  Identities=22%  Similarity=0.525  Sum_probs=69.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      +.++|||+|||.++++++|+++|++||.|.++.+..+      +++|||+|.+.++|++|++. ++|..++|+.|+|.|+
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ-MGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTTCEETTEECEEEEE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHH-cCCCEECCeEEEEEec
Confidence            3579999999999999999999999999999999875      58999999999999999997 6999999999999999


Q ss_pred             cCCC
Q psy14139        286 RAQA  289 (327)
Q Consensus       286 k~~~  289 (327)
                      ++++
T Consensus        84 ~~kp   87 (87)
T 3bs9_A           84 TRKP   87 (87)
T ss_dssp             C---
T ss_pred             CCCC
Confidence            8763

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

Probab=99.67  E-value=2e-16  Score=124.84  Aligned_cols=80  Identities=24%  Similarity=0.451  Sum_probs=73.5

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      ....++|||+|||.++++++|+++|++||.|.++.+..+      +|+|||+|.+.++|++|++. ++|..++|+.|+|.
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~V~   98 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG-LNGQDLMGQPISVD   98 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHH-HTTCBSSSSBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHH-hcCCEECCcEEEEE
Confidence            455689999999999999999999999999999999864      68999999999999999997 69999999999999


Q ss_pred             eccCCCC
Q psy14139        284 WGRAQAN  290 (327)
Q Consensus       284 ~ak~~~~  290 (327)
                      |+++++.
T Consensus        99 ~a~~~~~  105 (106)
T 1p27_B           99 WCFVRGP  105 (106)
T ss_dssp             ESEESSC
T ss_pred             eecCCCC
Confidence            9988754

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

Probab=99.67  E-value=5.4e-16  Score=118.90  Aligned_cols=80  Identities=23%  Similarity=0.437  Sum_probs=73.3

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      +...++|||+|||.++++++|+++|++||.|.++.+.  +++|||+|.+.++|++|++. +++..++|+.|+|.|+++..
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~--~~~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~v~~a~~~~   82 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--KDYAFVHMEKEADAKAAIAQ-LNGKEVKGKRINVELSTKGQ   82 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--SSCEEEEESCHHHHHHHHHH-HTTCEETTEECEEEESCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--CCEEEEEECCHHHHHHHHHH-hCCCEECCcEEEEEECCCCC
Confidence            3456899999999999999999999999999999998  56999999999999999997 69999999999999999876


Q ss_pred             CCC
Q psy14139        290 NRG  292 (327)
Q Consensus       290 ~~~  292 (327)
                      .+.
T Consensus        83 ~~~   85 (90)
T 2dnp_A           83 KKS   85 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            554

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

Probab=99.67  E-value=2.8e-16  Score=121.59  Aligned_cols=81  Identities=28%  Similarity=0.504  Sum_probs=74.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEE-EEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSV-TILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v-~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ..++|||+|||.++++++|+++|++||.|.++ +|..+      ++||||+|.+.++|++|++. +++..++|+.|+|.|
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA-MNGQYLCNRPITVSY   82 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHT-TTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            34799999999999999999999999999999 88874      78999999999999999997 799999999999999


Q ss_pred             ccCCCCCCC
Q psy14139        285 GRAQANRGE  293 (327)
Q Consensus       285 ak~~~~~~~  293 (327)
                      ++++..++.
T Consensus        83 a~~~~~~~~   91 (96)
T 1x5t_A           83 AFKKDSKGS   91 (96)
T ss_dssp             SCCCCCCCC
T ss_pred             ecccCCCCC
Confidence            998876543

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

Probab=99.67  E-value=3.6e-16  Score=124.22  Aligned_cols=83  Identities=19%  Similarity=0.426  Sum_probs=75.5

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      +.....++|||+|||.++++++|+++|++||.|.++.+..+      +|||||+|.+.++|++|+.. ++|..++|+.|+
T Consensus        21 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~-l~g~~~~g~~l~   99 (110)
T 1oo0_B           21 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA-LNGAEIMGQTIQ   99 (110)
T ss_dssp             CCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHH-HTTCEETTEECE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHH-cCCCEECCcEEE
Confidence            34456789999999999999999999999999999999764      69999999999999999997 699999999999


Q ss_pred             EEeccCCCCC
Q psy14139        282 IKWGRAQANR  291 (327)
Q Consensus       282 V~~ak~~~~~  291 (327)
                      |.|++++..+
T Consensus       100 V~~a~~~~~~  109 (110)
T 1oo0_B          100 VDWCFVKGPK  109 (110)
T ss_dssp             EEESEESSCC
T ss_pred             EEEcccCCCC
Confidence            9999987654

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

Probab=99.67  E-value=2.9e-16  Score=125.14  Aligned_cols=80  Identities=24%  Similarity=0.435  Sum_probs=72.9

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      .+...++|||+|||.++++++|+++|++||.|.++.+.  +|||||+|.+.++|++|++. ++|..++|+.|+|.|++++
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--kg~afV~f~~~~~A~~Ai~~-l~g~~~~g~~l~V~~a~~~  103 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--NGFAFVEFEEAESAAKAIEE-VHGKSFANQPLEVVYSKLP  103 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--TTEEEEECSSHHHHHHHHHH-HTTCEETTEECEEESCSCC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--CCEEEEEECCHHHHHHHHHH-cCCCEECCeEEEEEEecCC
Confidence            34566899999999999999999999999999999998  99999999999999999997 6999999999999999987


Q ss_pred             CCC
Q psy14139        289 ANR  291 (327)
Q Consensus       289 ~~~  291 (327)
                      ..+
T Consensus       104 ~~r  106 (108)
T 2jvo_A          104 AKR  106 (108)
T ss_dssp             C--
T ss_pred             CCC
Confidence            654

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

Probab=99.67  E-value=6.2e-16  Score=121.75  Aligned_cols=83  Identities=24%  Similarity=0.392  Sum_probs=75.5

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      .....++|||+|||.++++++|+++|++||.|.++.+..+      ++||||+|.+.++|++|++. +++..+.|+.|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~v   89 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI-MDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHH-SSSCBCSSCBCEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHH-hCCCeECCeEEEE
Confidence            4456689999999999999999999999999999999874      58999999999999999997 7999999999999


Q ss_pred             EeccCCCCCC
Q psy14139        283 KWGRAQANRG  292 (327)
Q Consensus       283 ~~ak~~~~~~  292 (327)
                      .|++++....
T Consensus        90 ~~a~~~~~~~   99 (105)
T 1x5u_A           90 NKASAHNKNL   99 (105)
T ss_dssp             EETTTTSCCC
T ss_pred             EECCCCCcCC
Confidence            9999877653

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.9e-16  Score=122.11  Aligned_cols=81  Identities=26%  Similarity=0.421  Sum_probs=71.6

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCC-eEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCC-eEECCeeEEEEeccC
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGE-IRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNK-VILGGRRLNIKWGRA  287 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~-I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g-~~i~G~~L~V~~ak~  287 (327)
                      ....++|||+|||.++++++|+++|++||. |..+.+ ..++||||+|.+.++|++|++. +++ ..++|+.|+|.|+++
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~-~~~g~afV~f~~~~~A~~A~~~-l~g~~~~~g~~l~v~~a~~   82 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-LKSGYAFVDYPDQNWAIRAIET-LSGKVELHGKIMEVDYSVS   82 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE-EETTEEEECCSCHHHHHHHHHH-HTTTCEETTEECEEEECCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE-cCCCEEEEEECCHHHHHHHHHH-ccCCeeECCEEEEEEEccC
Confidence            345689999999999999999999999999 555544 5789999999999999999997 699 999999999999998


Q ss_pred             CCCCC
Q psy14139        288 QANRG  292 (327)
Q Consensus       288 ~~~~~  292 (327)
                      +..++
T Consensus        83 ~~~~~   87 (93)
T 2cqh_A           83 KKLRS   87 (93)
T ss_dssp             CCCCC
T ss_pred             ccccC
Confidence            76654

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

Probab=99.67  E-value=6.1e-16  Score=120.58  Aligned_cols=82  Identities=18%  Similarity=0.438  Sum_probs=74.5

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      .+...++|||+|||.++++++|+++|++||.|.++.|+.+      ++||||+|.+.++|++|++  +++..++|+.|+|
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~~~~~g~~l~V   83 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN--MHFHDIMGKKVEV   83 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH--HCCCBSSSCBCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH--hCCCEECCeEEEE
Confidence            4456689999999999999999999999999999999863      6899999999999999997  4999999999999


Q ss_pred             EeccCCCCCC
Q psy14139        283 KWGRAQANRG  292 (327)
Q Consensus       283 ~~ak~~~~~~  292 (327)
                      .|++++..+.
T Consensus        84 ~~a~~~~~~~   93 (99)
T 2dgs_A           84 KRAEPRDSKS   93 (99)
T ss_dssp             EECCCCCCCC
T ss_pred             EECCCCcccC
Confidence            9999877654

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

Probab=99.67  E-value=2.7e-16  Score=120.75  Aligned_cols=81  Identities=23%  Similarity=0.411  Sum_probs=74.1

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      +...++|||+|||.++++++|+++|++||.|.++.+..+    +++|||+|.+.++|++|++. +++..++|+.|+|.|+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~-l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRM-MNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHH-HTTCCBTTBCCCCEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHH-hCCCEECCcEEEEEEc
Confidence            445689999999999999999999999999999999863    68999999999999999997 6999999999999999


Q ss_pred             cCCCCC
Q psy14139        286 RAQANR  291 (327)
Q Consensus       286 k~~~~~  291 (327)
                      ++....
T Consensus        84 ~~~~~~   89 (92)
T 2dgv_A           84 RNASGP   89 (92)
T ss_dssp             SCCSSC
T ss_pred             CCCCCC
Confidence            987643

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

Probab=99.67  E-value=7.2e-16  Score=124.32  Aligned_cols=81  Identities=21%  Similarity=0.392  Sum_probs=74.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ...++|||+|||.++++++|+++|++||.|.+|.|..+     ++||||+|.+.++|++|++. ++|..++|+.|+|.|+
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~-l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKD-MNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHH-CSSCBCSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            34589999999999999999999999999999999885     49999999999999999997 7999999999999999


Q ss_pred             cCCCCCC
Q psy14139        286 RAQANRG  292 (327)
Q Consensus       286 k~~~~~~  292 (327)
                      +++....
T Consensus        84 ~~~~~~~   90 (116)
T 2fy1_A           84 KKPSFQS   90 (116)
T ss_dssp             CCSSCSS
T ss_pred             CCCCCCC
Confidence            9876543

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

Probab=99.66  E-value=1e-15  Score=121.46  Aligned_cols=84  Identities=29%  Similarity=0.549  Sum_probs=75.7

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC---CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK---QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~---kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      +.+...++|||+|||.++++++|+++|++||.|.++.|..+   ++||||+|.+.++|++|++. +++..++|+.|+|.|
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYG-RDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHH-HTTCEETTEECEEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHH-cCCCEECCeEEEEEE
Confidence            34556689999999999999999999999999999999764   67999999999999999987 699999999999999


Q ss_pred             ccCCCCCC
Q psy14139        285 GRAQANRG  292 (327)
Q Consensus       285 ak~~~~~~  292 (327)
                      ++++....
T Consensus        96 a~~~~~~~  103 (109)
T 1x4a_A           96 PRSGRGTG  103 (109)
T ss_dssp             CCCCCCCC
T ss_pred             cccCCCCC
Confidence            99876543

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

Probab=99.66  E-value=5.2e-16  Score=119.83  Aligned_cols=80  Identities=29%  Similarity=0.504  Sum_probs=73.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.++++++|+++|++||.|.++.+..+      +++|||+|.+.++|++|++. +++..++|+.|+|.|+
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ-LNGFELAGRPMRVGHV   82 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHH-HTTCCSSSSCCEEEES
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHH-hCCCeeCCcEEEEEEc
Confidence            3479999999999999999999999999999999875      58999999999999999997 6999999999999999


Q ss_pred             cCCCCCC
Q psy14139        286 RAQANRG  292 (327)
Q Consensus       286 k~~~~~~  292 (327)
                      +++...+
T Consensus        83 ~~~~~~~   89 (95)
T 2dnz_A           83 TERLDGG   89 (95)
T ss_dssp             SCCCCCC
T ss_pred             ccccCCC
Confidence            9887654

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

Probab=99.66  E-value=4.6e-16  Score=121.87  Aligned_cols=81  Identities=26%  Similarity=0.483  Sum_probs=74.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ...++|||+|||.++++++|+++|++||.|.++.|..+      ++||||+|.+.++|++|++. +++..++|+.|+|.|
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN-MNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHH-HTTEEETTEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHH-hCCCEECCcEEEEEe
Confidence            45689999999999999999999999999999999764      78999999999999999997 699999999999999


Q ss_pred             ccCCCCCC
Q psy14139        285 GRAQANRG  292 (327)
Q Consensus       285 ak~~~~~~  292 (327)
                      ++++..+.
T Consensus        89 a~~~~~~~   96 (102)
T 2cqb_A           89 AKPMRIKE   96 (102)
T ss_dssp             CCCCCCCC
T ss_pred             CCCCCCCC
Confidence            99887654

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

Probab=99.66  E-value=4e-16  Score=122.51  Aligned_cols=82  Identities=27%  Similarity=0.477  Sum_probs=75.3

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      +...++|||+|||.++++++|+++|++||.|.++.+..+    ++||||+|.+.++|++|++. +++..+.|+.|+|.|+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~V~~a   90 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTE-MNGRIVATKPLYVALA   90 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHH-HTTCBSSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHH-hCCCEeCCcEEEEEEe
Confidence            346689999999999999999999999999999999854    79999999999999999997 6999999999999999


Q ss_pred             cCCCCCC
Q psy14139        286 RAQANRG  292 (327)
Q Consensus       286 k~~~~~~  292 (327)
                      +++..+.
T Consensus        91 ~~~~~~~   97 (103)
T 2d9p_A           91 QRKEERQ   97 (103)
T ss_dssp             SSCCCCC
T ss_pred             cccccCC
Confidence            9877654

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

Probab=99.66  E-value=3.2e-16  Score=123.10  Aligned_cols=84  Identities=26%  Similarity=0.400  Sum_probs=75.6

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      +.....++|||+|||.++++++|+++|++||.|.++.|..+      +++|||+|.+.++|++|++. +++..++|+.|+
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~   86 (103)
T 2dnm_A            8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA-MDGAELDGRELR   86 (103)
T ss_dssp             SCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHH-HSSCCBTTBCCE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHH-cCCCEECCcEEE
Confidence            34456789999999999999999999999999999999763      68999999999999999997 699999999999


Q ss_pred             EEeccCCCCCC
Q psy14139        282 IKWGRAQANRG  292 (327)
Q Consensus       282 V~~ak~~~~~~  292 (327)
                      |.|+++.....
T Consensus        87 V~~a~~~~~~~   97 (103)
T 2dnm_A           87 VQVARYGRRDL   97 (103)
T ss_dssp             EEECSSCCSCC
T ss_pred             EEECCcCCCCC
Confidence            99999876543

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

Probab=99.66  E-value=4.5e-16  Score=117.60  Aligned_cols=75  Identities=28%  Similarity=0.531  Sum_probs=69.7

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      .+.++|||+|||.++++++|+++|++||.|.++.+..+      +++|||+|.+.++|++|++. ++|..++|+.|+|.|
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN-MNESELFGRTIRVNL   83 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHH-HTTCEETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHH-hCCCEECCcEEEEEE
Confidence            45689999999999999999999999999999998653      79999999999999999987 699999999999999


Q ss_pred             cc
Q psy14139        285 GR  286 (327)
Q Consensus       285 ak  286 (327)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            85

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

Probab=99.66  E-value=6.1e-16  Score=124.00  Aligned_cols=82  Identities=23%  Similarity=0.455  Sum_probs=74.6

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      +...++|||+|||.++++++|+++|++||.|.+++|..+      ++||||+|.+.++|++|++. +++..+.|+.|+|.
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS-MNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHH-HTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHH-cCCCEECCEEEEEE
Confidence            445689999999999999999999999999999999875      37999999999999999997 69999999999999


Q ss_pred             eccCCCCCC
Q psy14139        284 WGRAQANRG  292 (327)
Q Consensus       284 ~ak~~~~~~  292 (327)
                      |++++..+.
T Consensus       101 ~a~~~~~~~  109 (115)
T 2cpz_A          101 LKRSKNDSK  109 (115)
T ss_dssp             CCCCSCCCC
T ss_pred             EcCCCCcCC
Confidence            999876543

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

Probab=99.66  E-value=6.4e-16  Score=121.35  Aligned_cols=82  Identities=27%  Similarity=0.457  Sum_probs=75.0

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      ....++|||+|||.++++++|+++|++||.|.+|.|..+      ++||||+|.+.++|++|++. +++..++|+.|+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG-VSGFGYDHLILNVE   90 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHH-TTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHH-cCCCeeCCcEEEEE
Confidence            345689999999999999999999999999999999865      57999999999999999997 79999999999999


Q ss_pred             eccCCCCCC
Q psy14139        284 WGRAQANRG  292 (327)
Q Consensus       284 ~ak~~~~~~  292 (327)
                      |++++..+.
T Consensus        91 ~a~~~~~~~   99 (103)
T 2cq0_A           91 WAKPSTNSG   99 (103)
T ss_dssp             ESSCCCCSC
T ss_pred             ECCCCCCCC
Confidence            999887654

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

Probab=99.66  E-value=5.2e-16  Score=120.65  Aligned_cols=80  Identities=23%  Similarity=0.407  Sum_probs=72.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec---------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS---------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~---------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      ..++|||+|||.++++++|+++|++||.|.++.+..         .++||||+|.+.++|++|++. +++..++|+.|+|
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~V   82 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQ-LQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHH-STTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHH-hCCCeeCCeEEEE
Confidence            347999999999999999999999999999999984         257999999999999999997 7999999999999


Q ss_pred             EeccCCCCCC
Q psy14139        283 KWGRAQANRG  292 (327)
Q Consensus       283 ~~ak~~~~~~  292 (327)
                      .|++++....
T Consensus        83 ~~a~~~~~~~   92 (98)
T 2cpf_A           83 RISERATKPA   92 (98)
T ss_dssp             ECSSCSSCCC
T ss_pred             EEccCCCCCC
Confidence            9998876543

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

Probab=99.66  E-value=9.2e-16  Score=121.84  Aligned_cols=83  Identities=23%  Similarity=0.434  Sum_probs=75.2

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcC------CeEEC
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFN------KVILG  276 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~------g~~i~  276 (327)
                      .....++|||+|||.++++++|+++|++||.|.+|.|+.+      ++||||+|.+.++|++|++. ++      +..++
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~~~~~~~~   89 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA-ASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHH-HCTTTTTCCEESS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHH-hccccccCCcEEc
Confidence            3455689999999999999999999999999999999853      78999999999999999997 68      99999


Q ss_pred             CeeEEEEeccCCCCCC
Q psy14139        277 GRRLNIKWGRAQANRG  292 (327)
Q Consensus       277 G~~L~V~~ak~~~~~~  292 (327)
                      |+.|+|.|++++....
T Consensus        90 g~~l~v~~a~~~~~~~  105 (111)
T 1x4h_A           90 GRQLKVDLAVTRDEAA  105 (111)
T ss_dssp             SCEEEEECCCCCCCCC
T ss_pred             CEEEEEEECCCCccCC
Confidence            9999999999876654

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.66  E-value=5e-16  Score=118.01  Aligned_cols=77  Identities=18%  Similarity=0.351  Sum_probs=71.3

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec-------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS-------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~-------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      .++|||+|||.++++++|+++|++||.|.++.+..       .+++|||+|.+.++|++|++. ++|..++|+.|+|.|+
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH-MDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHH-HTTCEETTEECEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHH-cCCCeECCeEEEEEEC
Confidence            47999999999999999999999999999999864       478999999999999999997 6999999999999999


Q ss_pred             cCCCC
Q psy14139        286 RAQAN  290 (327)
Q Consensus       286 k~~~~  290 (327)
                      .+...
T Consensus        83 ~~~~~   87 (88)
T 4a8x_A           83 LAPWP   87 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

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

Probab=99.66  E-value=9.8e-16  Score=118.05  Aligned_cols=77  Identities=29%  Similarity=0.409  Sum_probs=70.9

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      .....++|||+|||.++++++|+++|++||.|.++.+..+      +++|||+|.+.++|++|++. +++..+.|+.|+|
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~v   90 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA-INNKQLFGRVIKA   90 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHH-TTTEEETTEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHH-cCCCeeCCcEEEE
Confidence            3455689999999999999999999999999999999764      68999999999999999997 7999999999999


Q ss_pred             Eecc
Q psy14139        283 KWGR  286 (327)
Q Consensus       283 ~~ak  286 (327)
                      .|++
T Consensus        91 ~~ak   94 (94)
T 2e5h_A           91 SIAI   94 (94)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9985

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

Probab=99.66  E-value=6.1e-16  Score=120.03  Aligned_cols=78  Identities=21%  Similarity=0.357  Sum_probs=72.3

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      .++|||+|||.++++++|+++|++||.|.++++..+      +|+|||+|.+.++|++|++. ++|..++|+.|+|.|++
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~-l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN-LNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHH-HTTCEETTEECEEEECS
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHH-hCCCeECCeEEEEEEcC
Confidence            479999999999999999999999999999999864      79999999999999999997 69999999999999999


Q ss_pred             CCCCC
Q psy14139        287 AQANR  291 (327)
Q Consensus       287 ~~~~~  291 (327)
                      +++..
T Consensus        81 ~~~~~   85 (96)
T 2x1f_A           81 NSDIS   85 (96)
T ss_dssp             CSSGG
T ss_pred             CCCCC
Confidence            87643

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

Probab=99.66  E-value=3.8e-16  Score=124.42  Aligned_cols=80  Identities=25%  Similarity=0.457  Sum_probs=73.9

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      .+...++|||+|||.++++++|+++|++||.|.++++..+    +|||||+|.+.++|++|++. ++|..++|+.|+|.|
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~-l~g~~~~g~~l~V~~  103 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREK-LHGTVVEGRKIEVNN  103 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHH-HTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            4456789999999999999999999999999999999875    79999999999999999997 699999999999999


Q ss_pred             ccCCC
Q psy14139        285 GRAQA  289 (327)
Q Consensus       285 ak~~~  289 (327)
                      ++++.
T Consensus       104 a~~~~  108 (109)
T 2err_A          104 ATARV  108 (109)
T ss_dssp             CCCSC
T ss_pred             CCCCc
Confidence            98763

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.66  E-value=4.5e-16  Score=127.92  Aligned_cols=81  Identities=17%  Similarity=0.302  Sum_probs=72.4

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHH----HHHhhcCCeEEEEEec---CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLR----DHFYQFGEIRSVTILS---KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr----~~F~~fG~I~~v~i~~---~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      .....++|||+|||..+++++|+    ++|++||.|.+|.+..   .+|||||+|.+.++|+.|+.. +||..+.|++|+
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~-lng~~l~gr~l~  103 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEA-FQGYPFQGNPLV  103 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHH-STTCCCTTSCCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHH-HCCCEeCCCEEE
Confidence            34556899999999999999876    6999999999998864   489999999999999999998 799999999999


Q ss_pred             EEeccCCCC
Q psy14139        282 IKWGRAQAN  290 (327)
Q Consensus       282 V~~ak~~~~  290 (327)
                      |.|++++..
T Consensus       104 V~~a~~~~~  112 (127)
T 2a3j_A          104 ITFSETPQS  112 (127)
T ss_dssp             EEECCCCCH
T ss_pred             EEEccCcch
Confidence            999987654

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.66  E-value=9.4e-16  Score=130.97  Aligned_cols=86  Identities=20%  Similarity=0.245  Sum_probs=74.5

Q ss_pred             CCCCCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC--CCeEEEEeCCHHHHHHHHHHhcCCeEECC--eeE
Q psy14139        205 LDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK--QQCAFIQYTSRPAAEAAVEHSFNKVILGG--RRL  280 (327)
Q Consensus       205 ~~~p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~--kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G--~~L  280 (327)
                      +.++......+|||+||+..+++++|+++|++||+|.+|.|..+  +++|||+|.+.++|+.|++. ++|..|.|  +.|
T Consensus        38 ~~~~~ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~-LnG~~i~g~g~~L  116 (164)
T 1sjr_A           38 MAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLS-LDGQNIYNACCTL  116 (164)
T ss_dssp             --CCCCCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHH-STTBCSSSSCSCE
T ss_pred             CCCCCCCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHH-hCCCEecCCCcEE
Confidence            33344556789999999999999999999999999999998754  57999999999999999998 79999965  999


Q ss_pred             EEEeccCCCCC
Q psy14139        281 NIKWGRAQANR  291 (327)
Q Consensus       281 ~V~~ak~~~~~  291 (327)
                      +|.|++++...
T Consensus       117 ~V~~Ak~~~l~  127 (164)
T 1sjr_A          117 RIDFSKLTSLN  127 (164)
T ss_dssp             EEEECSSSSCC
T ss_pred             EEEEecCCccc
Confidence            99999987643

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

Probab=99.66  E-value=6.6e-16  Score=123.31  Aligned_cols=84  Identities=31%  Similarity=0.481  Sum_probs=75.7

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeE--------EEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCe
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIR--------SVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKV  273 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~--------~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~  273 (327)
                      .++...++|||+|||.++++++|+++|++||.|.        .++|..+      ++||||+|.+.++|++|++. +++.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~-l~g~   88 (113)
T 2cpe_A           10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEW-FDGK   88 (113)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHH-HTTC
T ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHH-cCCC
Confidence            3456678999999999999999999999999999        5888764      68999999999999999997 6999


Q ss_pred             EECCeeEEEEeccCCCCCC
Q psy14139        274 ILGGRRLNIKWGRAQANRG  292 (327)
Q Consensus       274 ~i~G~~L~V~~ak~~~~~~  292 (327)
                      .+.|+.|+|.|++++....
T Consensus        89 ~~~g~~l~V~~a~~~~~~~  107 (113)
T 2cpe_A           89 DFQGSKLKVSLARKKPPMN  107 (113)
T ss_dssp             EETTEECEEECSSCCCCST
T ss_pred             ccCCCEEEEEECCCCCCCC
Confidence            9999999999999877654

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

Probab=99.65  E-value=8.8e-16  Score=127.03  Aligned_cols=85  Identities=25%  Similarity=0.443  Sum_probs=76.9

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      +.+...++|||+|||.++++++|+++|+.||+|.+|+|+.+      ++||||+|.+.++|++|++. +++..+.|+.|+
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~  115 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG-LNGFNILNKRLK  115 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHH-TTTEECSSCEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHH-hCCCEECCeEEE
Confidence            34566789999999999999999999999999999999864      68999999999999999997 799999999999


Q ss_pred             EEeccCCCCCCC
Q psy14139        282 IKWGRAQANRGE  293 (327)
Q Consensus       282 V~~ak~~~~~~~  293 (327)
                      |.|++++..+..
T Consensus       116 v~~a~~~~~~~~  127 (139)
T 1u6f_A          116 VALAASGHQRPG  127 (139)
T ss_dssp             EEESSCCCCCCC
T ss_pred             EEECCCCCCCCC
Confidence            999998876543

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

Probab=99.65  E-value=8.5e-16  Score=119.93  Aligned_cols=77  Identities=23%  Similarity=0.408  Sum_probs=71.6

Q ss_pred             CCCccEEEEcCCCC-CCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        210 DKTITTLYVGNLGD-KLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       210 d~~~~tLfVgnLp~-~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      .+..++|||+|||. ++++++|+++|++||.|.++.+.  +|||||+|.+.++|++|++. ++|..++|+.|+|.|++++
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--~g~afV~f~~~~~A~~Ai~~-l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIEX-ESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--SSEEEEEESSHHHHHHHHHH-HTTSEETTEECEEEECCCC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--CCEEEEEECCHHHHHHHHHH-cCCCEECCEEEEEEecCCC
Confidence            35568999999998 99999999999999999999985  89999999999999999998 6999999999999999876


Q ss_pred             C
Q psy14139        289 A  289 (327)
Q Consensus       289 ~  289 (327)
                      .
T Consensus        96 ~   96 (97)
T 2xnq_A           96 A   96 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.65  E-value=6.2e-16  Score=123.76  Aligned_cols=77  Identities=21%  Similarity=0.305  Sum_probs=70.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.+++|++|+++|++||.|.++.|+.+      +|||||+|.+.++|++|++. +||..+.|+.|+|.++
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~-lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN-LHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTTCEETTEECEEEEC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHH-hCCCEECCeEEEEEEC
Confidence            3479999999999999999999999999999999764      58999999999999999998 6999999999999999


Q ss_pred             cCCC
Q psy14139        286 RAQA  289 (327)
Q Consensus       286 k~~~  289 (327)
                      +...
T Consensus        84 ~~~~   87 (110)
T 3s8s_A           84 IKGQ   87 (110)
T ss_dssp             STTH
T ss_pred             CCCc
Confidence            7554

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.65  E-value=5.4e-16  Score=120.21  Aligned_cols=81  Identities=20%  Similarity=0.456  Sum_probs=73.0

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHH----HHHhhcCCeEEEEEec---CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLR----DHFYQFGEIRSVTILS---KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr----~~F~~fG~I~~v~i~~---~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      +....++|||+|||.++++++|+    ++|++||.|.++.+..   .+|+|||+|.+.++|+.|++. ++|..++|+.|+
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~   82 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS-MQGFPFYDKPMR   82 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHH-HTTCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHH-hCCCEECCcEEE
Confidence            44566899999999999999999    9999999999999873   589999999999999999997 699999999999


Q ss_pred             EEeccCCCC
Q psy14139        282 IKWGRAQAN  290 (327)
Q Consensus       282 V~~ak~~~~  290 (327)
                      |.|++++..
T Consensus        83 v~~a~~~~~   91 (97)
T 1nu4_A           83 IQYAKTDSD   91 (97)
T ss_dssp             EEECSSCCT
T ss_pred             EEEccCCCc
Confidence            999998654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=2.8e-15  Score=116.53  Aligned_cols=79  Identities=28%  Similarity=0.426  Sum_probs=73.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQAN  290 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~  290 (327)
                      ...++|||+||  ++++++|+++|++||+|.+|.|...++||||+|.+.++|++|+.. +++..+.|+.|+|.|++++..
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~Ai~~-l~g~~~~g~~l~v~~a~~~~~   89 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAE-LNGTQVESVQLKVNIARKQPM   89 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHH-TTTEEETTEEEEEECCSSCCC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecCCCCEEEEEECCHHHHHHHHHH-hCCCeECCeEEEEEECCCCCC
Confidence            34589999996  899999999999999999999998999999999999999999997 799999999999999998765


Q ss_pred             CC
Q psy14139        291 RG  292 (327)
Q Consensus       291 ~~  292 (327)
                      ..
T Consensus        90 ~~   91 (97)
T 1x5p_A           90 LD   91 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

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

Probab=99.65  E-value=3e-16  Score=125.62  Aligned_cols=80  Identities=16%  Similarity=0.280  Sum_probs=74.5

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      +.+.++|||+|||.++++++|+++|++||.|.++.|...+++|||+|.+.++|+.|++. ++|..+.|+.|+|.|++...
T Consensus         7 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~A~~Ai~~-l~g~~~~g~~l~V~~a~~~~   85 (111)
T 1whx_A            7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRH-LAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHH-HTTCBSSSSBCEEEEEETTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEeCCHHHHHHHHHH-hCCCEECCeEEEEEECCCCc
Confidence            44568999999999999999999999999999999999999999999999999999998 69999999999999998754


Q ss_pred             C
Q psy14139        290 N  290 (327)
Q Consensus       290 ~  290 (327)
                      .
T Consensus        86 ~   86 (111)
T 1whx_A           86 F   86 (111)
T ss_dssp             T
T ss_pred             c
Confidence            4

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

Probab=99.65  E-value=2.7e-15  Score=116.97  Aligned_cols=78  Identities=22%  Similarity=0.440  Sum_probs=72.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhc--CCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQF--GEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~f--G~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      ...++|||+|||.++++++|+++|++|  |.|.++.+.  ++||||+|.+.++|++|+.. +++..+.|+.|+|.|++++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~v~~a~~~   89 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--RDYAFVHFSNREDAVEAMKA-LNGKVLDGSPIEVTLAKPV   89 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--SSEEEEEESSHHHHHHHHHH-HSSEEETTEEEEEECCCCC
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--CCeEEEEeCCHHHHHHHHHH-hCCCEeCCcEEEEEECCCC
Confidence            456899999999999999999999999  999998876  78999999999999999997 6999999999999999987


Q ss_pred             CCC
Q psy14139        289 ANR  291 (327)
Q Consensus       289 ~~~  291 (327)
                      ...
T Consensus        90 ~~~   92 (99)
T 2cpd_A           90 DKD   92 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=1.5e-16  Score=124.95  Aligned_cols=83  Identities=24%  Similarity=0.476  Sum_probs=75.6

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      +.+...++|||+|||.++++++|+++|++||.|.++.+..+      +|||||+|.+.++|++|++. ++|..++|+.|+
T Consensus         3 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~   81 (104)
T 1p1t_A            3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN-LNGREFSGRALR   81 (104)
T ss_dssp             CSHHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHH-SSSBSCSSSCBE
T ss_pred             CcCCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHH-hCCCeeCCcEEE
Confidence            44566789999999999999999999999999999999864      68999999999999999997 799999999999


Q ss_pred             EEeccCCCCC
Q psy14139        282 IKWGRAQANR  291 (327)
Q Consensus       282 V~~ak~~~~~  291 (327)
                      |.|++++..+
T Consensus        82 v~~a~~~~~~   91 (104)
T 1p1t_A           82 VDNAASEKNK   91 (104)
T ss_dssp             EEETTCTTHH
T ss_pred             EEeCCCccch
Confidence            9999987643

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

Probab=99.65  E-value=2.9e-16  Score=122.61  Aligned_cols=79  Identities=10%  Similarity=0.337  Sum_probs=69.4

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhcCC--eEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCe----EE
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGE--IRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKV----IL  275 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~--I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~----~i  275 (327)
                      .......||||+|||.+++|++|+++|++||.  |.+|+++.+      +|||||+|.+.++|++|++. ++|.    .+
T Consensus         4 ~~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~-lng~~~~~~i   82 (95)
T 2lkz_A            4 HHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQI-LQSLHPPLKI   82 (95)
T ss_dssp             CSSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHH-HHSSSSCEEE
T ss_pred             ccCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHH-hcCCCCCceE
Confidence            34556789999999999999999999999995  678888764      68999999999999999998 5664    69


Q ss_pred             CCeeEEEEeccC
Q psy14139        276 GGRRLNIKWGRA  287 (327)
Q Consensus       276 ~G~~L~V~~ak~  287 (327)
                      +|++|+|.||++
T Consensus        83 ~Gr~i~V~~Aks   94 (95)
T 2lkz_A           83 DGKTIGVDFAKS   94 (95)
T ss_dssp             TTEEEEEEECCC
T ss_pred             CCEEEEEEEccC
Confidence            999999999985

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

Probab=99.65  E-value=3.7e-15  Score=119.58  Aligned_cols=81  Identities=31%  Similarity=0.527  Sum_probs=73.4

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      ..+...++|||+|||.++++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++. +++ .+.|+.|+
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~-~~~g~~l~   89 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD-PNP-IIDGRKAN   89 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTC-SSC-EETTEECE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHh-CCC-cCCCEEEE
Confidence            45667799999999999999999999999999999999874      58999999999999999996 688 89999999


Q ss_pred             EEeccCCCC
Q psy14139        282 IKWGRAQAN  290 (327)
Q Consensus       282 V~~ak~~~~  290 (327)
                      |.|+++...
T Consensus        90 V~~a~~~~~   98 (116)
T 2cqd_A           90 VNLAYLGAK   98 (116)
T ss_dssp             EEESTTTCC
T ss_pred             EEEcccCCC
Confidence            999987543

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

Probab=99.64  E-value=7.1e-16  Score=119.07  Aligned_cols=78  Identities=26%  Similarity=0.423  Sum_probs=72.1

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      .+...++|||+|||.++++++|+++|++||+|.++.|..+     +++|||+|.+.++|++|++. +++..+.|+.|+|.
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~V~   90 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIAL-LNGIRLYGRPINVS   90 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHH-HTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-hCCCEECCCEEEEE
Confidence            4456689999999999999999999999999999999875     68999999999999999997 69999999999999


Q ss_pred             eccC
Q psy14139        284 WGRA  287 (327)
Q Consensus       284 ~ak~  287 (327)
                      |++.
T Consensus        91 ~a~~   94 (95)
T 2ywk_A           91 GPSS   94 (95)
T ss_dssp             CCCC
T ss_pred             EcCC
Confidence            9874

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

Probab=99.64  E-value=8.2e-16  Score=120.40  Aligned_cols=81  Identities=21%  Similarity=0.401  Sum_probs=74.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ...++|||+|||.++++++|+++|++||.|.++.+..+      ++||||+|.+.++|++|++. +++..++|+.|+|.|
T Consensus        10 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA-MNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHH-HTTCCTTSCCCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHH-hCCCEECCeEEEEEE
Confidence            45589999999999999999999999999999999874      68999999999999999987 699999999999999


Q ss_pred             ccCCCCCC
Q psy14139        285 GRAQANRG  292 (327)
Q Consensus       285 ak~~~~~~  292 (327)
                      ++++....
T Consensus        89 a~~~~~~~   96 (102)
T 1x5s_A           89 AGKSSDNR   96 (102)
T ss_dssp             EECCCCCC
T ss_pred             CCCCCCCC
Confidence            99876543

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

Probab=99.64  E-value=9.5e-16  Score=120.86  Aligned_cols=83  Identities=28%  Similarity=0.527  Sum_probs=74.4

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEE---CCee
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVIL---GGRR  279 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i---~G~~  279 (327)
                      .+...++|||+|||.++++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++. +++..+   .|+.
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-l~g~~~~~~~g~~   87 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA-LHEQKTLPGMNRP   87 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHH-HTTTCCCTTCSSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHH-hcCCcccCCCCce
Confidence            3456689999999999999999999999999999999873      68999999999999999997 688777   8899


Q ss_pred             EEEEeccCCCCCC
Q psy14139        280 LNIKWGRAQANRG  292 (327)
Q Consensus       280 L~V~~ak~~~~~~  292 (327)
                      |+|.|++++..+.
T Consensus        88 l~v~~a~~~~~~~  100 (106)
T 2dgp_A           88 IQVKPADSESRGG  100 (106)
T ss_dssp             CEEEECCCCSCCC
T ss_pred             EEEEECCcccccC
Confidence            9999999877654

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

Probab=99.64  E-value=8.1e-16  Score=125.14  Aligned_cols=83  Identities=23%  Similarity=0.429  Sum_probs=75.6

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      .....++|||+|||.++++++|+++|++||.|.+|.|+.+      +++|||+|.+.++|++|++. ++|..|+|+.|+|
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~v   96 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG-LNGQDLMGQPISV   96 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHH-HTTCBSSSSBCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHH-hCCCeeCCeEEEE
Confidence            4456789999999999999999999999999999999865      79999999999999999997 6999999999999


Q ss_pred             EeccCCCCCC
Q psy14139        283 KWGRAQANRG  292 (327)
Q Consensus       283 ~~ak~~~~~~  292 (327)
                      .|++++....
T Consensus        97 ~~a~~~~~~~  106 (126)
T 3ex7_B           97 DWCFVRGPPK  106 (126)
T ss_dssp             EESEESSSCC
T ss_pred             EEecCCCCCC
Confidence            9998776543

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

Probab=99.64  E-value=2.4e-15  Score=120.11  Aligned_cols=82  Identities=22%  Similarity=0.326  Sum_probs=74.4

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ....++|||+|||.++++++|+++|++||.|.++.|..+     ++||||+|.+.++|++|++. +++..++|+.|+|.|
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM-FNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHH-HTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHH-hCCCEeCCCEEEEEE
Confidence            345689999999999999999999999999999999875     68999999999999999997 699999999999999


Q ss_pred             ccCCCCCC
Q psy14139        285 GRAQANRG  292 (327)
Q Consensus       285 ak~~~~~~  292 (327)
                      ++....+.
T Consensus        91 a~~~~~~~   98 (114)
T 2do0_A           91 DERALPKG   98 (114)
T ss_dssp             CSCCCCCS
T ss_pred             cccCCCCC
Confidence            98765543

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

Probab=99.64  E-value=1.9e-15  Score=116.57  Aligned_cols=77  Identities=30%  Similarity=0.379  Sum_probs=71.1

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      ....++|||+|||.++++++|+++|++||.|.++.+..+      +++|||+|.+.++|++|++. +++..++|+.|+|.
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~v~   90 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER-ANGMELDGRRIRVS   90 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHH-HTTEEETTEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHH-hCCCEECCEEEEEE
Confidence            355689999999999999999999999999999999754      57999999999999999997 69999999999999


Q ss_pred             eccC
Q psy14139        284 WGRA  287 (327)
Q Consensus       284 ~ak~  287 (327)
                      |+++
T Consensus        91 ~a~~   94 (95)
T 2cqc_A           91 GPSS   94 (95)
T ss_dssp             CCSC
T ss_pred             ecCC
Confidence            9875

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.64  E-value=3.8e-16  Score=125.52  Aligned_cols=79  Identities=18%  Similarity=0.293  Sum_probs=71.9

Q ss_pred             CccEEEEcCCCCC-CCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHh-cCCeEECCeeEEEEeccCCC
Q psy14139        212 TITTLYVGNLGDK-LTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHS-FNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       212 ~~~tLfVgnLp~~-ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~-l~g~~i~G~~L~V~~ak~~~  289 (327)
                      ..++|||+|||.+ ++|++|+++|++||+|.+|+|+..++||||+|.+.++|+.|++.+ .++..+.|++|+|.|++.+.
T Consensus        24 p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~~  103 (112)
T 1x4f_A           24 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYK  103 (112)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCS
T ss_pred             CCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECcccc
Confidence            3579999999998 999999999999999999999999999999999999999999974 24677999999999998765


Q ss_pred             C
Q psy14139        290 N  290 (327)
Q Consensus       290 ~  290 (327)
                      .
T Consensus       104 ~  104 (112)
T 1x4f_A          104 K  104 (112)
T ss_dssp             S
T ss_pred             c
Confidence            4

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

Probab=99.64  E-value=1.3e-15  Score=118.65  Aligned_cols=79  Identities=20%  Similarity=0.381  Sum_probs=72.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeE-EEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCee----
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIR-SVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRR----  279 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~-~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~----  279 (327)
                      ...++|||+|||.++++++|+++|++||.|. +++++.+      ++||||+|.+.++|++|++. ++|..+.|+.    
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~~~~~   85 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK-INGKPLPGATPAKR   85 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHT-TTTSEESSCSSCEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHH-HcCCccCCCCccee
Confidence            3458999999999999999999999999999 9999875      38999999999999999997 7999999998    


Q ss_pred             EEEEeccCCCC
Q psy14139        280 LNIKWGRAQAN  290 (327)
Q Consensus       280 L~V~~ak~~~~  290 (327)
                      |+|.|+++...
T Consensus        86 l~v~~a~~~~~   96 (99)
T 2div_A           86 FKLNYATYSGP   96 (99)
T ss_dssp             CCEEETTCCSS
T ss_pred             EEEeecCCCCC
Confidence            99999987754

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.63  E-value=1.3e-15  Score=121.25  Aligned_cols=77  Identities=25%  Similarity=0.468  Sum_probs=71.0

Q ss_pred             CccEEEEcCCCCC-CCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCC
Q psy14139        212 TITTLYVGNLGDK-LTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQAN  290 (327)
Q Consensus       212 ~~~tLfVgnLp~~-ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~  290 (327)
                      ..++|||+|||.+ +++++|+++|++||.|.++.+  .+++|||+|.+.++|++|++. +++..++|+.|+|.|+++...
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~V~~a~~~~~  102 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--HKGYAFVQYSNERHARAAVLG-ENGRVLAGQTLDINMAGEPKP  102 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--ETTEEEEECSSSHHHHHHHHH-HTTCEETTEECCEEESCCCCS
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--eCCEEEEEECCHHHHHHHHHH-cCCCEECCeEEEEEECCCCCC
Confidence            4579999999999 999999999999999999998  689999999999999999987 699999999999999986544


Q ss_pred             C
Q psy14139        291 R  291 (327)
Q Consensus       291 ~  291 (327)
                      .
T Consensus       103 ~  103 (110)
T 1wf1_A          103 D  103 (110)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.63  E-value=1.6e-15  Score=115.53  Aligned_cols=76  Identities=24%  Similarity=0.517  Sum_probs=70.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      +.++|||+|||.++++++|+++|++||.|.++.+..+      +++|||+|.+.++|++|+ . +++..++|+.|+|.|+
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~-~~g~~~~g~~l~V~~a   82 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A-LDESLFRGRQIKVIPK   82 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-G-GTTCEETTEECEEEET
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-h-cCCCEECCcEEEEEEc
Confidence            3479999999999999999999999999999999864      789999999999999999 6 7999999999999999


Q ss_pred             cCCC
Q psy14139        286 RAQA  289 (327)
Q Consensus       286 k~~~  289 (327)
                      ++..
T Consensus        83 ~~~~   86 (89)
T 3ucg_A           83 RTNR   86 (89)
T ss_dssp             TTTS
T ss_pred             cCCC
Confidence            8753

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

Probab=99.63  E-value=8.7e-16  Score=120.68  Aligned_cols=82  Identities=17%  Similarity=0.351  Sum_probs=74.7

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhh-cCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeE-ECCeeEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQ-FGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVI-LGGRRLNI  282 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~-fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~-i~G~~L~V  282 (327)
                      ....++|||+|||.++++++|+++|++ ||.|.++.|+.+     ++||||+|.+.++|++|++. +++.. ++|+.|+|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~-l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE-CQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHH-TTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHH-ccCCcccCCEeEEE
Confidence            345689999999999999999999999 999999999875     78999999999999999997 79998 99999999


Q ss_pred             EeccCCCCCC
Q psy14139        283 KWGRAQANRG  292 (327)
Q Consensus       283 ~~ak~~~~~~  292 (327)
                      .|++++..+.
T Consensus        85 ~~a~~~~~~~   94 (104)
T 2dhg_A           85 SVAIPKASRV   94 (104)
T ss_dssp             CBCCCCCSCC
T ss_pred             EEccCCCcCC
Confidence            9998876554

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

Probab=99.63  E-value=6.6e-16  Score=124.23  Aligned_cols=77  Identities=22%  Similarity=0.470  Sum_probs=70.9

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      .+...++|||+|||.++++++|+++|++||.|.++++..+      ++||||+|.+.++|++|++. ++|..++|+.|+|
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~V  114 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA-MNGFQVGTKRLKV  114 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHH-CCCCEETTEECCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHH-cCCCEECCEEEEE
Confidence            4556789999999999999999999999999999999864      68999999999999999997 7999999999999


Q ss_pred             Eecc
Q psy14139        283 KWGR  286 (327)
Q Consensus       283 ~~ak  286 (327)
                      .|++
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            9985

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

Probab=99.63  E-value=9.3e-16  Score=122.12  Aligned_cols=79  Identities=29%  Similarity=0.482  Sum_probs=72.8

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      +...++|||+|||..+++++|+++|++||.|.++.+..+      +|||||+|.+.++|++|++. ++|..++|+.|+|.
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~-l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ-LNGFELAGRPMKVG  101 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHH-HTTCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHH-cCCCEECCEEEEEE
Confidence            445689999999999999999999999999999999864      58999999999999999997 69999999999999


Q ss_pred             eccCCC
Q psy14139        284 WGRAQA  289 (327)
Q Consensus       284 ~ak~~~  289 (327)
                      |++++.
T Consensus       102 ~a~~k~  107 (108)
T 2jrs_A          102 HVTERT  107 (108)
T ss_dssp             CSCSSC
T ss_pred             EcccCC
Confidence            998874

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

Probab=99.63  E-value=6.6e-16  Score=119.99  Aligned_cols=79  Identities=23%  Similarity=0.385  Sum_probs=71.4

Q ss_pred             CCccEEEEcCCCC-CCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        211 KTITTLYVGNLGD-KLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       211 ~~~~tLfVgnLp~-~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      ...++|||+|||. ++++++|+++|++||.|.++.+.  ++||||+|.+.++|+.|++. +++..+.|+.|+|.|++++.
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~V~~a~~~~   84 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIEC-ESQEMNFGKKLILEVSSSNA   84 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--TTEEEEEESCHHHHHHHHHH-HTCSSCBTTTBCEEEEECCC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--CCEEEEEECCHHHHHHHHHH-cCCCeeCCcEEEEEEcCcCC
Confidence            4568999999998 99999999999999999999986  89999999999999999998 69999999999999998776


Q ss_pred             CCC
Q psy14139        290 NRG  292 (327)
Q Consensus       290 ~~~  292 (327)
                      ...
T Consensus        85 ~~~   87 (96)
T 2kvi_A           85 RPQ   87 (96)
T ss_dssp             C--
T ss_pred             CCC
Confidence            543

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

Probab=99.62  E-value=3.3e-15  Score=117.51  Aligned_cols=79  Identities=18%  Similarity=0.382  Sum_probs=72.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      ...++|||+|||.++++++|+++|++|| |.+|.|+.+       ++||||+|.+.++|++|+ . +++..+.|+.|+|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~-l~g~~~~g~~l~V~   89 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S-LNEESLGNKRIRVD   89 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-G-GGTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-h-cCCCEeCCcEEEEE
Confidence            4558999999999999999999999999 999999754       689999999999999999 6 79999999999999


Q ss_pred             eccCCCCCC
Q psy14139        284 WGRAQANRG  292 (327)
Q Consensus       284 ~ak~~~~~~  292 (327)
                      |++++..+.
T Consensus        90 ~a~~~~~~~   98 (104)
T 1wi8_A           90 VADQAQDKD   98 (104)
T ss_dssp             ECCCCCCCC
T ss_pred             EccCCCCCC
Confidence            999887654

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

Probab=99.62  E-value=1.5e-15  Score=118.43  Aligned_cols=77  Identities=22%  Similarity=0.490  Sum_probs=70.3

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEE--------EEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRS--------VTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVI  274 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~--------v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~  274 (327)
                      .....++|||+|||.++++++|+++|++||.|.+        +++..+      +|+|||+|.+.++|++|++. ++|..
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~-l~g~~   87 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDW-FDGKE   87 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHH-HTTCB
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHH-hCCCE
Confidence            3455689999999999999999999999999999        888764      58999999999999999997 69999


Q ss_pred             ECCeeEEEEecc
Q psy14139        275 LGGRRLNIKWGR  286 (327)
Q Consensus       275 i~G~~L~V~~ak  286 (327)
                      +.|+.|+|.|++
T Consensus        88 ~~g~~l~V~~A~   99 (99)
T 2la6_A           88 FSGNPIKVSFAT   99 (99)
T ss_dssp             SSSSBCEEEECC
T ss_pred             eCCcEEEEEecC
Confidence            999999999985

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.62  E-value=2.4e-15  Score=114.31  Aligned_cols=75  Identities=25%  Similarity=0.453  Sum_probs=68.2

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      .+...++|||+|||.++++++|+++|++||.|.++.++.+      +|||||+|.+.++|++|++  +++..++|+.|+|
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~~g~~i~v   84 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD--QKEHRLDGRVIDP   84 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH--SSCEEETTEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH--hCCCEECCEEEEE
Confidence            3456689999999999999999999999999999999864      5799999999999999997  4788999999999


Q ss_pred             Eec
Q psy14139        283 KWG  285 (327)
Q Consensus       283 ~~a  285 (327)
                      +||
T Consensus        85 ~~A   87 (87)
T 3s7r_A           85 KKA   87 (87)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

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

Probab=99.62  E-value=1.8e-15  Score=119.20  Aligned_cols=83  Identities=22%  Similarity=0.378  Sum_probs=75.1

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      ..+...++|||+|||.++++++|+++|++||+|.+|.|+.+      ++||||+|.+.++|++|++.  ++..++|+.|+
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~--~~~~~~g~~l~   88 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS--RPHTLDGRNID   88 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH--CSEEETTEEEB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh--CCCeECCEEEE
Confidence            34566789999999999999999999999999999999875      47999999999999999984  99999999999


Q ss_pred             EEeccCCCCCC
Q psy14139        282 IKWGRAQANRG  292 (327)
Q Consensus       282 V~~ak~~~~~~  292 (327)
                      |.|++++....
T Consensus        89 V~~a~~~~~~~   99 (105)
T 2dh8_A           89 PKPCTPRGMQP   99 (105)
T ss_dssp             CCCSCCSSCCT
T ss_pred             EEEccCCCCCC
Confidence            99999877553

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.62  E-value=1.7e-15  Score=127.11  Aligned_cols=79  Identities=25%  Similarity=0.422  Sum_probs=74.0

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      ....++|||+|||.++++++|+++|++||.|.++++..+ +|||||+|.+.++|+.|+.. ++|..++|++|+|.|++++
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRE-LDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHH-HSSSCSSSSCCEEEECCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHH-cCCCEECCeEEEEEEcCCC
Confidence            345689999999999999999999999999999999987 99999999999999999997 6999999999999999887


Q ss_pred             C
Q psy14139        289 A  289 (327)
Q Consensus       289 ~  289 (327)
                      +
T Consensus       149 ~  149 (150)
T 2i2y_A          149 K  149 (150)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=2e-15  Score=121.62  Aligned_cols=79  Identities=15%  Similarity=0.245  Sum_probs=72.3

Q ss_pred             CccEEEE--cCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEE-----CCeeEEEEe
Q psy14139        212 TITTLYV--GNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL-----GGRRLNIKW  284 (327)
Q Consensus       212 ~~~tLfV--gnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i-----~G~~L~V~~  284 (327)
                      ..++|||  |||+.+++|++|+++|++||+|.+|.|..+++||||+|.+.++|++|+++ +||..+     .|++|.|.+
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~rgfaFV~f~~~~~A~~Ai~~-lnG~~~~~~lg~g~~l~v~~  102 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVT-LNGKEVVDDLGQKITLYLNF  102 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHH-TTTCEEECTTSCEEECEEEE
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHH-hCCCEEccccCCCcEEEEEe
Confidence            4578999  88999999999999999999999999998999999999999999999998 699988     689999999


Q ss_pred             ccCCCCC
Q psy14139        285 GRAQANR  291 (327)
Q Consensus       285 ak~~~~~  291 (327)
                      ++..+..
T Consensus       103 a~~~p~~  109 (114)
T 2cq2_A          103 VEKVQWS  109 (114)
T ss_dssp             ESCCCCS
T ss_pred             cccCccc
Confidence            9866544

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

Probab=99.61  E-value=2e-15  Score=121.19  Aligned_cols=77  Identities=16%  Similarity=0.188  Sum_probs=69.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcC-CeEEEEEec--CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFG-EIRSVTILS--KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG-~I~~v~i~~--~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      ...+|||+|||.++++++|+++|++|| +|..+.+..  .+|||||+|.+.++|++|++. +||..++|+.|+|.+++..
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~-lng~~l~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALER-LNNIEFRGSVITVERDDNP  105 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHH-TTTEEETTEEEEEEESCC-
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHH-cCCCEECCeEEEEEECCCC
Confidence            457999999999999999999999999 999999863  589999999999999999997 7999999999999998755


Q ss_pred             C
Q psy14139        289 A  289 (327)
Q Consensus       289 ~  289 (327)
                      +
T Consensus       106 p  106 (111)
T 2jvr_A          106 P  106 (111)
T ss_dssp             -
T ss_pred             C
Confidence            4

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

Probab=99.61  E-value=2.8e-15  Score=118.31  Aligned_cols=76  Identities=25%  Similarity=0.397  Sum_probs=70.7

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ....++|||+|||..+++++|+++|++||.|.++.|..+     +++|||+|.+.++|++|++. +++..+.|+.|+|.|
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ-YNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHH-HTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHH-hCCCEeCCcEEEEEE
Confidence            455689999999999999999999999999999999864     68999999999999999997 699999999999999


Q ss_pred             cc
Q psy14139        285 GR  286 (327)
Q Consensus       285 ak  286 (327)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=3.8e-15  Score=117.96  Aligned_cols=79  Identities=18%  Similarity=0.408  Sum_probs=71.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCC-eEEEEEe-------cCCCeEEEEeCCHHHHHHHHHHhcC--CeEECCeeEE
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGE-IRSVTIL-------SKQQCAFIQYTSRPAAEAAVEHSFN--KVILGGRRLN  281 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~-I~~v~i~-------~~kg~aFV~F~~~~~Ae~A~~~~l~--g~~i~G~~L~  281 (327)
                      ..++|||+|||.++++++|+++|++||. |.++.+.       ..++||||+|.+.++|+.|++. ++  +..++|+.|+
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~-l~~g~~~~~g~~l~   85 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRK-LMPGRIQLWGHQIA   85 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTT-TTTCCSCBTTBCCE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHH-hhCCCceecCCeEE
Confidence            4589999999999999999999999998 9999998       4589999999999999999997 54  5899999999


Q ss_pred             EEeccCCCCC
Q psy14139        282 IKWGRAQANR  291 (327)
Q Consensus       282 V~~ak~~~~~  291 (327)
                      |.|++++...
T Consensus        86 V~~a~~~~~~   95 (109)
T 2dis_A           86 VDWAEPEIDV   95 (109)
T ss_dssp             EEESCSSCST
T ss_pred             EEEcCCCCCc
Confidence            9999987654

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

Probab=99.61  E-value=3.8e-15  Score=125.78  Aligned_cols=80  Identities=30%  Similarity=0.441  Sum_probs=73.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ...++|||+|||.++++++|+++|++||.|.+|.|+.+      ++||||+|.+.++|++|++. +++..|+|+.|+|.|
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~-l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY-INGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-TTTSEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHH-hCCCEECCeEEEEEE
Confidence            35689999999999999999999999999999999764      47999999999999999997 799999999999999


Q ss_pred             ccCCCCC
Q psy14139        285 GRAQANR  291 (327)
Q Consensus       285 ak~~~~~  291 (327)
                      +++....
T Consensus       116 a~~~~~~  122 (156)
T 1h2v_Z          116 DAGFKEG  122 (156)
T ss_dssp             ESCCCTT
T ss_pred             CCCCCCc
Confidence            9876553

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.61  E-value=4.1e-15  Score=118.48  Aligned_cols=81  Identities=16%  Similarity=0.370  Sum_probs=70.9

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      +...++|||+|||.++++++|+++|++||.|.+++|..+      +|||||+|.+.++|++|++. + +..++|+.|+|.
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~-~-~~~l~g~~l~V~   99 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ-S-RHELDSKTIDPK   99 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHS-S-CEEETTEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHH-C-CCcCCCEEEEEE
Confidence            345689999999999999999999999999999999864      68999999999999999995 3 599999999999


Q ss_pred             eccCCCCCC
Q psy14139        284 WGRAQANRG  292 (327)
Q Consensus       284 ~ak~~~~~~  292 (327)
                      |+.++..+.
T Consensus       100 ~a~~~~~~~  108 (109)
T 2rs2_A          100 VAFPRRAQP  108 (109)
T ss_dssp             ECCCCCCCC
T ss_pred             EccCCCCCC
Confidence            999876553

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

Probab=99.60  E-value=4.1e-15  Score=115.63  Aligned_cols=78  Identities=26%  Similarity=0.455  Sum_probs=69.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEe--cCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL--SKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~--~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      ...++|||+|||.++++++|+++|++||.|. +.++  ..++||||+|.+.++|++|++. ++|..++|+.|+|.|++++
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~V~~a~~~   94 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSC-LQGLRLGTDTLRVALARQQ   94 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHH-HTTCCSSSSCCEEEECCCC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHH-hCCCEECCcEEEEEEcCCC
Confidence            3457999999999999999999999999996 4554  4589999999999999999997 6999999999999999987


Q ss_pred             CC
Q psy14139        289 AN  290 (327)
Q Consensus       289 ~~  290 (327)
                      ..
T Consensus        95 ~~   96 (97)
T 2e5j_A           95 RD   96 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

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

Probab=99.60  E-value=1.8e-15  Score=124.44  Aligned_cols=80  Identities=29%  Similarity=0.395  Sum_probs=73.4

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      ....++|||+|||.++++++|+++|++||+|.+|.+..+      ++||||+|.+.++|++|++. ++|..|+|+.|+|.
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~-lng~~i~g~~l~V~  121 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER-ANGMELDGRRIRVD  121 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHH-HTTCCSSSSCCEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHH-hCCCEECCEEEEEE
Confidence            345689999999999999999999999999999999853      68999999999999999997 69999999999999


Q ss_pred             eccCCCC
Q psy14139        284 WGRAQAN  290 (327)
Q Consensus       284 ~ak~~~~  290 (327)
                      |++++..
T Consensus       122 ~a~~~~p  128 (129)
T 2kxn_B          122 FSITKRP  128 (129)
T ss_dssp             CCSSSSC
T ss_pred             EecCCCC
Confidence            9988764

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=2e-15  Score=119.39  Aligned_cols=77  Identities=16%  Similarity=0.219  Sum_probs=70.7

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec-----CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS-----KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~-----~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      .+...++|||+|||.++++++|+++|++||.|.+|+|+.     .+|||||+|.+.++|++|+.  +++..++|+.|+|.
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~--~~~~~~~gr~l~V~   84 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE--TPGQKYKETDLLIL   84 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT--SSCCCCTTTTCEEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH--cCCCEECCEEEEEE
Confidence            345568999999999999999999999999999999986     37999999999999999998  59999999999999


Q ss_pred             eccC
Q psy14139        284 WGRA  287 (327)
Q Consensus       284 ~ak~  287 (327)
                      |+..
T Consensus        85 ~~~~   88 (103)
T 1s79_A           85 FKDD   88 (103)
T ss_dssp             EHHH
T ss_pred             EchH
Confidence            9875

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

Probab=99.60  E-value=9.2e-15  Score=114.75  Aligned_cols=80  Identities=21%  Similarity=0.416  Sum_probs=72.3

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      +...++|||+|||.++++++|+++|++|| |.+|.|+.+      ++||||+|.+.++|++|+ . +++..+.|+.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~-l~g~~~~g~~l~V~   88 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-T-YDGALLGDRSLRVD   88 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-G-GTTCEETTEECEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-h-hCCCeECCeEEEEE
Confidence            34568999999999999999999999997 999999865      579999999999999999 6 79999999999999


Q ss_pred             eccCCCCCC
Q psy14139        284 WGRAQANRG  292 (327)
Q Consensus       284 ~ak~~~~~~  292 (327)
                      |++++....
T Consensus        89 ~a~~~~~~~   97 (103)
T 2dng_A           89 IAEGRKQDK   97 (103)
T ss_dssp             ECCCCCCCC
T ss_pred             EecCCCCCC
Confidence            999876554

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.60  E-value=3.8e-15  Score=118.89  Aligned_cols=79  Identities=24%  Similarity=0.438  Sum_probs=72.5

Q ss_pred             CCccEEEEcCCCCCCCHHHHH---HHHhhcCCeEEEEEecCC---------CeEEEEeCCHHHHHHHHHHhcCCeEECCe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLR---DHFYQFGEIRSVTILSKQ---------QCAFIQYTSRPAAEAAVEHSFNKVILGGR  278 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr---~~F~~fG~I~~v~i~~~k---------g~aFV~F~~~~~Ae~A~~~~l~g~~i~G~  278 (327)
                      ...++|||+|||.++++++|+   ++|++||+|.++.|..++         |||||+|.+.++|++|++. ++|..++|+
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~-lng~~~~gr   91 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQC-VNNVVVDGR   91 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHH-HTTEEETTE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHH-hCCCEECCE
Confidence            345799999999999999999   999999999999998643         6999999999999999997 699999999


Q ss_pred             eEEEEeccCCCC
Q psy14139        279 RLNIKWGRAQAN  290 (327)
Q Consensus       279 ~L~V~~ak~~~~  290 (327)
                      .|+|.|++++..
T Consensus        92 ~l~V~~a~~k~~  103 (111)
T 2cpi_A           92 TLKASLGTTKYC  103 (111)
T ss_dssp             EEEEESCCCCSC
T ss_pred             EEEEEecccccc
Confidence            999999998763

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.60  E-value=4.9e-16  Score=119.32  Aligned_cols=77  Identities=19%  Similarity=0.305  Sum_probs=64.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcC--CeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFG--EIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG--~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      .+|||+|||.++++++|+++|++||  .|.+++++.+      +|||||+|.+.++|++|++. ++|..++|+.|+|.++
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~-l~g~~~~gr~i~V~~~   80 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDL-LPKRELHGQNPVVTPS   80 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHH-GGGSCSSSCCCEECCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHH-cCCCeeCCEEEEEEEC
Confidence            4899999999999999999999999  9999999874      58999999999999999997 7999999999999998


Q ss_pred             cCCCCC
Q psy14139        286 RAQANR  291 (327)
Q Consensus       286 k~~~~~  291 (327)
                      .+....
T Consensus        81 ~~~~~~   86 (90)
T 3p5t_L           81 NKLEHH   86 (90)
T ss_dssp             ------
T ss_pred             CCCccc
Confidence            876543

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

Probab=99.60  E-value=8.9e-15  Score=112.14  Aligned_cols=79  Identities=14%  Similarity=0.299  Sum_probs=72.0

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ....++|||+|||.++++++|+++|++| .|.+++|+.+     +|+|||+|.+.++|++|+.  +++..++|+.|+|.|
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~--~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK--CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH--SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH--hCCceeCCcEEEEEE
Confidence            4456899999999999999999999999 9999999875     6899999999999999998  599999999999999


Q ss_pred             ccCCCCC
Q psy14139        285 GRAQANR  291 (327)
Q Consensus       285 ak~~~~~  291 (327)
                      +++++..
T Consensus        84 a~~~~~s   90 (91)
T 2dgw_A           84 EKSGPSS   90 (91)
T ss_dssp             ESSCCCC
T ss_pred             CCcCCCC
Confidence            9887543

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

Probab=99.60  E-value=7e-15  Score=114.93  Aligned_cols=79  Identities=24%  Similarity=0.302  Sum_probs=69.8

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec-----CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS-----KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~-----~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      .+...++|||+|||.++++++|+++|++||.|   +++.     .++||||+|.+.++|++|++. +++..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNS-CNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHH-TSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHH-hCCCEeCCeEEEEE
Confidence            34556899999999999999999999999988   3333     379999999999999999997 79999999999999


Q ss_pred             eccCCCCC
Q psy14139        284 WGRAQANR  291 (327)
Q Consensus       284 ~ak~~~~~  291 (327)
                      |++++...
T Consensus        87 ~a~~~~~~   94 (101)
T 2fc9_A           87 LQGPRGSP   94 (101)
T ss_dssp             ECSSCCCC
T ss_pred             EcCCCCCC
Confidence            99987654

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.59  E-value=3.7e-15  Score=120.84  Aligned_cols=78  Identities=31%  Similarity=0.532  Sum_probs=71.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.++++++|+++|++||.|.++.+..+      +|||||+|.+.++|++|+ . ++|..++|+.|+|.|+
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~-l~g~~~~g~~l~V~~a  112 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-A-MDETVFRGRTIKVLPK  112 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-T-TTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-h-cCCCeECCeEEEEEEC
Confidence            3579999999999999999999999999999999864      689999999999999999 6 7999999999999999


Q ss_pred             cCCCCC
Q psy14139        286 RAQANR  291 (327)
Q Consensus       286 k~~~~~  291 (327)
                      ++....
T Consensus       113 ~~~~~~  118 (124)
T 2jwn_A          113 RTNMPG  118 (124)
T ss_dssp             SCCCSS
T ss_pred             CCCCCC
Confidence            876543

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=2.3e-14  Score=112.37  Aligned_cols=81  Identities=23%  Similarity=0.365  Sum_probs=72.6

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      .+...++|||+|||.++++++|+++|++||.|.++.|+.+      ++||||+|.+.++|++|+.   ++..++|+.|+|
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~---~~~~~~g~~l~v   87 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS---QRHMIDGRWCDC   87 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH---SCEEETTEEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH---cCCeeCCeEEEE
Confidence            4456689999999999999999999999999999999875      5799999999999999997   468999999999


Q ss_pred             EeccCCCCCC
Q psy14139        283 KWGRAQANRG  292 (327)
Q Consensus       283 ~~ak~~~~~~  292 (327)
                      .|++++....
T Consensus        88 ~~a~~~~~~~   97 (103)
T 2cqg_A           88 KLPNSKQSQD   97 (103)
T ss_dssp             ECCCTTCCCC
T ss_pred             EecCCCCcCC
Confidence            9999876543

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

Probab=99.59  E-value=6.8e-15  Score=117.99  Aligned_cols=81  Identities=22%  Similarity=0.452  Sum_probs=73.7

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ...++|||+|||.++++++|+++|++||.|.+|.|+.+      +|||||+|.+.++|++|++.  ++..++|+.|+|.|
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~--~~~~~~g~~l~V~~  102 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA--RPHSIDGRVVEPKR  102 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS--CSEEETTEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh--CCcEECCEEEEEEE
Confidence            34589999999999999999999999999999999874      68999999999999999984  99999999999999


Q ss_pred             ccCCCCCCC
Q psy14139        285 GRAQANRGE  293 (327)
Q Consensus       285 ak~~~~~~~  293 (327)
                      ++++.....
T Consensus       103 a~~~~~~~~  111 (116)
T 1x4b_A          103 AVAREESGS  111 (116)
T ss_dssp             CSSCCCCCC
T ss_pred             CCCCccCCC
Confidence            998876543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.59  E-value=1.4e-14  Score=118.39  Aligned_cols=79  Identities=18%  Similarity=0.215  Sum_probs=71.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCe-EEEEeCCHHHHHHHHHHhcCCeEECC--eeEEEEeccCC
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-AFIQYTSRPAAEAAVEHSFNKVILGG--RRLNIKWGRAQ  288 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~-aFV~F~~~~~Ae~A~~~~l~g~~i~G--~~L~V~~ak~~  288 (327)
                      .+..|||+||+..+++++|+++|++||+|.+|+|....|+ |||+|.+.++|+.|+++ |+|..|.|  +.|+|.|++++
T Consensus        24 ~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~~Gf~aFVef~~~~~A~~A~~~-LnG~~i~g~~~~l~V~~Ak~~  102 (124)
T 2e5i_A           24 KVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAA-LNGADIYAGCCTLKIEYARPT  102 (124)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEESSSEEEEEEESSHHHHHHHHHH-HTTCCCBTTBSEEEEECCSCS
T ss_pred             cEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHH-hCCCEecCCCeEEEEEEecCC
Confidence            3456889999999999999999999999999999877796 99999999999999998 69999987  68999999987


Q ss_pred             CCC
Q psy14139        289 ANR  291 (327)
Q Consensus       289 ~~~  291 (327)
                      .-.
T Consensus       103 ~l~  105 (124)
T 2e5i_A          103 RLN  105 (124)
T ss_dssp             CCC
T ss_pred             cce
Confidence            643

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

Probab=99.59  E-value=1e-14  Score=123.11  Aligned_cols=81  Identities=26%  Similarity=0.445  Sum_probs=74.1

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      ....++|||+|||.++++++|+++|++||.|.+++|..+      +|||||+|.+.++|++|++. ++|..++|+.|+|.
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~v~  145 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA-MDGAVLDGRELRVQ  145 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHH-STTEESSSSEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHH-hCCCEECCeEEEEE
Confidence            345689999999999999999999999999999999864      68999999999999999997 79999999999999


Q ss_pred             eccCCCCC
Q psy14139        284 WGRAQANR  291 (327)
Q Consensus       284 ~ak~~~~~  291 (327)
                      |++++..+
T Consensus       146 ~a~~~~~~  153 (158)
T 2kn4_A          146 MARYGRPP  153 (158)
T ss_dssp             EECCSSCC
T ss_pred             ECCCCCCC
Confidence            99987654

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.59  E-value=3.8e-15  Score=115.72  Aligned_cols=79  Identities=24%  Similarity=0.350  Sum_probs=70.4

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      +...++|||+|||.++++++|+++|++||.|.++.++.+      +++|||+|.+.++|++|++. +++..+.|+.|+|.
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-l~g~~~~g~~l~V~   90 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID-LNDRPIGSRKVKLV   90 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHH-TTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHH-hCCCeeCCeEEEEE
Confidence            345689999999999999999999999999987666542      69999999999999999997 79999999999999


Q ss_pred             eccCCC
Q psy14139        284 WGRAQA  289 (327)
Q Consensus       284 ~ak~~~  289 (327)
                      |++.+.
T Consensus        91 ~a~~~~   96 (98)
T 2cqp_A           91 LGSGPS   96 (98)
T ss_dssp             ESSCSS
T ss_pred             EcCCCC
Confidence            988654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.59  E-value=6.5e-15  Score=116.40  Aligned_cols=78  Identities=17%  Similarity=0.185  Sum_probs=70.6

Q ss_pred             CCccEEEEcCCCCCC------CHHHHHHHHhhcCCeEEEEEec----CCCeEEEEeCCHHHHHHHHHHhcCCeEECCe-e
Q psy14139        211 KTITTLYVGNLGDKL------TEQDLRDHFYQFGEIRSVTILS----KQQCAFIQYTSRPAAEAAVEHSFNKVILGGR-R  279 (327)
Q Consensus       211 ~~~~tLfVgnLp~~i------te~~Lr~~F~~fG~I~~v~i~~----~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~-~  279 (327)
                      ...++|||+|||..+      ++++|+++|++||.|.++.|..    .+|||||+|.+.++|++|+.. ++|..+.|+ .
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~-l~g~~~~g~~~   91 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKN-ADGYKLDKQHT   91 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHH-CSSEECSTTCE
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHH-hCCcccCCCce
Confidence            345799999999999      7899999999999999999884    379999999999999999997 799999998 9


Q ss_pred             EEEEeccCCC
Q psy14139        280 LNIKWGRAQA  289 (327)
Q Consensus       280 L~V~~ak~~~  289 (327)
                      |+|.|+....
T Consensus        92 l~V~~a~~~~  101 (105)
T 2nlw_A           92 FRVNLFTDFD  101 (105)
T ss_dssp             EEEECSCCCC
T ss_pred             EEEEEcchHh
Confidence            9999997654

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.59  E-value=6.1e-15  Score=125.91  Aligned_cols=82  Identities=20%  Similarity=0.426  Sum_probs=73.1

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      ....++|||+|||..+++++|+++|++||.|.+|.|+.+      +|||||+|.+.++|+.|+.. ++|..|.|+.|+|.
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~-l~g~~~~g~~l~V~  147 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA-LNGAEIMGQTIQVD  147 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHH-HTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHH-hCCCEECCEEEEEE
Confidence            455689999999999999999999999999999999875      69999999999999999997 69999999999999


Q ss_pred             eccCCCCCC
Q psy14139        284 WGRAQANRG  292 (327)
Q Consensus       284 ~ak~~~~~~  292 (327)
                      |++++..+.
T Consensus       148 ~a~~~~~~~  156 (165)
T 1rk8_A          148 WCFVKGPKR  156 (165)
T ss_dssp             ESEECC---
T ss_pred             EecCCCCCC
Confidence            999876654

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

Probab=99.58  E-value=4.6e-15  Score=118.52  Aligned_cols=80  Identities=28%  Similarity=0.450  Sum_probs=71.8

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEE--------
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVIL--------  275 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i--------  275 (327)
                      .+...++|||+|||.++++++|+++|++||.|.+++|..+     ++||||+|.+.++|++|++. ++|..+        
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~-l~g~~~~~~~~~~~   99 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH-FNGKFIKTPPGVSA   99 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHH-HBTCCCCCCTTSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHH-hCCCEEcCCccccC
Confidence            3455689999999999999999999999999999999875     68999999999999999997 699988        


Q ss_pred             CCeeEEEEeccCCC
Q psy14139        276 GGRRLNIKWGRAQA  289 (327)
Q Consensus       276 ~G~~L~V~~ak~~~  289 (327)
                      .+++|+|.|++++.
T Consensus       100 ~~~~l~v~~a~p~~  113 (114)
T 1x5o_A          100 PTEPLLCKFSGPSS  113 (114)
T ss_dssp             CSSCBEEEECCCSC
T ss_pred             CCCceeEEccCCCC
Confidence            57889999998653

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

Probab=99.58  E-value=1.1e-14  Score=118.13  Aligned_cols=78  Identities=24%  Similarity=0.398  Sum_probs=72.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ...++|||+|||.++++++|+++|++||.|.++.|..+     +|+|||+|.+.++|++|++. ++|..++|+.|+|.|+
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~-l~g~~~~g~~l~V~~a  111 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ-YKGVPLDGRPMDIQLV  111 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHH-HTTEESSSCEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHH-cCCCEECCcEEEEEEe
Confidence            45689999999999999999999999999999999873     79999999999999999997 6999999999999999


Q ss_pred             cCCC
Q psy14139        286 RAQA  289 (327)
Q Consensus       286 k~~~  289 (327)
                      .+..
T Consensus       112 ~~~~  115 (124)
T 2kt5_A          112 ASQI  115 (124)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            8654

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

Probab=99.58  E-value=4.7e-15  Score=113.31  Aligned_cols=76  Identities=17%  Similarity=0.320  Sum_probs=70.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      ..++|||+|||.++++++|+++|++| +|.++++...+|+|||+|.+.++|++|++. ++|..++|+.|+|.|+....
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~~~~g~afV~f~~~~~a~~Ai~~-l~g~~~~g~~l~V~~a~~~~   79 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDRNKRTAFVTLLNGEQAQNAIQM-FHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEEGGGTEEEECCSCHHHHHHHHHH-HTTEEETTEEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEeCCCcEEEEEECCHHHHHHHHHH-hCCCeECCcEEEEEEcCCCc
Confidence            45799999999999999999999999 999999988899999999999999999997 69999999999999986543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.58  E-value=1.6e-15  Score=118.95  Aligned_cols=77  Identities=14%  Similarity=0.139  Sum_probs=70.7

Q ss_pred             CccEEEEcCCCC------CCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECC-e
Q psy14139        212 TITTLYVGNLGD------KLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGG-R  278 (327)
Q Consensus       212 ~~~tLfVgnLp~------~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G-~  278 (327)
                      ..++|||+|||.      ++++++|+++|++||.|.+++|+.+      +|||||+|.+.++|++|++. ++|..+.| +
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~-lng~~~~g~r   83 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS-FHGKRLDLKH   83 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHH-HTTCBSSSSC
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHH-hCCcccCCCe
Confidence            357999999999      9999999999999999999998753      69999999999999999997 69999999 9


Q ss_pred             eEEEEeccCCC
Q psy14139        279 RLNIKWGRAQA  289 (327)
Q Consensus       279 ~L~V~~ak~~~  289 (327)
                      .|+|.|+.+..
T Consensus        84 ~l~V~~a~~~~   94 (100)
T 3ns6_A           84 RLFLYTMKDVE   94 (100)
T ss_dssp             BCEEEESHHHH
T ss_pred             EEEEEECchhh
Confidence            99999998753

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

Probab=99.58  E-value=7.4e-15  Score=113.63  Aligned_cols=82  Identities=24%  Similarity=0.348  Sum_probs=71.7

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEe-cCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-SKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~-~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      .+...++|||+|||.++++++|+++|++||.|..+... ..+|+|||+|.+.++|++|++. ++|..++|+.|+|.|+++
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~v~~a~~   90 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEE-KQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHH-TTEEEETTEEEEEEECSS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHH-hCCCEECCeEEEEEEcCC
Confidence            34567899999999999999999999999998877111 1378999999999999999997 799999999999999998


Q ss_pred             CCCC
Q psy14139        288 QANR  291 (327)
Q Consensus       288 ~~~~  291 (327)
                      +...
T Consensus        91 ~~~~   94 (96)
T 1fjc_A           91 KGGT   94 (96)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7654

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.58  E-value=1.5e-15  Score=118.95  Aligned_cols=77  Identities=19%  Similarity=0.381  Sum_probs=68.6

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      ....++|||+|||.++++++|+++|++|| |.+++|..+       +|||||+|.+.++|++|+ . ++|..++|+.|+|
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~-l~g~~~~g~~l~V   92 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S-LNEESLGNRRIRV   92 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-H-TTTCCBTTBCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-h-cCCCEECCeEEEE
Confidence            35568999999999999999999999999 999999764       589999999999999999 6 7999999999999


Q ss_pred             EeccCCC
Q psy14139        283 KWGRAQA  289 (327)
Q Consensus       283 ~~ak~~~  289 (327)
                      .|++++.
T Consensus        93 ~~a~~~~   99 (100)
T 2j76_E           93 DVADQAQ   99 (100)
T ss_dssp             EECCCSC
T ss_pred             EeccCCC
Confidence            9998764

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

Probab=99.58  E-value=2e-15  Score=125.02  Aligned_cols=85  Identities=27%  Similarity=0.495  Sum_probs=76.2

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeE
Q psy14139        207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRL  280 (327)
Q Consensus       207 ~p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L  280 (327)
                      ++.+...++|||+|||.++++++|+++|++||.|.+|.|..+      +|||||+|.+.++|++|++. +++..++|+.|
T Consensus        41 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~-l~g~~i~g~~l  119 (135)
T 2lea_A           41 PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA-MDGAVLDGREL  119 (135)
T ss_dssp             CSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTT-TTTCCSSSSCC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHH-cCCCEECCEEE
Confidence            345566789999999999999999999999999999999764      68999999999999999997 79999999999


Q ss_pred             EEEeccCCCCCC
Q psy14139        281 NIKWGRAQANRG  292 (327)
Q Consensus       281 ~V~~ak~~~~~~  292 (327)
                      +|.|+++.....
T Consensus       120 ~V~~a~~~~~~~  131 (135)
T 2lea_A          120 RVQMARYGRPPD  131 (135)
T ss_dssp             EEEECCCCCCCT
T ss_pred             EEEECCCCCCCc
Confidence            999999876543

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

Probab=99.58  E-value=1.2e-14  Score=119.83  Aligned_cols=75  Identities=28%  Similarity=0.518  Sum_probs=69.0

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      +...++|||+|||.++++++|+++|++||.|.++++..+      +++|||+|.+.++|++|++. ++|..++|+.|+|.
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN-MNESELFGRTIRVN  138 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHH-STEEEETTEEEEEE
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHH-hCCCEECCEEEEEE
Confidence            345689999999999999999999999999999999764      79999999999999999997 79999999999999


Q ss_pred             ec
Q psy14139        284 WG  285 (327)
Q Consensus       284 ~a  285 (327)
                      ||
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            86

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

Probab=99.57  E-value=8.7e-15  Score=117.09  Aligned_cols=79  Identities=25%  Similarity=0.392  Sum_probs=72.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC---CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK---QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~---kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      ..++|||+|||.++++++|+++|++||.|.++.+..+   +|+|||+|.+.++|++|++. ++|..++|+.|+|.|++++
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~v~~a~~~   85 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDH-LSGFNVSNRYLVVLYYNAN   85 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHH-HTTCBSSSCBCEEEECCHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHH-cCCCEECCeEEEEEEecCC
Confidence            3479999999999999999999999999999999764   68999999999999999997 6999999999999999976


Q ss_pred             CCC
Q psy14139        289 ANR  291 (327)
Q Consensus       289 ~~~  291 (327)
                      ...
T Consensus        86 ~~~   88 (115)
T 3lqv_A           86 RAF   88 (115)
T ss_dssp             HHT
T ss_pred             hhh
Confidence            544

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.57  E-value=7.7e-15  Score=112.75  Aligned_cols=77  Identities=22%  Similarity=0.430  Sum_probs=62.5

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      ....+|||+|||.+++|++|+++|++||.|.+++|+.+ +|||||+|.+.++|+++.   -....+.|+.|.|.+++++.
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~~~---~~~~~~~g~~v~v~~a~~k~   85 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLC---GEDLIIKGISVHISNAEPKH   85 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHHHT---TCEEEETTEEEEEEECC---
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHHHc---CCCcccCCEEEEEEEcCCCC
Confidence            44579999999999999999999999999999999875 899999999999998431   12345679999999999875


Q ss_pred             C
Q psy14139        290 N  290 (327)
Q Consensus       290 ~  290 (327)
                      .
T Consensus        86 ~   86 (89)
T 3d2w_A           86 N   86 (89)
T ss_dssp             -
T ss_pred             c
Confidence            4

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=2.6e-15  Score=120.10  Aligned_cols=80  Identities=23%  Similarity=0.426  Sum_probs=72.4

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      +...++|||+|||.++++++|+++|++||.|.+|.|+.      .+|||||+|.+.++|++|+ . +++..|+|+.|+|.
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~-l~g~~~~g~~l~V~   99 (114)
T 2cq4_A           22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-G-LTGQRLLGVPIIVQ   99 (114)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-H-HTTEEETTEEEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-H-cCCCEeCCeEEEEE
Confidence            34568999999999999999999999999999999975      3689999999999999999 6 69999999999999


Q ss_pred             eccCCCCC
Q psy14139        284 WGRAQANR  291 (327)
Q Consensus       284 ~ak~~~~~  291 (327)
                      |++++..+
T Consensus       100 ~a~~~~~~  107 (114)
T 2cq4_A          100 ASQAEKNR  107 (114)
T ss_dssp             EHHHHHHH
T ss_pred             ecCCCccC
Confidence            99876543

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

Probab=99.57  E-value=5.3e-15  Score=118.94  Aligned_cols=81  Identities=15%  Similarity=0.299  Sum_probs=67.4

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCee-----EEE
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRR-----LNI  282 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~-----L~V  282 (327)
                      |......+|||+|||.++++++|+++|++||+|.++.|+.+ +||||+|.+.++|++|++. +++..|+|+.     |+|
T Consensus        11 p~~r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-g~afV~f~~~~~a~~Ai~~-l~g~~~~gr~~~~~~i~v   88 (115)
T 3beg_B           11 PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRK-LDNTKFRSHEGETAYIRV   88 (115)
T ss_dssp             ------CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-SEEEEEESSHHHHHHHHHH-HTTCBCCCTTSCCCBCEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-CEEEEEECCHHHHHHHHHH-hCCCEECCcEeeeEEEEe
Confidence            33456689999999999999999999999999999999877 9999999999999999997 6999999988     888


Q ss_pred             EeccCCCC
Q psy14139        283 KWGRAQAN  290 (327)
Q Consensus       283 ~~ak~~~~  290 (327)
                      ..+.++..
T Consensus        89 ~~~~~~~~   96 (115)
T 3beg_B           89 KVDGPRSP   96 (115)
T ss_dssp             EECC----
T ss_pred             ccCCCCCC
Confidence            87776544

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

Probab=99.56  E-value=1.4e-15  Score=115.15  Aligned_cols=75  Identities=21%  Similarity=0.269  Sum_probs=68.7

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.++++++|+++|++||.|.++.+..+      ++||||+|.+.++|++|++. ++|..+.|+.|+|.|+
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA-LKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHH-HHHHTCCEESCCSSCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHH-hcCCeEeeEEEeecCC
Confidence            4579999999999999999999999999999999875      68999999999999999997 6999999999998776


Q ss_pred             cC
Q psy14139        286 RA  287 (327)
Q Consensus       286 k~  287 (327)
                      ++
T Consensus        83 ~s   84 (85)
T 1x4e_A           83 SS   84 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=1.3e-14  Score=116.04  Aligned_cols=80  Identities=29%  Similarity=0.436  Sum_probs=71.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCe----EEEEEec--CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEI----RSVTILS--KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I----~~v~i~~--~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.++++++|+++|++||.|    ..+.+..  .++||||+|.+.++|++|++. +++..+.|+.|+|.|+
T Consensus        24 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           24 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL-VNGYKLYGKILVIEFG  102 (115)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHH-STTCBCSSCBCEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHH-hCCCEeCCcEEEEEEc
Confidence            45899999999999999999999999998    5666554  379999999999999999997 7999999999999999


Q ss_pred             cCCCCCC
Q psy14139        286 RAQANRG  292 (327)
Q Consensus       286 k~~~~~~  292 (327)
                      +++..+.
T Consensus       103 ~~~~~~~  109 (115)
T 2cpx_A          103 KNKKQRS  109 (115)
T ss_dssp             CCCSCCC
T ss_pred             cCCCCCC
Confidence            9877654

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.56  E-value=1.4e-15  Score=116.33  Aligned_cols=76  Identities=20%  Similarity=0.423  Sum_probs=66.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      ++|||+|||.++++++|+++|++||.|.++.+..+      +|+|||+|.+.+ |++|+.. ++|..++|+.|+|.|+.+
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~-l~g~~~~g~~l~V~~a~~   79 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAK-LDNTDFMGRTIRVTEANP   79 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHT-SCSSCCSSSSCSEEEC--
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHH-hCCCEECCeEEEEEEcCC
Confidence            68999999999999999999999999999999864      689999999999 9999997 799999999999999987


Q ss_pred             CCCC
Q psy14139        288 QANR  291 (327)
Q Consensus       288 ~~~~  291 (327)
                      ....
T Consensus        80 ~~~~   83 (90)
T 2ki2_A           80 KKSL   83 (90)
T ss_dssp             ----
T ss_pred             CCCC
Confidence            6543

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=2.2e-14  Score=110.83  Aligned_cols=79  Identities=20%  Similarity=0.353  Sum_probs=68.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCC-eEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg-~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      ...++|||+|||.++++++|+++|++||.|.+|.+....+ ||||+|.+.++|++|++  +++..++|+.|+|.++.++.
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~--l~g~~~~g~~l~V~~a~~~~   83 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS--QSQHSLGGHRLRVRPREQKE   83 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT--CSCCEETTEECCCBCSCCSC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh--cCCeEECCEEEEEEECCcCC
Confidence            3457999999999999999999999999999983332222 99999999999999998  69999999999999887665


Q ss_pred             CC
Q psy14139        290 NR  291 (327)
Q Consensus       290 ~~  291 (327)
                      ..
T Consensus        84 ~~   85 (94)
T 2e5g_A           84 FQ   85 (94)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

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

Probab=99.56  E-value=2e-14  Score=111.23  Aligned_cols=79  Identities=19%  Similarity=0.294  Sum_probs=70.9

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEE-EecC--CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVT-ILSK--QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~-i~~~--kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      ....++|||+|||.++++++|+++|++||.|.+++ ++.+  .+.|||+|.+.++|++|+.. ++|..++|+.|+|.|+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~-l~g~~~~g~~l~V~~a~   90 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDK-LNGFQLENFTLKVAYIP   90 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHH-HTTCBCSSCBCEEEECC
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHH-hCCCEECCcEEEEEEcC
Confidence            34568999999999999999999999999999994 7665  35599999999999999997 69999999999999999


Q ss_pred             CCC
Q psy14139        287 AQA  289 (327)
Q Consensus       287 ~~~  289 (327)
                      ++.
T Consensus        91 ~~~   93 (96)
T 2e44_A           91 DEM   93 (96)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            873

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.56  E-value=1e-14  Score=123.85  Aligned_cols=77  Identities=17%  Similarity=0.269  Sum_probs=70.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcC--CeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFG--EIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG--~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      ..++|||+|||.+++|++|+++|++||  .|.+|+|+.+      +|||||+|.+.++|++|++. ++|..|+|+.|+|.
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~-lng~~~~Gr~l~V~  132 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLEL-LPGKVLNGEKVDVR  132 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHH-STTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHH-cCCCEECCeEeEEE
Confidence            457999999999999999999999999  9999999864      58999999999999999997 79999999999999


Q ss_pred             eccCCC
Q psy14139        284 WGRAQA  289 (327)
Q Consensus       284 ~ak~~~  289 (327)
                      |+.++.
T Consensus       133 ~a~~~~  138 (156)
T 3n9u_C          133 PATRQN  138 (156)
T ss_dssp             ECCHHH
T ss_pred             EcCCCc
Confidence            998654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.55  E-value=3.6e-14  Score=116.81  Aligned_cols=80  Identities=21%  Similarity=0.282  Sum_probs=72.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-CCe-EEEEeCCHHHHHHHHHHhcCCeEECC--eeEEEEecc
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-QQC-AFIQYTSRPAAEAAVEHSFNKVILGG--RRLNIKWGR  286 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-kg~-aFV~F~~~~~Ae~A~~~~l~g~~i~G--~~L~V~~ak  286 (327)
                      ...-.|||+||+..+++++|+++|++||+|.+|++..+ +++ |||+|.+.++|+.|+++ ++|..|.|  +.|+|.|++
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~-LnG~~i~g~~~~LrI~~ak  104 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLS-LDGQNIYNACCTLRIDFSK  104 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHH-HTTCEEETTEEEEEEEECS
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHH-cCCCeecCCCcEEEEEecC
Confidence            45678999999999999999999999999999988764 677 99999999999999998 69999988  899999999


Q ss_pred             CCCCC
Q psy14139        287 AQANR  291 (327)
Q Consensus       287 ~~~~~  291 (327)
                      +..-.
T Consensus       105 ~~~l~  109 (130)
T 3zzy_A          105 LTSLN  109 (130)
T ss_dssp             CSSCC
T ss_pred             CCcee
Confidence            87654

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.55  E-value=2e-14  Score=108.94  Aligned_cols=72  Identities=29%  Similarity=0.508  Sum_probs=67.7

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhc----C-------CeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCee
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQF----G-------EIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRR  279 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~f----G-------~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~  279 (327)
                      ...++|||+|||.++++++|+++|++|    |       .|.++.+..+++||||+|.+.++|++|+ . ++|..++|+.
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~kg~afV~f~~~~~a~~A~-~-l~g~~~~g~~   81 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-A-FDGIIFQGQS   81 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSSSSEEEEEESSHHHHHHHG-G-GTTCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCCCcEEEEEcCCHHHHHHHH-h-cCCCEECCeE
Confidence            456899999999999999999999999    8       9999999999999999999999999999 6 7999999999


Q ss_pred             EEEEe
Q psy14139        280 LNIKW  284 (327)
Q Consensus       280 L~V~~  284 (327)
                      |+|+.
T Consensus        82 l~V~r   86 (87)
T 2hzc_A           82 LKIRR   86 (87)
T ss_dssp             CEEEC
T ss_pred             EEEeC
Confidence            99963

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.55  E-value=9.4e-15  Score=120.04  Aligned_cols=81  Identities=16%  Similarity=0.350  Sum_probs=72.6

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEE--EEEecC------CCeEEEEeCCHHHHHHHHHHhcCCe----EEC
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRS--VTILSK------QQCAFIQYTSRPAAEAAVEHSFNKV----ILG  276 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~--v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~----~i~  276 (327)
                      .+...++|||+|||.+++|++|+++|++||.|..  |+|+.+      +|||||+|.+. +|++|+.. ++|.    .++
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~-l~g~~~~~~~~   96 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQI-LQALHPPLTID   96 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHH-HTTCCCSCCGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHH-hcCCCCCccCC
Confidence            3455689999999999999999999999999977  888764      69999999999 99999997 6999    999


Q ss_pred             CeeEEEEeccCCCCC
Q psy14139        277 GRRLNIKWGRAQANR  291 (327)
Q Consensus       277 G~~L~V~~ak~~~~~  291 (327)
                      |+.|+|.|+++....
T Consensus        97 gr~l~V~~a~~~~~~  111 (131)
T 2m2b_A           97 GKTINVEFAKGSKRD  111 (131)
T ss_dssp             GCCCCCEECCCSCCC
T ss_pred             CEEEEEEECCCCCCC
Confidence            999999999987554

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=1.1e-14  Score=111.14  Aligned_cols=77  Identities=23%  Similarity=0.466  Sum_probs=67.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCCC
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR  291 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~~  291 (327)
                      .++|||+|||.++++++|+++|++||.|.++++..+ ++||||+|.+.++|++|..   ....+.|+.|+|.|++++...
T Consensus         5 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~~~---~~~~~~g~~l~v~~a~~~~~~   81 (88)
T 1wf0_A            5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG---EDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT---CEEEETTEEEEEECCCCCCCC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhc---CCceeCCEEEEEEecCCCCCC
Confidence            489999999999999999999999999999999875 8999999999999986532   346779999999999987654


Q ss_pred             C
Q psy14139        292 G  292 (327)
Q Consensus       292 ~  292 (327)
                      .
T Consensus        82 ~   82 (88)
T 1wf0_A           82 N   82 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.54  E-value=4.8e-15  Score=109.78  Aligned_cols=70  Identities=19%  Similarity=0.441  Sum_probs=65.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ++|||+|||.++++++|+++|++||+|.++.+..+      +|+|||+|.+.++|++|++. ++ ..++|+.|+|+|+
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~-~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ-SR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHT-TT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHh-CC-CccCCEEEEEEec
Confidence            47999999999999999999999999999999874      58999999999999999997 57 9999999999987

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

Probab=99.54  E-value=2.6e-14  Score=111.79  Aligned_cols=80  Identities=23%  Similarity=0.471  Sum_probs=69.0

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      ....++|||+|||.++++++|+++|+.|+.   +.++.+      ++||||+|.+.++|++|++. +++..|.|+.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~---~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~V~   87 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSVR---ARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA-MEDGEIDGNKVTLD   87 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCSE---EEEEECSSSCSEEEEEEEECSSHHHHHHHHHH-HTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCeE---EEEEecCCCCCcCcEEEEEECCHHHHHHHHHH-hCCCeECCeEEEEE
Confidence            455689999999999999999999998864   444433      58999999999999999997 69999999999999


Q ss_pred             eccCCCCCCC
Q psy14139        284 WGRAQANRGE  293 (327)
Q Consensus       284 ~ak~~~~~~~  293 (327)
                      |++++..++.
T Consensus        88 ~a~~~~~~~~   97 (102)
T 2fc8_A           88 WAKPKGEGGS   97 (102)
T ss_dssp             ECCCCCSSSC
T ss_pred             EecCCCCCCC
Confidence            9998876543

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

Probab=99.54  E-value=6.4e-15  Score=108.78  Aligned_cols=69  Identities=20%  Similarity=0.393  Sum_probs=64.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       215 tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      +|||+|||.++++++|+++|++||.|.++.+..+      +|+|||+|.+.++|++|++  +++..++|+.|+|+||
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~--~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE--IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS--SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH--CCCCEECCEEEEEEeC
Confidence            5899999999999999999999999999998764      5899999999999999987  6999999999999986

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.53  E-value=4.9e-14  Score=118.30  Aligned_cols=91  Identities=25%  Similarity=0.426  Sum_probs=77.7

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCC------CeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ------QCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~k------g~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      .++|||+|||.++++++|+++|++||.|.++.+..++      |+|||+|.+.++|++|++. ++|..+.|+.|+|.|+.
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~-l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT-LNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTTCEETTEECEEEECC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHH-cCCCccCCceEEEEecC
Confidence            4799999999999999999999999999999998764      8999999999999999997 69999999999999998


Q ss_pred             CCCCCCCCcccccccccCCCCCCC
Q psy14139        287 AQANRGEDTAELKVRLEPVPGLPG  310 (327)
Q Consensus       287 ~~~~~~~~~~~~~~~~~pv~Glp~  310 (327)
                      +.....    .....+  |.|||.
T Consensus        81 ~~~~~~----~~~~l~--v~nl~~   98 (167)
T 1fxl_A           81 PSSASI----RDANLY--VSGLPK   98 (167)
T ss_dssp             CCCGGG----TTCEEE--EESCCT
T ss_pred             CCcccC----CCCcEE--ECCCCC
Confidence            765322    122234  667753

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.53  E-value=8.7e-15  Score=112.90  Aligned_cols=75  Identities=24%  Similarity=0.334  Sum_probs=67.1

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.++++++|+++|++||.|.++.++.      .+++|||+|.+.++|++|++. +++..+.|+.|+|.++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID-LNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHH-HTTCEETTEECEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHH-hCCCeECCcEEEEEec
Confidence            348999999999999999999999999998777664      268999999999999999997 6999999999999987


Q ss_pred             cC
Q psy14139        286 RA  287 (327)
Q Consensus       286 k~  287 (327)
                      .+
T Consensus        93 ~s   94 (95)
T 2ek1_A           93 SS   94 (95)
T ss_dssp             C-
T ss_pred             cC
Confidence            64

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.52  E-value=1.5e-14  Score=108.68  Aligned_cols=68  Identities=19%  Similarity=0.280  Sum_probs=63.0

Q ss_pred             cEEEEcCCCCCC------CHHHHHHHHhhcCCeEEEEEec----CCCeEEEEeCCHHHHHHHHHHhcCCeEECCe-eEEE
Q psy14139        214 TTLYVGNLGDKL------TEQDLRDHFYQFGEIRSVTILS----KQQCAFIQYTSRPAAEAAVEHSFNKVILGGR-RLNI  282 (327)
Q Consensus       214 ~tLfVgnLp~~i------te~~Lr~~F~~fG~I~~v~i~~----~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~-~L~V  282 (327)
                      ++|||+|||..+      ++++|+++|++||.|.++.+..    .+|||||+|.+.++|++|++. ++|..++|+ +|+|
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~-lng~~~~g~~~l~V   80 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKN-ADGYKLDKQHTFRV   80 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTT-SSSCCCSSSSCCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHH-hcCcccCCceeEEe
Confidence            689999999999      7799999999999999999874    379999999999999999997 799999999 8876

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.52  E-value=3.2e-14  Score=118.35  Aligned_cols=81  Identities=23%  Similarity=0.406  Sum_probs=70.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEE--------EEEe---cCCCeEEEEeCCHHHHHHHHHHhcCCeEECCee
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRS--------VTIL---SKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRR  279 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~--------v~i~---~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~  279 (327)
                      ...++|||+|||.++++++|+++|++||.|.+        +++.   ..+|||||+|.+.++|++|+.. ++|..+.|+.
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~-lng~~~~g~~  121 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKE-ANGYVLFGKP  121 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHH-HTTBEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHH-hCCCEeCCcE
Confidence            44589999999999999999999999999876        3333   2479999999999999999997 6999999999


Q ss_pred             EEEEeccCCCCCC
Q psy14139        280 LNIKWGRAQANRG  292 (327)
Q Consensus       280 L~V~~ak~~~~~~  292 (327)
                      |+|.|+++...+.
T Consensus       122 l~V~~a~~~~~~~  134 (143)
T 3egn_A          122 MVVQFARSARPKQ  134 (143)
T ss_dssp             CEEEECCCSCC--
T ss_pred             EEEEECCCCCCcc
Confidence            9999998876554

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=2.5e-14  Score=114.64  Aligned_cols=77  Identities=14%  Similarity=0.132  Sum_probs=70.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCe-EEEEEec-----CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEI-RSVTILS-----KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I-~~v~i~~-----~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ...++|||+|||.++++++|+++|++||.| .+|+|+.     .+|||||+|.+.++|++|++.  ++..|+|+.|+|.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~--~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL--HRKKLNGREAFVHV   90 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG--CSEEETTEEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh--CCCccCCeEEEEEE
Confidence            345799999999999999999999999999 8898876     479999999999999999983  99999999999999


Q ss_pred             ccCCC
Q psy14139        285 GRAQA  289 (327)
Q Consensus       285 ak~~~  289 (327)
                      +.++.
T Consensus        91 a~~~~   95 (114)
T 2cpy_A           91 VTLED   95 (114)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            98654

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.27  E-value=1e-15  Score=122.89  Aligned_cols=81  Identities=22%  Similarity=0.474  Sum_probs=73.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEE--------EEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEEC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRS--------VTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILG  276 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~--------v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~  276 (327)
                      ...++|||+|||.++++++|+++|++||.|.+        +.+..+      ++||||+|.+.++|++|++. +++..+.
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~-l~g~~~~   83 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDW-FDGKEFS   83 (116)
Confidence            45689999999999999999999999999998        777754      68999999999999999997 7999999


Q ss_pred             CeeEEEEeccCCCCCC
Q psy14139        277 GRRLNIKWGRAQANRG  292 (327)
Q Consensus       277 G~~L~V~~ak~~~~~~  292 (327)
                      |+.|+|.|++++....
T Consensus        84 g~~l~V~~a~~~~~~~   99 (116)
T 2lcw_A           84 GNPIKVSFATRRADFN   99 (116)
Confidence            9999999999877654

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.51  E-value=6.1e-14  Score=109.53  Aligned_cols=78  Identities=14%  Similarity=0.284  Sum_probs=68.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~------~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ...++|||+|||.++++++|+++|++||.|.+ .++      ..+|||||+|.+.++|++|++  +++..+.|+.|+|.|
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~--l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE--LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH--GGGCCBTTBCCEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh--cCCcEECCcEEEEEE
Confidence            34689999999999999999999999998766 332      348999999999999999997  599999999999999


Q ss_pred             ccCCCCC
Q psy14139        285 GRAQANR  291 (327)
Q Consensus       285 ak~~~~~  291 (327)
                      ++++..+
T Consensus        92 a~~~~~~   98 (101)
T 1fj7_A           92 PKGRDGT   98 (101)
T ss_dssp             CSCCCCS
T ss_pred             cCCCCCC
Confidence            9987654

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.51  E-value=6.7e-14  Score=123.84  Aligned_cols=77  Identities=19%  Similarity=0.357  Sum_probs=71.5

Q ss_pred             CccEEEEcCCC-CCCCHHHHHHHHhhcCCeEEEEEecC-CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        212 TITTLYVGNLG-DKLTEQDLRDHFYQFGEIRSVTILSK-QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       212 ~~~tLfVgnLp-~~ite~~Lr~~F~~fG~I~~v~i~~~-kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      ..++|||+||| ..+++++|+++|++||.|.+|+++.+ +|+|||+|.+.++|+.|++. +||..+.|+.|+|.|++.+.
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~-lng~~~~g~~l~v~~s~~~~   81 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITH-LNNNFMFGQKMNVCVSKQPA   81 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHH-HTTCEETTEECEEEECSCSC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHH-hCCCEECCceEEEEEccCCc
Confidence            34799999999 89999999999999999999999875 79999999999999999998 69999999999999998554

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.51  E-value=1.1e-14  Score=107.36  Aligned_cols=69  Identities=23%  Similarity=0.418  Sum_probs=64.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       215 tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      +|||+|||.++++++|+++|++||.|.++.+..+      +|+|||+|.+.++|++|++  .++..++|+.|+|++|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~--~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME--KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT--TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH--hCCCeECCEEEEEEEC
Confidence            5899999999999999999999999999998753      7899999999999999998  3889999999999885

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.51  E-value=8.3e-14  Score=117.31  Aligned_cols=91  Identities=24%  Similarity=0.396  Sum_probs=77.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      .++|||+|||.++++++|+++|++||.|.++.+..+      +|+|||+|.+.++|++|++. ++|..+.|+.|+|.|++
T Consensus         3 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~-l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV-LNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHH-HTTCEETTEECEEEECC
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHh-cCCCEeCCcEEEEEecC
Confidence            479999999999999999999999999999998764      48999999999999999997 69999999999999998


Q ss_pred             CCCCCCCCcccccccccCCCCCCC
Q psy14139        287 AQANRGEDTAELKVRLEPVPGLPG  310 (327)
Q Consensus       287 ~~~~~~~~~~~~~~~~~pv~Glp~  310 (327)
                      +......    ....+  |.|||.
T Consensus        82 ~~~~~~~----~~~l~--v~nl~~   99 (168)
T 1b7f_A           82 PGGESIK----DTNLY--VTNLPR   99 (168)
T ss_dssp             CCSSTTT----TCEEE--EESCCT
T ss_pred             CCcccCC----CCCEE--EeCCCC
Confidence            7664322    22233  667753

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=6.9e-14  Score=110.24  Aligned_cols=78  Identities=18%  Similarity=0.216  Sum_probs=69.5

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEE-EEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRS-VTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~-v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      .....+|||+|||.+++|++|+++|++||.|.+ |+|+.+     +|||||+|.+.++|++|++.  ++..++|+.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~--~~~~~~gr~i~v~   89 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK--HKERIGHRYIEIF   89 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT--TTCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh--CcchhCCcEEEEE
Confidence            345689999999999999999999999999987 777643     79999999999999999983  8999999999999


Q ss_pred             eccCCC
Q psy14139        284 WGRAQA  289 (327)
Q Consensus       284 ~ak~~~  289 (327)
                      ++.++.
T Consensus        90 ~~~~~~   95 (104)
T 1wg5_A           90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            987654

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

Probab=99.50  E-value=8.1e-14  Score=116.84  Aligned_cols=92  Identities=26%  Similarity=0.396  Sum_probs=77.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      ++|||+|||.++++++|+++|++||.|.++.+..+     +|+|||+|.+.++|++|++. ++|..+.|+.|+|.|+.+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT-LNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHH-HTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHH-cCCCccCCCeeEEEEcCCC
Confidence            58999999999999999999999999999999864     48999999999999999987 6999999999999999877


Q ss_pred             CCCCCCcccccccccCCCCCCC
Q psy14139        289 ANRGEDTAELKVRLEPVPGLPG  310 (327)
Q Consensus       289 ~~~~~~~~~~~~~~~pv~Glp~  310 (327)
                      ......  .....+  |.|||.
T Consensus        80 ~~~~~~--~~~~l~--v~nl~~   97 (166)
T 3md3_A           80 QQSSSD--DTFNLF--VGDLNV   97 (166)
T ss_dssp             CCCCCT--TCEEEE--EESCCT
T ss_pred             CCCCCC--CCceEE--ECCCCC
Confidence            654322  222334  677753

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.50  E-value=7.8e-14  Score=120.59  Aligned_cols=98  Identities=21%  Similarity=0.417  Sum_probs=76.7

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      +....++|||+|||.++++++|+++|++||.|.++.++.+      +|||||+|.+.++|++|++.  ++..+.|+.|.|
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~--~~~~~~g~~l~v   86 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA--RPHKVDGRVVEP   86 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT--CSCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc--CCCEECCEEeee
Confidence            4456789999999999999999999999999999999864      57999999999999999983  889999999999


Q ss_pred             EeccCCCCCCCCc--ccccccccCCCCCCC
Q psy14139        283 KWGRAQANRGEDT--AELKVRLEPVPGLPG  310 (327)
Q Consensus       283 ~~ak~~~~~~~~~--~~~~~~~~pv~Glp~  310 (327)
                      .|+.+......+.  .....++  |.|||.
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~l~--V~nLp~  114 (196)
T 1l3k_A           87 KRAVSREDSQRPGAHLTVKKIF--VGGIKE  114 (196)
T ss_dssp             EECCC-----------CCSEEE--EECCTT
T ss_pred             ecccCcccccccccCCCcceEE--EeCCCC
Confidence            9998765433221  1223344  677753

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.50  E-value=1.6e-14  Score=113.11  Aligned_cols=79  Identities=19%  Similarity=0.461  Sum_probs=70.6

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      +...++|||+|||.++++++|+++|++||.|.++.+..+     +|||||+|.+.++|++|++   ++..++|+.|.|.+
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~---~~~~~~g~~l~v~~   82 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE---SQINFHGKKLKLGP   82 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT---CCCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh---CCCeECCEEEEEEE
Confidence            345689999999999999999999999999999999874     6999999999999999986   88999999999999


Q ss_pred             ccCCCCC
Q psy14139        285 GRAQANR  291 (327)
Q Consensus       285 ak~~~~~  291 (327)
                      +.++...
T Consensus        83 a~~~~~~   89 (102)
T 2xs2_A           83 AIRKQNL   89 (102)
T ss_dssp             EEECC--
T ss_pred             CCcCcch
Confidence            9876543

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.49  E-value=4.9e-14  Score=124.79  Aligned_cols=94  Identities=22%  Similarity=0.421  Sum_probs=77.7

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.+++|++|+++|++||+|.+|+|+.+      +|||||+|.+.++|++|++. +++..+.|+.|+|.|+
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~-~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT-MNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTTCEETTEECEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHH-hhhhhcCCcccccccc
Confidence            4579999999999999999999999999999999864      58999999999999999997 6999999999999998


Q ss_pred             cCCCCCCCCcccccccccCCCCCCC
Q psy14139        286 RAQANRGEDTAELKVRLEPVPGLPG  310 (327)
Q Consensus       286 k~~~~~~~~~~~~~~~~~pv~Glp~  310 (327)
                      .......  ......++  |.+||.
T Consensus        93 ~~~~~~~--~~~~~~l~--v~nl~~  113 (213)
T 4f02_A           93 QRDPSLR--KSGVGNIF--IKNLDK  113 (213)
T ss_dssp             CCCTHHH--HHCTTEEE--EESCCT
T ss_pred             ccccccc--ccccccce--ECCccc
Confidence            7654321  11223345  677753

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.49  E-value=5.4e-14  Score=113.59  Aligned_cols=78  Identities=13%  Similarity=0.149  Sum_probs=70.4

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCC---eEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGE---IRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRL  280 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~---I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L  280 (327)
                      .....++|||+|||.++++++|+++|++||.   |.+|+|+.+     +|||||+|.+.++|++|++  +++..|+|+.|
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~--~~g~~~~gr~i   90 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK--KDRESMGHRYI   90 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG--GTTEEETTEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh--cCCCeECCeEE
Confidence            3455689999999999999999999999999   899998864     6899999999999999998  59999999999


Q ss_pred             EEEeccCC
Q psy14139        281 NIKWGRAQ  288 (327)
Q Consensus       281 ~V~~ak~~  288 (327)
                      +|.++..+
T Consensus        91 ~V~~a~~~   98 (118)
T 2db1_A           91 EVFKSHRT   98 (118)
T ss_dssp             EEEEECHH
T ss_pred             EEEECCHH
Confidence            99998654

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.48  E-value=4.2e-13  Score=123.12  Aligned_cols=81  Identities=22%  Similarity=0.483  Sum_probs=73.7

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHH----HHHhhcCCeEEEEEec---CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeE
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLR----DHFYQFGEIRSVTILS---KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRL  280 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr----~~F~~fG~I~~v~i~~---~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L  280 (327)
                      ++....++|||+|||.++++++|+    ++|++||.|.+|++..   .+|||||+|.+.++|++|++. ++|..+.|+.|
T Consensus         4 ~~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l   82 (282)
T 3pgw_A            4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS-MQGFPFYDKPM   82 (282)
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHH-hcCCeeCCcEE
Confidence            455667899999999999999977    8999999999999876   479999999999999999987 79999999999


Q ss_pred             EEEeccCCC
Q psy14139        281 NIKWGRAQA  289 (327)
Q Consensus       281 ~V~~ak~~~  289 (327)
                      +|.|++...
T Consensus        83 ~v~~a~~~~   91 (282)
T 3pgw_A           83 RIQYAKTDS   91 (282)
T ss_pred             EEEEeccCc
Confidence            999998765

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=1.7e-13  Score=106.05  Aligned_cols=75  Identities=23%  Similarity=0.275  Sum_probs=66.5

Q ss_pred             CccEEEEcCCCCCCCHHH----HHHHHhhc-CCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        212 TITTLYVGNLGDKLTEQD----LRDHFYQF-GEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~----Lr~~F~~f-G~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      ..+.|||+|||..+++++    |+++|++| |+|.+|.    .|+|||.|.+.++|++|++. ++|..+.|++|+|.+++
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt----gG~AfV~F~~~esA~~A~~~-l~G~~l~gr~i~v~~A~   82 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSIT----GCSAILRFINQDSAERAQKR-MENEDVFGNRIIVSFTP   82 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEECC----TTCEEEEESSHHHHHHHHHH-HTTCCSSSSCCEEESSC
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEEe----cCEEEEEECCHHHHHHHHHH-hcCCccCCceEEEEecC
Confidence            335599999999999988    55899999 5999983    49999999999999999998 69999999999999999


Q ss_pred             CCCCC
Q psy14139        287 AQANR  291 (327)
Q Consensus       287 ~~~~~  291 (327)
                      .++.-
T Consensus        83 ~~sd~   87 (96)
T 2diu_A           83 KNREL   87 (96)
T ss_dssp             CSCCC
T ss_pred             CCcce
Confidence            87653

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.47  E-value=1.1e-13  Score=122.45  Aligned_cols=77  Identities=23%  Similarity=0.514  Sum_probs=71.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      ..+|||+|||.++++++|+++|++||.|.+++|+.+    +|||||+|.+.++|++|++. +||..|+|+.|+|.|++++
T Consensus       103 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~-lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK-MNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHH-HTTCEETTEECEEEECCCH
T ss_pred             cccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHH-hCCCEECCEEEEEEEcCCC
Confidence            468999999999999999999999999999999864    68999999999999999998 6999999999999999876


Q ss_pred             CC
Q psy14139        289 AN  290 (327)
Q Consensus       289 ~~  290 (327)
                      ..
T Consensus       182 ~~  183 (213)
T 4f02_A          182 KE  183 (213)
T ss_dssp             HH
T ss_pred             cc
Confidence            54

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

Probab=99.47  E-value=2.4e-13  Score=113.93  Aligned_cols=77  Identities=26%  Similarity=0.493  Sum_probs=70.8

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      ....++|||+|||.++++++|+++|++||.|.++.+..+      +|+|||+|.+.++|++|+.. ++|..++|+.|+|.
T Consensus        84 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~i~v~  162 (166)
T 3md3_A           84 SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS-MQGQDLNGRPLRIN  162 (166)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHH-HTTCEETTEECEEE
T ss_pred             CCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHH-hCCCccCCcEEEEE
Confidence            345679999999999999999999999999999999864      67999999999999999997 69999999999999


Q ss_pred             eccC
Q psy14139        284 WGRA  287 (327)
Q Consensus       284 ~ak~  287 (327)
                      |++.
T Consensus       163 ~a~~  166 (166)
T 3md3_A          163 WAAK  166 (166)
T ss_dssp             ESCC
T ss_pred             ecCC
Confidence            9863

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=2e-13  Score=109.06  Aligned_cols=78  Identities=17%  Similarity=0.257  Sum_probs=69.5

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      |......+|||+|||.+++|++|+++|++| .|.+|+|+.+     +|+|||+|.+.++|++|+.  +++..++|+.|.|
T Consensus        11 ~~~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~--~~~~~~~gr~i~V   87 (109)
T 2dnn_A           11 PINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALK--RNRMLMIQRYVEV   87 (109)
T ss_dssp             CCCHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHHH--TTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh--cCCCeECCeEEEE
Confidence            334456799999999999999999999999 8999999863     7999999999999999994  6999999999999


Q ss_pred             EeccCC
Q psy14139        283 KWGRAQ  288 (327)
Q Consensus       283 ~~ak~~  288 (327)
                      ..+.++
T Consensus        88 ~~a~~~   93 (109)
T 2dnn_A           88 SPATER   93 (109)
T ss_dssp             EECCHH
T ss_pred             EECCcc
Confidence            888654

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.47  E-value=5.1e-14  Score=116.95  Aligned_cols=79  Identities=14%  Similarity=0.163  Sum_probs=71.0

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhcCC---eEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCee
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGE---IRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRR  279 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~---I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~  279 (327)
                      +.....++|||+|||.+++|++|+++|++||.   |.+|+|+.+     +|||||+|.+.++|++|++  +++..++|+.
T Consensus        39 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~--~~g~~l~gr~  116 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK--KDRESMGHRY  116 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT--TTEEESSSSE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh--cCCCEECCEE
Confidence            34556789999999999999999999999999   889998864     6899999999999999998  5999999999


Q ss_pred             EEEEeccCC
Q psy14139        280 LNIKWGRAQ  288 (327)
Q Consensus       280 L~V~~ak~~  288 (327)
                      |+|.++.++
T Consensus       117 i~V~~a~~~  125 (136)
T 2hgl_A          117 IEVFKSHRT  125 (136)
T ss_dssp             EEEEECCHH
T ss_pred             EEEEECChH
Confidence            999998654

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

Probab=99.47  E-value=2e-13  Score=118.15  Aligned_cols=80  Identities=19%  Similarity=0.470  Sum_probs=74.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ...++|||+|||.++++++|+++|++||.|.++.+..+      +|+|||+|.+.++|++|++. ++|..++|+.|+|.|
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g~~~~g~~l~v~~  190 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG-LNGMQLGDKKLLVQR  190 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHH-HTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            45689999999999999999999999999999999875      68999999999999999997 699999999999999


Q ss_pred             ccCCCCC
Q psy14139        285 GRAQANR  291 (327)
Q Consensus       285 ak~~~~~  291 (327)
                      ++++.++
T Consensus       191 a~~~~~~  197 (198)
T 2yh0_A          191 ASVGAKN  197 (198)
T ss_dssp             SCCCCCC
T ss_pred             CCCCCCC
Confidence            9987654

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=9.2e-14  Score=109.45  Aligned_cols=78  Identities=18%  Similarity=0.165  Sum_probs=68.7

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ...++|||+|||.+++|++|+++|++||. .+|+|+.+     +|||||+|.+.++|++|++  +++..++|+.|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~--~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA--KDKANMQHRYVELFLN   89 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT--TSSCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECCCCCEeeEEEEEECCHHHHHHHHH--hCCCeECCcEEEEEEC
Confidence            34579999999999999999999999995 48988764     6899999999999999995  4999999999999998


Q ss_pred             cCCCCC
Q psy14139        286 RAQANR  291 (327)
Q Consensus       286 k~~~~~  291 (327)
                      .+....
T Consensus        90 ~~~~~~   95 (102)
T 1wez_A           90 STAGTS   95 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.46  E-value=6.2e-14  Score=126.27  Aligned_cols=75  Identities=20%  Similarity=0.285  Sum_probs=68.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcC--CeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFG--EIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG--~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      ..++|||+||+.+++|++|+++|++||  .|.+|+|+.+      ++||||+|.+.++|++|++. +++..|.|+.|+|.
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~-lng~~~~Gr~l~V~  145 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDL-LPKRELHGQNPVVT  145 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTT-STTSCBTTBCCEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHH-cCCCeECCEEeEEE
Confidence            457999999999999999999999999  9999999875      58999999999999999997 79999999999999


Q ss_pred             eccC
Q psy14139        284 WGRA  287 (327)
Q Consensus       284 ~ak~  287 (327)
                      |+++
T Consensus       146 ~a~~  149 (229)
T 3q2s_C          146 PVNK  149 (229)
T ss_dssp             ECCH
T ss_pred             ECCC
Confidence            9864

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

Probab=99.46  E-value=1.7e-13  Score=118.68  Aligned_cols=78  Identities=24%  Similarity=0.398  Sum_probs=71.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ...++|||+|||.++++++|+++|++||.|.+|.|..+     +++|||+|.+.++|++|++. +++..++|+.|+|.|+
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~-lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ-YKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHH-STTCBCSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHH-hCCCEECCEEEEEEEe
Confidence            44689999999999999999999999999999999763     69999999999999999997 7999999999999998


Q ss_pred             cCCC
Q psy14139        286 RAQA  289 (327)
Q Consensus       286 k~~~  289 (327)
                      .+..
T Consensus       165 ~~~~  168 (177)
T 2f3j_A          165 ASQI  168 (177)
T ss_dssp             SSGG
T ss_pred             cCCC
Confidence            7653

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.46  E-value=3.1e-13  Score=123.33  Aligned_cols=76  Identities=33%  Similarity=0.503  Sum_probs=72.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      ...++|||+|||.++++++|+++|++||.|.+|.+..++|+|||+|.+.++|+.|+.. ++|..+.|+.|+|.|+.+
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~A~~A~~~-l~g~~i~g~~l~v~~a~~   95 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAE-LDGTILKSRPLRIRFATH   95 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETTTTEEEEECSSHHHHHHHHHH-HTTCEETTEECEEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCCCcEEEEEECCHHHHHHHHHH-cCCcEECCceeEeeeccc
Confidence            4557999999999999999999999999999999999999999999999999999997 699999999999999875

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.46  E-value=3.7e-13  Score=113.88  Aligned_cols=91  Identities=26%  Similarity=0.439  Sum_probs=77.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhc----C-------CeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeE
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQF----G-------EIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRL  280 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~f----G-------~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L  280 (327)
                      ..++|||+|||.++++++|+++|++|    |       .|.++.+..++|+|||+|.+.++|++|+ . ++|..+.|+.|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~~g~afV~f~~~~~A~~A~-~-~~~~~~~g~~i   80 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-A-FDGIIFQGQSL   80 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETTTTEEEEEESSHHHHHHHG-G-GTTCEETTEEC
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCCCCEEEEEeCCHHHHHHHH-H-hCCcEecCcee
Confidence            45899999999999999999999999    7       8999999999999999999999999999 5 79999999999


Q ss_pred             EEEeccCCCCCCCCcccccccccCCCCCCC
Q psy14139        281 NIKWGRAQANRGEDTAELKVRLEPVPGLPG  310 (327)
Q Consensus       281 ~V~~ak~~~~~~~~~~~~~~~~~pv~Glp~  310 (327)
                      +|.|+.+......    ....+  |.|||.
T Consensus        81 ~v~~~~~~~~~~~----~~~l~--v~nlp~  104 (172)
T 2g4b_A           81 KIRRPHDYQPLPG----AHKLF--IGGLPN  104 (172)
T ss_dssp             EEECCSSCCCCTT----TTCEE--EECCCT
T ss_pred             eecCCcccCCCCC----CCEEE--EEcCCC
Confidence            9999876543321    22344  677753

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

Probab=99.44  E-value=3.3e-13  Score=118.41  Aligned_cols=77  Identities=26%  Similarity=0.509  Sum_probs=71.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.++++++|+++|++||.|.++++..+      +++|||+|.+.++|++|++. ++|..++|+.|+|.|+
T Consensus       124 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS-MNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTTCBCSSSBCEEEEC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHH-ccCCEeCCcEEEEEEe
Confidence            4479999999999999999999999999999999875      68999999999999999998 6999999999999999


Q ss_pred             cCCC
Q psy14139        286 RAQA  289 (327)
Q Consensus       286 k~~~  289 (327)
                      +++.
T Consensus       203 ~~~~  206 (216)
T 2qfj_A          203 VTPP  206 (216)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8764

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.43  E-value=4.8e-13  Score=115.56  Aligned_cols=81  Identities=20%  Similarity=0.443  Sum_probs=68.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ...++|||+|||.++++++|+++|++||.|.++.+..+      +|+|||+|.+.++|++|+..  ++..++|+.|.|.|
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~--~~~~~~G~~i~v~~  179 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ--KYHTVNGHNCEVRK  179 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC--SCCEETTEECEEEE
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh--CCcEECCEEEEEEe
Confidence            34589999999999999999999999999999999864      68999999999999999984  79999999999999


Q ss_pred             ccCCCCCCC
Q psy14139        285 GRAQANRGE  293 (327)
Q Consensus       285 ak~~~~~~~  293 (327)
                      +.++.....
T Consensus       180 a~~k~~~~~  188 (196)
T 1l3k_A          180 ALSKQEMAS  188 (196)
T ss_dssp             CC-------
T ss_pred             cCChhHhcc
Confidence            998876543

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.43  E-value=4.8e-13  Score=131.36  Aligned_cols=79  Identities=25%  Similarity=0.453  Sum_probs=72.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|++|+.. |||..|.|+.|.|.|
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~-lng~~i~gr~i~V~~  178 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH-ADGKKIDGRRVLVDV  178 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            34579999999999999999999999999999999864      79999999999999999997 799999999999999


Q ss_pred             ccCCCC
Q psy14139        285 GRAQAN  290 (327)
Q Consensus       285 ak~~~~  290 (327)
                      +++...
T Consensus       179 a~~~~~  184 (437)
T 3pgw_S          179 ERGRTV  184 (437)
T ss_pred             eCCCCC
Confidence            987654

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.43  E-value=9.8e-14  Score=109.91  Aligned_cols=78  Identities=15%  Similarity=0.154  Sum_probs=69.9

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCC---eEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGE---IRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~---I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      .....+|||+|||.++++++|+++|+.||.   |.+|+|+.+     +|+|||+|.+.++|++|++  +++..++|+.|+
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~--~~~~~~~gr~i~   85 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE--KHRMYMGQRYVE   85 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT--TTTCCSSSSCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH--hCcceeCCeEEE
Confidence            345689999999999999999999999988   899998763     6899999999999999998  599999999999


Q ss_pred             EEeccCCC
Q psy14139        282 IKWGRAQA  289 (327)
Q Consensus       282 V~~ak~~~  289 (327)
                      |.++.++.
T Consensus        86 V~~a~~~~   93 (107)
T 2lmi_A           86 VYEINNED   93 (107)
T ss_dssp             CEECCHHH
T ss_pred             EEECCHHH
Confidence            99987643

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.43  E-value=6.9e-13  Score=121.69  Aligned_cols=76  Identities=20%  Similarity=0.357  Sum_probs=71.3

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCC-CeEEEEeCCHHHHHHHHHHhcCCeEEC-CeeEEEEecc
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ-QCAFIQYTSRPAAEAAVEHSFNKVILG-GRRLNIKWGR  286 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~k-g~aFV~F~~~~~Ae~A~~~~l~g~~i~-G~~L~V~~ak  286 (327)
                      ....++|||+|||.++++++|+++|++||.|.++++..++ |+|||+|.+.++|++|++. ++|..+. |+.|+|.|++
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~-l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDA-LQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCCcEEEEEeCCHHHHHHHHHH-cCCcEeCCCCEEEEEEec
Confidence            4556899999999999999999999999999999999876 9999999999999999997 7999999 9999999986

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.43  E-value=4.4e-14  Score=114.82  Aligned_cols=77  Identities=13%  Similarity=0.207  Sum_probs=67.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ...++|||+|||.++++++|+++|++||.|.++.++.      .+|||||+|.+.++|++|++  +++..|+|+.|+|.|
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~--~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC--RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT--SCSBCSTTSCBEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH--hCCCeECCcEEEEEE
Confidence            3458999999999999999999999999998743332      26899999999999999998  599999999999999


Q ss_pred             ccCCC
Q psy14139        285 GRAQA  289 (327)
Q Consensus       285 ak~~~  289 (327)
                      +.++.
T Consensus       101 a~~~~  105 (124)
T 1wel_A          101 ITKKG  105 (124)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            87654

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.41  E-value=4.5e-13  Score=116.46  Aligned_cols=76  Identities=29%  Similarity=0.417  Sum_probs=71.3

Q ss_pred             ccEEEEcCCCC-CCCHHHHHHHHhhcCCeEEEEEecC-CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        213 ITTLYVGNLGD-KLTEQDLRDHFYQFGEIRSVTILSK-QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       213 ~~tLfVgnLp~-~ite~~Lr~~F~~fG~I~~v~i~~~-kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      .++|||+|||. ++++++|+++|++||.|.++++..+ +|+|||+|.+.++|++|++. ++|..+.|+.|+|.|+++..
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~-l~~~~~~g~~l~v~~a~~~~   80 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSH-LNGHKLHGKPIRITLSKHQN   80 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHH-HTTCCCSSCCCEEEECCCCS
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHH-hCCCeecCeEEEEEEecCCC
Confidence            47999999999 9999999999999999999999887 59999999999999999997 69999999999999998764

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.41  E-value=4.8e-13  Score=119.71  Aligned_cols=78  Identities=28%  Similarity=0.400  Sum_probs=72.7

Q ss_pred             CCccEEEEcCCCC-CCCHHHHHHHHhhcCCeEEEEEecC-CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        211 KTITTLYVGNLGD-KLTEQDLRDHFYQFGEIRSVTILSK-QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       211 ~~~~tLfVgnLp~-~ite~~Lr~~F~~fG~I~~v~i~~~-kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      ...++|||+|||. ++++++|+++|++||.|.+|++..+ +++|||+|.+.++|++|++. ++|..+.|+.|+|.|+++.
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~-l~g~~~~g~~l~v~~a~~~  110 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSH-LNGHKLHGKPIRITLSKHQ  110 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHH-HTTCBCSSSBCEEECCSCC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHH-hCCCeECCeEEEEEEecCc
Confidence            4568999999999 9999999999999999999999987 59999999999999999997 6999999999999999866


Q ss_pred             C
Q psy14139        289 A  289 (327)
Q Consensus       289 ~  289 (327)
                      .
T Consensus       111 ~  111 (229)
T 2adc_A          111 N  111 (229)
T ss_dssp             C
T ss_pred             c
Confidence            3

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.41  E-value=4.9e-13  Score=113.15  Aligned_cols=73  Identities=19%  Similarity=0.489  Sum_probs=68.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.++++++|+++|++||.|.++.+..+      +|+|||+|.+.++|++|++. ++|..++|+.|+|.||
T Consensus        93 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG-LNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHH-HTTCEETTEECEEEEC
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHH-cCCCEECCeEEEEEeC
Confidence            3589999999999999999999999999999999876      58999999999999999997 6999999999999997

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.40  E-value=3.8e-13  Score=113.26  Aligned_cols=74  Identities=19%  Similarity=0.451  Sum_probs=69.3

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      .++|||+|||.++++++|+++|++||.|.++.+..+      +|+|||+|.+.++|++|++  +++..++|+.|+|.|++
T Consensus        87 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ--NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH--CSEECSSSSCEEEEECC
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh--CCCEEeCCeEEEEeecC
Confidence            469999999999999999999999999999999864      5899999999999999997  59999999999999998


Q ss_pred             CC
Q psy14139        287 AQ  288 (327)
Q Consensus       287 ~~  288 (327)
                      |+
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            86

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.40  E-value=7.9e-13  Score=111.85  Aligned_cols=93  Identities=20%  Similarity=0.409  Sum_probs=75.1

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec--------CCCeEEEEeCCHHHHHHHHHHhcCCeEEC---CeeE
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS--------KQQCAFIQYTSRPAAEAAVEHSFNKVILG---GRRL  280 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~--------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~---G~~L  280 (327)
                      +.++|||+|||.++++++|+++|++||.|.+++++.        .+|+|||+|.+.++|++|++. +++..+.   ++.+
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~~~~~~~~~~~~~   80 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA-LHNMKVLPGMHHPI   80 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHH-HTTTCCCTTCSSCC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHH-hcCcEEccCCccce
Confidence            347999999999999999999999999999999984        368999999999999999997 5876655   5788


Q ss_pred             EEEeccCCCCCCCCcccccccccCCCCCCC
Q psy14139        281 NIKWGRAQANRGEDTAELKVRLEPVPGLPG  310 (327)
Q Consensus       281 ~V~~ak~~~~~~~~~~~~~~~~~pv~Glp~  310 (327)
                      .+.++.+.....   ......+  |.|||.
T Consensus        81 ~~~~~~~~~~~~---~~~~~l~--v~nl~~  105 (175)
T 3nmr_A           81 QMKPADSEKNNA---VEDRKLF--IGMISK  105 (175)
T ss_dssp             EEEECGGGCCSC---GGGSEEE--EESCCT
T ss_pred             EEcccccccccc---CCCCeEE--EcCCCC
Confidence            998887765432   1223344  677763

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.38  E-value=1.3e-12  Score=116.91  Aligned_cols=76  Identities=22%  Similarity=0.359  Sum_probs=71.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcC-CeEEEEEec-CCCeEEEEeCCHHHHHHHHHHhcCCeEEC-CeeEEEEeccCC
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFG-EIRSVTILS-KQQCAFIQYTSRPAAEAAVEHSFNKVILG-GRRLNIKWGRAQ  288 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG-~I~~v~i~~-~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~-G~~L~V~~ak~~  288 (327)
                      ..++|||+|||.++++++|+++|++|| .|.+++++. ++++|||+|.+.++|++|++. ++|..++ |+.|+|.|++++
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~~A~~Ai~~-l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALID-LHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHH-HTTCBSSSSCBCEEEECSSC
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHHHHHHHHHH-HCCCccCCCCeEEEEEecCC
Confidence            458999999999999999999999999 999999965 799999999999999999998 6999999 999999999875

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.38  E-value=1.5e-12  Score=110.74  Aligned_cols=77  Identities=26%  Similarity=0.381  Sum_probs=69.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEe--cCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL--SKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~--~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      ...++|||+|||.++++++|+++|++||.|..+ ..  ..+|+|||+|.+.++|++|++. ++|..++|+.|+|.|++++
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGKSKGIAYIEFKSEADAEKNLEE-KQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-CSSSSCCSEEEEECSSHHHHHHHHHH-HTEEEETTEEEEEEECSSC
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-cCCCCCceEEEEEECCHHHHHHHHHH-hCCCEECCeEEEEEecCCC
Confidence            456899999999999999999999999999877 11  2479999999999999999997 6999999999999999876


Q ss_pred             C
Q psy14139        289 A  289 (327)
Q Consensus       289 ~  289 (327)
                      +
T Consensus       175 ~  175 (175)
T 1fje_B          175 G  175 (175)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=99.38  E-value=4.2e-12  Score=109.80  Aligned_cols=76  Identities=28%  Similarity=0.462  Sum_probs=70.7

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhc----C-------CeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQF----G-------EIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~f----G-------~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      .++|||+|||.++++++|+++|++|    |       .|.++.+..++|||||+|.+.++|++|+ . ++|..+.|+.|+
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al-~-l~g~~~~g~~i~   81 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-A-FDGIIFQGQSLK   81 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTTTEEEEEESCSHHHHHHG-G-GTTEEETTEEEE
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCCCEEEEEeCCHHHHHHHH-H-hcCCEEcCceEE
Confidence            4799999999999999999999999    6       7899999999999999999999999999 5 799999999999


Q ss_pred             EEeccCCCC
Q psy14139        282 IKWGRAQAN  290 (327)
Q Consensus       282 V~~ak~~~~  290 (327)
                      |.|+++...
T Consensus        82 v~~~~~~~~   90 (198)
T 2yh0_A           82 IRRPHDYQP   90 (198)
T ss_dssp             EECCCCCCC
T ss_pred             EeCCCCCCC
Confidence            999887644

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.38  E-value=8e-13  Score=114.87  Aligned_cols=77  Identities=22%  Similarity=0.352  Sum_probs=71.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcC-CeEEEEEec-CCCeEEEEeCCHHHHHHHHHHhcCCeEEC-CeeEEEEeccC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFG-EIRSVTILS-KQQCAFIQYTSRPAAEAAVEHSFNKVILG-GRRLNIKWGRA  287 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG-~I~~v~i~~-~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~-G~~L~V~~ak~  287 (327)
                      ...++|||+|||..+++++|+++|++|| .|.++++.. ++|+|||+|.+.++|++|+.. ++|..++ |+.|+|.|+++
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~afV~f~~~~~A~~A~~~-l~g~~~~~g~~l~v~~a~~  196 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALID-LHNHDLGENHHLRVSFSKS  196 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHHHHHHHHH-HTSSCCSSCCSCCEEEECC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHH-hcCCccCCCCeEEEEeecc
Confidence            3468999999999999999999999999 999999966 689999999999999999997 6999999 99999999987


Q ss_pred             C
Q psy14139        288 Q  288 (327)
Q Consensus       288 ~  288 (327)
                      +
T Consensus       197 ~  197 (198)
T 1qm9_A          197 T  197 (198)
T ss_dssp             C
T ss_pred             c
Confidence            4

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.38  E-value=1.3e-12  Score=110.47  Aligned_cols=74  Identities=28%  Similarity=0.544  Sum_probs=66.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEEC---CeeEEEE
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILG---GRRLNIK  283 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~---G~~L~V~  283 (327)
                      ..++|||+|||.++++++|+++|++||.|.++.+..+     +|+|||+|.+.++|++|++. ++|..+.   |++|+|.
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~-l~g~~~~~g~~~~l~V~  172 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKA-MHQAQTMEGCSSPMVVK  172 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHH-HTTSCCCTTCSSCCEEE
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHH-hcCCcccCCCCCCeEEE
Confidence            4579999999999999999999999999999999875     78999999999999999998 6876555   3999999


Q ss_pred             ecc
Q psy14139        284 WGR  286 (327)
Q Consensus       284 ~ak  286 (327)
                      ||.
T Consensus       173 ~ad  175 (175)
T 3nmr_A          173 FAD  175 (175)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            984

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.37  E-value=2.2e-13  Score=113.46  Aligned_cols=78  Identities=18%  Similarity=0.157  Sum_probs=68.7

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ...++|||+|||.+++|++|+++|++|| |.+|+|+.+     +|||||+|.+.++|++|+ . +++..++|+.|+|.++
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~-~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-S-KDRANMQHRYIELFLN  120 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-T-CCSCSSSSCCCCCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-h-hCCCEECCEEEEEEEC
Confidence            3457999999999999999999999999 779998763     789999999999999999 4 6999999999999998


Q ss_pred             cCCCCC
Q psy14139        286 RAQANR  291 (327)
Q Consensus       286 k~~~~~  291 (327)
                      .+....
T Consensus       121 ~~~~~~  126 (139)
T 2hgn_A          121 STTGAS  126 (139)
T ss_dssp             CCSCC-
T ss_pred             CCCCCC
Confidence            876543

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.37  E-value=2.7e-12  Score=109.06  Aligned_cols=96  Identities=16%  Similarity=0.249  Sum_probs=76.6

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEE-----EEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRS-----VTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~-----v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      .....++|||+|||.++++++|+++|++||.+..     ......+|+|||+|.+.++|++|++  ++|..+.|+.|+|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~--l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE--LTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH--GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHh--cCCCEeCCeEEEEe
Confidence            3456689999999999999999999999985443     3444468999999999999999994  79999999999999


Q ss_pred             eccCCCCCCCCcccccccccCCCCCCC
Q psy14139        284 WGRAQANRGEDTAELKVRLEPVPGLPG  310 (327)
Q Consensus       284 ~ak~~~~~~~~~~~~~~~~~pv~Glp~  310 (327)
                      |+.++......  .....+  |.|||.
T Consensus        87 ~~~~~~~~~~~--~~~~l~--v~nlp~  109 (175)
T 1fje_B           87 KPKGRDSKKVR--AARTLL--AKNLSF  109 (175)
T ss_dssp             CCCCSSCSTTG--GGGEEE--EESCCS
T ss_pred             cCCCccccccc--cCCEEE--EeCCCC
Confidence            99887654322  233344  777763

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.37  E-value=1.8e-12  Score=113.69  Aligned_cols=75  Identities=15%  Similarity=0.208  Sum_probs=67.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec-----CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS-----KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~-----~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      ..++|||+|||.++++++|+++|++||.|.+|+|..     .+|||||+|.+.++|++|++.  .+..++|+.|+|.|++
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~--~~~~~~Gr~l~V~~~~  185 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET--PGQKYKETDLLILFKD  185 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHC--TTCEETTEECEEEETT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHh--CCCeECCEEEEEEEhH
Confidence            357999999999999999999999999999999986     369999999999999999984  3459999999999987


Q ss_pred             CC
Q psy14139        287 AQ  288 (327)
Q Consensus       287 ~~  288 (327)
                      .-
T Consensus       186 ~y  187 (193)
T 2voo_A          186 DY  187 (193)
T ss_dssp             TC
T ss_pred             HH
Confidence            64

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.37  E-value=2.2e-12  Score=108.52  Aligned_cols=74  Identities=32%  Similarity=0.537  Sum_probs=68.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECC--eeEEE
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGG--RRLNI  282 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G--~~L~V  282 (327)
                      ...++|||+|||.++++++|+++|++||.|.++.+..+      +|+|||+|.+.++|++|++. ++|..+.|  ++|+|
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~~~l~V  165 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA-LNNVIPEGGSQPLSV  165 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTTCCCTTCSSCCEE
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHH-hcCCEecCCCeEEEE
Confidence            34579999999999999999999999999999999875      38999999999999999997 69999988  99999


Q ss_pred             Eec
Q psy14139        283 KWG  285 (327)
Q Consensus       283 ~~a  285 (327)
                      .||
T Consensus       166 ~~A  168 (168)
T 1b7f_A          166 RLA  168 (168)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.36  E-value=6.6e-13  Score=108.81  Aligned_cols=75  Identities=21%  Similarity=0.260  Sum_probs=66.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeE--EEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIR--SVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~--~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      ....+|||+|||.+++|++|+++|++| .|.  +|+|+.+     +|||||+|.+.++|++|++.  ++..|+|+.|+|.
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~--~~~~l~gR~I~V~  116 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK--HKERIGHRYIEVF  116 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT--TTCCBTTBCCCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH--CCCEECCEEEEEE
Confidence            345789999999999999999999999 677  8888763     79999999999999999983  6799999999998


Q ss_pred             eccCC
Q psy14139        284 WGRAQ  288 (327)
Q Consensus       284 ~ak~~  288 (327)
                      ++.++
T Consensus       117 ~a~~~  121 (126)
T 2hgm_A          117 KSSQE  121 (126)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            87543

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

Probab=99.36  E-value=1.8e-12  Score=113.62  Aligned_cols=77  Identities=31%  Similarity=0.567  Sum_probs=69.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.++++++|+++|++||.|.+++++.+      +++|||+|.+.++|++|++. +++..+.|+.|+|.++
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ-MNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHH-HSSCCCC-CCCEEECC
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHH-ccCCeeCCeeEEEecC
Confidence            3579999999999999999999999999999999753      79999999999999999997 6999999999999988


Q ss_pred             cCCC
Q psy14139        286 RAQA  289 (327)
Q Consensus       286 k~~~  289 (327)
                      ....
T Consensus       106 ~~~~  109 (216)
T 2qfj_A          106 SNIG  109 (216)
T ss_dssp             SCCG
T ss_pred             CCcc
Confidence            7654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.36  E-value=2.2e-12  Score=103.27  Aligned_cols=74  Identities=16%  Similarity=0.296  Sum_probs=62.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec---------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS---------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~---------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      ...++|||+|||.++++++|+++|++||.|. +.++.         .+|||||+|.+.++|++|++. +  ..++|+.|.
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~-~--~~~~G~~~~   81 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDA-C--LEEDGKLYL   81 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHH-S--EEETTEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHh-h--hhcCCcEEE
Confidence            3458999999999999999999999999999 76654         379999999999999999997 4  347888888


Q ss_pred             EEeccCC
Q psy14139        282 IKWGRAQ  288 (327)
Q Consensus       282 V~~ak~~  288 (327)
                      +..+.+.
T Consensus        82 ~~~~~~~   88 (114)
T 2dnl_A           82 CVSSPTI   88 (114)
T ss_dssp             EECCSSS
T ss_pred             eccCCCc
Confidence            8755433

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.35  E-value=6.3e-13  Score=108.44  Aligned_cols=75  Identities=19%  Similarity=0.241  Sum_probs=66.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCe----EEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEI----RSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I----~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      ...+|||+|||.+++|++|+++|++||.|    .+|+|+.+     +|||||+|.+.++|++|++.  ++..++|+.|.|
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~--~~~~l~gR~i~V   99 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK--HKDLLGKRYIEL   99 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT--TTEESSSCEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh--CCCeeCCeEEEE
Confidence            34799999999999999999999999985    68888753     68999999999999999983  899999999999


Q ss_pred             EeccCC
Q psy14139        283 KWGRAQ  288 (327)
Q Consensus       283 ~~ak~~  288 (327)
                      ..+.++
T Consensus       100 ~~a~~~  105 (123)
T 2dha_A          100 FRSTAA  105 (123)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            887543

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.33  E-value=2.9e-12  Score=107.81  Aligned_cols=75  Identities=20%  Similarity=0.462  Sum_probs=67.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.++++++|+++|++||.|.+++++.+      +|+|||+|.+.++|++|++   ++..++|+.|.|.++
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~---~~~~~~g~~i~v~~~   78 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK---TQHILDGKVIDPKRA   78 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH---SCCEETTEECCCEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh---cccccCCeEcccccc
Confidence            4589999999999999999999999999999999864      5899999999999999998   357899999999998


Q ss_pred             cCCC
Q psy14139        286 RAQA  289 (327)
Q Consensus       286 k~~~  289 (327)
                      .++.
T Consensus        79 ~~~~   82 (167)
T 2cjk_A           79 IPRD   82 (167)
T ss_dssp             CCHH
T ss_pred             cchh
Confidence            7654

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.33  E-value=1.1e-11  Score=98.91  Aligned_cols=79  Identities=16%  Similarity=0.349  Sum_probs=67.9

Q ss_pred             CCccEEEEcCCCCCCC-----------HHHHHHHHhhcCCeEEEEEec--CCCeEEEEeCCHHHHHHHHHHhcCCeEECC
Q psy14139        211 KTITTLYVGNLGDKLT-----------EQDLRDHFYQFGEIRSVTILS--KQQCAFIQYTSRPAAEAAVEHSFNKVILGG  277 (327)
Q Consensus       211 ~~~~tLfVgnLp~~it-----------e~~Lr~~F~~fG~I~~v~i~~--~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G  277 (327)
                      ...++|+|.||.....           +++|+++|++||.|.++.|..  .+|||||+|.+.++|++|+.. ++|..++|
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~-lng~~~~g   91 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQT-LDGRWFGG   91 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHH-STTCEETT
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHH-cCCCEECC
Confidence            3457999999954322           589999999999999997753  379999999999999999997 79999999


Q ss_pred             eeEEEEeccCCCC
Q psy14139        278 RRLNIKWGRAQAN  290 (327)
Q Consensus       278 ~~L~V~~ak~~~~  290 (327)
                      +.|+|.|+.++..
T Consensus        92 r~l~v~~a~~~~~  104 (112)
T 2dit_A           92 RQITAQAWDGTTD  104 (112)
T ss_dssp             EECEEEECCSCCC
T ss_pred             cEEEEEEeCCCCC
Confidence            9999999988654

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.33  E-value=3.6e-12  Score=106.78  Aligned_cols=73  Identities=29%  Similarity=0.504  Sum_probs=66.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCe--eEEEE
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGR--RLNIK  283 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~--~L~V~  283 (327)
                      ..++|||+|||.++++++|+++|++||.|.++++..+      +|+|||+|.+.++|++|++. ++|..+.|+  +|+|.
T Consensus        87 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~~~i~v~  165 (167)
T 1fxl_A           87 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG-LNGQKPSGATEPITVK  165 (167)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTTCCCTTCSSCCEEE
T ss_pred             CCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHH-hcCCccCCCccceEEE
Confidence            4579999999999999999999999999999999864      58999999999999999998 699999996  58998


Q ss_pred             ec
Q psy14139        284 WG  285 (327)
Q Consensus       284 ~a  285 (327)
                      ||
T Consensus       166 ~A  167 (167)
T 1fxl_A          166 FA  167 (167)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.33  E-value=3.3e-12  Score=117.29  Aligned_cols=81  Identities=16%  Similarity=0.169  Sum_probs=74.1

Q ss_pred             CCCccEEEEcCCCCCC-CHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKL-TEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~i-te~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      ....++|||+|||.++ ++++|+++|++||.|.++.+..+     +|+|||+|.+.++|++|+.. ++|..++|+.|+|.
T Consensus       181 ~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~l~v~  259 (284)
T 3smz_A          181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQ-ADGLSLGGSHLRVS  259 (284)
T ss_dssp             TTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHH-HTTCEETTEECEEE
T ss_pred             cCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHH-hCCCccCCeEEEEE
Confidence            3456899999999996 99999999999999999999875     79999999999999999998 69999999999999


Q ss_pred             eccCCCCC
Q psy14139        284 WGRAQANR  291 (327)
Q Consensus       284 ~ak~~~~~  291 (327)
                      |++++..+
T Consensus       260 ~a~~~~~~  267 (284)
T 3smz_A          260 FCAPGPPG  267 (284)
T ss_dssp             ECCSSSCH
T ss_pred             EecCCCcc
Confidence            99987653

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.31  E-value=8.9e-12  Score=98.73  Aligned_cols=75  Identities=16%  Similarity=0.269  Sum_probs=65.8

Q ss_pred             ccEEEEcCCCC-----CCCHHHHHHHHhhcCCeEEEEEecC-------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeE
Q psy14139        213 ITTLYVGNLGD-----KLTEQDLRDHFYQFGEIRSVTILSK-------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRL  280 (327)
Q Consensus       213 ~~tLfVgnLp~-----~ite~~Lr~~F~~fG~I~~v~i~~~-------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L  280 (327)
                      .++|+|.|+..     +-.+++|++.|++||.|.++.|..+       +|+|||+|.+.++|++|+++ +||..++|+.|
T Consensus         8 s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~-lnG~~~~Gr~i   86 (105)
T 2pe8_A            8 TKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVD-LNGRYFGGRVV   86 (105)
T ss_dssp             CSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHH-HTTCEETTEEC
T ss_pred             CCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHH-HCCCEECCcEE
Confidence            47999999963     2368999999999999999999752       68999999999999999998 69999999999


Q ss_pred             EEEeccCC
Q psy14139        281 NIKWGRAQ  288 (327)
Q Consensus       281 ~V~~ak~~  288 (327)
                      +|.|+.+.
T Consensus        87 ~v~~a~~~   94 (105)
T 2pe8_A           87 KACFYNLD   94 (105)
T ss_dssp             EEEECCHH
T ss_pred             EEEEcCHH
Confidence            99998753

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.31  E-value=4.8e-12  Score=116.60  Aligned_cols=76  Identities=20%  Similarity=0.282  Sum_probs=67.3

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec----CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS----KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~----~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      .+...++|||+|||.++++++|+++|++||.|.+|+|..    .+|+|||+|.+.++|++|++  +++..++|+.|.|.|
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~--~~~~~~~g~~i~v~~  114 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT--KTHKVVGQNEIIVSH  114 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT--TTTCEETTEECEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHHH--hCCcEeCCcEEEEEE
Confidence            345678999999999999999999999999999999987    47999999999999999995  699999999999998


Q ss_pred             cc
Q psy14139        285 GR  286 (327)
Q Consensus       285 ak  286 (327)
                      +.
T Consensus       115 ~~  116 (292)
T 2ghp_A          115 LT  116 (292)
T ss_dssp             CC
T ss_pred             CC
Confidence            74

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.30  E-value=6.6e-12  Score=115.67  Aligned_cols=77  Identities=27%  Similarity=0.535  Sum_probs=70.9

Q ss_pred             CCccEEEEcCCCCC-CCHHHHHHHHhhcCCeEEEEEecC-------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        211 KTITTLYVGNLGDK-LTEQDLRDHFYQFGEIRSVTILSK-------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       211 ~~~~tLfVgnLp~~-ite~~Lr~~F~~fG~I~~v~i~~~-------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      ...++|||+|||.+ +++++|+++|++||.|.++++..+       +|+|||+|.+.++|++|+ . ++|..++|+.|+|
T Consensus       208 ~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~-l~g~~~~g~~i~V  285 (292)
T 2ghp_A          208 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-Q-MNRSLLGNREISV  285 (292)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-G-GTTEEETTEEEEE
T ss_pred             CCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-H-hcCCEECCcEEEE
Confidence            44589999999999 999999999999999999999753       689999999999999999 7 7999999999999


Q ss_pred             EeccCCC
Q psy14139        283 KWGRAQA  289 (327)
Q Consensus       283 ~~ak~~~  289 (327)
                      .|+++++
T Consensus       286 ~~a~~k~  292 (292)
T 2ghp_A          286 SLADKKP  292 (292)
T ss_dssp             EECCCCC
T ss_pred             EEecCCC
Confidence            9999863

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.30  E-value=4.5e-12  Score=103.57  Aligned_cols=73  Identities=18%  Similarity=0.301  Sum_probs=63.3

Q ss_pred             cEEEEcCC----CCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCC----H-HH---HHHHHH--HhcCCe
Q psy14139        214 TTLYVGNL----GDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTS----R-PA---AEAAVE--HSFNKV  273 (327)
Q Consensus       214 ~tLfVgnL----p~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~----~-~~---Ae~A~~--~~l~g~  273 (327)
                      ++|||+||    |..++|.+|+++|++||+|.++.++.+      +|||||+|.+    . ++   |.+|+.  . ++|.
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~-lng~   81 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHE-SSGC   81 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTT-TTCE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhh-hcCC
Confidence            68999999    999999999999999999999999875      6999999995    2 32   777877  4 6999


Q ss_pred             EECCeeEEEEeccC
Q psy14139        274 ILGGRRLNIKWGRA  287 (327)
Q Consensus       274 ~i~G~~L~V~~ak~  287 (327)
                      .|+|+.|+|.+-+.
T Consensus        82 ~I~Gr~irV~ln~~   95 (136)
T 2j8a_A           82 FIMGFKFEVILNKH   95 (136)
T ss_dssp             EETTEEEEEEECCT
T ss_pred             eecCcEEEEEECcc
Confidence            99999999987653

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.29  E-value=1.1e-11  Score=113.65  Aligned_cols=74  Identities=19%  Similarity=0.323  Sum_probs=69.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      ..++|||+|||.++++++|+++|++|| |.++.+...+|+|||+|.+.++|++|++. ++|..+.|+.|+|.|+.+
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~~~~~~g~~i~v~~~~~   94 (284)
T 3smz_A           21 NRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINA-FHQSRLRERELSVQLQPT   94 (284)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHH-HTTCEETTEECEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEEecCCCEEEEEeCCHHHHHHHHHH-cCCCeeCCeEEEEEecCC
Confidence            347999999999999999999999999 99999988999999999999999999997 799999999999999653

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.27  E-value=5.3e-11  Score=93.51  Aligned_cols=66  Identities=24%  Similarity=0.346  Sum_probs=58.2

Q ss_pred             CCCCHHHHHHHHhhcCCeEEEEEec-CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCCC
Q psy14139        223 DKLTEQDLRDHFYQFGEIRSVTILS-KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR  291 (327)
Q Consensus       223 ~~ite~~Lr~~F~~fG~I~~v~i~~-~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~~  291 (327)
                      .+++|++|+++|++||+|.+|.|+. .+|||||+|.+.++|+.|++. +++  +.|++|+|.|+++++..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~-~~~--~~g~~l~V~~a~~~~~~   93 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQN-EVG--LVDNPLKISWLEGQPQD   93 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHT-CCB--CSSSBCEEECSSCCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHh-cCC--CCCCeEEEEEccCCCCC
Confidence            4689999999999999999999984 589999999999999999986 444  57999999999887654

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.25  E-value=9.8e-12  Score=109.85  Aligned_cols=72  Identities=17%  Similarity=0.207  Sum_probs=65.6

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCe--EEEEEecC----CCeEEEEeCCHHHHHHHHHHhcCCeEECCe----eEEE
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEI--RSVTILSK----QQCAFIQYTSRPAAEAAVEHSFNKVILGGR----RLNI  282 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I--~~v~i~~~----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~----~L~V  282 (327)
                      .++|||+|||.++++++|+++|++||.|  .++++..+    +++|||+|.+.++|.+|+.. +||..+.|.    ++.|
T Consensus       123 ~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~-lng~~~~g~~~~~p~~v  201 (205)
T 3tyt_A          123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGF-LNHYQMKNPNGPYPYTL  201 (205)
T ss_dssp             CSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHH-HTTCEECCSSSSSCEEC
T ss_pred             cceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHH-hCCCCccCCCCCcceEE
Confidence            4799999999999999999999999999  89998875    48999999999999999998 799999885    6888


Q ss_pred             Eec
Q psy14139        283 KWG  285 (327)
Q Consensus       283 ~~a  285 (327)
                      +|+
T Consensus       202 k~~  204 (205)
T 3tyt_A          202 KLC  204 (205)
T ss_dssp             EEE
T ss_pred             Eec
Confidence            775

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.21  E-value=3.4e-11  Score=114.44  Aligned_cols=75  Identities=17%  Similarity=0.304  Sum_probs=65.6

Q ss_pred             CCccEEEEcC--CCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEEC---Ce--eEEEE
Q psy14139        211 KTITTLYVGN--LGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILG---GR--RLNIK  283 (327)
Q Consensus       211 ~~~~tLfVgn--Lp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~---G~--~L~V~  283 (327)
                      ....+|||||  |+..++|++|+++|++||+|.+|.+..++|||||+|.+.++|++|+++ +||..+-   |+  .|.|.
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~~kgfaFV~f~~~~~A~~Ai~~-lnG~~~~~~~g~~~~ly~~   94 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVT-LNGKEVVDDLGQKITLYLN   94 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCTTCSEEEEEESSHHHHHHHHHH-TTTCEEECTTSCEEECEEE
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHH-hCCCccccccCCceEEEEE
Confidence            4457999998  578999999999999999999999988999999999999999999998 6988772   44  67777


Q ss_pred             ecc
Q psy14139        284 WGR  286 (327)
Q Consensus       284 ~ak  286 (327)
                      +..
T Consensus        95 ~~~   97 (345)
T 3tht_A           95 FVE   97 (345)
T ss_dssp             ECS
T ss_pred             Eee
Confidence            774

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.19  E-value=4.4e-11  Score=109.04  Aligned_cols=79  Identities=20%  Similarity=0.308  Sum_probs=70.4

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEEC---CeeEEEEe
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILG---GRRLNIKW  284 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~---G~~L~V~~  284 (327)
                      .++|||+|||..+++++|+++|++||.|.++.++.+     +|+|||+|.+.++|.+|+..+.++..+.   |++|.|.|
T Consensus        96 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~  175 (261)
T 3sde_A           96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEP  175 (261)
T ss_dssp             SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEE
T ss_pred             CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEee
Confidence            479999999999999999999999999999999875     7999999999999999999854676666   89999999


Q ss_pred             ccCCCCC
Q psy14139        285 GRAQANR  291 (327)
Q Consensus       285 ak~~~~~  291 (327)
                      +.+....
T Consensus       176 ~~~~~~~  182 (261)
T 3sde_A          176 MEQFDDE  182 (261)
T ss_dssp             CCCEESS
T ss_pred             ccccCcc
Confidence            9876543

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.18  E-value=1.3e-11  Score=97.58  Aligned_cols=67  Identities=15%  Similarity=0.435  Sum_probs=59.1

Q ss_pred             EcCCCCCCCHHHHHHHH------------hhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeE
Q psy14139        218 VGNLGDKLTEQDLRDHF------------YQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRL  280 (327)
Q Consensus       218 VgnLp~~ite~~Lr~~F------------~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L  280 (327)
                      +.||+..+++++|+++|            ++||.|.++.|..+     +|+|||+|.+.++|++|+.+ +||..++|+.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~-lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVID-LNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHH-HTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHH-HCCCEECCEEE
Confidence            56777778887777666            99999999999864     79999999999999999998 69999999999


Q ss_pred             EEEec
Q psy14139        281 NIKWG  285 (327)
Q Consensus       281 ~V~~a  285 (327)
                      +|.|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.13  E-value=1.6e-10  Score=91.37  Aligned_cols=75  Identities=20%  Similarity=0.317  Sum_probs=63.9

Q ss_pred             ccEEEEcCC--CCCCC--------HHHHHHHHhhcCCeEEEEEecC--------CCeEEEEeCCHHHHHHHHHHhcCCeE
Q psy14139        213 ITTLYVGNL--GDKLT--------EQDLRDHFYQFGEIRSVTILSK--------QQCAFIQYTSRPAAEAAVEHSFNKVI  274 (327)
Q Consensus       213 ~~tLfVgnL--p~~it--------e~~Lr~~F~~fG~I~~v~i~~~--------kg~aFV~F~~~~~Ae~A~~~~l~g~~  274 (327)
                      .+.|.+.|+  +.++.        +++|++.|++||.|.+|.|..+        +|+|||+|.+.++|++|+.+ +||..
T Consensus         5 s~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~-lnG~~   83 (105)
T 3v4m_A            5 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQG-LTGRK   83 (105)
T ss_dssp             CSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHH-HTTCE
T ss_pred             CeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHH-hCCCE
Confidence            467888887  33333        4689999999999999999753        69999999999999999998 69999


Q ss_pred             ECCeeEEEEeccCC
Q psy14139        275 LGGRRLNIKWGRAQ  288 (327)
Q Consensus       275 i~G~~L~V~~ak~~  288 (327)
                      ++|+.|+|.+....
T Consensus        84 f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           84 FANRVVVTKYCDPD   97 (105)
T ss_dssp             ETTEECEEEEECHH
T ss_pred             eCCCEEEEEEeCHH
Confidence            99999999997643

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.04  E-value=7.9e-10  Score=89.33  Aligned_cols=74  Identities=18%  Similarity=0.324  Sum_probs=64.0

Q ss_pred             ccEEEEcCCCC--CC---CHHHHHHHHhhcCCeEEEEEecC----------CCeEEEEeCCHHHHHHHHHHhcCCeEECC
Q psy14139        213 ITTLYVGNLGD--KL---TEQDLRDHFYQFGEIRSVTILSK----------QQCAFIQYTSRPAAEAAVEHSFNKVILGG  277 (327)
Q Consensus       213 ~~tLfVgnLp~--~i---te~~Lr~~F~~fG~I~~v~i~~~----------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G  277 (327)
                      .+.|++.|+-.  ++   -+++|++.|++||.|.+|.|..+          +|++||+|.+.++|++|+.+ +||..++|
T Consensus        20 s~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~-LnGr~f~G   98 (118)
T 3ue2_A           20 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQA-LNGRWFAG   98 (118)
T ss_dssp             CCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHH-HTTCEETT
T ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHH-HCCCEECC
Confidence            36899999843  22   36899999999999999999763          38999999999999999998 69999999


Q ss_pred             eeEEEEeccC
Q psy14139        278 RRLNIKWGRA  287 (327)
Q Consensus       278 ~~L~V~~ak~  287 (327)
                      +.|+|.+...
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999998764

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.01  E-value=6.6e-10  Score=89.26  Aligned_cols=61  Identities=16%  Similarity=0.247  Sum_probs=55.7

Q ss_pred             HHHHHHHHhhcCCeEEEEEecC--CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        227 EQDLRDHFYQFGEIRSVTILSK--QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       227 e~~Lr~~F~~fG~I~~v~i~~~--kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      +++|++.|++||.|.+|.|..+  +|+|||+|.+.++|++|++. +||..++|+.|+|.|+...
T Consensus        31 ~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~-lnG~~f~GR~i~v~~~~~~   93 (114)
T 3s6e_A           31 KDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNA-LHGRWFAGKMITAAYVPLP   93 (114)
T ss_dssp             HHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHH-HTTCEETTEECEEEEECHH
T ss_pred             HHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHH-hCCCEECCEEEEEEEEcHH
Confidence            4689999999999999999775  69999999999999999998 6999999999999998643

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.96  E-value=3.4e-09  Score=81.11  Aligned_cols=71  Identities=17%  Similarity=0.305  Sum_probs=60.9

Q ss_pred             cEEEEcCCCC----CCCH----HHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        214 TTLYVGNLGD----KLTE----QDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       214 ~tLfVgnLp~----~ite----~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      .|++|.-.+.    ++-.    .+|.+.|++||+|..+++..++  +||+|.+.++|.+|++  ++|..++|+.|+|+++
T Consensus         8 ~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--~fVtF~d~~sAlaAi~--mnG~~v~Gr~LkV~lk   83 (91)
T 2dnr_A            8 GTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--MWVTFLEGSSALNVLS--LNGKELLNRTITIALK   83 (91)
T ss_dssp             CEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--EEEEESSHHHHHHGGG--GTTCEETTEEEEEEEC
T ss_pred             CeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--EEEEECChHHHHHHHh--cCCeEeCCeEEEEEeC
Confidence            4888877662    3333    5789999999999999999876  8999999999999997  6999999999999998


Q ss_pred             cCC
Q psy14139        286 RAQ  288 (327)
Q Consensus       286 k~~  288 (327)
                      ++.
T Consensus        84 t~d   86 (91)
T 2dnr_A           84 SPS   86 (91)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            865

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.91  E-value=4e-09  Score=85.40  Aligned_cols=75  Identities=16%  Similarity=0.143  Sum_probs=66.8

Q ss_pred             CCccEEEEcCCCCC-CCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCC-HHHHHHHHHHhc-CCeEECCeeEEEEec
Q psy14139        211 KTITTLYVGNLGDK-LTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTS-RPAAEAAVEHSF-NKVILGGRRLNIKWG  285 (327)
Q Consensus       211 ~~~~tLfVgnLp~~-ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~-~~~Ae~A~~~~l-~g~~i~G~~L~V~~a  285 (327)
                      +...-|||+||+.+ +++++|+++|++||+|..|.+..+...|||.|.+ ..+|+.|+.++- +++.|+|..++++..
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL   93 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   93 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEEC
Confidence            45689999999999 9999999999999999999999999999999999 899999999831 478999988777653

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.69  E-value=4.5e-08  Score=75.30  Aligned_cols=69  Identities=19%  Similarity=0.284  Sum_probs=59.4

Q ss_pred             cEEEEcCCCCC------CCH---HHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        214 TTLYVGNLGDK------LTE---QDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       214 ~tLfVgnLp~~------ite---~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      .|++|.-++..      ..+   .+|.+.|.+||+|..+++..++  +||+|.+.++|.+|++  ++|..++|+.|+|++
T Consensus        16 ~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--~fVtF~d~~sAl~AI~--ldG~~v~Gr~L~V~~   91 (95)
T 1ufw_A           16 ATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--MLVTFADSHSALSVLD--VDGMKVKGRAVKISG   91 (95)
T ss_dssp             CEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--EEEECSCSHHHHHHHH--GGGSEETTEEEEEEC
T ss_pred             CeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--EEEEEcChHHHHHHHh--cCCeeeCCeEEEEec
Confidence            49999887643      222   4689999999999999999877  9999999999999997  699999999999987


Q ss_pred             cc
Q psy14139        285 GR  286 (327)
Q Consensus       285 ak  286 (327)
                      -.
T Consensus        92 k~   93 (95)
T 1ufw_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            44

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.40  E-value=4e-07  Score=80.55  Aligned_cols=63  Identities=16%  Similarity=0.268  Sum_probs=56.1

Q ss_pred             CCCHHHHHHHHhhcCCeEEEEEe----------cCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        224 KLTEQDLRDHFYQFGEIRSVTIL----------SKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       224 ~ite~~Lr~~F~~fG~I~~v~i~----------~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      +-.+++|++.|++||.|.++.|.          +.+|++||+|.+.++|++|+.. ++|..++|+.|+|.+...
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~-l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQA-LNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHH-HTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHH-hcCceECCeEEEEEEcCH
Confidence            34568999999999999999997          3468999999999999999998 799999999999998754

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.36  E-value=2.6e-06  Score=66.98  Aligned_cols=70  Identities=17%  Similarity=0.192  Sum_probs=66.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhc-----CCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQF-----GEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~f-----G~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      .++|-+-+||+.++...|+.+..++     |.|..|.+.++-+-|+|+|.+...|-+|.-+ ++|..|+|+.|++.
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~GAivef~d~~~AgKasLa-L~G~ef~gr~Lr~g   95 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMI-LNGSQFQGKVIRSG   95 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTEEEEECSCHHHHHHHHHH-HSSEEETTEEEEEE
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCCceEEEEccchhhHHHHhh-cCCeeecCeEEEec
Confidence            4788899999999999999999999     9999999999999999999999999999876 79999999999984

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.80  E-value=0.00033  Score=54.46  Aligned_cols=85  Identities=19%  Similarity=0.185  Sum_probs=68.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhc-----CCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQF-----GEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~f-----G~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      .++|.|.|||++++++.|.-+|+.-     |+|.++....  +-|+|+|.+.+.|++.++.  ..+.++|.+|.|.-.-+
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--~~AvItF~d~~va~rVL~k--~~H~L~~~~LsV~P~~~   83 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--CGGVLTFREPADAERVLAQ--ADHELHGAQLSLRPAPP   83 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--TEEEEEESSHHHHHHHHTC--SCCBSSSSBCEEEECCC
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--CcEEEEEcChHHHHHHhcC--CcceecCeEEEEEcCCC
Confidence            4799999999999999999999872     6899998876  8899999999999999873  57899999999966444


Q ss_pred             CCCCCCCcccccccccCCCCCCCC
Q psy14139        288 QANRGEDTAELKVRLEPVPGLPGA  311 (327)
Q Consensus       288 ~~~~~~~~~~~~~~~~pv~Glp~~  311 (327)
                      ....        ..  .+.||+..
T Consensus        84 ~~~~--------r~--ll~gl~~~   97 (104)
T 2dhx_A           84 RAPA--------RL--LLQGLPPG   97 (104)
T ss_dssp             CCCC--------CC--CCCSCCCC
T ss_pred             CCcc--------eE--eeecCCCC
Confidence            4322        12  37888633

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.77  E-value=0.00015  Score=56.54  Aligned_cols=75  Identities=11%  Similarity=0.192  Sum_probs=65.4

Q ss_pred             cEEEEcCCCCCC-C----HHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        214 TTLYVGNLGDKL-T----EQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       214 ~tLfVgnLp~~i-t----e~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      ++|+|.||+.++ .    .+.++++|..|+++.+....++=.-..|.|.+.++|.+|-.. +++..+.|+.++|.++.+.
T Consensus         6 ntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFRRirv~F~~~~~A~~AR~~-Lh~~~f~g~~~r~YFgq~~   84 (104)
T 1wey_A            6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLR-LHKTEFLGKEMKLYFAQTL   84 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHT-STTSEETTEECEEECCCCS
T ss_pred             ceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcceEEEEEeCChHHHHHHHHH-hccceecCceeEEEecCCC
Confidence            689999998754 2    257899999999999999998877889999999999999887 7999999999999999844


Q ss_pred             C
Q psy14139        289 A  289 (327)
Q Consensus       289 ~  289 (327)
                      .
T Consensus        85 ~   85 (104)
T 1wey_A           85 H   85 (104)
T ss_dssp             S
T ss_pred             C
Confidence            3

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.57  E-value=0.00038  Score=55.64  Aligned_cols=73  Identities=19%  Similarity=0.144  Sum_probs=61.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECC-eeEEEEecc
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGG-RRLNIKWGR  286 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G-~~L~V~~ak  286 (327)
                      ...+-+.|.|+|... -..|.++|++||+|.+........+-.|.|.++.+|++|+.  .||..++| ..|-|.+-.
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~~~NWihI~Y~s~~~A~rAL~--kNG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS--KDGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT--TTTCEETTTEECEEEECC
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCCCCCeEEEEeCCHHHHHHHHH--hCCeEecCCEEEEEEECC
Confidence            345788999999986 46677889999999999886678999999999999999998  49999985 677887743

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.75  E-value=0.0011  Score=53.74  Aligned_cols=71  Identities=20%  Similarity=0.232  Sum_probs=56.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEE-EEEe-------------------cCCCeEEEEeCCHHHHHHHHHHhcCCe
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRS-VTIL-------------------SKQQCAFIQYTSRPAAEAAVEHSFNKV  273 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~-v~i~-------------------~~kg~aFV~F~~~~~Ae~A~~~~l~g~  273 (327)
                      +.+.|.|.|++.+ ..+.++|++||.|.+ +.+.                   ...++..|+|+++.+|.+|+.  .||.
T Consensus         8 ~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~--~NG~   84 (132)
T 3p3d_A            8 LAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL--ENGA   84 (132)
T ss_dssp             CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT--TTTC
T ss_pred             eEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH--hCCe
Confidence            5778889987765 667778999999966 2111                   136788999999999999998  4999


Q ss_pred             EECCeeEEEEeccC
Q psy14139        274 ILGGRRLNIKWGRA  287 (327)
Q Consensus       274 ~i~G~~L~V~~ak~  287 (327)
                      +++|..|-|.+-++
T Consensus        85 ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           85 VFNGVLLGVIPYTK   98 (132)
T ss_dssp             EETTEECEEEECCH
T ss_pred             EeCcEEEEEEECCH
Confidence            99999888887753

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.44  E-value=0.0015  Score=48.16  Aligned_cols=31  Identities=26%  Similarity=0.866  Sum_probs=24.8

Q ss_pred             CccCCCccccccccccccCCCCCCCCCCCCC
Q psy14139        138 YYKRNRPHICSFWVKGECRRGEECPYRHEKP  168 (327)
Q Consensus       138 ~y~r~~~~~C~ff~kG~C~rG~~Cpy~H~~p  168 (327)
                      .-+..+..+|.||.+|.|.+|+.|+|.|...
T Consensus         4 ~~~~~k~~~C~~fl~G~C~~G~~C~fsH~~~   34 (77)
T 2d9n_A            4 GSSGEKTVVCKHWLRGLCKKGDQCEFLHEYD   34 (77)
T ss_dssp             CCSCCTTSBCHHHHTTCCSCTTSSSSBCSCC
T ss_pred             CCCCCcceeCHhHccCcCCCCCCCCCccccc
Confidence            3334567899999999999999999999754

>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens}

Probab=95.85  E-value=0.0021  Score=46.78  Aligned_cols=26  Identities=31%  Similarity=1.128  Sum_probs=23.0

Q ss_pred             CCccccccccccccCCCCCCCCCCCC
Q psy14139        142 NRPHICSFWVKGECRRGEECPYRHEK  167 (327)
Q Consensus       142 ~~~~~C~ff~kG~C~rG~~Cpy~H~~  167 (327)
                      .+..+|.||.+|.|.+|+.|+|.|..
T Consensus        14 ~k~~vCk~fl~G~C~~G~~C~fsH~~   39 (72)
T 2rhk_C           14 EKTVVCKHWLRGLCKKGDQCEFLHEY   39 (72)
T ss_dssp             CCCSBCHHHHTTCCCCGGGSSSBCSC
T ss_pred             CcCeeCHHHhcCCCCCCCCCCCcccc
Confidence            35679999999999999999999974

>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1

Probab=95.72  E-value=0.0051  Score=47.48  Aligned_cols=24  Identities=42%  Similarity=1.173  Sum_probs=20.1

Q ss_pred             CccccccccccccCCCCCCCCCCC
Q psy14139        143 RPHICSFWVKGECRRGEECPYRHE  166 (327)
Q Consensus       143 ~~~~C~ff~kG~C~rG~~Cpy~H~  166 (327)
                      +..+|.||.+|.|.+|+.|+|.|.
T Consensus        12 k~~lC~~f~~G~C~~G~~C~f~H~   35 (98)
T 2cqe_A           12 KRELCKFYITGFCARAENCPYMHG   35 (98)
T ss_dssp             CCSBCTTTTTTCCSCSTTCSSBSS
T ss_pred             CCccCcccccCcCCCCCCCCCCCC
Confidence            467888888888888888888886

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=95.68  E-value=0.046  Score=41.97  Aligned_cols=52  Identities=23%  Similarity=0.410  Sum_probs=43.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHH
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH  268 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~  268 (327)
                      .-++| ++|.++...||.++|+.||.| .|+.+. ---|||.|.+++.|..|+..
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~Wid-DTsAlvvf~~~~~a~~al~~   68 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWID-DTSAFVSLSQPEQVQIAVNT   68 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEE-TTEEEEECSCHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEc-CCeEEEEecCHHHHHHHHHh
Confidence            34555 999999999999999999954 455554 45799999999999999985

>3d2q_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 1.50A {Homo sapiens} PDB: 3d2s_A

Probab=95.67  E-value=0.0027  Score=45.93  Aligned_cols=25  Identities=36%  Similarity=1.008  Sum_probs=22.1

Q ss_pred             CccccccccccccCCCC-CCCCCCCC
Q psy14139        143 RPHICSFWVKGECRRGE-ECPYRHEK  167 (327)
Q Consensus       143 ~~~~C~ff~kG~C~rG~-~Cpy~H~~  167 (327)
                      +..+|.+|.+|.|.+|+ +|+|.|..
T Consensus         5 k~~vC~~f~~G~C~rg~~~C~f~H~~   30 (70)
T 3d2q_A            5 RLEVCREYQRGNCNRGENDCRFAHPA   30 (70)
T ss_dssp             EEEBCHHHHTTCCSSCTTTCSSBCCC
T ss_pred             cchhCHHHhcCCCCCCCCCCCCccCc
Confidence            45799999999999999 59999964

>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=95.51  E-value=0.087  Score=39.92  Aligned_cols=63  Identities=16%  Similarity=0.284  Sum_probs=52.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC--------CCeEEEEeCCHHHHHHHHHHhcCCeEECC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK--------QQCAFIQYTSRPAAEAAVEHSFNKVILGG  277 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~--------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G  277 (327)
                      ++|.|.+||+.++|+++.+.++...++.....+..        -.-|||.|.+.+++....+. ++|..+-+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~-~~g~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDR-FDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHH-HTTCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHH-hCCcEEEc
Confidence            57899999999999999999999888776666542        25799999999999999887 68876643

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=95.41  E-value=0.017  Score=44.47  Aligned_cols=52  Identities=23%  Similarity=0.379  Sum_probs=43.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHh
Q psy14139        215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHS  269 (327)
Q Consensus       215 tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~  269 (327)
                      -|+| ++|.++...||.++|+.||. ..|+.+.+ .-|||.|.+++.|..|+..+
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidD-TsAlvvf~~~~~a~~al~~i   59 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDD-TSAFVSLSQPEQVKIAVNTS   59 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEET-TEEEEEEEEECHHHHHHHHH
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcC-CeEEEEecCHHHHHHHHHhc
Confidence            3455 99999999999999999994 45666644 57999999999999999853

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.34  E-value=0.0096  Score=58.33  Aligned_cols=53  Identities=15%  Similarity=0.268  Sum_probs=41.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCC-CeEEEEeCCHHHHHHHHH
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ-QCAFIQYTSRPAAEAAVE  267 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~k-g~aFV~F~~~~~Ae~A~~  267 (327)
                      +++||. .+..+++.+|.++|++||.|.++.+-.++ .||.|+|.+.+++..++.
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHh
Confidence            799997 79999999999999999999999988765 589999999999987764

>3d2n_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 2.70A {Homo sapiens}

Probab=95.02  E-value=0.012  Score=44.02  Aligned_cols=25  Identities=28%  Similarity=0.813  Sum_probs=22.2

Q ss_pred             ccccccccccccCCCC-CCCCCCCCC
Q psy14139        144 PHICSFWVKGECRRGE-ECPYRHEKP  168 (327)
Q Consensus       144 ~~~C~ff~kG~C~rG~-~Cpy~H~~p  168 (327)
                      -.+|.+|.+|.|.||+ +|+|.|...
T Consensus         9 ~~VCr~FlrG~C~r~d~~C~f~H~~~   34 (83)
T 3d2n_A            9 LEVCREFQRGTCSRPDTECKFAHPSK   34 (83)
T ss_dssp             EEBCTTGGGTCCCSCTTTCSSBCCCT
T ss_pred             chhcHHHhcCCCCCCCCCCCCcCCCc
Confidence            5699999999999997 999999754

>3d2q_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 1.50A {Homo sapiens} PDB: 3d2s_A

Probab=94.55  E-value=0.0078  Score=43.42  Aligned_cols=25  Identities=36%  Similarity=0.858  Sum_probs=22.0

Q ss_pred             CCccccccccccccCCCCCCCCCCCC
Q psy14139        142 NRPHICSFWVKGECRRGEECPYRHEK  167 (327)
Q Consensus       142 ~~~~~C~ff~kG~C~rG~~Cpy~H~~  167 (327)
                      .+..+|.+|.+|.|.+| .|+|.|..
T Consensus        40 ~~~~vC~~flkG~C~r~-~C~y~H~~   64 (70)
T 3d2q_A           40 NTVTVCMDYIKGRCSRE-KCKYFHPP   64 (70)
T ss_dssp             TEEEBCHHHHTTCCCCT-TCCSBCCC
T ss_pred             CcceeccccCcCCCCCC-CcCeeCCH
Confidence            35679999999999999 89999974

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=94.36  E-value=0.016  Score=47.40  Aligned_cols=39  Identities=10%  Similarity=0.006  Sum_probs=34.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        249 QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       249 kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      +|+++|+|.+.++|++|++++.+|..++| .+++.++..+
T Consensus        13 ~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~   51 (150)
T 2i2y_A           13 KGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKT   51 (150)
T ss_dssp             CEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTE
T ss_pred             cccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCc
Confidence            78999999999999999998339999999 9999988753

>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens}

Probab=94.12  E-value=0.017  Score=41.95  Aligned_cols=26  Identities=42%  Similarity=1.027  Sum_probs=22.7

Q ss_pred             Cccccccccc-cccCCCCCCCCCCCCCC
Q psy14139        143 RPHICSFWVK-GECRRGEECPYRHEKPT  169 (327)
Q Consensus       143 ~~~~C~ff~k-G~C~rG~~Cpy~H~~p~  169 (327)
                      +..+|.||.+ |.|.+ +.|+|.|..|.
T Consensus        43 ~~~~C~~f~~~G~C~~-~~C~y~H~~p~   69 (72)
T 2rhk_C           43 KMSECYFYSKFGECSN-KECPFLHIDPE   69 (72)
T ss_dssp             SCCBCHHHHHHSCCSB-TTCCSBCCCCC
T ss_pred             cCCcccccCCCCCCCC-CCeeccCCCcc
Confidence            3568999999 99999 99999998764

>2e5s_A Otthump00000018578; ZF-CCCHX2 domain, muscleblind-like 2, isoform 1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=94.01  E-value=0.0058  Score=47.19  Aligned_cols=28  Identities=29%  Similarity=0.876  Sum_probs=23.9

Q ss_pred             CCCccccccccccccCCCC-CCCCCCCCC
Q psy14139        141 RNRPHICSFWVKGECRRGE-ECPYRHEKP  168 (327)
Q Consensus       141 r~~~~~C~ff~kG~C~rG~-~Cpy~H~~p  168 (327)
                      ..+-.+|.+|.+|.|.||+ +|+|.|...
T Consensus        17 ~~k~~VCr~FlrG~C~rgd~~C~FsH~~~   45 (98)
T 2e5s_A           17 TDKLEVCREFQRGNCARGETDCRFAHPAD   45 (98)
T ss_dssp             SSEEEBCSHHHHTCCSSHHHHCSSBCCSS
T ss_pred             hhhhhhhHHHhcCcCCCCCCCCCCcCCch
Confidence            3456899999999999999 799999754

>2rpp_A Muscleblind-like protein 2; zinc finger domain, C3H, alternative splicing, cytoplasm, metal-binding, nucleus, RNA-binding, zinc, zinc-finger; NMR {Homo sapiens}

Probab=94.00  E-value=0.018  Score=43.57  Aligned_cols=25  Identities=28%  Similarity=0.848  Sum_probs=22.5

Q ss_pred             ccccccccccccCCCC-CCCCCCCCC
Q psy14139        144 PHICSFWVKGECRRGE-ECPYRHEKP  168 (327)
Q Consensus       144 ~~~C~ff~kG~C~rG~-~Cpy~H~~p  168 (327)
                      -.+|.+|.+|.|.||+ +|+|.|...
T Consensus        17 ~~VCrdFlrG~C~r~d~~CrfsH~~~   42 (89)
T 2rpp_A           17 LEVCRQFQRGTCSRSDEECKFAHPPK   42 (89)
T ss_dssp             ECBCHHHHHTCCCCCTTTSSSBCCCS
T ss_pred             hhhchHHhcCCCCCCCCCCCCcCCCc
Confidence            5799999999999998 999999744

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=93.99  E-value=0.025  Score=41.48  Aligned_cols=25  Identities=44%  Similarity=1.022  Sum_probs=21.9

Q ss_pred             ccccccccc-cccCCCCCCCCCCCCCC
Q psy14139        144 PHICSFWVK-GECRRGEECPYRHEKPT  169 (327)
Q Consensus       144 ~~~C~ff~k-G~C~rG~~Cpy~H~~p~  169 (327)
                      ..+|.||.+ |.|. |+.|+|.|..|.
T Consensus        38 ~~~C~~f~~~G~C~-~~~C~f~H~~~~   63 (77)
T 2d9n_A           38 MPECYFYSKFGECS-NKECPFLHIDPE   63 (77)
T ss_dssp             SCBCHHHHHTCCCC-CSSCSSBCCCTT
T ss_pred             CCCCcccCCCCccC-CCCeeccCCCcc
Confidence            358999988 9999 899999998764

>2e5s_A Otthump00000018578; ZF-CCCHX2 domain, muscleblind-like 2, isoform 1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=93.42  E-value=0.015  Score=44.85  Aligned_cols=26  Identities=35%  Similarity=0.810  Sum_probs=22.4

Q ss_pred             CCccccccccccccCCCCCCCCCCCCC
Q psy14139        142 NRPHICSFWVKGECRRGEECPYRHEKP  168 (327)
Q Consensus       142 ~~~~~C~ff~kG~C~rG~~Cpy~H~~p  168 (327)
                      .+..+|.+|.+|.|.|| .|+|.|..+
T Consensus        54 ~~~~vC~~flkG~C~r~-~C~y~H~~~   79 (98)
T 2e5s_A           54 NTVTVCMDYIKGRCMRE-KCKYFHPPA   79 (98)
T ss_dssp             CEEEBCHHHHHTCCCCT-TCCSBCCCH
T ss_pred             CccccchhhccCCCCCC-CcCccCChH
Confidence            35679999999999999 899999643

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A

Probab=93.02  E-value=0.07  Score=38.70  Aligned_cols=25  Identities=28%  Similarity=0.873  Sum_probs=22.0

Q ss_pred             Cccccccc-cccccCCCCCCCCCCCC
Q psy14139        143 RPHICSFW-VKGECRRGEECPYRHEK  167 (327)
Q Consensus       143 ~~~~C~ff-~kG~C~rG~~Cpy~H~~  167 (327)
                      +..+|.+| ..|.|..|+.|.|.|..
T Consensus        11 kt~~C~~f~~~G~C~~G~~C~f~H~~   36 (77)
T 1m9o_A           11 KTELCRTYSESGRCRYGAKCQFAHGL   36 (77)
T ss_dssp             CSCCCSGGGGTSCCTTTTTCSSCSSS
T ss_pred             cchhCHHhhhCCCcCCCCCccCCCCC
Confidence            46799999 58999999999999974

>3d2n_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 2.70A {Homo sapiens}

Probab=92.43  E-value=0.038  Score=41.23  Aligned_cols=23  Identities=39%  Similarity=0.738  Sum_probs=20.9

Q ss_pred             CccccccccccccCCCCCCCCCCC
Q psy14139        143 RPHICSFWVKGECRRGEECPYRHE  166 (327)
Q Consensus       143 ~~~~C~ff~kG~C~rG~~Cpy~H~  166 (327)
                      +..+|.+|.+|.|.|+ .|+|.|.
T Consensus        42 ~~~vC~dflkG~C~r~-~C~y~H~   64 (83)
T 3d2n_A           42 RVIACFDSLKGRCSRE-NCKYLHP   64 (83)
T ss_dssp             EEECCHHHHTTCCCCS-SCSSCCC
T ss_pred             ceeehhHhhhccccCC-CcceeCC
Confidence            4579999999999999 8999996

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

Probab=92.34  E-value=0.27  Score=37.61  Aligned_cols=63  Identities=13%  Similarity=0.194  Sum_probs=47.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC--------CCeEEEEeCCHHHHHHHHHHhcCCeEECC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK--------QQCAFIQYTSRPAAEAAVEHSFNKVILGG  277 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~--------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G  277 (327)
                      -+|.|..||+.+||+++.+.++.+=++.....+..        -.-|||.|.+.++.....+. ++|..+-+
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~-f~g~~F~D   80 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDR-FDGYIFLD   80 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHH-STTEEEEC
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHH-cCCcEEEe
Confidence            47899999999999998887776544322222211        25699999999999999987 79877644

>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=90.78  E-value=0.2  Score=40.84  Aligned_cols=22  Identities=9%  Similarity=-0.001  Sum_probs=19.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHh
Q psy14139        248 KQQCAFIQYTSRPAAEAAVEHS  269 (327)
Q Consensus       248 ~kg~aFV~F~~~~~Ae~A~~~~  269 (327)
                      .+|+|||+|.+.++|++|++.+
T Consensus        12 ~~G~~fV~f~~~~~A~~al~~~   33 (158)
T 2kn4_A           12 LKGETTTEAVDAATAEKVFKQY   33 (158)
T ss_dssp             CEEEEEEECSSHHHHHHHHHHH
T ss_pred             ccchhHHHHHHHHhHHHHHHhh
Confidence            3799999999999999999873

>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1

Probab=90.09  E-value=0.13  Score=39.44  Aligned_cols=24  Identities=25%  Similarity=0.908  Sum_probs=21.2

Q ss_pred             ccccccc-cccccCCCCCCCCCCCC
Q psy14139        144 PHICSFW-VKGECRRGEECPYRHEK  167 (327)
Q Consensus       144 ~~~C~ff-~kG~C~rG~~Cpy~H~~  167 (327)
                      ..+|.|| .+|.|.+|+.|.|.|..
T Consensus        36 ~~~C~~f~~~G~C~~G~~C~f~H~~   60 (98)
T 2cqe_A           36 DFPCKLYHTTGNCINGDDCMFSHDP   60 (98)
T ss_dssp             SSBCSHHHHTSCCSSCTTCSSBCCC
T ss_pred             CCcCcCcccCCcCCCCCCCcccCCC
Confidence            4579999 69999999999999973

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A

Probab=89.79  E-value=0.061  Score=39.01  Aligned_cols=25  Identities=24%  Similarity=0.809  Sum_probs=0.0

Q ss_pred             ccccccc-cccccCCCCCCCCCCCCC
Q psy14139        144 PHICSFW-VKGECRRGEECPYRHEKP  168 (327)
Q Consensus       144 ~~~C~ff-~kG~C~rG~~Cpy~H~~p  168 (327)
                      ..+|.+| ..|.|.+|..|.|.|...
T Consensus        50 ~~~C~~f~~~G~C~~G~~C~f~H~~~   75 (77)
T 1m9o_A           50 TELCHKFKLQGRCPYGSRCHFIHNPT   75 (77)
T ss_dssp             --------------------------
T ss_pred             CCcccchhhCcCCCCcCcCCCCCCCC
Confidence            4689755 789999999999999753

>2rpp_A Muscleblind-like protein 2; zinc finger domain, C3H, alternative splicing, cytoplasm, metal-binding, nucleus, RNA-binding, zinc, zinc-finger; NMR {Homo sapiens}

Probab=88.83  E-value=0.1  Score=39.32  Aligned_cols=23  Identities=39%  Similarity=0.738  Sum_probs=20.9

Q ss_pred             CccccccccccccCCCCCCCCCCC
Q psy14139        143 RPHICSFWVKGECRRGEECPYRHE  166 (327)
Q Consensus       143 ~~~~C~ff~kG~C~rG~~Cpy~H~  166 (327)
                      +..+|.+|.+|.|.|+ .|+|.|.
T Consensus        50 ~~~vC~dflkG~C~r~-~Cky~H~   72 (89)
T 2rpp_A           50 RVIACFDSLKGRCSRE-NCKYLHP   72 (89)
T ss_dssp             BEEBCHHHHHTCCCCT-TCCSBCC
T ss_pred             ceeeehhhhhCcCCCC-CcceecC
Confidence            4679999999999999 7999996

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}

Probab=88.72  E-value=0.037  Score=41.22  Aligned_cols=45  Identities=20%  Similarity=0.451  Sum_probs=30.8

Q ss_pred             cccchhhhhccccCCcccccCCcceeEEecCCCCCcccchhhhhhhhccc
Q psy14139         11 NRQSWEDATKEKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLK   60 (327)
Q Consensus        11 ~~~~~e~~~k~~~g~eckic~rpft~f~w~~~~~~~~kkt~ic~~ca~~k   60 (327)
                      .+..|..   .....+|.+|..+||+|+.+  .+-|.=--++|..|+..+
T Consensus        11 ~~~~W~p---d~~~~~C~~C~~~Fs~~~Rr--HHCR~CG~v~C~~Cs~~~   55 (84)
T 1z2q_A           11 SKGYWQE---DEDAPACNGCGCVFTTTVRR--HHCRNCGYVLCGDCSRHR   55 (84)
T ss_dssp             CCSCCCC---TTTCCBCTTTCCBCCTTSCC--EECTTTCCEECTGGGCCE
T ss_pred             CCCcccc---CCCCCCCcCcCCccccchhc--ccccCCCcEEChHHhCCe
Confidence            4567753   34567999999999998754  234444457788887654

>2d9m_A Zinc finger CCCH-type domain containing protein 7A; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=88.21  E-value=0.15  Score=36.44  Aligned_cols=22  Identities=32%  Similarity=0.982  Sum_probs=20.9

Q ss_pred             cccccccccccCCCCCCCCCCC
Q psy14139        145 HICSFWVKGECRRGEECPYRHE  166 (327)
Q Consensus       145 ~~C~ff~kG~C~rG~~Cpy~H~  166 (327)
                      .+|..|.+|.|..|+.|.|.|.
T Consensus        21 ~LC~~~~~G~C~~G~~C~FAHG   42 (69)
T 2d9m_A           21 SICDRYMNGTCPEGNSCKFAHG   42 (69)
T ss_dssp             SBCHHHHHSCCSSCSSCSSBSS
T ss_pred             ccCcccCcCCCCCCCccCCcCC
Confidence            6999999999999999999996

>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics, structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB: 2yqm_A

Probab=87.83  E-value=0.063  Score=39.75  Aligned_cols=38  Identities=21%  Similarity=0.486  Sum_probs=26.2

Q ss_pred             cccCCcccccCCcceeEEecCCCCCcccchhhhhhhhccc
Q psy14139         21 EKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLK   60 (327)
Q Consensus        21 ~~~g~eckic~rpft~f~w~~~~~~~~kkt~ic~~ca~~k   60 (327)
                      ......|.+|..+||+|+.+=  +-|.=--++|..|+..+
T Consensus        16 d~~~~~C~~C~~~Fs~~~RrH--HCR~CG~v~C~~Cs~~~   53 (82)
T 2yw8_A           16 DDEATHCRQCEKEFSISRRKH--HCRNCGHIFCNTCSSNE   53 (82)
T ss_dssp             CCCCCBCTTTCCBCBTTBCCE--ECTTTCCEECSGGGCEE
T ss_pred             CccCCcccCcCCcccCccccc--cCCCCCCEEChHHhCCe
Confidence            345568999999999987652  23433446777777654

>2fc6_A Nuclear, target of EGR1, member 1; structure genomics, ZF-CCCH domain, member 1(nuclear), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.66.1.1

Probab=87.32  E-value=0.22  Score=33.04  Aligned_cols=26  Identities=31%  Similarity=0.721  Sum_probs=22.8

Q ss_pred             Cccccccc-cccccCCCCCCCCCCCCC
Q psy14139        143 RPHICSFW-VKGECRRGEECPYRHEKP  168 (327)
Q Consensus       143 ~~~~C~ff-~kG~C~rG~~Cpy~H~~p  168 (327)
                      ...||.-| +-|.|..|..||+.|...
T Consensus        19 ~~~iC~~FSayGwCp~G~~Cp~SHDiD   45 (50)
T 2fc6_A           19 PTSICDNFSAYGWCPLGPQCPQSHDIS   45 (50)
T ss_dssp             CSCBCSHHHHTCCCTTGGGCSSBCCCC
T ss_pred             ccchhhhccccccCCCCCCCCccccCC
Confidence            46799999 889999999999999754

>1y02_A CARP2, FYVE-ring finger protein sakura; zinc-binding module, phosphoinositide binding, caspase regulation, metal binding protein; 1.80A {Homo sapiens} SCOP: a.140.2.1 g.50.1.1

Probab=86.48  E-value=0.088  Score=41.99  Aligned_cols=46  Identities=22%  Similarity=0.345  Sum_probs=32.6

Q ss_pred             cCCcccccCCcceeEEecCCCCCcccchhhhhhhhccc----Cccccccccc
Q psy14139         23 YGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLK----NVCQTCLLDL   70 (327)
Q Consensus        23 ~g~eckic~rpft~f~w~~~~~~~~kkt~ic~~ca~~k----n~cq~c~ldl   70 (327)
                      ....|..|..+||+|+++  .+-|.=--++|.+|+..+    .||..|..-+
T Consensus        18 ~~~~C~~C~~~Fs~~~Rk--HHCR~CG~ifC~~Cs~~~~~~vRVC~~C~~~~   67 (120)
T 1y02_A           18 LEPSCKSCGAHFANTARK--QTCLDCKKNFCMTCSSQVGNGPRLCLLCQRFR   67 (120)
T ss_dssp             --CCCTTTCCCCSSGGGC--EECTTTCCEECGGGEEC----CCEEHHHHHHH
T ss_pred             ccCcccCcCCcccccccc--ccCCCCCCeeCHHHhCCCCCCceECHHHHHHH
Confidence            346899999999998765  234444567899998765    7899996443

>1vfy_A Phosphatidylinositol-3-phosphate binding FYVE domain of protein VPS27; endosome maturation, intracellular trafficking; 1.15A {Saccharomyces cerevisiae} SCOP: g.50.1.1

Probab=85.79  E-value=0.064  Score=38.80  Aligned_cols=32  Identities=22%  Similarity=0.472  Sum_probs=21.6

Q ss_pred             CcccccCCcceeEEecCCCCCcccchhhhhhhhc
Q psy14139         25 KECKICARPFTVFRWCPGARMRFKKTEVCQTCAR   58 (327)
Q Consensus        25 ~eckic~rpft~f~w~~~~~~~~kkt~ic~~ca~   58 (327)
                      .+|.+|.++||+|+.+  .+-|.=--++|..|+.
T Consensus        12 ~~C~~C~~~F~~~~Rr--HHCR~CG~v~C~~Cs~   43 (73)
T 1vfy_A           12 DACMICSKKFSLLNRK--HHCRSCGGVFCQEHSS   43 (73)
T ss_dssp             SBCTTTCCBCBTTBCC--EECTTTCCEECGGGSC
T ss_pred             CcccCCCCccCCcccc--ccCCCCCEEEcccccC
Confidence            5899999999998653  2233333456666664

>3t7l_A Zinc finger FYVE domain-containing protein 16; structural genomics consortium, SGC, lipid BIND protein, transport protein; 1.09A {Homo sapiens}

Probab=84.89  E-value=0.14  Score=38.55  Aligned_cols=38  Identities=21%  Similarity=0.376  Sum_probs=25.9

Q ss_pred             cccCCcccccCCcceeEEecCCCCCcccchhhhhhhhccc
Q psy14139         21 EKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLK   60 (327)
Q Consensus        21 ~~~g~eckic~rpft~f~w~~~~~~~~kkt~ic~~ca~~k   60 (327)
                      .....+|.+|..+|++|+.+  .+-|.=--++|..|+..+
T Consensus        17 d~~~~~C~~C~~~F~~~~Rr--hhCr~CG~v~C~~Cs~~~   54 (90)
T 3t7l_A           17 DSEAPNCMNCQVKFTFTKRR--HHCRACGKVFCGVCCNRK   54 (90)
T ss_dssp             GGGCCBCTTTCCBCCSSSCC--EECTTTCCEECGGGSCEE
T ss_pred             cccCCcCcCCCCcccchhhC--ccccCCCCEECCcccCCe
Confidence            34567899999999987654  234444556777776653

>1joc_A EEA1, early endosomal autoantigen 1; FYVE domain, inositol 3-phosphate binding, membrane protein; HET: ITP; 2.20A {Homo sapiens} SCOP: g.50.1.1 h.1.21.1 PDB: 1hyi_A* 1hyj_A

Probab=82.82  E-value=0.17  Score=40.60  Aligned_cols=38  Identities=18%  Similarity=0.379  Sum_probs=24.7

Q ss_pred             cccCCcccccCCcceeEEecCCCCCcccchhhhhhhhccc
Q psy14139         21 EKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLK   60 (327)
Q Consensus        21 ~~~g~eckic~rpft~f~w~~~~~~~~kkt~ic~~ca~~k   60 (327)
                      ...-..|.+|..+||+|+.+  .+-|.=--++|..|+..+
T Consensus        66 d~~~~~C~~C~~~Fs~~~Rr--HHCR~CG~vfC~~Cs~~~  103 (125)
T 1joc_A           66 DNEVQNCMACGKGFSVTVRR--HHCRQCGNIFCAECSAKN  103 (125)
T ss_dssp             GGGCCBCTTTCCBCCSSSCC--EECTTTCCEECGGGSCEE
T ss_pred             CCCCCCCcCcCCcccccccc--ccCCCCCeEEChHHhCCc
Confidence            34567899999999998643  223333346677776543

>1wfk_A Zinc finger, FYVE domain containing 19; riken structural genomics/proteomics initiative, RSGI, structural genomics, unknown function; NMR {Mus musculus} SCOP: g.50.1.1

Probab=80.99  E-value=0.12  Score=38.76  Aligned_cols=35  Identities=23%  Similarity=0.420  Sum_probs=22.1

Q ss_pred             cCCcccccCCcceeEEecCCCCCcccchhhhhhhhcc
Q psy14139         23 YGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARL   59 (327)
Q Consensus        23 ~g~eckic~rpft~f~w~~~~~~~~kkt~ic~~ca~~   59 (327)
                      ...+|.+|..+||+|+.+-  +-|.=--++|..|+..
T Consensus         8 ~~~~C~~C~~~F~~~~RrH--HCR~CG~vfC~~Cs~~   42 (88)
T 1wfk_A            8 MESRCYGCAVKFTLFKKEY--GCKNCGRAFCNGCLSF   42 (88)
T ss_dssp             CCSBCTTTCCBCCSSSCEE--ECSSSCCEEETTTSCE
T ss_pred             cCCCCcCcCCcccCccccc--cCCCCCCEEChhHcCC
Confidence            3468999999999986542  2232233556666543

>1x4u_A Zinc finger, FYVE domain containing 27 isoform B; phosphoinositide binding, zinc binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=80.74  E-value=0.16  Score=37.76  Aligned_cols=37  Identities=16%  Similarity=0.372  Sum_probs=24.2

Q ss_pred             cccCCcccccCCcceeEEecCCCCCcccchhhhhhhhcc
Q psy14139         21 EKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARL   59 (327)
Q Consensus        21 ~~~g~eckic~rpft~f~w~~~~~~~~kkt~ic~~ca~~   59 (327)
                      ...-.+|-+|..+||+|+.+  .+-|.=--++|..|+..
T Consensus        11 d~~~~~C~~C~~~F~~~~Rr--HHCR~CG~vfC~~Cs~~   47 (84)
T 1x4u_A           11 TNNFGNCTGCSATFSVLKKR--RSCSNCGNSFCSRCCSF   47 (84)
T ss_dssp             CCCCSSCSSSCCCCCSSSCC--EECSSSCCEECTTTSCE
T ss_pred             CCCCCcCcCcCCccccchhh--hhhcCCCcEEChhhcCC
Confidence            34567899999999998543  22333344666666643

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=80.37  E-value=5.2  Score=39.37  Aligned_cols=53  Identities=25%  Similarity=0.406  Sum_probs=43.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHh
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHS  269 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~  269 (327)
                      ..++|+ +|..+...+|.+.|+.||.+ +|+.+ +..+|||.|.+.+.|+.++.++
T Consensus       441 ~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~wi-ddt~a~V~~~~~~~a~~~l~~~  493 (507)
T 3d45_A          441 HVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWI-DDTSAFVSLSQPEQVQIAVNTS  493 (507)
T ss_dssp             GEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEEC-SSSEEEEECSCHHHHHHHHHHH
T ss_pred             cEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEE-cCCeEEEEECCHHHHHHHHHHH
Confidence            466666 99999999999999999954 45544 4577999999999999999874

---

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	327
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-17
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-17
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-16
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-15
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-15
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-14
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-14
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-14
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	6e-14
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-13
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-13
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-13
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-13
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-13
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	9e-13
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	9e-13
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-12
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	1e-12
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-12
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-12
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-12
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-12
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	4e-12
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	4e-12
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-12
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	8e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	8e-12
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	9e-12
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	9e-12
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-11
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-11
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-11
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-11
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-11
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-11
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-11
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	6e-11
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	7e-11
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-10
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	2e-10
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-10
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-10
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-10
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	4e-10
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	4e-10
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	5e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	6e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	7e-10
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-09
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-09
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-09
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-09
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-09
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-09
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	8e-09
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	1e-08
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-08
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-08
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-08
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-08
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	8e-08
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	2e-07
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	4e-07
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	4e-07
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	8e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-06
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-06
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	1e-06
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	3e-06
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-06
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	5e-05
d1x4fa1	99	d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus)	9e-05
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	3e-04
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	0.002
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	0.002
d2cqea2	29	g.66.1.1 (A:429-457) Zinc finger CCCH domain-conta	0.002

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 74.6 bits (183), Expect = 1e-17
 Identities = 20/91 (21%), Positives = 45/91 (49%), Gaps = 7/91 (7%)

Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-------CAFIQYTSRP 260
           P+ +T + + V N+  +  ++++R+ F  FGE+++V +  K           F+ + ++ 
Sbjct: 3   PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 62

Query: 261 AAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
            A+ A     +   L GRRL ++W  ++   
Sbjct: 63  DAKKAFNALCHSTHLYGRRLVLEWADSEVTV 93

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 74.2 bits (182), Expect = 2e-17
 Identities = 18/78 (23%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
            T+Y G +   LT+Q +R  F  FG+I  + +  ++  +F+++++  +A  A+    N  
Sbjct: 19  CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVS-VNGT 77

Query: 274 ILGGRRLNIKWGRAQANR 291
            + G  +   WG+   + 
Sbjct: 78  TIEGHVVKCYWGKESPDM 95

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.8 bits (176), Expect = 1e-16
 Identities = 18/87 (20%), Positives = 38/87 (43%), Gaps = 4/87 (4%)

Query: 206 DPPEDKTITTLYVGNLG-DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEA 264
                   + +++GNL    + + D+   F ++G+I   ++   +  AF+QY +   A A
Sbjct: 8   KTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--HKGFAFVQYVNERNARA 65

Query: 265 AVEHSFNKVILGGRRLNIKWGRAQANR 291
           AV    +  ++ G+ L+I         
Sbjct: 66  AVAG-EDGRMIAGQVLDINLAAEPKVN 91

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.8 bits (168), Expect = 1e-15
 Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
           + L+VGNL   +TE+++R  F ++G+   V I   +   FI+  +R  AE A     + +
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVE-LDNM 67

Query: 274 ILGGRRLNIKWGRAQAN 290
            L G++L +++    A+
Sbjct: 68  PLRGKQLRVRFACHSAS 84

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.6 bits (165), Expect = 3e-15
 Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 7/76 (9%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVEH 268
           +LYVG+L   +TE  L + F   G I S+ +            A++ +     AE A++ 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 269 SFNKVILGGRRLNIKW 284
             N  ++ G+ + I W
Sbjct: 62  -MNFDVIKGKPVRIMW 76

>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 = 65.7 bits (160), Expect = 1e-14
 Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 7/83 (8%)

Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAA 262
           E    T LYV NL   +T+  L   F ++G I    IL  +        AF++Y  R  A
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 263 EAAVEHSFNKVILGG-RRLNIKW 284
           + A+    N +  GG + L+++ 
Sbjct: 62  QEAISALNNVIPEGGSQPLSVRL 84

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.6 bits (162), Expect = 2e-14
 Identities = 30/115 (26%), Positives = 55/115 (47%), Gaps = 7/115 (6%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC---AFIQYTSRPAAE 263
           PPE      LY+ NL  K+T +++ D F ++G IR + + +  +    A++ Y     A+
Sbjct: 3   PPEVNR--ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAK 60

Query: 264 AAVEHSFNKVILGGRRLNIKWGRAQ-ANRGEDTAELKVRLEPVPGLPGALPPPPK 317
            A +H  +   +  R L + +  A  A +  DT + + +L+ +    G    PPK
Sbjct: 61  NACDH-LSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPPK 114

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 64.6 bits (157), Expect = 4e-14
 Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
           T L V  L   +T+++L   F   G I +  I+   +       AF+ +TS   ++ A++
Sbjct: 3   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

Query: 268 HSFNKVILGGRRLNIKWGR 286
              N + +  +RL + + R
Sbjct: 63  V-LNGITVRNKRLKVSYAR 80

>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 = 64.2 bits (156), Expect = 6e-14
 Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----SKQQCAFIQYTSRPAAEAAVEHSF 270
           L V NL   +++ D+++ F +FG ++   +           A + +  +  A  A++  +
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ-Y 61

Query: 271 NKVILGGRRLNIKW 284
           N V L GR +NI+ 
Sbjct: 62  NGVPLDGRPMNIQL 75

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.0 bits (155), Expect = 1e-13
 Identities = 27/100 (27%), Positives = 40/100 (40%), Gaps = 15/100 (15%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK--------------QQC 251
           DP ED   + +YV  L D +T  DL D F Q G ++      +              +  
Sbjct: 1   DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 60

Query: 252 AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
           A + Y   P A+AAVE  F+     G +L +   R +   
Sbjct: 61  ATVSYEDPPTAKAAVEW-FDGKDFQGSKLKVSLARKKPPM 99

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.2 bits (153), Expect = 1e-13
 Identities = 23/77 (29%), Positives = 36/77 (46%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVI 274
            LY+GNL   +T  DLR  F       +  +L K   AF+ Y  +  A  A+E    KV 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVE 62

Query: 275 LGGRRLNIKWGRAQANR 291
           L G+ + + +  ++  R
Sbjct: 63  LHGKIMEVDYSVSKKLR 79

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.5 bits (151), Expect = 2e-13
 Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 8/84 (9%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-------CAFIQYTSRPAAEAAVEH 268
           +++GNL  ++ E+ L D F  FG I     + +          AFI + S  A++AA+E 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 269 SFNKVILGGRRLNIKWGRAQANRG 292
             N   L  R + + +   + ++G
Sbjct: 61  -MNGQYLCNRPITVSYAFKKDSKG 83

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.0 bits (150), Expect = 5e-13
 Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 5/87 (5%)

Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK----QQCAFIQYTSRPAAEA 264
           +D    TLYVGNL   +TE  +   F Q G  +S  ++++        F+++     A A
Sbjct: 4   DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAA 63

Query: 265 AVEHSFNKVILGGRRLNIKWGRAQANR 291
           A+    N   + G+ + + W    +++
Sbjct: 64  ALAA-MNGRKILGKEVKVNWATTPSSQ 89

>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 = 62.0 bits (150), Expect = 5e-13
 Identities = 21/92 (22%), Positives = 42/92 (45%), Gaps = 10/92 (10%)

Query: 203 PKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQY 256
           P  +  +D    T+YVG L +K++E  L + F Q G + +  +         Q   F+++
Sbjct: 2   PISERNQD---ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 58

Query: 257 TSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ 288
            S   A+ A++   + + L G+ + +    A 
Sbjct: 59  LSEEDADYAIKI-MDMIKLYGKPIRVNKASAH 89

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.1 bits (148), Expect = 9e-13
 Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
            TLYVGNL    TE+ + + F + G+I+ + +   +         F++Y SR  AE A+ 
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 268 HSFNKVILGGRRLNIKWGR 286
           +  N   L  R +   W  
Sbjct: 68  Y-INGTRLDDRIIRTDWDA 85

>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 = 60.9 bits (147), Expect = 9e-13
 Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 7/79 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
           T L V  L   +T+++ R  F   GEI S  ++  +         F+ Y     AE A+ 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 268 HSFNKVILGGRRLNIKWGR 286
              N + L  + + + + R
Sbjct: 63  T-LNGLRLQTKTIKVSYAR 80

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.2 bits (148), Expect = 1e-12
 Identities = 24/88 (27%), Positives = 43/88 (48%), Gaps = 4/88 (4%)

Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ---CAFIQYTSRPAAEA 264
           P       +YVGNL   +  +D+ D FY++G IR + + +++     AF+++     AE 
Sbjct: 9   PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAED 68

Query: 265 AVEHSFNKVILGGRRLNIKWGRAQANRG 292
           AV    +     G RL +++ R+    G
Sbjct: 69  AVYG-RDGYDYDGYRLRVEFPRSGRGTG 95

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.8 bits (147), Expect = 1e-12
 Identities = 28/81 (34%), Positives = 41/81 (50%), Gaps = 3/81 (3%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
           T L+VG LG   +   L   F +FG IR++  +     A+IQY S  AA+AA        
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAK-MRGF 76

Query: 274 ILGG--RRLNIKWGRAQANRG 292
            LGG  RRL + + ++  + G
Sbjct: 77  PLGGPDRRLRVDFAKSGPSSG 97

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.4 bits (146), Expect = 1e-12
 Identities = 18/80 (22%), Positives = 37/80 (46%), Gaps = 4/80 (5%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-CAFIQYTSRPAAEAAVEHSFNK 272
           + ++VG     +TE +LR+ F Q+G++  V I    +  AF+ +     A++        
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG---ED 62

Query: 273 VILGGRRLNIKWGRAQANRG 292
           +I+ G  ++I     + N  
Sbjct: 63  LIIKGISVHISNAEPKHNSN 82

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.4 bits (146), Expect = 1e-12
 Identities = 16/86 (18%), Positives = 33/86 (38%), Gaps = 1/86 (1%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAA 265
           D     ++  LYV NL    +E+ +   F          +   +  AF+ +++R  A  A
Sbjct: 1   DEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEA 60

Query: 266 VEHSFNKVILGGRRLNIKWGRAQANR 291
           ++   N  +L G  + +   +     
Sbjct: 61  MKA-LNGKVLDGSPIEVTLAKPVDKD 85

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.4 bits (146), Expect = 2e-12
 Identities = 21/90 (23%), Positives = 44/90 (48%), Gaps = 6/90 (6%)

Query: 207 PPEDKT-ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL----SKQQCAFIQYTSRPA 261
           P   K+ +  +++ NL   +  + L D F  FG I S  ++      +   F+ + ++ A
Sbjct: 1   PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEA 60

Query: 262 AEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
           AE A+E   N ++L  R++ +   +++  R
Sbjct: 61  AERAIEK-MNGMLLNDRKVFVGRFKSRKER 89

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.6 bits (146), Expect = 2e-12
 Identities = 14/84 (16%), Positives = 38/84 (45%), Gaps = 1/84 (1%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAA 265
              +      ++V  L + + E DL +   +FG I  V ++  ++ A +++ +  +A+  
Sbjct: 8   SHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKEC 67

Query: 266 VEH-SFNKVILGGRRLNIKWGRAQ 288
           V   +   V + G++    +  ++
Sbjct: 68  VTFAADVPVYIAGQQAFFNYSTSK 91

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.0 bits (145), Expect = 2e-12
 Identities = 21/90 (23%), Positives = 38/90 (42%), Gaps = 14/90 (15%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC---------AFIQYTSRPAAEAAV 266
           L++ NL    TE+ L+  F + G I+S TI  K+            F++Y     A+ A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 267 EHSFNKVILGGRRLNIKWGRAQANRGEDTA 296
           +       + G +L ++     + R    A
Sbjct: 61  KQ-LQGHTVDGHKLEVRI----SERATKPA 85

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 59.7 bits (144), Expect = 4e-12
 Identities = 26/92 (28%), Positives = 43/92 (46%), Gaps = 6/92 (6%)

Query: 206 DPPEDKTI---TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-CAFIQYTSRPA 261
           DP   K +    TL   NL   +TE +L++ F    EIR V+   K +  A+I++ S   
Sbjct: 6   DPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEAD 65

Query: 262 AEAAVEHSFNKVILGGRRLNIKWGRAQ-ANRG 292
           AE  +E       + GR +++ +   +   RG
Sbjct: 66  AEKNLEE-KQGAEIDGRSVSLYYTGEKGGTRG 96

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.2 bits (143), Expect = 4e-12
 Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 9/84 (10%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
           + L V  L  K TEQDL+++F  FGE+  V +    +        F+++T        + 
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 268 HSFNKVILGGRRLNIKWGRAQANR 291
               + ++ GR  + K   ++ ++
Sbjct: 69  ---QRHMIDGRWCDCKLPNSKQSQ 89

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 5e-12
 Identities = 20/90 (22%), Positives = 42/90 (46%), Gaps = 8/90 (8%)

Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPA 261
           PE++   T++   L  ++  +DL D F   G++R V I+S +        A++++    +
Sbjct: 13  PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 72

Query: 262 AEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
              A+        L G  + ++  +A+ NR
Sbjct: 73  VPLAIG--LTGQRLLGVPIIVQASQAEKNR 100

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.1 bits (140), Expect = 8e-12
 Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
            TLYV      +T   LR  F  FG I  +++   + CAF+ Y    +A+ AV    N  
Sbjct: 6   NTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAE-LNGT 62

Query: 274 ILGGRRLNIKWGRAQ 288
            +   +L +   R Q
Sbjct: 63  QVESVQLKVNIARKQ 77

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 8e-12
 Identities = 21/89 (23%), Positives = 39/89 (43%), Gaps = 5/89 (5%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI----LSKQQCAFIQYTSRPA 261
           +     T   L+V N+  +  + DLR  F QFG+I  V I       +   F+ + +   
Sbjct: 4   NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSAD 63

Query: 262 AEAAVEHSFNKVILGGRRLNIKWGRAQAN 290
           A+ A E   +  ++ GR++ +    A+  
Sbjct: 64  ADRAREK-LHGTVVEGRKIEVNNATARVM 91

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 9e-12
 Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 7/87 (8%)

Query: 211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEA 264
            T   LYVG L +++ ++ L   F  FG+I  + I         +  AF+++     A A
Sbjct: 3   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62

Query: 265 AVEHSFNKVILGGRRLNIKWGRAQANR 291
           A+++  N+  L GR + +   +    +
Sbjct: 63  AIDN-MNESELFGRTIRVNLAKPMRIK 88

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.1 bits (140), Expect = 9e-12
 Identities = 13/75 (17%), Positives = 35/75 (46%), Gaps = 8/75 (10%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVEHS 269
           +++G L  + T++ LR++F QFGE++   ++            F+ +  +   +  +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 61

Query: 270 FNKVILGGRRLNIKW 284
            ++  L  + ++ K 
Sbjct: 62  -SRHELDSKTIDPKV 75

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.6 bits (141), Expect = 1e-11
 Identities = 21/99 (21%), Positives = 45/99 (45%), Gaps = 10/99 (10%)

Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCA 252
            +   + + PE      L++ +L  +  +QDL   F  FG + S  +         +   
Sbjct: 7   GAAGSQKEGPEG---ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFG 63

Query: 253 FIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
           F+ Y +  +A+AA++   N   +G +RL ++  R++ + 
Sbjct: 64  FVSYDNPVSAQAAIQS-MNGFQIGMKRLKVQLKRSKNDS 101

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 1e-11
 Identities = 17/93 (18%), Positives = 35/93 (37%), Gaps = 9/93 (9%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC--------AFIQYTSRPAAEAA 265
             L++G +      +++ +   +  E     I+             AF++Y S  AA  A
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 266 VEH-SFNKVILGGRRLNIKWGRAQANRGEDTAE 297
                  ++ L G ++ + W   + +  ED  E
Sbjct: 62  RRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVME 94

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.8 bits (139), Expect = 1e-11
 Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 7/78 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
             LYV  L   +T+++L   F Q+G I +  IL  Q         FI++  R  AE A++
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 268 HSFNKVILG-GRRLNIKW 284
               +   G    + +K+
Sbjct: 67  GLNGQKPSGATEPITVKF 84

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.6 bits (141), Expect = 1e-11
 Identities = 23/94 (24%), Positives = 48/94 (51%), Gaps = 7/94 (7%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSR 259
           DP  D+++ +++VGN+  + TE+ L+D F + G + S  ++  ++        F +Y  +
Sbjct: 1   DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGE 293
             A +A+ +  N     GR L +    ++ N+ E
Sbjct: 61  ETALSAMRN-LNGREFSGRALRVDNAASEKNKEE 93

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.3 bits (138), Expect = 1e-11
 Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 8/74 (10%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ------QCAFIQYTSRPAAEAAVEHS 269
           ++VG L     E+ +R++F  FGE+ S+ +             FI +      +  +E  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 270 FNKVILGGRRLNIK 283
           ++   +G  +  IK
Sbjct: 62  YHN--VGLSKCEIK 73

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.8 bits (139), Expect = 2e-11
 Identities = 10/76 (13%), Positives = 27/76 (35%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAV 266
                    +  G LG+ ++   L     + G + ++ +   +  +F +Y +   ++ A 
Sbjct: 14  VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAY 73

Query: 267 EHSFNKVILGGRRLNI 282
                K ++      I
Sbjct: 74  VTLNGKEVVDDLGQKI 89

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.8 bits (139), Expect = 2e-11
 Identities = 19/93 (20%), Positives = 40/93 (43%), Gaps = 8/93 (8%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSR 259
              E +    L++G L  + TE+ LR+++ Q+G++    ++            F+ ++S 
Sbjct: 13  KKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSM 72

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANRG 292
              +AA+        + GR +  K   A+   G
Sbjct: 73  AEVDAAMA--ARPHSIDGRVVEPKRAVAREESG 103

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 3e-11
 Identities = 25/75 (33%), Positives = 38/75 (50%), Gaps = 7/75 (9%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
             L V  L    TE+DLR+ F ++G I  V+I+  QQ       AF+ + +   A+ A E
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 268 HSFNKVILGGRRLNI 282
              N + L GRR+ +
Sbjct: 70  R-ANGMELDGRRIRV 83

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 3e-11
 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 9/82 (10%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSV-------TILSKQQCAFIQYTSRPAAEAAVEH 268
           L++G L + L +  +++    FG +++        T LSK   AF +Y      + A+  
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK-GYAFCEYVDINVTDQAIAG 62

Query: 269 SFNKVILGGRRLNIKWGRAQAN 290
             N + LG ++L ++     A 
Sbjct: 63  -LNGMQLGDKKLLVQRASVGAK 83

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.6 bits (136), Expect = 5e-11
 Identities = 16/86 (18%), Positives = 30/86 (34%), Gaps = 7/86 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
             L+V NL    +E+DL   F  +G +  +              AF+ +     A  A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 268 HSFNKVILGGRRLNIKWGRAQANRGE 293
              +  +  GR L++     +    +
Sbjct: 69  E-VDGQVFQGRMLHVLPSTIKKEASQ 93

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.5 bits (133), Expect = 6e-11
 Identities = 14/75 (18%), Positives = 31/75 (41%), Gaps = 8/75 (10%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVEHS 269
           ++VG L    T +D++ +F QFG++    ++  +         F+ + S    E   E  
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-- 59

Query: 270 FNKVILGGRRLNIKW 284
            +   +  + +  K 
Sbjct: 60  IHFHEINNKMVECKK 74

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 7e-11
 Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 7/83 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
            T+ V NL +   E DL++ F  FG I  + +   +        AFI +  R  A  A+ 
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 268 HSFNKVILGGRRLNIKWGRAQAN 290
              +        LN++W +   N
Sbjct: 69  G-VSGFGYDHLILNVEWAKPSTN 90

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 55.1 bits (132), Expect = 1e-10
 Identities = 17/84 (20%), Positives = 40/84 (47%), Gaps = 7/84 (8%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRP 260
           P        L+V ++ ++  E ++++ F  +GEI+++ +   ++       A ++Y +  
Sbjct: 1   PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 60

Query: 261 AAEAAVEHSFNKVILGGRRLNIKW 284
            A AA E   N   + G+ + + W
Sbjct: 61  QALAAKEA-LNGAEIMGQTIQVDW 83

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.6 bits (133), Expect = 2e-10
 Identities = 15/83 (18%), Positives = 27/83 (32%)

Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH 268
           E       + G+L D+   +DL   F   GEI+ +  +   +   I +  +         
Sbjct: 7   EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAK 66

Query: 269 SFNKVILGGRRLNIKWGRAQANR 291
             N   L  R   + W   +   
Sbjct: 67  DANNGNLQLRNKEVTWEVLEGEV 89

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.4 bits (130), Expect = 2e-10
 Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 2/77 (2%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL--SKQQCAFIQYTSRPAAEAAVEHSFN 271
            TL++ N+   ++E+DL+  F   G +          ++ A IQ  S   A  A+    N
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHN 70

Query: 272 KVILGGRRLNIKWGRAQ 288
             +     L + + ++ 
Sbjct: 71  HDLGENHHLRVSFSKST 87

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.7 bits (131), Expect = 2e-10
 Identities = 15/85 (17%), Positives = 38/85 (44%), Gaps = 8/85 (9%)

Query: 214 TTLYVGNLGDKLTEQDLRDH----FYQFGEIRSVTILSKQQ---CAFIQYTSRPAAEAAV 266
            T+Y+ NL +K+ + +L+      F +FG+I  + +    +    AF+ +    +A  A+
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 267 EHSFNKVILGGRRLNIKWGRAQANR 291
                      + + I++ +  ++ 
Sbjct: 64  RS-MQGFPFYDKPMRIQYAKTDSDI 87

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.8 bits (129), Expect = 2e-10
 Identities = 15/74 (20%), Positives = 35/74 (47%), Gaps = 8/74 (10%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVEHS 269
           +++G L    T++DL+D+F +FGE+   T+             F+ +    + +  ++  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ- 60

Query: 270 FNKVILGGRRLNIK 283
             +  L G+ ++ K
Sbjct: 61  -KEHKLNGKVIDPK 73

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 54.9 bits (131), Expect = 4e-10
 Identities = 27/124 (21%), Positives = 47/124 (37%), Gaps = 9/124 (7%)

Query: 174 PLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDH 233
           PL  Q   D Y         +   +    P    PE   +  L V  +   + E  LR  
Sbjct: 5   PLVSQY--DPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQL 62

Query: 234 FYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA 287
           F ++G I SV I+  ++        F+++ S  +A+ A+    N   +  +RL +    +
Sbjct: 63  FERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG-LNGFNILNKRLKVALAAS 121

Query: 288 QANR 291
              R
Sbjct: 122 GHQR 125

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.0 bits (129), Expect = 4e-10
 Identities = 26/91 (28%), Positives = 41/91 (45%), Gaps = 8/91 (8%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSR 259
              +D T T ++VG L    T+  LR +F  FG+I    +++ +Q        F+    R
Sbjct: 3   GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 62

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQAN 290
            AAE A +   N +I  GR+ N+      A 
Sbjct: 63  AAAERACKD-PNPII-DGRKANVNLAYLGAK 91

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.0 bits (129), Expect = 5e-10
 Identities = 10/108 (9%), Positives = 26/108 (24%), Gaps = 17/108 (15%)

Query: 214 TTLYVGNLGDKLTE-----QDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH 268
           + L      D +             F  + +  +       +   I +++  +A  A   
Sbjct: 6   SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLR 65

Query: 269 SFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLEPVPGLPGALPPPP 316
             +K    G+ + + + +                      P      P
Sbjct: 66  -LHKTEFLGKEMKLYFAQTLHIG-----------SSHLAPPNPDKSGP 101

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.9 bits (129), Expect = 6e-10
 Identities = 17/84 (20%), Positives = 30/84 (35%), Gaps = 3/84 (3%)

Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS--KQQCAFIQYTSRPAAEAA 265
                +  + V NL   +T   L   F +FG +  +   +   Q  A +QY    +A+ A
Sbjct: 2   AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHA 61

Query: 266 VEHSFNKVIL-GGRRLNIKWGRAQ 288
                 + I      L I + +  
Sbjct: 62  KLSLDGQNIYNACCTLRIDFSKLT 85

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 52.9 bits (126), Expect = 7e-10
 Identities = 18/79 (22%), Positives = 33/79 (41%), Gaps = 7/79 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIR------SVTILSKQQCAFIQYTSRPAAEAAVE 267
            TL++ N     T++++RD       +       S+   + ++ A+I  TS+  A   VE
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 268 HSFNKVILGGRRLNIKWGR 286
              N + + G  L  K   
Sbjct: 62  K-LNGLKIEGYTLVTKVSN 79

>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 = 51.6 bits (123), Expect = 2e-09
 Identities = 18/85 (21%), Positives = 36/85 (42%), Gaps = 11/85 (12%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ------QCAFIQYTSR 259
           +P + +    L++G L  + T++ LR HF Q+G +    ++            F+ Y + 
Sbjct: 2   EPEQLRK---LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 58

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKW 284
              +AA+        + GR +  K 
Sbjct: 59  EEVDAAMN--ARPHKVDGRVVEPKR 81

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.7 bits (123), Expect = 2e-09
 Identities = 19/83 (22%), Positives = 33/83 (39%), Gaps = 13/83 (15%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-----------AFIQYTSRPAAE 263
            LYVGN+   +TE+ + D F     +  +T                  AF+++ S     
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 264 AAVEHSFNKVILGGRRLNIKWGR 286
            A+   F+ +I  G+ L I+   
Sbjct: 63  QAMA--FDGIIFQGQSLKIRRPH 83

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.1 bits (124), Expect = 2e-09
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 3/77 (3%)

Query: 214 TTLYVGNLG-DKLTEQDLRDHFYQFGEIRSVTI-LSKQQCAFIQYTSRPAAEAAVEHSFN 271
           + L V NL  +++T Q L   F  +G+++ V I  +K++ A +Q      A+ A+ H  N
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSH-LN 61

Query: 272 KVILGGRRLNIKWGRAQ 288
              L G+ + I   + Q
Sbjct: 62  GHKLHGKPIRITLSKHQ 78

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.0 bits (124), Expect = 2e-09
 Identities = 17/101 (16%), Positives = 39/101 (38%), Gaps = 14/101 (13%)

Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQ 250
           +  S +PK  PP      T ++GNL   +TE+ +++ F                    + 
Sbjct: 5   SSGSRLPK-SPP-----YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKG 58

Query: 251 CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
             + ++    +  +A+    N+  LG +R+ +       ++
Sbjct: 59  FGYAEFEDLDSLLSALS--LNEESLGNKRIRVDVADQAQDK 97

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.7 bits (123), Expect = 2e-09
 Identities = 16/86 (18%), Positives = 31/86 (36%), Gaps = 2/86 (2%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAV 266
           PP  ++   + V  L    + QDL+DH  + G++    +  K     ++Y  +   E A+
Sbjct: 9   PPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADV-QKDGMGMVEYLRKEDMEYAL 67

Query: 267 EHSFNKVILGGRRLNIKWGRAQANRG 292
               +            + R    R 
Sbjct: 68  RK-LDDTKFRSHEGETSYIRVYPERS 92

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.3 bits (122), Expect = 2e-09
 Identities = 13/76 (17%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
           + + V NL      Q++ D    +  ++   +   ++ AF+   +   A+ A++  F++ 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQM-FHQY 63

Query: 274 ILGGRRLNIKWGRAQA 289
              G+ L ++     A
Sbjct: 64  SFRGKDLIVQLQPTDA 79

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.4 bits (122), Expect = 3e-09
 Identities = 20/91 (21%), Positives = 40/91 (43%), Gaps = 11/91 (12%)

Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRP 260
           P +     T+++ NL     E+ L +   QFG+++ V ++        + CAF Q+ ++ 
Sbjct: 2   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 261 AAEAAVE-----HSFNKVILGGRRLNIKWGR 286
           AA+  +           + L GR+L +    
Sbjct: 62  AAQKCLAAASLEAEGGGLKLDGRQLKVDLAV 92

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.1 bits (119), Expect = 8e-09
 Identities = 16/79 (20%), Positives = 34/79 (43%), Gaps = 2/79 (2%)

Query: 215 TLYVGNLG-DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH-SFNK 272
            +++ +    K     L      FG I +  IL+K   AFI+  +   A+AAV++ +   
Sbjct: 10  VVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTP 69

Query: 273 VILGGRRLNIKWGRAQANR 291
            ++ G+ + +   +     
Sbjct: 70  ALVFGKPVRVHLSQKYKRI 88

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.3 bits (117), Expect = 1e-08
 Identities = 12/81 (14%), Positives = 29/81 (35%), Gaps = 7/81 (8%)

Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAE 263
            D    ++Y+       T  D+++     G++ ++ +        +   F+ + S  +A+
Sbjct: 2   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 61

Query: 264 AAVEHSFNKVILGGRRLNIKW 284
             VE            L I +
Sbjct: 62  KFVET--PGQKYKETDLLILF 80

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 2e-08
 Identities = 20/83 (24%), Positives = 32/83 (38%), Gaps = 5/83 (6%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAEAAVEH 268
             LY+ NL  ++TE+DL   F +F E +   I  +                        H
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 269 SFNKVILGGRRLNIKWGRAQANR 291
             N   L G+ L I++G+ +  R
Sbjct: 79  LVNGYKLYGKILVIEFGKNKKQR 101

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.3 bits (117), Expect = 2e-08
 Identities = 10/80 (12%), Positives = 30/80 (37%), Gaps = 6/80 (7%)

Query: 210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----SKQQCAFIQYTSRPAAEA 264
              ++ + +    D+  E+   +   ++GE+  + +            ++++     AE 
Sbjct: 24  RSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEK 83

Query: 265 AVEHSFNKVILGGRRLNIKW 284
           AV    N     G+ ++ + 
Sbjct: 84  AVID-LNNRWFNGQPIHAEL 102

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.9 bits (116), Expect = 2e-08
 Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 7/78 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
           T + V N+   ++  ++ D FY +  I     L   +       A + + SR  A AAV 
Sbjct: 10  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 268 HSFNKVILGGRRLNIKWG 285
              N   +G R++ +  G
Sbjct: 70  D-LNDRPIGSRKVKLVLG 86

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (114), Expect = 3e-08
 Identities = 16/78 (20%), Positives = 35/78 (44%), Gaps = 8/78 (10%)

Query: 212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAA 265
           T+  ++VG + +   E  LRD+F Q+G+I  + I++       +  AF+ +    + +  
Sbjct: 1   TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 60

Query: 266 VEHSFNKVILGGRRLNIK 283
           V        + G    ++
Sbjct: 61  VI--QKYHTVNGHNCEVR 76

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (111), Expect = 8e-08
 Identities = 17/83 (20%), Positives = 36/83 (43%), Gaps = 7/83 (8%)

Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVEH 268
            L+VG L     EQ L   F ++G+I  V ++  ++        F+ + +   A+ A+  
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 269 SFNKVILGGRRLNIKWGRAQANR 291
             N   + GR++ +      ++ 
Sbjct: 67  -MNGKSVDGRQIRVDQAGKSSDN 88

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 46.0 bits (108), Expect = 2e-07
 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 5/82 (6%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIR-SVTILSKQQCAFIQYTSRPAAEA 264
            PP       L++ NL ++  E  L   F QF   +    + ++   AF+++T+   + A
Sbjct: 5   QPPN----QILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNA 60

Query: 265 AVEHSFNKVILGGRRLNIKWGR 286
           A E      I     + I + +
Sbjct: 61  AKEALQGFKITPTHAMKITFAK 82

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 44.8 bits (105), Expect = 4e-07
 Identities = 15/74 (20%), Positives = 28/74 (37%), Gaps = 6/74 (8%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC----AFIQYTSRPAAEAAVEHS 269
           TT+ V NL     +  +  +F   G I  V +    +     A I++     A AA+  +
Sbjct: 1   TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKT 60

Query: 270 FNKVILGGRRLNIK 283
                +G   + + 
Sbjct: 61  HKV--VGQNEIIVS 72

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.2 bits (106), Expect = 4e-07
 Identities = 16/84 (19%), Positives = 38/84 (45%), Gaps = 1/84 (1%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAA 265
           D  +      L++  L  ++TE ++      FG++ ++ +L  +  AF++  +  AA   
Sbjct: 1   DKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITM 60

Query: 266 VEH-SFNKVILGGRRLNIKWGRAQ 288
           V + S     L  + + I++   +
Sbjct: 61  VNYYSAVTPHLRNQPIYIQYSNHK 84

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.7 bits (107), Expect = 5e-07
 Identities = 13/85 (15%), Positives = 28/85 (32%), Gaps = 1/85 (1%)

Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH 268
             ++ T +   NL       ++++ F +FG +  V +      A +++     A  A  H
Sbjct: 6   SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRH 65

Query: 269 SFNKVILGGRRLNIKWGRAQANRGE 293
                      L ++W         
Sbjct: 66  -LAYSKFHHVPLYLEWAPIGVFGAA 89

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (103), Expect = 8e-07
 Identities = 16/71 (22%), Positives = 27/71 (38%), Gaps = 7/71 (9%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVEHS 269
           LY+  L    T+QDL      +G+I S   +  +         F+ + S  AA+ AV   
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA- 59

Query: 270 FNKVILGGRRL 280
                +  +  
Sbjct: 60  LKASGVQAQMA 70

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.1 bits (108), Expect = 1e-06
 Identities = 21/153 (13%), Positives = 52/153 (33%), Gaps = 11/153 (7%)

Query: 145 HICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPK 204
            +    V  +        +        ++  A  N +           ++ ++R      
Sbjct: 32  TLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSR---EDS 88

Query: 205 LDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTS 258
             P    T+  ++VG + +   E  LRD+F Q+G+I  + I++ +        AF+ +  
Sbjct: 89  QRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 148

Query: 259 RPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
             + +  V        + G    ++   ++   
Sbjct: 149 HDSVDKIVIQ--KYHTVNGHNCEVRKALSKQEM 179

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (107), Expect = 1e-06
 Identities = 17/105 (16%), Positives = 38/105 (36%), Gaps = 12/105 (11%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ---------CAFIQY 256
           +P + +    L++G L  + T++ LR HF Q+G +    ++               +   
Sbjct: 2   EPEQLRK---LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 58

Query: 257 TSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVR 301
               AA  A  H  +  ++  +R   +    +        ++ V 
Sbjct: 59  EEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVG 103

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 44.2 bits (103), Expect = 1e-06
 Identities = 12/87 (13%), Positives = 35/87 (40%), Gaps = 7/87 (8%)

Query: 205 LDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ-----QCAFIQYTSR 259
           ++  E  T   L++GNL    +  +L+    +      + ++  +     +  ++ + S 
Sbjct: 5   VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESA 64

Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGR 286
              E A+E     + + G  + ++  +
Sbjct: 65  EDLEKALE--LTGLKVFGNEIKLEKPK 89

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (103), Expect = 1e-06
 Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 6/88 (6%)

Query: 204 KLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGE-----IRSVTILSKQQCAFIQYTS 258
           ++   +++  T LY+ NL   + EQ+L +    FG+     I   +  + +   F +  S
Sbjct: 9   QMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMES 68

Query: 259 RPAAEAAVEHSFNKVILGGRRLNIKWGR 286
               EA + H FN   +           
Sbjct: 69  TEKCEAVIGH-FNGKFIKTPPGVSAPTE 95

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.0 bits (101), Expect = 2e-06
 Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 2/76 (2%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
           T + V           L   F Q+G I    + +      I+Y S+  A  A+     ++
Sbjct: 5   TWVTVFGFPQASASYILL-QFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSK-DGRI 62

Query: 274 ILGGRRLNIKWGRAQA 289
                 + +K    + 
Sbjct: 63  FGESIMIGVKPCIDKN 78

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 42.8 bits (100), Expect = 3e-06
 Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 10/81 (12%)

Query: 214 TTLYVGNLGDKLT-EQDLRDHFYQFGEIRSVTILS-------KQQCAFIQYTSRPAAEAA 265
             + + NL  +L  E  LR+ F  FG I  + I +          CAF+ + ++ +AE A
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 266 VEHSFNKVILGGRRLNIKWGR 286
           ++   N+ +LG R +++    
Sbjct: 65  LQ--MNRSLLGNREISVSLAD 83

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.7 bits (97), Expect = 8e-06
 Identities = 14/91 (15%), Positives = 32/91 (35%), Gaps = 6/91 (6%)

Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC----AFIQYTSRPA 261
              +  T   +++  L  + TE D+ + F     +R    +         A +++ +   
Sbjct: 8   SSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHED 67

Query: 262 AEAAVEHSFNKVILGGRRLNIKWGRAQANRG 292
           A AA+    +K  +  R + +         G
Sbjct: 68  AVAAMAK--DKANMQHRYVELFLNSTAGTSG 96

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.7 bits (89), Expect = 5e-05
 Identities = 16/74 (21%), Positives = 34/74 (45%), Gaps = 2/74 (2%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL 275
           + +  L   +T Q++ D    + E++   +   +  AF+   +   AEAA+   F++  L
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDY-ELKYCFVDKYKGTAFVTLLNGEQAEAAINT-FHQSRL 58

Query: 276 GGRRLNIKWGRAQA 289
             R L+++     A
Sbjct: 59  RERELSVQLQPTDA 72

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.8 bits (89), Expect = 9e-05
 Identities = 14/86 (16%), Positives = 35/86 (40%), Gaps = 2/86 (2%)

Query: 207 PPEDKTITTLYVGNLGD-KLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAA 265
             + +    +++ NL     ++  +      +G+I++  ++  +  AFI+  +R  A A 
Sbjct: 12  DQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAM 71

Query: 266 VEH-SFNKVILGGRRLNIKWGRAQAN 290
           V+H     +   GR + +        
Sbjct: 72  VDHCLKKALWFQGRCVKVDLSEKYKK 97

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.2 bits (85), Expect = 3e-04
 Identities = 11/77 (14%), Positives = 27/77 (35%), Gaps = 2/77 (2%)

Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL 275
           + V  L    + QDL+DH  + G++    +  +     +++  +     AV    +    
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVCYADV-YRDGTGVVEFVRKEDMTYAVRK-LDNTKF 60

Query: 276 GGRRLNIKWGRAQANRG 292
                   + R + +  
Sbjct: 61  RSHEGETAYIRVKVDGP 77

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.2 bits (80), Expect = 0.002
 Identities = 10/84 (11%), Positives = 26/84 (30%), Gaps = 8/84 (9%)

Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
              ++ N+   +T+ D+           +   +           A +Q+ +   A  +  
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER 68

Query: 268 HSFNKVILGGRRLNIKWGRAQANR 291
              ++  L GR   +     +  R
Sbjct: 69  --LHRKKLNGREAFVHVVTLEDMR 90

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.8 bits (79), Expect = 0.002
 Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 13/78 (16%)

Query: 215 TLYVGNLGDKLTEQDLRDHFY---QFGEIRSVTILSKQQ---------CAFIQYTSRPAA 262
            ++V  L  +L + ++        +FG+I  V I +             A++ Y     A
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 263 EAAVEHSFNKVILGGRRL 280
             A++   N V++ GR L
Sbjct: 70  LRAIQC-VNNVVVDGRTL 86

>d2cqea2 g.66.1.1 (A:429-457) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]} Length = 29

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.9 bits (75), Expect = 0.002
 Identities = 10/23 (43%), Positives = 14/23 (60%)

Query: 143 RPHICSFWVKGECRRGEECPYRH 165
           +  +C F++ G C R E CPY H
Sbjct: 5   KRELCKFYITGFCARAENCPYMH 27

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	327
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.77
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.75
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.75
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.74
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.73
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.73
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.73
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.73
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.72
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.72
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.72
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.72
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.71
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.71
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.71
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.71
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.71
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.7
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.7
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.7
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.7
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.7
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.7
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.69
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.69
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.69
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.69
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.68
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.68
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.68
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.68
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.68
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.68
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.67
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.67
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.67
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.67
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.67
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.67
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.67
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.66
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.66
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.66
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.66
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.66
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.65
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.65
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.65
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.65
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.65
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.64
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.64
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.63
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.63
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.63
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.63
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.63
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.63
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.62
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.62
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.61
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.61
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.61
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.6
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.6
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.6
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.6
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.6
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.59
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.58
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.58
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.55
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.5
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.49
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.48
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.47
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.44
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.42
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.42
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.4
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.39
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.36
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.27
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.26
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.26
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.24
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.9
d2cqea2	29	Zinc finger CCCH domain-containing protein C19orf7	97.87
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.68
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.38
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.02
d1m9oa_	40	Tristetraproline (ttp, tis11, nup475) {Mouse (Mus	95.09
d1rgoa1	36	Butyrate response factor 2 (Tis11D) {Human (Homo s	94.57
d1rgoa2	34	Butyrate response factor 2 (Tis11D) {Human (Homo s	93.67
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	91.36
d1joca1	64	Eea1 {Human (Homo sapiens) [TaxId: 9606]}	90.25
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	86.42
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	82.5
d2cqea1	56	Zinc finger CCCH domain-containing protein C19orf7	82.12

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.1e-18  Score=134.77  Aligned_cols=77  Identities=23%  Similarity=0.558  Sum_probs=73.2

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCC
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQAN  290 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~  290 (327)
                      .++|||+|||.+++|++|+++|++||+|.+|++..++|||||+|.+.++|+.|+.. ++|..++|+.|+|.|+++++.
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~kg~afV~f~~~~~A~~Ai~~-l~~~~i~g~~l~v~~ak~~p~   94 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVS-VNGTTIEGHVVKCYWGKESPD   94 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHH-HTTCEETTEECEEECCCCCCS
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEecceEEEEEECCHHHHHHHHHH-hCCCEECCEEEEEEEcCCCCC
Confidence            47899999999999999999999999999999999999999999999999999998 699999999999999987654

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=7.7e-18  Score=128.21  Aligned_cols=81  Identities=26%  Similarity=0.491  Sum_probs=73.6

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      +...++|||+|||.+++|++|+++|++||.|.++++..+    ++||||+|.+.++|+.|++. ++|..+.|+.|+|.||
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~-l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAA-MNGRKILGKEVKVNWA   83 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHH-HTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            344579999999999999999999999999999999763    78999999999999999997 6999999999999999


Q ss_pred             cCCCCC
Q psy14139        286 RAQANR  291 (327)
Q Consensus       286 k~~~~~  291 (327)
                      +++..+
T Consensus        84 ~~~~~~   89 (90)
T d2cqia1          84 TTPSSQ   89 (90)
T ss_dssp             CCTTCC
T ss_pred             CCCCCC
Confidence            876643

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.75  E-value=3e-18  Score=128.03  Aligned_cols=74  Identities=26%  Similarity=0.473  Sum_probs=69.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      .++|||+|||.++++++|+++|++||.|.++++..+      ++||||+|.+.++|++|++. ++|..+.|+.|+|.|++
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~-lng~~~~g~~l~v~~a~   80 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV-LNGITVRNKRLKVSYAR   80 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHH-HTTCEETTEECEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHH-hCCCEECCEEEEEEEcC
Confidence            478999999999999999999999999999998753      68999999999999999997 69999999999999998


Q ss_pred             C
Q psy14139        287 A  287 (327)
Q Consensus       287 ~  287 (327)
                      |
T Consensus        81 p   81 (82)
T d1b7fa1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
Confidence            6

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=4.9e-18  Score=126.78  Aligned_cols=74  Identities=26%  Similarity=0.470  Sum_probs=69.3

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      .++|||+|||.+++|++|+++|++||.|.++++..+      +|||||+|.+.++|+.|++. ++|..+.|+.|+|.||+
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~-l~g~~~~g~~l~v~~Ak   80 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT-LNGLRLQTKTIKVSYAR   80 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTTCEETTEECEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHH-hCCCEECCEEEEEEEee
Confidence            368999999999999999999999999999999753      57999999999999999997 69999999999999998


Q ss_pred             C
Q psy14139        287 A  287 (327)
Q Consensus       287 ~  287 (327)
                      |
T Consensus        81 P   81 (82)
T d1fxla1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
Confidence            6

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=4.1e-18  Score=129.51  Aligned_cols=79  Identities=27%  Similarity=0.498  Sum_probs=72.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      +.++|||+|||.++++++|+++|++||+|.+++++.+      +|||||+|.+.++|+.|++. ++|..++|+.|+|.|+
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~-l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN-MNESELFGRTIRVNLA   82 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHH-HTTEEETTEEEEEEEC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHH-cCCCEECCEEEEEEEe
Confidence            4579999999999999999999999999999999753      68999999999999999998 6999999999999999


Q ss_pred             cCCCCC
Q psy14139        286 RAQANR  291 (327)
Q Consensus       286 k~~~~~  291 (327)
                      +|+..+
T Consensus        83 ~p~~~k   88 (89)
T d2cqba1          83 KPMRIK   88 (89)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            986543

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=1.4e-17  Score=125.66  Aligned_cols=79  Identities=19%  Similarity=0.330  Sum_probs=73.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCCC
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR  291 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~~  291 (327)
                      ..++|||+|||.++++++|+++|++||.|..+.+...+|||||+|.+.++|+.|+.. ++|..+.|+.|+|.|++|..+.
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~rg~afV~f~~~~~A~~Ai~~-l~~~~i~g~~i~V~~akP~~~~   85 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKA-LNGKVLDGSPIEVTLAKPVDKD   85 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECSSEEEEEESSHHHHHHHHHH-HSSEEETTEEEEEECCCCCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccccEEEEEEeCCHHHHHHHHHH-cCCCEECCEEEEEEeccCCCCC
Confidence            457999999999999999999999999999999999999999999999999999998 6999999999999999987643

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=9.1e-18  Score=128.68  Aligned_cols=78  Identities=24%  Similarity=0.417  Sum_probs=72.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.++++++|+++|++||.|.+++++.+      +|||||+|.+.++|+.|++. ++|..++|+.|+|.||
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~-l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI-MDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHH-SSSCBCSSCBCEEEET
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            3579999999999999999999999999999998763      68999999999999999997 7999999999999999


Q ss_pred             cCCCC
Q psy14139        286 RAQAN  290 (327)
Q Consensus       286 k~~~~  290 (327)
                      +++.+
T Consensus        87 ~~~~~   91 (93)
T d1x5ua1          87 SAHNK   91 (93)
T ss_dssp             TTTSC
T ss_pred             CCCCC
Confidence            98763

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=4.7e-18  Score=126.36  Aligned_cols=75  Identities=29%  Similarity=0.453  Sum_probs=70.6

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      +.++|||+|++  ++|++|+++|++||+|.++.+..+++||||+|.+.++|+.|++. +||..++|+.|+|.|+++++
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~~~~afV~f~~~~~A~~Ai~~-lng~~~~g~~l~V~~a~~~P   78 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAE-LNGTQVESVQLKVNIARKQP   78 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTTTEEEEECSSHHHHHHHHHH-HTTCBCSSCBCEEEECCSSC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccCCCEEEEEEcccHHHHHHHHH-hCCCEECCEEEEEEEecCCC
Confidence            45799999996  89999999999999999999999999999999999999999998 69999999999999998764

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.72  E-value=1.2e-17  Score=126.70  Aligned_cols=78  Identities=21%  Similarity=0.443  Sum_probs=71.3

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      ..+..+|||+|||.++++++|+++|++||+|.+++++.+      +|||||+|.+.++|++|+.. +||..++|+.|+|.
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~-lng~~l~g~~l~V~   82 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA-LNGAEIMGQTIQVD   82 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHH-HTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHH-cCCCEECCEEEEEE
Confidence            345579999999999999999999999999999999864      57999999999999999997 69999999999999


Q ss_pred             eccCC
Q psy14139        284 WGRAQ  288 (327)
Q Consensus       284 ~ak~~  288 (327)
                      |+.++
T Consensus        83 ~a~~k   87 (88)
T d1rk8a_          83 WCFVK   87 (88)
T ss_dssp             ESEEC
T ss_pred             EecCC
Confidence            99876

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=1.1e-17  Score=128.53  Aligned_cols=82  Identities=23%  Similarity=0.508  Sum_probs=73.8

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      .....++|||+|||.+++|++|+++|++||.|.+++|+.+       +|||||+|.+.++|++|++.|.++..+.|++|+
T Consensus         4 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~   83 (94)
T d2cpha1           4 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   83 (94)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEE
Confidence            3455689999999999999999999999999999998652       689999999999999999985599999999999


Q ss_pred             EEeccCCCC
Q psy14139        282 IKWGRAQAN  290 (327)
Q Consensus       282 V~~ak~~~~  290 (327)
                      |.||+++..
T Consensus        84 V~~A~~~~~   92 (94)
T d2cpha1          84 LEWADSEVT   92 (94)
T ss_dssp             EEECCCCCC
T ss_pred             EEEcCCCCC
Confidence            999988753

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=3.6e-18  Score=127.30  Aligned_cols=77  Identities=29%  Similarity=0.416  Sum_probs=71.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCC-eEECCeeEEEEeccCCCCC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNK-VILGGRRLNIKWGRAQANR  291 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g-~~i~G~~L~V~~ak~~~~~  291 (327)
                      .+|||+|||.+++|++|+++|++||.|.++++..++|||||+|.+.++|++|++. +|| ..++|++|+|.|+.|+..+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~rg~aFV~f~~~~~A~~Ai~~-lng~~~~~G~~i~V~~a~~k~~r   79 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIET-LSGKVELHGKIMEVDYSVSKKLR   79 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEETTEEEECCSCHHHHHHHHHH-HTTTCEETTEECEEEECCCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecccceEEEEECCHHHHHHHHHH-hCCCeEECCEEEEEEEcCCcCcC
Confidence            4799999999999999999999999999999999999999999999999999998 687 5799999999999987655

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=4.8e-17  Score=124.54  Aligned_cols=80  Identities=26%  Similarity=0.454  Sum_probs=73.3

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      +...++|||+|||.++++++|+++|++||+|.++++..+    +++|||+|.+.++|++|++. +++..++|+.|+|.||
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~-l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREK-LHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHH-HTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHH-cCCCEECCEEEEEEec
Confidence            344578999999999999999999999999999999874    78999999999999999997 6999999999999999


Q ss_pred             cCCCC
Q psy14139        286 RAQAN  290 (327)
Q Consensus       286 k~~~~  290 (327)
                      +++..
T Consensus        87 ~~r~~   91 (93)
T d2cq3a1          87 TARVM   91 (93)
T ss_dssp             CSSCC
T ss_pred             CcCCC
Confidence            98753

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=1.3e-17  Score=125.95  Aligned_cols=76  Identities=29%  Similarity=0.519  Sum_probs=72.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      .++|||+|||.++++++|+++|++||+|.++++..+++||||+|.+.++|++|++. ++|..++|+.|+|+||.+..
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~k~~afV~f~~~~~A~~A~~~-l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVE-LDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHH-HTTCCBTTBCCEEEESSCCS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecccceEEEEECCHHHHHHHHHH-hCCCEECCEEEEEEECCCcC
Confidence            36899999999999999999999999999999999999999999999999999998 69999999999999998765

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=2.3e-17  Score=126.36  Aligned_cols=77  Identities=30%  Similarity=0.445  Sum_probs=70.7

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.++++++|+++|++||+|.+|.++.+      +|||||+|.+.++|+.|++. ++|..++|++|+|.|+
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~-l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY-INGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-TTTSEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHH-hCCCEECCEEEEEEEc
Confidence            4579999999999999999999999999999999864      57999999999999999997 6999999999999998


Q ss_pred             cCCC
Q psy14139        286 RAQA  289 (327)
Q Consensus       286 k~~~  289 (327)
                      .+..
T Consensus        85 ~~~~   88 (93)
T d1h2vz_          85 AGFK   88 (93)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7543

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.7e-17  Score=126.31  Aligned_cols=77  Identities=26%  Similarity=0.442  Sum_probs=71.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.++++++|+++|++||+|.+++|+.+      +|||||+|.+.++|++|++. ++|..++|+.|+|.|+
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~-l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG-VSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHH-TTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHH-hCCCEECCEEEEEEee
Confidence            3478999999999999999999999999999999864      57999999999999999998 7999999999999999


Q ss_pred             cCCC
Q psy14139        286 RAQA  289 (327)
Q Consensus       286 k~~~  289 (327)
                      +|+.
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            9875

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.8e-17  Score=125.81  Aligned_cols=76  Identities=24%  Similarity=0.507  Sum_probs=71.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      .+|||+|||.++++++|+++|++||.|.+++|..+    +|||||+|.+.++|++|++. ++|..++|+.|+|.|++++.
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~-l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2           9 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK-MNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             TEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTS-SSEEEETTEEEEEEECCCTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHH-cCCCEECCEEEEEEECCCCC
Confidence            58999999999999999999999999999999874    78999999999999999987 79999999999999999876


Q ss_pred             C
Q psy14139        290 N  290 (327)
Q Consensus       290 ~  290 (327)
                      .
T Consensus        88 ~   88 (89)
T d1cvja2          88 E   88 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=4.4e-17  Score=125.18  Aligned_cols=80  Identities=28%  Similarity=0.501  Sum_probs=72.5

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec---CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS---KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~---~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      .....++|||+|||.++++++|+++|++||.|..+.+..   .+++|||+|.+.++|+.|++. +++..+.|++|+|.|+
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~-l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYG-RDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHH-HTTCEETTEECEEECC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHH-hCCCEECCEEEEEEec
Confidence            344557899999999999999999999999999999875   379999999999999999997 6999999999999999


Q ss_pred             cCCC
Q psy14139        286 RAQA  289 (327)
Q Consensus       286 k~~~  289 (327)
                      ++..
T Consensus        89 ~~~r   92 (95)
T d1x4aa1          89 RSGR   92 (95)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8754

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.70  E-value=4.4e-17  Score=133.63  Aligned_cols=81  Identities=23%  Similarity=0.425  Sum_probs=73.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ...++|||+|||.+++|++|+++|++||.|.+|+|+.+      +|||||+|.+.++|+.|++. +||..|+|+.|+|.|
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~-lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG-LNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHH-TTTEECSSCEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHH-hCCCEECCEEEEEEE
Confidence            34578999999999999999999999999999999763      68999999999999999997 799999999999999


Q ss_pred             ccCCCCCC
Q psy14139        285 GRAQANRG  292 (327)
Q Consensus       285 ak~~~~~~  292 (327)
                      ++++..+.
T Consensus       119 a~~~~~~p  126 (139)
T d1u6fa1         119 AASGHQRP  126 (139)
T ss_dssp             SSCCCCCC
T ss_pred             cCCCCCCC
Confidence            98776553

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=7.1e-17  Score=124.86  Aligned_cols=79  Identities=20%  Similarity=0.298  Sum_probs=72.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.++++++|+++|++||.|.+++|+.+      +|||||+|.+.++|+.|++. +++..++|+.|+|.|+
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~-l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE-VDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHH-TTTEESSSCEEEEEEC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHH-cCCCEECCEEEEEEEC
Confidence            3468999999999999999999999999999999763      68999999999999999997 7999999999999999


Q ss_pred             cCCCCC
Q psy14139        286 RAQANR  291 (327)
Q Consensus       286 k~~~~~  291 (327)
                      +++...
T Consensus        86 ~~~~~~   91 (99)
T d1whwa_          86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCCcc
Confidence            987644

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=2.7e-17  Score=122.39  Aligned_cols=72  Identities=28%  Similarity=0.523  Sum_probs=67.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       215 tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      +|||||||.+++|++|+++|++||+|.+++|+.+      +|+|||+|.+.++|+.|++. ++|..++|++|+|.|++.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~-l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT-MNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTT-STTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHH-cCCCEECCEEEEEEEeCC
Confidence            7999999999999999999999999999999864      58999999999999999997 799999999999999863

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=7.9e-17  Score=121.93  Aligned_cols=80  Identities=18%  Similarity=0.253  Sum_probs=73.6

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHh-cCCeEECCeeEEEEeccCC
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHS-FNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~-l~g~~i~G~~L~V~~ak~~  288 (327)
                      .+..++|||+|||.++++++|+++|++||.|.++++..++++|||+|.+.++|+.|++.+ .++..++|++|+|.|++.+
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~   84 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK   84 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCC
Confidence            345689999999999999999999999999999999999999999999999999999864 4688999999999999876


Q ss_pred             C
Q psy14139        289 A  289 (327)
Q Consensus       289 ~  289 (327)
                      .
T Consensus        85 ~   85 (88)
T d2cq1a1          85 E   85 (88)
T ss_dssp             S
T ss_pred             C
Confidence            5

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=3.2e-17  Score=127.70  Aligned_cols=79  Identities=24%  Similarity=0.479  Sum_probs=72.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.++++++|+++|++||.|.++.++.+      +|+|||+|.+.++|+.|++. ++|..+.|+.|+|+|+
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~-lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS-MNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHH-HTTCEETTEECEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHH-hCCCEECCEEEEEEEe
Confidence            3468999999999999999999999999999998763      57999999999999999998 6999999999999999


Q ss_pred             cCCCCC
Q psy14139        286 RAQANR  291 (327)
Q Consensus       286 k~~~~~  291 (327)
                      +++..+
T Consensus        96 ~~k~~~  101 (102)
T d2cpza1          96 RSKNDS  101 (102)
T ss_dssp             CCSCCC
T ss_pred             CCCCCC
Confidence            988653

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=9.5e-17  Score=125.18  Aligned_cols=79  Identities=32%  Similarity=0.538  Sum_probs=71.3

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       209 ~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      .|.+.++|||+|||..++|++|+++|++||+|.+++|+.+      +|||||+|.+.++|++|++. +++ .++|+.|+|
T Consensus         6 ~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~-~~~-~l~Gr~l~V   83 (103)
T d2cqda1           6 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD-PNP-IIDGRKANV   83 (103)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTC-SSC-EETTEECEE
T ss_pred             CCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHH-CCC-cCCCEEEEE
Confidence            4566789999999999999999999999999999999763      78999999999999999986 576 799999999


Q ss_pred             EeccCCC
Q psy14139        283 KWGRAQA  289 (327)
Q Consensus       283 ~~ak~~~  289 (327)
                      .|+.+..
T Consensus        84 ~~a~~~~   90 (103)
T d2cqda1          84 NLAYLGA   90 (103)
T ss_dssp             EESTTTC
T ss_pred             EEcCCCC
Confidence            9998654

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=5.2e-17  Score=126.81  Aligned_cols=78  Identities=23%  Similarity=0.456  Sum_probs=71.4

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      .++|||+|||.++++++|+++|++||+|.++.|..      .+|||||+|.+.++|++|++  +++..|+|+.|.|++++
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~--~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA--ARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT--SCSEEETTEEEEEECCS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH--hCCCeECCEEEEEEECc
Confidence            47999999999999999999999999999999975      37999999999999999986  59999999999999999


Q ss_pred             CCCCCC
Q psy14139        287 AQANRG  292 (327)
Q Consensus       287 ~~~~~~  292 (327)
                      ++...|
T Consensus        98 ~ke~~g  103 (103)
T d1x4ba1          98 AREESG  103 (103)
T ss_dssp             SCCCCC
T ss_pred             ccCCCc
Confidence            887553

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=8.4e-17  Score=124.10  Aligned_cols=78  Identities=35%  Similarity=0.586  Sum_probs=72.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECC--eeEEEEeccCCC
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGG--RRLNIKWGRAQA  289 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G--~~L~V~~ak~~~  289 (327)
                      ..++|||+|||.++++++|+++|++||+|..+++.+++++|||+|.+.++|+.|++. +++..|.|  ++|+|.|+++.+
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~afV~f~~~~~A~~A~~~-l~~~~i~g~~~~l~v~~ak~~~   94 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAK-MRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHH-HTTCBCSSSSCBCEEEECCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeeccccEEEeccCCHHHHHHHHHH-hCCCEeCCCceEEEEEeCCCCC
Confidence            357999999999999999999999999999999999999999999999999999998 69999987  589999999765


Q ss_pred             C
Q psy14139        290 N  290 (327)
Q Consensus       290 ~  290 (327)
                      .
T Consensus        95 ~   95 (97)
T d1whya_          95 S   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=2.9e-17  Score=129.27  Aligned_cols=80  Identities=16%  Similarity=0.276  Sum_probs=74.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQAN  290 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~  290 (327)
                      ++.++|||+|||.++++++|+++|++||+|..|.|...+++|||+|.+.++|++|++. |||..|.|++|+|.|+.....
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~~kg~afV~f~~~~~A~~A~~~-lng~~~~gr~l~v~~a~~~~~   86 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRH-LAYSKFHHVPLYLEWAPIGVF   86 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHH-HTTCBSSSSBCEEEEEETTTT
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeeccCceEEEEEcCHHHHHHHHHH-HcCCccCCCeEEEEECCCCcc
Confidence            4568999999999999999999999999999999999999999999999999999997 699999999999999976554


Q ss_pred             C
Q psy14139        291 R  291 (327)
Q Consensus       291 ~  291 (327)
                      .
T Consensus        87 ~   87 (111)
T d1whxa_          87 G   87 (111)
T ss_dssp             C
T ss_pred             c
Confidence            3

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.3e-17  Score=130.13  Aligned_cols=82  Identities=24%  Similarity=0.471  Sum_probs=73.8

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       208 p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      ..+++.++|||+|||.++++++|+++|++||+|.+|+|+.+      +|||||+|.+.++|+.|++. ++|..+.|+.|+
T Consensus         3 ~~~~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~-l~~~~~~g~~i~   81 (104)
T d1p1ta_           3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN-LNGREFSGRALR   81 (104)
T ss_dssp             CSHHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHH-SSSBSCSSSCBE
T ss_pred             CCCCCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHH-cCCCEECCEEEE
Confidence            34556689999999999999999999999999999998763      57999999999999999997 799999999999


Q ss_pred             EEeccCCCC
Q psy14139        282 IKWGRAQAN  290 (327)
Q Consensus       282 V~~ak~~~~  290 (327)
                      |.|+.++..
T Consensus        82 V~~a~~~~~   90 (104)
T d1p1ta_          82 VDNAASEKN   90 (104)
T ss_dssp             EEETTCTTH
T ss_pred             EEECCCCCC
Confidence            999987643

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.68  E-value=6.8e-17  Score=121.03  Aligned_cols=75  Identities=21%  Similarity=0.374  Sum_probs=68.5

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-CCeEEEEeCCHHHHHHHHHHhcCCeEE-CCeeEEEEecc
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-QQCAFIQYTSRPAAEAAVEHSFNKVIL-GGRRLNIKWGR  286 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-kg~aFV~F~~~~~Ae~A~~~~l~g~~i-~G~~L~V~~ak  286 (327)
                      ++.++|||+|||.++++++|+++|++||.|.+++++.+ +++|||+|.+.++|+.|++. ++|..+ +|++|+|.||+
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~-l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEA-LQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHH-HTTCBSSTTCBCEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHH-hCCcEeCCCcEEEEEEec
Confidence            34579999999999999999999999999999999875 68999999999999999997 688777 56899999997

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.68  E-value=7.1e-17  Score=121.27  Aligned_cols=73  Identities=26%  Similarity=0.469  Sum_probs=67.4

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC---------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK---------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       216 LfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~---------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      |||+|||.++++++|+++|++||+|.++.|..+         +|||||+|.+.++|++|++. ++|..++|+.|+|.|++
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~-~~~~~~~g~~i~V~~a~   79 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQ-LQGHTVDGHKLEVRISE   79 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHH-STTCEETTEECEEECSS
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHH-hCCCEECCEEEEEEECC
Confidence            799999999999999999999999999998752         57999999999999999997 79999999999999986


Q ss_pred             CCC
Q psy14139        287 AQA  289 (327)
Q Consensus       287 ~~~  289 (327)
                      +..
T Consensus        80 ~~~   82 (85)
T d2cpfa1          80 RAT   82 (85)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            543

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.68  E-value=6.2e-17  Score=121.74  Aligned_cols=75  Identities=32%  Similarity=0.532  Sum_probs=68.2

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECC--eeEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGG--RRLN  281 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G--~~L~  281 (327)
                      +.+.++|||+|||.+++|++|+++|++||+|.+++++.+      +|||||+|.+.++|++|++. ++|..+.|  ++|+
T Consensus         3 ~~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~-l~g~~~~g~~~~l~   81 (85)
T d1b7fa2           3 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA-LNNVIPEGGSQPLS   81 (85)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHH-HCCCEeCCCCeEEE
Confidence            345578999999999999999999999999999999864      57999999999999999998 69988877  8899


Q ss_pred             EEec
Q psy14139        282 IKWG  285 (327)
Q Consensus       282 V~~a  285 (327)
                      |+||
T Consensus        82 V~~A   85 (85)
T d1b7fa2          82 VRLA   85 (85)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            9997

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=6.7e-17  Score=120.89  Aligned_cols=76  Identities=30%  Similarity=0.547  Sum_probs=68.4

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeEEE-EEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        216 LYVGNLGDKLTEQDLRDHFYQFGEIRSV-TILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       216 LfVgnLp~~ite~~Lr~~F~~fG~I~~v-~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      |||+|||.+++|++|+++|++||.|.++ +++.+      +|||||+|.+.++|+.|++. ++|..++|++|+|.|+.++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA-MNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHT-TTTCEETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHh-CCCcEECCEEEEEEEecCC
Confidence            7999999999999999999999999664 56542      68999999999999999997 6999999999999999988


Q ss_pred             CCCC
Q psy14139        289 ANRG  292 (327)
Q Consensus       289 ~~~~  292 (327)
                      ..+|
T Consensus        80 ~~kG   83 (83)
T d1x5ta1          80 DSKG   83 (83)
T ss_dssp             CCCC
T ss_pred             CcCC
Confidence            7653

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.68  E-value=7.5e-17  Score=120.03  Aligned_cols=73  Identities=25%  Similarity=0.351  Sum_probs=67.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      +||||+|||.++++++|+++|++||.|..+.++.      .+|||||+|.+.++|++|++. ++|..++|++|+|+|++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~-l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK-LNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHH-HTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHH-hCCCEECCEEEEEEEccC
Confidence            6999999999999999999999999998877754      379999999999999999997 699999999999999987

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=1e-16  Score=124.07  Aligned_cols=84  Identities=32%  Similarity=0.485  Sum_probs=72.2

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEE--------EEec------CCCeEEEEeCCHHHHHHHHHHhcCC
Q psy14139        207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSV--------TILS------KQQCAFIQYTSRPAAEAAVEHSFNK  272 (327)
Q Consensus       207 ~p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v--------~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g  272 (327)
                      |.++...++|||+|||..++|++|+++|++||.|..+        .+..      .+++|||+|.++++|++|++. ++|
T Consensus         2 p~~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~-l~g   80 (101)
T d2cpea1           2 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEW-FDG   80 (101)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHH-HTT
T ss_pred             CCCCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHH-hCC
Confidence            3455677899999999999999999999999998543        2222      268999999999999999997 799


Q ss_pred             eEECCeeEEEEeccCCCCC
Q psy14139        273 VILGGRRLNIKWGRAQANR  291 (327)
Q Consensus       273 ~~i~G~~L~V~~ak~~~~~  291 (327)
                      ..++|+.|+|+|++++..+
T Consensus        81 ~~~~gr~i~V~~a~~~~p~   99 (101)
T d2cpea1          81 KDFQGSKLKVSLARKKPPM   99 (101)
T ss_dssp             CEETTEECEEECSSCCCCS
T ss_pred             CEECCEEEEEEEcCCCCCC
Confidence            9999999999999987654

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=1.6e-16  Score=122.15  Aligned_cols=80  Identities=24%  Similarity=0.452  Sum_probs=71.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhc-----CCeEECCee
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSF-----NKVILGGRR  279 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l-----~g~~i~G~~  279 (327)
                      ...++|||+|||.+++|++|+++|++||.|.++.+..+      +|||||+|.+.++|++|++.+.     +|..++|+.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~   85 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   85 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEE
Confidence            45689999999999999999999999999999998763      7899999999999999999741     478899999


Q ss_pred             EEEEeccCCCC
Q psy14139        280 LNIKWGRAQAN  290 (327)
Q Consensus       280 L~V~~ak~~~~  290 (327)
                      |+|.|++++..
T Consensus        86 l~v~~a~~k~~   96 (98)
T d1x4ha1          86 LKVDLAVTRDE   96 (98)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCCc
Confidence            99999998653

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=8.6e-17  Score=121.05  Aligned_cols=72  Identities=29%  Similarity=0.516  Sum_probs=66.3

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECC--eeEEEEe
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGG--RRLNIKW  284 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G--~~L~V~~  284 (327)
                      .++|||+|||.++++++|+++|++||+|.+++++.+      +|||||+|.+.++|+.|++. +||..+.|  ++|+|+|
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~-lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG-LNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTTCCCTTCSSCCEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHH-hCCCEeCCCCEEEEEEe
Confidence            478999999999999999999999999999999863      57999999999999999998 69999998  5699999


Q ss_pred             c
Q psy14139        285 G  285 (327)
Q Consensus       285 a  285 (327)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.4e-16  Score=123.20  Aligned_cols=77  Identities=23%  Similarity=0.418  Sum_probs=69.2

Q ss_pred             CCccEEEEcCCC-CCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        211 KTITTLYVGNLG-DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       211 ~~~~tLfVgnLp-~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      ...++|||+||+ ..+++++|+++|++||.|.+++|.  ++||||+|.+.++|++|++. +||..+.|+.|+|.|++++.
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--rg~aFV~f~~~~~A~~Ai~~-lng~~~~g~~l~V~~a~~~~   89 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--KGFAFVQYVNERNARAAVAG-EDGRMIAGQVLDINLAAEPK   89 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--TEEEEEEESSHHHHHHHHHT-TTTCEETTEECEEEETTSCC
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--CCeEEEEECCHHHHHHHHHH-cCCCEECCEEEEEEECCCCC
Confidence            345689999997 578889999999999999999985  89999999999999999997 79999999999999998654


Q ss_pred             C
Q psy14139        290 N  290 (327)
Q Consensus       290 ~  290 (327)
                      .
T Consensus        90 ~   90 (98)
T d1wf2a_          90 V   90 (98)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=6.8e-17  Score=121.67  Aligned_cols=76  Identities=20%  Similarity=0.488  Sum_probs=70.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      .+|||+|||.+++|++|+++|++||+|.+++|+.+      ++||||+|.+.++|+.|++. ++|..++|++|+|.|+++
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~-l~~~~l~g~~l~V~~A~~   80 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG-LNGMQLGDKKLLVQRASV   80 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHT-SSSCCCSSSCCEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHH-hCCCEECCEEEEEEECCC
Confidence            37999999999999999999999999999999863      79999999999999999997 799999999999999987


Q ss_pred             CCC
Q psy14139        288 QAN  290 (327)
Q Consensus       288 ~~~  290 (327)
                      ..+
T Consensus        81 ~~~   83 (85)
T d2u2fa_          81 GAK   83 (85)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=1.6e-16  Score=117.65  Aligned_cols=72  Identities=25%  Similarity=0.446  Sum_probs=67.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       215 tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      +|||+|||.++++++|+++|++||.|.++++..+     +|+|||+|.+.++|+.|++. +||..++|++|+|+++.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~-l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ-YNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHH-HTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHH-hCCCEECCEEEEEEEeeC
Confidence            6999999999999999999999999999999864     68999999999999999997 699999999999999864

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1e-16  Score=121.74  Aligned_cols=77  Identities=22%  Similarity=0.424  Sum_probs=70.8

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      ..+|||+|||.++++++|+++|++||.|..+.++.+      +|||||+|.+.++|+.|++. ++|..++|+.|+|.|+.
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA-MNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHH-HTTCCTTSCCCEEEEEE
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHH-cCCCEECCEEEEEEEcC
Confidence            368999999999999999999999999999988762      78999999999999999997 69999999999999998


Q ss_pred             CCCC
Q psy14139        287 AQAN  290 (327)
Q Consensus       287 ~~~~  290 (327)
                      ++..
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=2.1e-16  Score=120.35  Aligned_cols=77  Identities=25%  Similarity=0.392  Sum_probs=69.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.+++|++|+++|++||.|.+++|+.+      +|||||+|.+.++|++|++.   ...++|+.|+|+|+
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~---~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ---RHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS---CEEETTEEEEEECC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc---CCccCCEEeEEEeC
Confidence            4479999999999999999999999999999999864      68999999999999999974   45899999999999


Q ss_pred             cCCCCC
Q psy14139        286 RAQANR  291 (327)
Q Consensus       286 k~~~~~  291 (327)
                      .++..+
T Consensus        84 ~~k~~~   89 (90)
T d2cqga1          84 NSKQSQ   89 (90)
T ss_dssp             CTTCCC
T ss_pred             CCCCCC
Confidence            887643

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=2.2e-16  Score=125.04  Aligned_cols=77  Identities=25%  Similarity=0.393  Sum_probs=71.1

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC---CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCC
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK---QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~---kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~  288 (327)
                      ..++|||+|||.++++++|+++|++||.|.+|++..+   +|||||+|.+.++|..|++. ++|..|.|+.|+|.|+.+.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~-l~g~~~~gr~l~V~~a~~~   84 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH-LSGFNVCNRYLVVLYYNAN   84 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHH-HTTCEETTEECEEEECCHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHH-hCCCEECCEEEEEEEcCCC
Confidence            3579999999999999999999999999999999864   78999999999999999998 6999999999999999764


Q ss_pred             C
Q psy14139        289 A  289 (327)
Q Consensus       289 ~  289 (327)
                      .
T Consensus        85 ~   85 (114)
T d2f9da1          85 R   85 (114)
T ss_dssp             H
T ss_pred             c
Confidence            3

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=2.3e-16  Score=118.48  Aligned_cols=74  Identities=23%  Similarity=0.471  Sum_probs=67.6

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||+|||.++++++|+++|++||.|.+++|+.+      +|||||+|.+.++|++|++  +++..|+|+.|+|+.|
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~--~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN--ARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH--TCSCEETTEECEEEEC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH--hCCCEECCEEEEEEee
Confidence            4479999999999999999999999999999999764      6899999999999999997  4888999999999887


Q ss_pred             cC
Q psy14139        286 RA  287 (327)
Q Consensus       286 k~  287 (327)
                      .+
T Consensus        83 ~s   84 (84)
T d1l3ka1          83 VS   84 (84)
T ss_dssp             CC
T ss_pred             eC
Confidence            53

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=2.1e-16  Score=123.95  Aligned_cols=77  Identities=29%  Similarity=0.402  Sum_probs=70.1

Q ss_pred             ccEEEEcCCCC-CCCHHHHHHHHhhcCCeEEEEEecC-CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCC
Q psy14139        213 ITTLYVGNLGD-KLTEQDLRDHFYQFGEIRSVTILSK-QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQAN  290 (327)
Q Consensus       213 ~~tLfVgnLp~-~ite~~Lr~~F~~fG~I~~v~i~~~-kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~  290 (327)
                      .++|||+||++ .++|++|+++|++||.|.++.|+.+ +|+|||+|.+.++|++|++. ++|..|.|+.|+|.|++....
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~ai~~-lng~~l~g~~l~v~~s~~~~~   80 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSH-LNGHKLHGKPIRITLSKHQNV   80 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHH-HTTCBCSSSBCEEECCSCCCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHH-hCCCEECCEEEEEEECCCCCC
Confidence            47999999965 6999999999999999999999876 68999999999999999997 699999999999999986543

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.66  E-value=1.4e-16  Score=122.59  Aligned_cols=80  Identities=25%  Similarity=0.363  Sum_probs=72.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEe-cCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-SKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~-~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      ...++|||+|||.++++++|+++|++||.|..+... ..++||||+|.+.++|++|++. ++|..++|++|+|.|+.++.
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~-l~~~~~~gr~i~V~~a~~k~   92 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEE-KQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHH-TTEEEETTEEEEEEECSSSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHH-cCCCEECCEEEEEEEeCCCC
Confidence            456899999999999999999999999998877654 3489999999999999999997 79999999999999999887


Q ss_pred             CC
Q psy14139        290 NR  291 (327)
Q Consensus       290 ~~  291 (327)
                      ..
T Consensus        93 ~~   94 (96)
T d1fjca_          93 GT   94 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=9.6e-17  Score=121.56  Aligned_cols=78  Identities=23%  Similarity=0.444  Sum_probs=70.0

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec-CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCC
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS-KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQAN  290 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~-~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~  290 (327)
                      ..++|||+|||.+++|++|+++|++||.|.++++.. .++||||+|.+.++|++|+.   ++..|+|+.|+|.|++++..
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~---~~~~i~g~~l~v~~a~~k~~   80 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG---EDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT---CEEEETTEEEEEECCCCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh---CCCEECCEEeEEEeCCCCCC
Confidence            357999999999999999999999999999998776 48999999999999999874   78899999999999988765


Q ss_pred             CC
Q psy14139        291 RG  292 (327)
Q Consensus       291 ~~  292 (327)
                      ..
T Consensus        81 ~~   82 (88)
T d1wf0a_          81 SN   82 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.65  E-value=2e-16  Score=119.25  Aligned_cols=75  Identities=28%  Similarity=0.563  Sum_probs=67.2

Q ss_pred             ccEEEEcCCCCCCC-HHHHHHHHhhcCCeEEEEEec-------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        213 ITTLYVGNLGDKLT-EQDLRDHFYQFGEIRSVTILS-------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       213 ~~tLfVgnLp~~it-e~~Lr~~F~~fG~I~~v~i~~-------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      .++|||+|||.+++ |++|+++|++||+|.+++|..       .+|+|||+|.+.++|++|++  +|+..++|+.|+|.|
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~--~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ--MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG--GTTEEETTEEEEEEE
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh--cCCCEECCEEEEEEE
Confidence            47999999999875 667999999999999999864       26899999999999999995  699999999999999


Q ss_pred             ccCCC
Q psy14139        285 GRAQA  289 (327)
Q Consensus       285 ak~~~  289 (327)
                      +++++
T Consensus        82 a~~kP   86 (86)
T d2ghpa3          82 ADKKP   86 (86)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98764

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.65  E-value=3.3e-16  Score=115.07  Aligned_cols=72  Identities=21%  Similarity=0.359  Sum_probs=67.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCC
Q psy14139        216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       216 LfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~  289 (327)
                      |||+|||.++++++|+++|++|| +..+.+...+++|||+|.+.++|++|++. +||..++|++|+|+|++.+.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~~~~g~afv~f~~~~~A~~Ai~~-ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINT-FHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHH-HTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecccceeEEEEECCHHHHHHHHHH-hCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999999 78888889999999999999999999998 69999999999999997654

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.65  E-value=3.3e-16  Score=121.07  Aligned_cols=83  Identities=19%  Similarity=0.323  Sum_probs=75.0

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       207 ~p~d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      ||...+..+|||+|||.++++++|+++|++||+|.++.+. .++||||+|.+.++|++|++. |||..++|+.|+|.+.+
T Consensus         9 p~~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~-~~g~afV~f~~~~~a~~Ai~~-lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_           9 PPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ-KDGMGMVEYLRKEDMEYALRK-LDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             CCCCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE-TTTEEEEEESSHHHHHHHHHH-HSSEEEECTTSCEEEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhhccccccccc-ccceEEEEECCHHHHHHHHHH-hCCCEeCCeEEEEEEEe
Confidence            4555666799999999999999999999999999999986 469999999999999999997 79999999999999998


Q ss_pred             CCCCC
Q psy14139        287 AQANR  291 (327)
Q Consensus       287 ~~~~~  291 (327)
                      ++..+
T Consensus        87 ~~~~~   91 (98)
T d1wg4a_          87 VYPER   91 (98)
T ss_dssp             EECCC
T ss_pred             cCCCC
Confidence            76654

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=2.6e-16  Score=119.16  Aligned_cols=76  Identities=17%  Similarity=0.301  Sum_probs=69.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCC
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQAN  290 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~  290 (327)
                      .++|||+|||.++++++|+++|++|| +..+.+...+++|||+|.+.++|++|++. +++..++|+.|+|+|++++..
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~~~kg~afV~f~~~~~A~~Ai~~-ln~~~~~G~~l~V~~a~~~~~   80 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQM-FHQYSFRGKDLIVQLQPTDAL   80 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEGGGTEEEECCSCHHHHHHHHHH-HTTEEETTEEEEEEECCCCCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeeccCCceEEEECCHHHHHHHHHH-hCCCEECCEEEEEEEcCCCCC
Confidence            46899999999999999999999999 55567777899999999999999999998 799999999999999976643

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=3.2e-16  Score=119.31  Aligned_cols=76  Identities=20%  Similarity=0.452  Sum_probs=69.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHH----HHhhcCCeEEEEEec---CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        213 ITTLYVGNLGDKLTEQDLRD----HFYQFGEIRSVTILS---KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~----~F~~fG~I~~v~i~~---~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      .++|||+|||.++++++|++    +|++||+|.+|++..   .+|+|||+|.+.++|..|++. ++|..++|+.|+|.||
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~-~~~~~~~g~~l~v~~a   81 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS-MQGFPFYDKPMRIQYA   81 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHH-HTTCEETTEECEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHH-hCCCEECCEEEEEEEe
Confidence            47999999999999998864    689999999999875   389999999999999999997 6999999999999999


Q ss_pred             cCCC
Q psy14139        286 RAQA  289 (327)
Q Consensus       286 k~~~  289 (327)
                      +++.
T Consensus        82 k~~~   85 (91)
T d1nu4a_          82 KTDS   85 (91)
T ss_dssp             SSCC
T ss_pred             CCCc
Confidence            8765

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=4.4e-16  Score=117.68  Aligned_cols=75  Identities=21%  Similarity=0.261  Sum_probs=67.7

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec--CCCeEEEEeCCHHHHHHHHHHhcCCeEE-CCeeEEEEeccCC
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS--KQQCAFIQYTSRPAAEAAVEHSFNKVIL-GGRRLNIKWGRAQ  288 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~--~kg~aFV~F~~~~~Ae~A~~~~l~g~~i-~G~~L~V~~ak~~  288 (327)
                      .++|||+|||.++++++|+++|++||.|..+.+..  ++++|||+|.+.++|.+|+.. ++|..+ +|+.|+|.|++++
T Consensus        10 s~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~-l~~~~i~~g~~l~v~~sk~~   87 (88)
T d2adca2          10 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALID-LHNHDLGENHHLRVSFSKST   87 (88)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHH-HTTCBSSSSCBCEEEECSSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHh-ccCCEecCCCEEEEEeCCCC
Confidence            46999999999999999999999999998887764  478999999999999999997 688777 6899999999864

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=6.4e-16  Score=115.50  Aligned_cols=70  Identities=33%  Similarity=0.440  Sum_probs=64.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      ..++|||+|||.+++|++|+++|++||.|.+++|+.+      +|+|||+|.+.++|+.|+++ ++|..++|+.|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~-l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER-ANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHH-HTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHH-cCCCEECCEEeEC
Confidence            3579999999999999999999999999999998764      57999999999999999997 6999999999987

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=6.2e-16  Score=114.34  Aligned_cols=71  Identities=21%  Similarity=0.485  Sum_probs=65.7

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      .++|||||||.++++++|+++|++||.|..+.+..+      +|+|||+|.+.++|++|++  ++|..|+|+.|+|+.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~--~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI--QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH--CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH--hCCCEECCEEEEEEEC
Confidence            579999999999999999999999999999998763      6899999999999999986  5999999999999875

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=1.3e-15  Score=118.78  Aligned_cols=80  Identities=18%  Similarity=0.294  Sum_probs=72.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHh-cCCeEECCeeEEEEeccCCC
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHS-FNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~-l~g~~i~G~~L~V~~ak~~~  289 (327)
                      ...++|||+|||.+++|++|+++|++||.|.++++.+++++|||+|.+.++|+.|+..+ .++..+.|++|+|.|++.+.
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~~   92 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKR   92 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCCc
Confidence            44579999999999999999999999999999999999999999999999999999864 36788999999999998754


Q ss_pred             C
Q psy14139        290 N  290 (327)
Q Consensus       290 ~  290 (327)
                      .
T Consensus        93 ~   93 (104)
T d1wexa_          93 I   93 (104)
T ss_dssp             C
T ss_pred             c
Confidence            3

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=4.6e-16  Score=121.55  Aligned_cols=79  Identities=10%  Similarity=0.154  Sum_probs=71.1

Q ss_pred             CccEEEEcCCCCCC-C----HHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        212 TITTLYVGNLGDKL-T----EQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       212 ~~~tLfVgnLp~~i-t----e~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      ...+|||+||+.++ +    +++|+++|++||.|.++++++.+++|||+|.+.++|++|++. +||..|+|++|+|.|++
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~~~~afV~f~~~~~A~~Ai~~-lng~~~~g~~l~v~~a~   82 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLR-LHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHT-STTSEETTEECEEECCC
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecCCCEEEEEECCHHHHHHHHHH-hcccccCCCEeEEeecc
Confidence            34799999999875 3    357999999999999999999999999999999999999998 79999999999999998


Q ss_pred             CCCCC
Q psy14139        287 AQANR  291 (327)
Q Consensus       287 ~~~~~  291 (327)
                      ++...
T Consensus        83 ~~~~~   87 (104)
T d1weya_          83 TLHIG   87 (104)
T ss_dssp             CSSCC
T ss_pred             cCCCC
Confidence            77544

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=7.9e-17  Score=125.34  Aligned_cols=76  Identities=21%  Similarity=0.406  Sum_probs=69.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ...++|||+|||.+++|++|+++|++||+|.+++++.+      +|||||+|.+.++|++|++  ++|..+.|+.|+|++
T Consensus        16 ~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~--l~g~~~~G~~l~V~~   93 (101)
T d2cq4a1          16 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG--LTGQRLLGVPIIVQA   93 (101)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH--HTTEEETTEEEEEEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH--HCCCEECCEEEEEEE
Confidence            34579999999999999999999999999999999863      6899999999999999995  699999999999999


Q ss_pred             ccCC
Q psy14139        285 GRAQ  288 (327)
Q Consensus       285 ak~~  288 (327)
                      ++++
T Consensus        94 a~~~   97 (101)
T d2cq4a1          94 SQAE   97 (101)
T ss_dssp             HHHH
T ss_pred             CCCC
Confidence            8764

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.63  E-value=1.4e-16  Score=121.55  Aligned_cols=77  Identities=14%  Similarity=0.319  Sum_probs=69.0

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec-----CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS-----KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~-----~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      .....+|||+|||.++++++|+++|++||.|.++.|+.     .+|||||+|.+.++|++|++  ++|..++|+.|+|.|
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~--~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE--LTGLKVFGNEIKLEK   87 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH--GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh--cCCcEECCEEEEEEe
Confidence            34457999999999999999999999999988877654     47999999999999999995  599999999999999


Q ss_pred             ccCC
Q psy14139        285 GRAQ  288 (327)
Q Consensus       285 ak~~  288 (327)
                      ++++
T Consensus        88 ak~k   91 (91)
T d1fjeb1          88 PKGR   91 (91)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            9864

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=1.2e-16  Score=120.85  Aligned_cols=75  Identities=15%  Similarity=0.259  Sum_probs=68.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEeccCCCCC
Q psy14139        215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR  291 (327)
Q Consensus       215 tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak~~~~~  291 (327)
                      +|||+|||.++++++|+++|++||+|.++.+.. .|||||+|.+.++|++|++. ++|..+.|+.|+|.+++++...
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-~g~afV~f~~~~~a~~Ai~~-l~g~~~~g~~i~v~~~~~~~~~   76 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-DGTGVVEFVRKEDMTYAVRK-LDNTKFRSHEGETAYIRVKVDG   76 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-TSEEEEEESSHHHHHHHHHH-HTTCBCCCTTSCCCBCEEEECC
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhcccccccccc-cceeeEEeCCHHHHHHHHHH-hCCCEECCcEeEEeEEecCcCC
Confidence            699999999999999999999999999999765 49999999999999999997 6999999999999888765543

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=5.8e-16  Score=118.96  Aligned_cols=79  Identities=18%  Similarity=0.418  Sum_probs=68.9

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCC-eEEEEEec-------CCCeEEEEeCCHHHHHHHHHHhc-CCeEECCeeEEEE
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGE-IRSVTILS-------KQQCAFIQYTSRPAAEAAVEHSF-NKVILGGRRLNIK  283 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~-I~~v~i~~-------~kg~aFV~F~~~~~Ae~A~~~~l-~g~~i~G~~L~V~  283 (327)
                      +++|||||||.++++++|+++|++||+ |.++.+..       ++|||||+|.+.++|+.|++.|. ++..+.|+.|+|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            368999999999999999999999996 89999865       36899999999999999998742 3567789999999


Q ss_pred             eccCCCCC
Q psy14139        284 WGRAQANR  291 (327)
Q Consensus       284 ~ak~~~~~  291 (327)
                      ||+|+...
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99886644

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.62  E-value=4.5e-16  Score=120.48  Aligned_cols=79  Identities=18%  Similarity=0.294  Sum_probs=71.6

Q ss_pred             CCccEEEEcCCCCC-CCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHh-cCCeEECCeeEEEEeccCC
Q psy14139        211 KTITTLYVGNLGDK-LTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHS-FNKVILGGRRLNIKWGRAQ  288 (327)
Q Consensus       211 ~~~~tLfVgnLp~~-ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~-l~g~~i~G~~L~V~~ak~~  288 (327)
                      ...++|||+|||.+ +++++|+++|++||.|.++.++.++++|||+|.+.++|+.|++.+ +++..++|+.|+|.|++..
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~~   95 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKY   95 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSC
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCCc
Confidence            44579999999975 899999999999999999999999999999999999999999742 5889999999999999765


Q ss_pred             C
Q psy14139        289 A  289 (327)
Q Consensus       289 ~  289 (327)
                      .
T Consensus        96 ~   96 (99)
T d1x4fa1          96 K   96 (99)
T ss_dssp             S
T ss_pred             c
Confidence            4

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=1.7e-16  Score=123.12  Aligned_cols=78  Identities=31%  Similarity=0.430  Sum_probs=71.3

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      .++|||+|||.++++++|+++|++||.|..+.+..      .++||||+|.+.++|+.|++. ++|..+.|++|+|.|++
T Consensus        18 s~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~-l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          18 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL-VNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHH-STTCBCSSCBCEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHH-hCCCEECCEEEEEEeCC
Confidence            47999999999999999999999999998877654      479999999999999999997 79999999999999999


Q ss_pred             CCCCC
Q psy14139        287 AQANR  291 (327)
Q Consensus       287 ~~~~~  291 (327)
                      ++..+
T Consensus        97 ~k~~r  101 (102)
T d2cpxa1          97 NKKQR  101 (102)
T ss_dssp             CCSCC
T ss_pred             CcccC
Confidence            87654

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.61  E-value=9e-16  Score=116.47  Aligned_cols=78  Identities=21%  Similarity=0.225  Sum_probs=71.2

Q ss_pred             CccEEEEcCCCCC-CCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHh-cCCeEECCeeEEEEeccCCC
Q psy14139        212 TITTLYVGNLGDK-LTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHS-FNKVILGGRRLNIKWGRAQA  289 (327)
Q Consensus       212 ~~~tLfVgnLp~~-ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~-l~g~~i~G~~L~V~~ak~~~  289 (327)
                      ..++|||+|||.. +++++|.++|++||.|.++.+..++++|||+|.+.++|+.|++.+ .++..++|++|+|.|+++..
T Consensus         7 ~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~~~   86 (89)
T d1x4da1           7 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYK   86 (89)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCT
T ss_pred             CCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCCcc
Confidence            3479999999985 889999999999999999999999999999999999999999864 47889999999999998654

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=2.6e-16  Score=122.19  Aligned_cols=76  Identities=26%  Similarity=0.355  Sum_probs=68.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ...++|||+|||.++++++|+++|++||.|.++.+..+     +|||||+|.+.++|++|++. +||..|.|+++.|.|+
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~-lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH-FNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHH-HBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHH-hCCCEECCcCCccCCC
Confidence            34579999999999999999999999999999988764     67999999999999999997 6999999999988777


Q ss_pred             cC
Q psy14139        286 RA  287 (327)
Q Consensus       286 k~  287 (327)
                      +|
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.60  E-value=3e-16  Score=115.91  Aligned_cols=70  Identities=19%  Similarity=0.452  Sum_probs=65.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ++|||+|||.+++|++|+++|++||.|.+++|+.+      +|+|||+|.+.++|++|++  +++..++|+.|+|++|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~--~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA--QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH--TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH--cCCCEECCeEEEEEEC
Confidence            47999999999999999999999999999999763      6999999999999999997  4999999999999876

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.5e-15  Score=119.21  Aligned_cols=80  Identities=20%  Similarity=0.260  Sum_probs=70.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec--CCCeEEEEeCCHHHHHHHHHHhcCCeEE--CCeeEEEEecc
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS--KQQCAFIQYTSRPAAEAAVEHSFNKVIL--GGRRLNIKWGR  286 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~--~kg~aFV~F~~~~~Ae~A~~~~l~g~~i--~G~~L~V~~ak  286 (327)
                      ....+|||+|||.+++|++|+++|++||.|.++.+..  ++|+|||+|.+.++|+.|+.. ++|..|  .|+.|+|.|++
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~-ln~~~l~~~~~~l~v~~s~   83 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLS-LDGQNIYNACCTLRIDFSK   83 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHH-HHSCCSSTTCCCCEEEECS
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHH-HCCCEeccCCcEEEEEecC
Confidence            3457899999999999999999999999999998876  468999999999999999998 688877  46899999998


Q ss_pred             CCCCC
Q psy14139        287 AQANR  291 (327)
Q Consensus       287 ~~~~~  291 (327)
                      ++...
T Consensus        84 ~~~~~   88 (108)
T d2adba1          84 LTSLN   88 (108)
T ss_dssp             SCSCC
T ss_pred             Ccccc
Confidence            76543

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=9.8e-16  Score=112.45  Aligned_cols=68  Identities=22%  Similarity=0.466  Sum_probs=62.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       215 tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      .|||+|||.+++|++|+++|++||+|.++.+..+      +|||||+|.+.++|++|++  +++..++|+.|+|+.
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~--~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD--QKEHKLNGKVIDPKR   74 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH--TCCCCBTTBCCEECC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh--cCCCEECCCEEEeeE
Confidence            4899999999999999999999999999998763      6999999999999999997  488899999999964

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.7e-15  Score=113.82  Aligned_cols=73  Identities=15%  Similarity=0.230  Sum_probs=67.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      ..++|||+|||.++++++|+++|+.||.|.+++|..+     +|+|||+|.+.++|++|++  +++..+.|+.|+|+|.+
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~--~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE--TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT--CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH--HCCCEECCEEEEEEEcC
Confidence            3479999999999999999999999999999999764     5899999999999999996  59999999999999965

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.60  E-value=8.6e-16  Score=112.28  Aligned_cols=69  Identities=20%  Similarity=0.393  Sum_probs=64.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       215 tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      .|||||||.+++|++|+++|++||.|..+.+..+      +++|||+|.+.++|++|++  ++|..++|+.|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~--~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE--IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH--CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh--cCCCEECCeEEEEEEC
Confidence            4899999999999999999999999999988653      6899999999999999996  6999999999999986

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=5e-15  Score=115.18  Aligned_cols=77  Identities=18%  Similarity=0.393  Sum_probs=67.4

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..+|||+|||.+++|++|+++|++|| |.+++++.+       +++|||+|.+.++|++|++  +++..|+|+.|+|.|+
T Consensus        15 ~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~--~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          15 PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS--LNEESLGNKRIRVDVA   91 (104)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG--GGTCEETTEECEEEEC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH--cCCCEECCEEEEEEEC
Confidence            47999999999999999999999999 777777642       5799999999999987664  6999999999999999


Q ss_pred             cCCCCCC
Q psy14139        286 RAQANRG  292 (327)
Q Consensus       286 k~~~~~~  292 (327)
                      +++..+.
T Consensus        92 ~~~~~~~   98 (104)
T d1wi8a_          92 DQAQDKD   98 (104)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9876553

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.58  E-value=3.5e-15  Score=109.52  Aligned_cols=70  Identities=21%  Similarity=0.266  Sum_probs=64.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ++|||+|||.++++++|+++|++||.|.++++..+    +++|||+|.+.++|++|+.  +++..|+|++|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~--~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT--KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT--TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH--hcCcEECCEEEEEEEC
Confidence            58999999999999999999999999999999864    5799999999999999985  5999999999999753

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=1.2e-15  Score=112.12  Aligned_cols=69  Identities=23%  Similarity=0.418  Sum_probs=63.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       215 tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      +|||||||.++++++|+++|++||.|.+++|+.+      +|||||+|.+.++|++|++  .++..++|+.|.|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~--~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME--KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT--CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh--hCCCEECCEEeEEEEC
Confidence            5899999999999999999999999999998764      6999999999999999997  3778899999999764

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=3.9e-15  Score=112.82  Aligned_cols=69  Identities=26%  Similarity=0.509  Sum_probs=63.5

Q ss_pred             cEEEEcCCCCCCCHHHH---HHHHhhcCCeEEEEEecC---------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        214 TTLYVGNLGDKLTEQDL---RDHFYQFGEIRSVTILSK---------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~L---r~~F~~fG~I~~v~i~~~---------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      ++|||+|||.++++++|   +++|++||+|.++.+..+         +++|||+|.+.++|++|++. +||..++|+.|+
T Consensus         9 n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~-lng~~~~gr~lk   87 (89)
T d2cpia1           9 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQC-VNNVVVDGRTLK   87 (89)
T ss_dssp             SCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHH-HTTEEETTEEEE
T ss_pred             CEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHH-hCCCEECCEEEE
Confidence            57999999999999999   678999999999999863         37999999999999999998 699999999999


Q ss_pred             EE
Q psy14139        282 IK  283 (327)
Q Consensus       282 V~  283 (327)
                      |.
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            84

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=6e-15  Score=107.03  Aligned_cols=65  Identities=25%  Similarity=0.356  Sum_probs=60.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEE
Q psy14139        216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLN  281 (327)
Q Consensus       216 LfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~  281 (327)
                      |||+|||.++++++|+++|++||.|.++++..+      +|+|||+|.+.++|++|++. +||..++|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~-lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA-LKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHH-HHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHH-hCCCEECCEECc
Confidence            799999999999999999999999999988763      79999999999999999998 799999998764

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.49  E-value=3.7e-14  Score=106.32  Aligned_cols=74  Identities=26%  Similarity=0.371  Sum_probs=65.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEE-EEEec-----CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRS-VTILS-----KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~-v~i~~-----~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      +..++|||+|||.++++++|+++|+.||.|.. +.+..     .+|+|||+|.+.++|++|++. +++..++|++|+|++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~-l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID-LNDRPIGSRKVKLVL   85 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHH-TTTCEETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            34578999999999999999999999999865 34443     268999999999999999997 799999999999987


Q ss_pred             c
Q psy14139        285 G  285 (327)
Q Consensus       285 a  285 (327)
                      |
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            5

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=9e-14  Score=108.06  Aligned_cols=80  Identities=19%  Similarity=0.188  Sum_probs=68.8

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~------~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      ......|||+|||.+++|++|+++|..+|.|....++.      .+|+|||+|.+.++|++|++  +++..|.|+.|+|.
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~--~~~~~i~gR~i~V~   89 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK--KHKERIGHRYIEIF   89 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT--TTTCCSSSSCCEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh--hCCCEEcceEEEEE
Confidence            34456899999999999999999999999988755443      26999999999999999886  59999999999999


Q ss_pred             eccCCCCC
Q psy14139        284 WGRAQANR  291 (327)
Q Consensus       284 ~ak~~~~~  291 (327)
                      ++.+...+
T Consensus        90 ~~~~~~~~   97 (104)
T d1wg5a_          90 KSSRAEVR   97 (104)
T ss_dssp             EECTTTSC
T ss_pred             ECCHHHhc
Confidence            99877544

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=4.5e-14  Score=109.42  Aligned_cols=79  Identities=19%  Similarity=0.190  Sum_probs=67.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ....+|||+|||.+++|++|+++|..||. ..+.++.+     +|+|||+|.+.++|++|++  +++..|+|+.|+|.|+
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~--~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA--KDKANMQHRYVELFLN   89 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT--TSSCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEecCCcceEEEEEEECCHHHHHHHHH--cCCCEECCEEEEEEEc
Confidence            44569999999999999999999999985 45666543     6899999999999999986  5999999999999999


Q ss_pred             cCCCCCC
Q psy14139        286 RAQANRG  292 (327)
Q Consensus       286 k~~~~~~  292 (327)
                      .+.....
T Consensus        90 ~~~~~~~   96 (102)
T d1weza_          90 STAGTSG   96 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            8776543

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=1.2e-13  Score=106.97  Aligned_cols=75  Identities=15%  Similarity=0.146  Sum_probs=65.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEE-EEEec-----CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRS-VTILS-----KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~-v~i~~-----~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      ...++|||+|||.++++++|+++|+.||.|.. +.+..     .+|+|||+|.+.++|++|++  +++..|+|+.|.|.+
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~--~n~~~i~gr~i~V~~   83 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER--LHRKKLNGREAFVHV   83 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG--GCSEEETTEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh--cCCCeECCcEEEEEE
Confidence            44578999999999999999999999999876 44443     37999999999999999996  699999999999998


Q ss_pred             ccC
Q psy14139        285 GRA  287 (327)
Q Consensus       285 ak~  287 (327)
                      +..
T Consensus        84 ~~~   86 (103)
T d2cpya1          84 VTL   86 (103)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            754

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=9.2e-14  Score=109.76  Aligned_cols=74  Identities=20%  Similarity=0.309  Sum_probs=64.7

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCH-HHHHHHHHHhcCCeEECCeeEEEEeccC
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSR-PAAEAAVEHSFNKVILGGRRLNIKWGRA  287 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~-~~Ae~A~~~~l~g~~i~G~~L~V~~ak~  287 (327)
                      ...+||||||.++|+++|+++|++||+|.+|.|+.+++||||+|.++ ++|..|+.. +++..+.++.+.|.|+..
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~kg~gfV~F~~~~~~A~~a~~~-~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKD-ANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHH-TTTSCBCTTSSSEEEEEC
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecCCceEEEEecCcHHHHHHHHHH-hcCCceecCceEEEEeec
Confidence            35779999999999999999999999999999999999999999985 678889887 688877777666766654

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=2.2e-13  Score=105.44  Aligned_cols=66  Identities=17%  Similarity=0.301  Sum_probs=59.1

Q ss_pred             CccEEEE--cCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEE-CCe
Q psy14139        212 TITTLYV--GNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL-GGR  278 (327)
Q Consensus       212 ~~~tLfV--gnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i-~G~  278 (327)
                      +.++|||  ||||.+++|++|+++|++||.|.++++..+++||||+|.+.++|+.|+.. +||..+ .+.
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k~~aFV~f~~~e~A~~A~~~-lng~~i~~~~   85 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVT-LNGKEVVDDL   85 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHH-TTTCEEECTT
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCccEEEEEECCHHHHHHHHHH-hCCCCCCCCC
Confidence            3468888  55999999999999999999999999999999999999999999999998 688655 553

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.40  E-value=5.2e-15  Score=112.09  Aligned_cols=69  Identities=28%  Similarity=0.477  Sum_probs=61.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEe-----------cCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEE
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----------SKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI  282 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~-----------~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V  282 (327)
                      ++|||||||.+++|++|+++|++||.|..+.+.           ..++||||+|.+.++|+.|++  ++|..+.|+.|+|
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~--l~g~~~~Gr~l~V   79 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA--FDGIIFQGQSLKI   79 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG--GSSCCSSSSCCCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh--hCCcEECCEEEEE
Confidence            689999999999999999999999987765543           248999999999999999984  6999999999999


Q ss_pred             Ee
Q psy14139        283 KW  284 (327)
Q Consensus       283 ~~  284 (327)
                      ++
T Consensus        80 ~r   81 (90)
T d1u2fa_          80 RR   81 (90)
T ss_dssp             BC
T ss_pred             CC
Confidence            64

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=7.9e-13  Score=111.79  Aligned_cols=78  Identities=21%  Similarity=0.446  Sum_probs=70.1

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEE
Q psy14139        210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK  283 (327)
Q Consensus       210 d~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~  283 (327)
                      ....++|||+|||..+++++|+++|+.||.|..+.+..+      +|+|||+|.+.++|++|++  +++..++|+.|+|.
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~--~~~~~~~G~~i~V~  171 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI--QKYHTVNGHNCEVR  171 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT--SSCEEETTEEEEEE
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH--hCCCeECCEEEEEE
Confidence            345679999999999999999999999999999998863      5799999999999999996  48889999999999


Q ss_pred             eccCCC
Q psy14139        284 WGRAQA  289 (327)
Q Consensus       284 ~ak~~~  289 (327)
                      ||.++.
T Consensus       172 ~A~~k~  177 (183)
T d1u1qa_         172 KALSKQ  177 (183)
T ss_dssp             ECCCHH
T ss_pred             ecCCcc
Confidence            998764

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.36  E-value=8.5e-13  Score=98.01  Aligned_cols=72  Identities=21%  Similarity=0.170  Sum_probs=63.0

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCe-eEEEEeccC
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGR-RLNIKWGRA  287 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~-~L~V~~ak~  287 (327)
                      .+.++|+|+|++.+++.| ++|++||+|.++++..+++||||+|.++++|++|++  +||..++|+ .|.|+....
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~~~~~fV~f~~~~~A~~Al~--~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS--KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT--TTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCCCCEEEEEEcccHHHHHHHh--cCCCeECCcEEEEEEeCCC
Confidence            368999999999987655 589999999999999999999999999999999995  699999997 467876543

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.27  E-value=8.6e-12  Score=105.23  Aligned_cols=95  Identities=21%  Similarity=0.419  Sum_probs=75.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK------QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       212 ~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      ..++|||||||.+++|++|+++|++||.|.++.++.+      +|+|||+|.+.++|+.|+..  .+..+.++.+.+.+.
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~--~~~~~~~~~~~~~~~   82 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA--RPHKVDGRVVEPKRA   82 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT--CSCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh--cCCcccccchhhhhh
Confidence            3479999999999999999999999999999998753      68999999999999999984  677888988888877


Q ss_pred             cCCCCCCCC--cccccccccCCCCCCC
Q psy14139        286 RAQANRGED--TAELKVRLEPVPGLPG  310 (327)
Q Consensus       286 k~~~~~~~~--~~~~~~~~~pv~Glp~  310 (327)
                      .+.......  ......++  |.|||.
T Consensus        83 ~~~~~~~~~~~~~~~~~i~--V~~lp~  107 (183)
T d1u1qa_          83 VSREDSQRPGAHLTVKKIF--VGGIKE  107 (183)
T ss_dssp             CCTTGGGSTTTTCCCSEEE--EECCCT
T ss_pred             hhcccccccccccccceeE--EccCCC
Confidence            665543322  12223344  788863

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=1.3e-11  Score=94.84  Aligned_cols=80  Identities=16%  Similarity=0.341  Sum_probs=68.3

Q ss_pred             CCCCccEEEEcCC--CCCCC---------HHHHHHHHhhcCCeEEEEEecC--CCeEEEEeCCHHHHHHHHHHhcCCeEE
Q psy14139        209 EDKTITTLYVGNL--GDKLT---------EQDLRDHFYQFGEIRSVTILSK--QQCAFIQYTSRPAAEAAVEHSFNKVIL  275 (327)
Q Consensus       209 ~d~~~~tLfVgnL--p~~it---------e~~Lr~~F~~fG~I~~v~i~~~--kg~aFV~F~~~~~Ae~A~~~~l~g~~i  275 (327)
                      .....++|+|.|+  |.++.         +++|++.|++||.|..|.+..+  +|+|||+|.+.++|++|+.. +||..+
T Consensus         4 ~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~-lng~~~   82 (99)
T d2dita1           4 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQT-LDGRWF   82 (99)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHH-STTCEE
T ss_pred             CCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHH-hCCcEE
Confidence            3456689999998  54321         3689999999999999998775  79999999999999999998 799999


Q ss_pred             CCeeEEEEeccCCC
Q psy14139        276 GGRRLNIKWGRAQA  289 (327)
Q Consensus       276 ~G~~L~V~~ak~~~  289 (327)
                      +|+.|+|.+..++.
T Consensus        83 ~gr~i~v~~~~g~~   96 (99)
T d2dita1          83 GGRQITAQAWDGTT   96 (99)
T ss_dssp             TTEECEEEECCSCC
T ss_pred             CCEEEEEEEeCCcC
Confidence            99999999987654

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=3.7e-13  Score=104.74  Aligned_cols=71  Identities=14%  Similarity=0.292  Sum_probs=65.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEec
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-----QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWG  285 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~-----kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~a  285 (327)
                      +.++|.+++.+++|++|+++|++||+|.+|+|..+     +|+|||+|.+.++|++|++. +||..++|++|+|.|.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~-lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVID-LNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHH-HTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHH-HCCCEECCEEEEEEEC
Confidence            46788888889999999999999999999999753     69999999999999999998 6999999999999885

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=1.5e-12  Score=102.42  Aligned_cols=74  Identities=15%  Similarity=0.189  Sum_probs=63.3

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhhcCCeEEE-EEec-----CCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSV-TILS-----KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       213 ~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v-~i~~-----~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      ..+|||+|||.++++++|+++|+.||.+..+ .+..     .+|+|||+|.+.++|++|++  +++..|+|+.|.|.++.
T Consensus        18 ~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~--~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          18 GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC--RHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT--SCSBCSTTSCBEEEEEC
T ss_pred             CeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH--cCCCcCCCEEEEEEEcC
Confidence            4589999999999999999999999988653 3332     26899999999999999986  69999999999998875


Q ss_pred             CC
Q psy14139        287 AQ  288 (327)
Q Consensus       287 ~~  288 (327)
                      ++
T Consensus        96 ~~   97 (112)
T d1wela1          96 KK   97 (112)
T ss_dssp             HH
T ss_pred             hH
Confidence            43

>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=98.90  E-value=1.7e-09  Score=83.35  Aligned_cols=74  Identities=20%  Similarity=0.318  Sum_probs=63.0

Q ss_pred             ccEEEEcCC--CCCCC--------HHHHHHHHhhcCCeEEEEEecC--------CCeEEEEeCCHHHHHHHHHHhcCCeE
Q psy14139        213 ITTLYVGNL--GDKLT--------EQDLRDHFYQFGEIRSVTILSK--------QQCAFIQYTSRPAAEAAVEHSFNKVI  274 (327)
Q Consensus       213 ~~tLfVgnL--p~~it--------e~~Lr~~F~~fG~I~~v~i~~~--------kg~aFV~F~~~~~Ae~A~~~~l~g~~  274 (327)
                      .+.|.+.|+  +.++.        .++|++.|++||.|.+|.|..+        .|++||.|.+.++|.+|+.. ++|..
T Consensus         4 s~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~-l~Gr~   82 (104)
T d1o0pa_           4 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQG-LTGRK   82 (104)
T ss_dssp             CSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHH-HSSCC
T ss_pred             CcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHH-HCCCE
Confidence            467899998  44443        3578999999999999998652        48999999999999999997 79999


Q ss_pred             ECCeeEEEEeccC
Q psy14139        275 LGGRRLNIKWGRA  287 (327)
Q Consensus       275 i~G~~L~V~~ak~  287 (327)
                      ++|+.|.|.+..+
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999998764

>d2cqea2 g.66.1.1 (A:429-457) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.87  E-value=3.3e-06  Score=47.64  Aligned_cols=24  Identities=42%  Similarity=1.173  Sum_probs=21.9

Q ss_pred             CccccccccccccCCCCCCCCCCC
Q psy14139        143 RPHICSFWVKGECRRGEECPYRHE  166 (327)
Q Consensus       143 ~~~~C~ff~kG~C~rG~~Cpy~H~  166 (327)
                      +..+|-||+.|.|.||+.|+|.|.
T Consensus         5 kkelCKfYvqGyCtrgenC~ymH~   28 (29)
T d2cqea2           5 KRELCKFYITGFCARAENCPYMHG   28 (29)
T ss_dssp             CCSBCTTTTTTCCSCSTTCSSBSS
T ss_pred             hhhhhhhheeeeecCCcCcccccC
Confidence            457999999999999999999995

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.68  E-value=0.0021  Score=46.80  Aligned_cols=53  Identities=19%  Similarity=0.312  Sum_probs=47.0

Q ss_pred             HHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEe
Q psy14139        228 QDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW  284 (327)
Q Consensus       228 ~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~  284 (327)
                      .+|.+.|.+||+|.-||++  ..-..|+|.+-++|.+|+.  ++|..+.|+.|+|..
T Consensus        39 ~~Llq~l~~~GeViLvRFv--~d~mwVTF~dG~SAL~al~--l~g~~v~G~~l~It~   91 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRIN--QGQMLVTFADSHSALSVLD--VDGMKVKGRAVKISG   91 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEE--TTEEEEECSCSHHHHHHHH--GGGSEETTEEEEEEC
T ss_pred             HHHHHHHhhCCeEEEEEEe--CCeEEEEECCcHHHHHHhc--cCCeEEcceEEEEec
Confidence            4677889999999999998  4567999999999999998  699999999999964

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.38  E-value=0.013  Score=40.47  Aligned_cols=57  Identities=21%  Similarity=0.364  Sum_probs=49.9

Q ss_pred             HHHHHHhhcCCeEEEEEecC---CCeEEEEeCCHHHHHHHHHHhcCCeEECCeeEEEEecc
Q psy14139        229 DLRDHFYQFGEIRSVTILSK---QQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR  286 (327)
Q Consensus       229 ~Lr~~F~~fG~I~~v~i~~~---kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G~~L~V~~ak  286 (327)
                      .|.+.|.++|.|.++.+...   .-.|-|...+..+|.-|+.. ++...+++++|.|.++.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~-LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNS-LHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHH-HTTEEETTEEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHH-HHHHhcCCeEEEEEEec
Confidence            45567889999999999774   45799999999999999998 79999999999998864

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.02  E-value=0.016  Score=42.16  Aligned_cols=63  Identities=16%  Similarity=0.284  Sum_probs=53.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecC--------CCeEEEEeCCHHHHHHHHHHhcCCeEECC
Q psy14139        214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK--------QQCAFIQYTSRPAAEAAVEHSFNKVILGG  277 (327)
Q Consensus       214 ~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~--------kg~aFV~F~~~~~Ae~A~~~~l~g~~i~G  277 (327)
                      ++|.|..||+.++|+++.+.++..|++........        -.-|+|.|.+.++.....+. ++|..+-+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~-f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDR-FDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHH-HTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHH-cCCcEEEc
Confidence            68999999999999999999999999887776652        25799999999999999887 78877643

>d1m9oa_ g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Tristetraproline (ttp, tis11, nup475)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.09  E-value=0.0095  Score=36.63  Aligned_cols=25  Identities=28%  Similarity=0.873  Sum_probs=21.6

Q ss_pred             Cccccccc-cccccCCCCCCCCCCCC
Q psy14139        143 RPHICSFW-VKGECRRGEECPYRHEK  167 (327)
Q Consensus       143 ~~~~C~ff-~kG~C~rG~~Cpy~H~~  167 (327)
                      +..+|.+| ..|.|..|+.|.|.|..
T Consensus         8 KT~lC~~~~~~g~C~~G~~C~FAHg~   33 (40)
T d1m9oa_           8 KTELCRTYSESGRCRYGAKCQFAHGL   33 (40)
T ss_dssp             CSCCCSGGGGTSCCTTTTTCSSCSSS
T ss_pred             ccccChhhhcCCcCCCCCCCCCCCCH
Confidence            36899999 56999999999999963

>d1rgoa1 g.66.1.1 (A:151-186) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.57  E-value=0.0041  Score=37.47  Aligned_cols=24  Identities=29%  Similarity=0.924  Sum_probs=21.4

Q ss_pred             Cccccccc-cccccCCCCCCCCCCC
Q psy14139        143 RPHICSFW-VKGECRRGEECPYRHE  166 (327)
Q Consensus       143 ~~~~C~ff-~kG~C~rG~~Cpy~H~  166 (327)
                      +..+|.+| ..|.|..|+.|.|.|.
T Consensus         5 KT~lC~~~~~~g~C~~G~~C~FAHg   29 (36)
T d1rgoa1           5 KTELCRPFEESGTCKYGEKCQFAHG   29 (36)
T ss_dssp             TSSBCHHHHHHSCCTTGGGCSSBSS
T ss_pred             chhhCcchhcCCcCCCCCcCCCcCC
Confidence            46899999 5799999999999996

>d1rgoa2 g.66.1.1 (A:187-220) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.67  E-value=0.0092  Score=35.34  Aligned_cols=24  Identities=25%  Similarity=0.758  Sum_probs=21.5

Q ss_pred             Cccccccc-cccccCCCCCCCCCCC
Q psy14139        143 RPHICSFW-VKGECRRGEECPYRHE  166 (327)
Q Consensus       143 ~~~~C~ff-~kG~C~rG~~Cpy~H~  166 (327)
                      +..+|..| ..|.|..|+.|.|.|.
T Consensus         7 KT~lC~~f~~~g~C~yG~~C~FaHg   31 (34)
T d1rgoa2           7 KTELCRTFHTIGFCPYGPRCHFIHN   31 (34)
T ss_dssp             TCSBCHHHHHHSCCTTGGGCSSBCC
T ss_pred             cchhccccCCCCcCCCCCcccCcCC
Confidence            37899999 5699999999999996

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.36  E-value=0.33  Score=35.30  Aligned_cols=56  Identities=20%  Similarity=0.273  Sum_probs=46.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCeEEEEeCCHHHHHHHHHH
Q psy14139        211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH  268 (327)
Q Consensus       211 ~~~~tLfVgnLp~~ite~~Lr~~F~~fG~I~~v~i~~~kg~aFV~F~~~~~Ae~A~~~  268 (327)
                      +....+|.-.+|..+...||.++|+.||.|.=-.|  +---|||.-.+++.|+.+...
T Consensus        13 p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI--ddTSa~V~L~~~e~~~~v~~~   68 (100)
T d1whva_          13 PKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI--DDTSAFVSLSQPEQVQIAVNT   68 (100)
T ss_dssp             CCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE--ETTEEEEECSCHHHHHHHHHH
T ss_pred             CCcceeEEEeCCcccchhHHHHHhcCCCceEEEEe--cCceEEEEecCHHHHHHHHHH
Confidence            33457888899999999999999999998753333  345799999999999998874

>d1joca1 g.50.1.1 (A:1348-1411) Eea1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Eea1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.25  E-value=0.016  Score=39.24  Aligned_cols=37  Identities=19%  Similarity=0.382  Sum_probs=23.0

Q ss_pred             cccCCcccccCCcceeEEecCCCCCcccchhhhhhhhcc
Q psy14139         21 EKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARL   59 (327)
Q Consensus        21 ~~~g~eckic~rpft~f~w~~~~~~~~kkt~ic~~ca~~   59 (327)
                      +..-..|-+|.++||+|+.+  .+=|.==-++|..|+..
T Consensus         5 d~~~~~C~~C~~~F~~~~rr--HHCR~CG~v~C~~Cs~~   41 (64)
T d1joca1           5 DNEVQNCMACGKGFSVTVRR--HHCRQCGNIFCAECSAK   41 (64)
T ss_dssp             GGGCCBCTTTCCBCCSSSCC--EECTTTCCEECGGGSCE
T ss_pred             cccCCcCcCcCCcccCCccc--cchhhhCCeecccccCC
Confidence            34456899999999998653  22332233456666553

>d1y02a2 g.50.1.1 (A:20-70) Rififylin (FYVE-RING finger protein Sakura) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Rififylin (FYVE-RING finger protein Sakura)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.42  E-value=0.036  Score=35.78  Aligned_cols=31  Identities=26%  Similarity=0.436  Sum_probs=19.9

Q ss_pred             cccccCCcceeEEecCCCCCcccchhhhhhhhc
Q psy14139         26 ECKICARPFTVFRWCPGARMRFKKTEVCQTCAR   58 (327)
Q Consensus        26 eckic~rpft~f~w~~~~~~~~kkt~ic~~ca~   58 (327)
                      .|.+|..+|++|+|+-  +=|.=--++|..|+.
T Consensus         2 ~C~~C~~~F~~~~rkh--hCr~CG~~fC~~Cs~   32 (51)
T d1y02a2           2 SCKSCGAHFANTARKQ--TCLDCKKNFCMTCSS   32 (51)
T ss_dssp             CCTTTCCCCSSGGGCE--ECTTTCCEECGGGEE
T ss_pred             CccccCCcccCCccCc--ccccCCcccCccccC
Confidence            5899999999998762  222222255666653

>d1v6ga2 g.39.1.3 (A:42-81) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.50  E-value=0.21  Score=29.63  Aligned_cols=28  Identities=39%  Similarity=0.927  Sum_probs=19.2

Q ss_pred             cccccCCcceeEEecCCCCCc-ccchhhhhhhhc
Q psy14139         26 ECKICARPFTVFRWCPGARMR-FKKTEVCQTCAR   58 (327)
Q Consensus        26 eckic~rpft~f~w~~~~~~~-~kkt~ic~~ca~   58 (327)
                      -|.+|-+||-     +|.+-- --|--+||.|+.
T Consensus         2 vC~vCr~pFP-----~GDRVTFnGKeC~CQ~Cs~   30 (40)
T d1v6ga2           2 VCAVCRLPFP-----PGDRVTFNGKECMCQKCSL   30 (40)
T ss_dssp             SCSSSCCCCC-----SSSCEEEETTEEEEHHHHS
T ss_pred             cccccCCCCC-----CCCeEEEcCceeehhhcCC
Confidence            4899999992     354433 347778888874

>d2cqea1 g.66.1.1 (A:458-513) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.12  E-value=0.26  Score=31.83  Aligned_cols=21  Identities=29%  Similarity=1.059  Sum_probs=18.3

Q ss_pred             ccccc-cccccCCCCCCCCCCC
Q psy14139        146 ICSFW-VKGECRRGEECPYRHE  166 (327)
Q Consensus       146 ~C~ff-~kG~C~rG~~Cpy~H~  166 (327)
                      .|-|| ..+.|..|+.|.|.|+
T Consensus         2 PCK~yHtg~kCy~gd~C~FSH~   23 (56)
T d2cqea1           2 PCKLYHTTGNCINGDDCMFSHD   23 (56)
T ss_dssp             BCSHHHHTSCCSSCTTCSSBCC
T ss_pred             CcceeecCCcccCCCcccccCC
Confidence            58899 5669999999999995