Psyllid ID: psy13533

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------
Protein Sequence
MSDQENSFIHEEENFENGDHIENGDMEADQSKCTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRGGPRGRGRGRVSRGAAMYGGYRPVRRAR
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHccccccEEEccccccccHHHHHHHHcccccEEEEEEEccccccccccEEEEEEccHHHHHHHHHcccccccccEEEEEEccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHcccEEEEEcccccccHHHHHHHHcccccEEEEEEEEcccccccccEEEEEEccHHHHHHHHHHcccHccccEEEEEcccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
msdqensfiheeenfengdhiengdmeadqskcTDEAELAAMKARVREMEEEAEKLKQLQSEVDkqmsmgsppnsnnllnlSIEEKKEADLRSIYVGNVDYGATAEELEshfhgcgsvnRVTILCnkfdghpkgfaYIEFADKDSVQTAMAMDEslfrgrqikvnpkrtnrpgisttnrggprgrgrgrvsrgaamyggyrpvrrar
Flexible Loop (DISEMBL)
msdqensfiheeenfengdhieNGDMEADQSKCTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESlfrgrqikvnpkrtnrpgisttnrggprgrgrgrvsrgaamyggyrpvrrar
Low Complexity Region (SEG)
MSDQENSFIHEEENFENGDHIENGDMEADQSKCTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGsppnsnnllnlsIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNrggprgrgrgrvsrgAAMYGGYRPVRRAR
Disordered region (IsUnstruct)
*****************************************************************************************DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSV*************************************************************
Disordered Region (DISOPRED)
*********************************************************************************************IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKV*******************************************
Disordered Region (DISEMBL)
********IHEEENFENGDHIENGDMEADQSKCTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTT************VSRGAAMYGGYRPVRRAR
Disordered Region (DISPRO)
***********************************EAELAAMKARVREMEEEAEKLKQLQSEVDKQ*********************EADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGI*********************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSDQENSFIHEEENFENGDHIENGDMEADQSKCTDEAExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxGSPPNSNNLLNLSIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRGGPRGRGRGRVSRGAAMYGGYRPVRRAR
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	207	2.2.26 [Sep-21-2011]
Q7KNF2	224	Polyadenylate-binding pro	yes	N/A	0.845	0.781	0.654	5e-61
Q28ZX3	225	Polyadenylate-binding pro	yes	N/A	0.801	0.737	0.686	1e-59
Q86U42	306	Polyadenylate-binding pro	no	N/A	0.768	0.519	0.748	6e-59
Q28165	306	Polyadenylate-binding pro	yes	N/A	0.816	0.552	0.717	7e-59
Q8CCS6	302	Polyadenylate-binding pro	yes	N/A	0.811	0.556	0.721	7e-59
Q7ZXB8	295	Polyadenylate-binding pro	N/A	N/A	0.729	0.511	0.754	8e-57
Q6NVP7	296	Polyadenylate-binding pro	yes	N/A	0.792	0.554	0.664	1e-56
Q9DDY9	296	Polyadenylate-binding pro	N/A	N/A	0.729	0.510	0.754	2e-56
Q6TY21	218	Embryonic polyadenylate-b	N/A	N/A	0.777	0.738	0.516	2e-46
Q804A5	218	Embryonic polyadenylate-b	N/A	N/A	0.772	0.733	0.518	1e-45

>sp|Q7KNF2|PABP2_DROME Polyadenylate-binding protein 2 OS=Drosophila melanogaster GN=Pabp2 PE=2 SV=1

 Score =  233 bits (595), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 123/188 (65%), Positives = 145/188 (77%), Gaps = 13/188 (6%)

Query: 22  ENGDMEADQSKCTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNL 81
           E G M+ D        EL A+KARV+EMEEEAEK+KQ+QSEVDKQM+ GS      +  L
Sbjct: 34  EEGSMQID-------PELEAIKARVKEMEEEAEKIKQMQSEVDKQMAGGSTTGLATV-PL 85

Query: 82  SIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFA 141
           S+EEK+E D RS+YVGNVDYGA+AEELE+HFHGCG++NRVTILCNK DGHPKGFAYIEF 
Sbjct: 86  SLEEKQEIDTRSVYVGNVDYGASAEELEAHFHGCGTINRVTILCNKADGHPKGFAYIEFG 145

Query: 142 DKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTN---RGGPRGRGRGRVSRGAAMYG 198
            K+ V+TA+AM+E+LFRGRQIKV  KRTNRPG+STTN   RG  RGRG  RVSR A  + 
Sbjct: 146 SKEFVETALAMNETLFRGRQIKVMSKRTNRPGLSTTNRFARGSFRGRG-ARVSR-ACCHS 203

Query: 199 GYRPVRRA 206
            +R  RRA
Sbjct: 204 TFRGARRA 211

Involved in the 3'-end formation of mRNA precursors (pre-mRNA) by the addition of a poly(A) tail of 200-250 nt to the upstream cleavage product. Stimulates poly(A) polymerase (PAPOLA) conferring processivity on the poly(A) tail elongation reaction and controls also the poly(A) tail length. Increases the affinity of poly(A) polymerase for RNA. Binds to poly(A) and to poly(G) with high affinity. May protect the poly(A) tail from degradation.
Drosophila melanogaster (taxid: 7227)

>sp|Q28ZX3|PABP2_DROPS Polyadenylate-binding protein 2 OS=Drosophila pseudoobscura pseudoobscura GN=Pabp2 PE=3 SV=1

 Score =  229 bits (584), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 118/172 (68%), Positives = 139/172 (80%), Gaps = 6/172 (3%)

Query: 38  ELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKEADLRSIYVG 97
           EL A+KARV+EMEEEAEK+KQ+QSEVDKQM+ GS       + LS+EEK+E D RS+YVG
Sbjct: 43  ELEAIKARVKEMEEEAEKIKQMQSEVDKQMAGGSTTGLA-AVPLSLEEKQEIDTRSVYVG 101

Query: 98  NVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLF 157
           NVDYGA+AEELE+HFHGCG++NRVTILCNK DGHPKGFAYIEF  K+ V+TA+AM+E+LF
Sbjct: 102 NVDYGASAEELEAHFHGCGTINRVTILCNKADGHPKGFAYIEFGSKEFVETALAMNETLF 161

Query: 158 RGRQIKVNPKRTNRPGISTTN---RGGPRGRGRGRVSRGAAMYGGYRPVRRA 206
           RGRQIKV  KRTNRPG+STTN   RG  RGRG  R SR A  +  +R  RRA
Sbjct: 162 RGRQIKVMSKRTNRPGLSTTNRFARGSFRGRG-ARASR-ACCHSTFRGARRA 211

Involved in the 3'-end formation of mRNA precursors (pre-mRNA) by the addition of a poly(A) tail of 200-250 nt to the upstream cleavage product. Stimulates poly(A) polymerase (PAPOLA) conferring processivity on the poly(A) tail elongation reaction and controls also the poly(A) tail length. Increases the affinity of poly(A) polymerase for RNA. Binds to poly(A) and to poly(G) with high affinity. May protect the poly(A) tail from degradation.

Drosophila pseudoobscura pseudoobscura (taxid: 46245)

>sp|Q86U42|PABP2_HUMAN Polyadenylate-binding protein 2 OS=Homo sapiens GN=PABPN1 PE=1 SV=3

 Score =  226 bits (577), Expect = 6e-59,   Method: Compositional matrix adjust.
 Identities = 119/159 (74%), Positives = 139/159 (87%)

Query: 33  CTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKEADLR 92
             ++ EL A+KARVREMEEEAEKLK+LQ+EV+KQM+M  PP +   + +SIEEK EAD R
Sbjct: 113 AIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMSIEEKMEADAR 172

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
           SIYVGNVDYGATAEELE+HFHGCGSVNRVTILC+KF GHPKGFAYIEF+DK+SV+T++A+
Sbjct: 173 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLAL 232

Query: 153 DESLFRGRQIKVNPKRTNRPGISTTNRGGPRGRGRGRVS 191
           DESLFRGRQIKV PKRTNRPGISTT+RG PR R R R +
Sbjct: 233 DESLFRGRQIKVIPKRTNRPGISTTDRGFPRARYRARTT 271

Involved in the 3'-end formation of mRNA precursors (pre-mRNA) by the addition of a poly(A) tail of 200-250 nt to the upstream cleavage product. Stimulates poly(A) polymerase (PAPOLA) conferring processivity on the poly(A) tail elongation reaction and controls also the poly(A) tail length. Increases the affinity of poly(A) polymerase for RNA. Is also present at various stages of mRNA metabolism including nucleocytoplasmic trafficking and nonsense-mediated decay (NMD) of mRNA. Cooperates with SKIP to synergistically activate E-box-mediated transcription through MYOD1 and may regulate the expression of muscle-specific genes. Binds to poly(A) and to poly(G) with high affinity. May protect the poly(A) tail from degradation.

Homo sapiens (taxid: 9606)

>sp|Q28165|PABP2_BOVIN Polyadenylate-binding protein 2 OS=Bos taurus GN=PABPN1 PE=1 SV=3

 Score =  226 bits (577), Expect = 7e-59,   Method: Compositional matrix adjust.
 Identities = 122/170 (71%), Positives = 144/170 (84%), Gaps = 1/170 (0%)

Query: 23  NGDMEADQSK-CTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNL 81
           +G +E D      ++ EL A+KARVREMEEEAEKLK+LQ+EV+KQM+M  PP +   + +
Sbjct: 102 SGLVEGDPGDGAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVIM 161

Query: 82  SIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFA 141
           SIEEK EAD RSIYVGNVDYGATAEELE+HFHGCGSVNRVTILC+KF GHPKGFAYIEF+
Sbjct: 162 SIEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFS 221

Query: 142 DKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRGGPRGRGRGRVS 191
           DK+SV+T++A+DESLFRGRQIKV PKRTNRPGISTT+RG PR R R R +
Sbjct: 222 DKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTDRGFPRARYRARTT 271

Involved in the 3'-end formation of mRNA precursors (pre-mRNA) by the addition of a poly(A) tail of 200-250 nt to the upstream cleavage product. Stimulates poly(A) polymerase (PAPOLA) conferring processivity on the poly(A) tail elongation reaction and controls also the poly(A) tail length. Increases the affinity of poly(A) polymerase for RNA. Is also present at various stages of mRNA metabolism including nucleocytoplasmic trafficking and nonsense-mediated decay (NMD) of mRNA. Cooperates with SKIP to synergistically activate E-box-mediated transcription through MYOD1 and may regulate the expression of muscle-specific genes. Binds to poly(A) and to poly(G) with high affinity. May protect the poly(A) tail from degradation.

Bos taurus (taxid: 9913)

>sp|Q8CCS6|PABP2_MOUSE Polyadenylate-binding protein 2 OS=Mus musculus GN=Pabpn1 PE=2 SV=3

 Score =  226 bits (577), Expect = 7e-59,   Method: Compositional matrix adjust.
 Identities = 122/169 (72%), Positives = 144/169 (85%), Gaps = 1/169 (0%)

Query: 24  GDMEADQSK-CTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNLS 82
           G +EAD      ++ EL A+KARVREMEEEAEKLK+LQ+EV+KQM+M  PP +   + +S
Sbjct: 99  GLVEADPGDGAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMS 158

Query: 83  IEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFAD 142
           +EEK EAD RSIYVGNVDYGATAEELE+HFHGCGSVNRVTILC+KF GHPKGFAYIEF+D
Sbjct: 159 LEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD 218

Query: 143 KDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRGGPRGRGRGRVS 191
           K+SV+T++A+DESLFRGRQIKV PKRTNRPGISTT+RG PR R R R +
Sbjct: 219 KESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTDRGFPRSRYRARTT 267

Involved in the 3'-end formation of mRNA precursors (pre-mRNA) by the addition of a poly(A) tail of 200-250 nt to the upstream cleavage product. Stimulates poly(A) polymerase (PAPOLA) conferring processivity on the poly(A) tail elongation reaction and controls also the poly(A) tail length. Increases the affinity of poly(A) polymerase for RNA. Is also present at various stages of mRNA metabolism including nucleocytoplasmic trafficking and nonsense-mediated decay (NMD) of mRNA. Cooperates with SKIP to synergistically activate E-box-mediated transcription through MYOD1 and may regulate the expression of muscle-specific genes. Binds to poly(A) and to poly(G) with high affinity. May protect the poly(A) tail from degradation.

Mus musculus (taxid: 10090)

>sp|Q7ZXB8|PAB2B_XENLA Polyadenylate-binding protein 2-B OS=Xenopus laevis GN=pabpn1-b PE=2 SV=1

 Score =  219 bits (559), Expect = 8e-57,   Method: Compositional matrix adjust.
 Identities = 114/151 (75%), Positives = 135/151 (89%)

Query: 32  KCTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKEADL 91
           +  ++ EL A+KARVREMEEEAEKLK+LQ+EV+KQM+M  PP +   + +S+EEK EAD 
Sbjct: 102 QTIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMSVEEKMEADA 161

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
           RSIYVGNVDYGATAEELE+HFHGCGSVNRVTILC+KF GHPKGFAYIEF+DK+SV+T++A
Sbjct: 162 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFTGHPKGFAYIEFSDKESVRTSLA 221

Query: 152 MDESLFRGRQIKVNPKRTNRPGISTTNRGGP 182
           +DESLFRGRQIKV PKRTNRPGISTT+RG P
Sbjct: 222 LDESLFRGRQIKVVPKRTNRPGISTTDRGFP 252

Involved in the 3'-end formation of mRNA precursors (pre-mRNA) by the addition of a poly(A) tail of 200-250 nt to the upstream cleavage product. Stimulates poly(A) polymerase (PAPOLA) conferring processivity on the poly(A) tail elongation reaction and controls also the poly(A) tail length. Increases the affinity of poly(A) polymerase for RNA. Binds to poly(A) and to poly(G) with high affinity. May protect the poly(A) tail from degradation.

Xenopus laevis (taxid: 8355)

>sp|Q6NVP7|PABP2_XENTR Polyadenylate-binding protein 2 OS=Xenopus tropicalis GN=pabpn1 PE=2 SV=1

 Score =  219 bits (557), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 123/185 (66%), Positives = 144/185 (77%), Gaps = 21/185 (11%)

Query: 32  KCTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKEADL 91
           +  ++ EL A+KARVREMEEEAEKLK+LQ+EV+KQM+M  PP +   + +SIEEK EAD 
Sbjct: 103 QTIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMSIEEKMEADA 162

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
           RSIYVGNVDYGATAEELE+HFHGCGSVNRVTILC+K+ GHPKGFAYIEF+DK+SV+T++A
Sbjct: 163 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKYTGHPKGFAYIEFSDKESVRTSLA 222

Query: 152 MDESLFRGRQIKVNPKRTNRPGISTTNRGGPRG---------------------RGRGRV 190
           +DESLFRGRQIKV PKRTNRPGISTT+RG PR                      R RGRV
Sbjct: 223 LDESLFRGRQIKVVPKRTNRPGISTTDRGFPRARYRARASSYSSRSRFYSGYTPRPRGRV 282

Query: 191 SRGAA 195
            RG A
Sbjct: 283 YRGRA 287

Involved in the 3'-end formation of mRNA precursors (pre-mRNA) by the addition of a poly(A) tail of 200-250 nt to the upstream cleavage product. Stimulates poly(A) polymerase (PAPOLA) conferring processivity on the poly(A) tail elongation reaction and controls also the poly(A) tail length. Increases the affinity of poly(A) polymerase for RNA. Binds to poly(A) and to poly(G) with high affinity. May protect the poly(A) tail from degradation.

Xenopus tropicalis (taxid: 8364)

>sp|Q9DDY9|PAB2A_XENLA Polyadenylate-binding protein 2-A OS=Xenopus laevis GN=pabpn1-a PE=2 SV=1

 Score =  218 bits (556), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 114/151 (75%), Positives = 134/151 (88%)

Query: 32  KCTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKEADL 91
           +  ++ EL A+KARVREMEEEAEKLK+LQ+EV+KQM+M  PP +   + +S+EEK EAD 
Sbjct: 103 QTIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMSVEEKMEADA 162

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
           RSIYVGNVDYGATAEELE+HFHGCGSVNRVTILC+KF GHPKGFAYIEF DK+SV+T++A
Sbjct: 163 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFTGHPKGFAYIEFCDKESVRTSLA 222

Query: 152 MDESLFRGRQIKVNPKRTNRPGISTTNRGGP 182
           +DESLFRGRQIKV PKRTNRPGISTT+RG P
Sbjct: 223 LDESLFRGRQIKVVPKRTNRPGISTTDRGFP 253

Involved in the 3'-end formation of mRNA precursors (pre-mRNA) by the addition of a poly(A) tail of 200-250 nt to the upstream cleavage product. Stimulates poly(A) polymerase (PAPOLA) conferring processivity on the poly(A) tail elongation reaction and controls also the poly(A) tail length. Increases the affinity of poly(A) polymerase for RNA. Binds to poly(A) and to poly(G) with high affinity. May protect the poly(A) tail from degradation.

Xenopus laevis (taxid: 8355)

>sp|Q6TY21|EPA2B_XENLA Embryonic polyadenylate-binding protein 2-B OS=Xenopus laevis GN=Pabpn1l-b PE=1 SV=1

 Score =  185 bits (470), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 95/184 (51%), Positives = 125/184 (67%), Gaps = 23/184 (12%)

Query: 9   IHEEENFENGDHIENGDMEADQSKCTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMS 68
           + EE   + GD  E  ++        D+ EL A++ RVREMEEEAE+LK L  + DK + 
Sbjct: 5   VSEEPGLDKGDRAEECEL--------DDPELKAIRMRVREMEEEAERLKGLSGQ-DKSIG 55

Query: 69  MGSPPNSNNLLN--------------LSIEEKKEADLRSIYVGNVDYGATAEELESHFHG 114
           + + P      +              LS EEKKE D RS+YVGNVDYG+TA++LE+HF  
Sbjct: 56  VSTRPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSS 115

Query: 115 CGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGI 174
           CGS+NR+TILC+KF GHPKG+AYIEFA+++SV  A+AMDE++FRGR IKV PKRTN PGI
Sbjct: 116 CGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRTNMPGI 175

Query: 175 STTN 178
           S+T+
Sbjct: 176 SSTD 179

Binds the poly(A) tail of mRNA. Unable to interact with the cap-binding complex and is therefore unlikely to be involved in translation initiation.

Xenopus laevis (taxid: 8355)

>sp|Q804A5|EPA2A_XENLA Embryonic polyadenylate-binding protein 2-A OS=Xenopus laevis GN=Pabpn1l-a PE=1 SV=1

 Score =  182 bits (462), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 96/185 (51%), Positives = 125/185 (67%), Gaps = 25/185 (13%)

Query: 9   IHEEENFENGDHIENGDMEADQSKCTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMS 68
           + EE   + GD  E  ++        D+ EL A++ RVREMEEEAE+LK L  + DK + 
Sbjct: 5   VSEEPGLDKGDGAEECEL--------DDPELKAIRMRVREMEEEAERLKGLSGQ-DKSIG 55

Query: 69  MGSPPNSNNLLN---------------LSIEEKKEADLRSIYVGNVDYGATAEELESHFH 113
           + SP     L++               LS EEKKE D RS+YVGNVDYG TA++LE+HF 
Sbjct: 56  V-SPRPCMKLIHSKMTAGEYTEGPPRPLSAEEKKEIDKRSVYVGNVDYGGTAQDLEAHFS 114

Query: 114 GCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPG 173
            CGS+NR+TILC+KF GHPKG+AYIEFA+++SV  A+ MDE++FRGR IKV PKRTN PG
Sbjct: 115 SCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVTMDETVFRGRTIKVLPKRTNMPG 174

Query: 174 ISTTN 178
           IS+T+
Sbjct: 175 ISSTD 179

Binds the poly(A) tail of mRNA. Unable to interact with the cap-binding complex and is therefore unlikely to be involved in translation initiation.

Xenopus laevis (taxid: 8355)

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	207
332374616	228	unknown [Dendroctonus ponderosae]	0.971	0.881	0.714	1e-73
270010566	225	hypothetical protein TcasGA2_TC009984 [T	0.980	0.902	0.674	3e-73
383855268	228	PREDICTED: polyadenylate-binding protein	0.917	0.833	0.717	9e-73
66512323	228	PREDICTED: polyadenylate-binding protein	0.913	0.828	0.713	1e-72
380018099	228	PREDICTED: polyadenylate-binding protein	0.913	0.828	0.713	1e-72
340716338	228	PREDICTED: polyadenylate-binding protein	0.913	0.828	0.703	5e-72
332026434	228	Polyadenylate-binding protein 2 [Acromyr	0.932	0.846	0.717	9e-72
307171015	228	Polyadenylate-binding protein 2 [Campono	0.937	0.850	0.716	1e-71
242004476	221	Polyadenylate-binding protein, putative	0.956	0.895	0.713	5e-70
189239479	222	PREDICTED: similar to polyadenylate bind	0.946	0.882	0.672	7e-70

>gi|332374616|gb|AEE62449.1| unknown [Dendroctonus ponderosae]

 Score =  281 bits (720), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 153/214 (71%), Positives = 170/214 (79%), Gaps = 13/214 (6%)

Query: 3   DQENSFIHEEE--NFE--NGDHIENGDMEADQSKCTDEAELAAMKARVREMEEEAEKLKQ 58
           D  N  I E++  +F+  NG H E+   +AD     D+ EL A+KARVREMEEEAEKLKQ
Sbjct: 8   DSGNPLIGEDQLDSFDETNGAHDESLLNDADMD-VKDDPELEAIKARVREMEEEAEKLKQ 66

Query: 59  LQSEVDKQMSMGSPPNSNNLLNLSIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSV 118
           LQSEVDKQM++GSPP   + LN+SIEEK E D RSIYVGNVDYGATAEELE HFHGCGS+
Sbjct: 67  LQSEVDKQMNLGSPPGITSPLNMSIEEKMEVDNRSIYVGNVDYGATAEELEQHFHGCGSI 126

Query: 119 NRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTN 178
           NRVTILCN+FDGHPKGFAYIEF D+DSVQTAMAMDESLFRGRQIKV PKRTNRPGISTTN
Sbjct: 127 NRVTILCNRFDGHPKGFAYIEFGDRDSVQTAMAMDESLFRGRQIKVMPKRTNRPGISTTN 186

Query: 179 RGGPRGRG----RGR-VSRGAAMYGGYRPVRRAR 207
           R  PRGRG    RGR  SRG   + GYRP+RR R
Sbjct: 187 R-PPRGRGVSTFRGRGASRGG--FYGYRPMRRPR 217

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270010566|gb|EFA07014.1| hypothetical protein TcasGA2_TC009984 [Tribolium castaneum]

 Score =  280 bits (715), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 147/218 (67%), Positives = 168/218 (77%), Gaps = 15/218 (6%)

Query: 1   MSDQENSFIHEEENFE-----NGDH----IENGDMEADQSKCTDEAELAAMKARVREMEE 51
           M+D E+  +  E++ E     NG H    + + D++       D+ EL A+KARVREMEE
Sbjct: 1   MADNEDLGLGPEDHLESLDETNGMHDDALLNDTDLDGTGG---DDPELEAIKARVREMEE 57

Query: 52  EAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKEADLRSIYVGNVDYGATAEELESH 111
           EAEKLKQLQSEVDKQM+MGSPP   + LN+S+EEK E D RSIYVGNVDYGATAEELE H
Sbjct: 58  EAEKLKQLQSEVDKQMNMGSPPGLTSPLNMSLEEKMEVDNRSIYVGNVDYGATAEELEQH 117

Query: 112 FHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNR 171
           FHGCGS+NRVTILCNK+DGHPKGFAYIEF D+DSVQTAMAMDESLFRGR IKV PKRTNR
Sbjct: 118 FHGCGSINRVTILCNKYDGHPKGFAYIEFGDRDSVQTAMAMDESLFRGRPIKVMPKRTNR 177

Query: 172 PGISTTNRGGPRGRGRGRVSRGA--AMYGGYRPVRRAR 207
           PG+STTNR  PRGRG  R +RG     Y GYRP+RR R
Sbjct: 178 PGLSTTNR-PPRGRGAFRGARGVGRGFYAGYRPMRRPR 214

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383855268|ref|XP_003703137.1| PREDICTED: polyadenylate-binding protein 2-like [Megachile rotundata]

 Score =  278 bits (711), Expect = 9e-73,   Method: Compositional matrix adjust.
 Identities = 147/205 (71%), Positives = 164/205 (80%), Gaps = 15/205 (7%)

Query: 13  ENFENGDHIENGDMEADQSK------CTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQ 66
           EN ++GD I    M+ D  K        D+ EL A+KARVREMEEEAEKLKQLQSEVDKQ
Sbjct: 19  ENGQDGDAI----MQCDGVKRELNEANIDDPELEAIKARVREMEEEAEKLKQLQSEVDKQ 74

Query: 67  MSMGSPPNSNNLLNLSIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCN 126
           M+MGSPP   + LN+S+E+K+E D RSIYVGNVDYGATAEELE HFHGCGSVNRVTILCN
Sbjct: 75  MNMGSPPGITSPLNMSLEDKREVDNRSIYVGNVDYGATAEELEQHFHGCGSVNRVTILCN 134

Query: 127 KFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRGGPRG-R 185
           KFDGHPKGFAYIEFA++DSVQTAMAMDES+FRGRQIKV PKRTNRPG+S TNR GPRG R
Sbjct: 135 KFDGHPKGFAYIEFAERDSVQTAMAMDESMFRGRQIKVMPKRTNRPGLSVTNR-GPRGTR 193

Query: 186 GRGRVSRG---AAMYGGYRPVRRAR 207
           G   V+RG    + Y GYRP RR R
Sbjct: 194 GYRGVARGIIRGSAYFGYRPTRRPR 218

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66512323|ref|XP_393066.2| PREDICTED: polyadenylate-binding protein 2 [Apis mellifera]

 Score =  278 bits (710), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 147/206 (71%), Positives = 164/206 (79%), Gaps = 17/206 (8%)

Query: 13  ENFENGDHIENGDMEADQSK------CTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQ 66
           EN ++GD I    M+ D  K        D+ EL A+KARVREMEEEAEKLKQLQSEVDKQ
Sbjct: 19  ENGQDGDAI----MQCDGVKRELNEANIDDPELEAIKARVREMEEEAEKLKQLQSEVDKQ 74

Query: 67  MSMGSPPNSNNLLNLSIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCN 126
           M+MGSPP   + LN+S+E+K E D RSIYVGNVDYGATAEELE HFHGCGSVNRVTILCN
Sbjct: 75  MNMGSPPGITSPLNMSLEDKMEVDNRSIYVGNVDYGATAEELEQHFHGCGSVNRVTILCN 134

Query: 127 KFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRG-----G 181
           KFDGHPKGFAYIEFA++DSVQTAMAMDES+FRGRQIKV PKRTNRPG+S TNRG     G
Sbjct: 135 KFDGHPKGFAYIEFAERDSVQTAMAMDESMFRGRQIKVMPKRTNRPGLSVTNRGPRGTRG 194

Query: 182 PRGRGRGRVSRGAAMYGGYRPVRRAR 207
            RG  RG + RG+A Y GYRP+RR R
Sbjct: 195 YRGIARG-IIRGSA-YFGYRPIRRPR 218

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380018099|ref|XP_003692973.1| PREDICTED: polyadenylate-binding protein 2-like [Apis florea]

 Score =  278 bits (710), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 147/206 (71%), Positives = 164/206 (79%), Gaps = 17/206 (8%)

Query: 13  ENFENGDHIENGDMEADQSK------CTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQ 66
           EN ++GD I    M+ D  K        D+ EL A+KARVREMEEEAEKLKQLQSEVDKQ
Sbjct: 19  ENGQDGDAI----MQCDGVKRELNEANIDDPELEAIKARVREMEEEAEKLKQLQSEVDKQ 74

Query: 67  MSMGSPPNSNNLLNLSIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCN 126
           M+MGSPP   + LN+S+E+K E D RSIYVGNVDYGATAEELE HFHGCGSVNRVTILCN
Sbjct: 75  MNMGSPPGITSPLNMSLEDKMEVDNRSIYVGNVDYGATAEELEQHFHGCGSVNRVTILCN 134

Query: 127 KFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRG-----G 181
           KFDGHPKGFAYIEFA++DSVQTAMAMDES+FRGRQIKV PKRTNRPG+S TNRG     G
Sbjct: 135 KFDGHPKGFAYIEFAERDSVQTAMAMDESMFRGRQIKVMPKRTNRPGLSVTNRGPRGTRG 194

Query: 182 PRGRGRGRVSRGAAMYGGYRPVRRAR 207
            RG  RG + RG+A Y GYRP+RR R
Sbjct: 195 YRGIARG-IIRGSA-YFGYRPIRRPR 218

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340716338|ref|XP_003396656.1| PREDICTED: polyadenylate-binding protein 2-like [Bombus terrestris] gi|350406230|ref|XP_003487700.1| PREDICTED: polyadenylate-binding protein 2-like [Bombus impatiens]

 Score =  276 bits (705), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 145/206 (70%), Positives = 164/206 (79%), Gaps = 17/206 (8%)

Query: 13  ENFENGDHIENGDMEADQSK------CTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQ 66
           EN ++GD I    M+ D  K        D+ EL A+KARVREMEEEAEKLKQLQSEVDKQ
Sbjct: 19  ENGQDGDAI----MQCDGVKRELNEANIDDPELEAIKARVREMEEEAEKLKQLQSEVDKQ 74

Query: 67  MSMGSPPNSNNLLNLSIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCN 126
           M+MGSPP   + LN+S+E+K E D RSIYVGNVDYGATAEELE HFHGCGS+NRVTILCN
Sbjct: 75  MNMGSPPGITSPLNMSLEDKMEVDNRSIYVGNVDYGATAEELEQHFHGCGSINRVTILCN 134

Query: 127 KFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRG-----G 181
           KFDGHPKGFAYIEFA++DSVQTAMA+DES+FRGRQIKV PKRTNRPG+S TNRG     G
Sbjct: 135 KFDGHPKGFAYIEFAERDSVQTAMAIDESMFRGRQIKVMPKRTNRPGLSVTNRGPRGARG 194

Query: 182 PRGRGRGRVSRGAAMYGGYRPVRRAR 207
            RG  RG + RG+A Y GYRP+RR R
Sbjct: 195 YRGIARG-IIRGSA-YFGYRPIRRPR 218

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332026434|gb|EGI66562.1| Polyadenylate-binding protein 2 [Acromyrmex echinatior]

 Score =  275 bits (703), Expect = 9e-72,   Method: Compositional matrix adjust.
 Identities = 145/202 (71%), Positives = 163/202 (80%), Gaps = 9/202 (4%)

Query: 13  ENFENGDHIENGD-MEADQSKC-TDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMG 70
           EN ++GD I   D ++ D  +   D+ EL A+KARVREMEEEAEKLKQLQSEVDKQM+MG
Sbjct: 19  ENGQDGDTIMQCDGVKRDLGEANVDDPELEAIKARVREMEEEAEKLKQLQSEVDKQMNMG 78

Query: 71  SPPNSNNLLNLSIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDG 130
           SPP   + LN+S+E+K E D RSIYVGNVDYGATAEELE HFHGCGSVNRVTILCNKFDG
Sbjct: 79  SPPGITSPLNMSLEDKMEVDNRSIYVGNVDYGATAEELEQHFHGCGSVNRVTILCNKFDG 138

Query: 131 HPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRG-----GPRGR 185
           HPKGFAYIEFA++DSVQTAMAMDES+FRGRQIKV PKRTN+PG S TNRG     G RG 
Sbjct: 139 HPKGFAYIEFAERDSVQTAMAMDESMFRGRQIKVMPKRTNKPGFSMTNRGPRGARGYRGM 198

Query: 186 GRGRVSRGAAMYGGYRPVRRAR 207
            RG + RG+A Y GYRP RR R
Sbjct: 199 ARG-IIRGSA-YFGYRPTRRPR 218

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307171015|gb|EFN63078.1| Polyadenylate-binding protein 2 [Camponotus floridanus]

 Score =  274 bits (701), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 144/201 (71%), Positives = 165/201 (82%), Gaps = 7/201 (3%)

Query: 13  ENFENGDHIENGD-MEADQSKC-TDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMG 70
           EN ++GD I   D ++ + S+   D+ EL A+KARVREMEEEAEKLKQLQSEVDKQM+MG
Sbjct: 19  ENGQDGDAIMQCDGVKRELSEANIDDPELEAIKARVREMEEEAEKLKQLQSEVDKQMNMG 78

Query: 71  SPPNSNNLLNLSIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDG 130
           SPP   + LN+S+E+K E D RSIYVGNVDYGATAEELE HFHGCGSVNRVTILCNKFDG
Sbjct: 79  SPPGITSPLNMSLEDKMEVDNRSIYVGNVDYGATAEELEQHFHGCGSVNRVTILCNKFDG 138

Query: 131 HPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRGGPRG-RGRGR 189
           HPKGFAYIEFA++DSVQTAMAMDES+FRGRQIKV PKRTN+PG S TNR GPRG RG   
Sbjct: 139 HPKGFAYIEFAERDSVQTAMAMDESMFRGRQIKVMPKRTNKPGFSMTNR-GPRGARGYRG 197

Query: 190 VSRG---AAMYGGYRPVRRAR 207
           ++RG   ++ Y GYRP RR R
Sbjct: 198 MTRGIIRSSAYFGYRPTRRPR 218

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242004476|ref|XP_002423109.1| Polyadenylate-binding protein, putative [Pediculus humanus corporis] gi|212506055|gb|EEB10371.1| Polyadenylate-binding protein, putative [Pediculus humanus corporis]

 Score =  269 bits (687), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 142/199 (71%), Positives = 162/199 (81%), Gaps = 1/199 (0%)

Query: 9   IHEEENFENGDHIENGDMEADQSKCTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMS 68
           + + EN  +GD   +GD E D+S   D+ EL A+KARVREMEEEAEKLKQLQ+EV+KQ++
Sbjct: 12  LEDMENDVDGDEPVDGDAEVDKSGNYDDTELEAIKARVREMEEEAEKLKQLQTEVEKQLN 71

Query: 69  MGSPPNSNNLLNLSIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKF 128
           +GSP    + LNLS+EEK E D RSIYVGNVDYGA AEELE HFHGCGS+NRVTILCNK+
Sbjct: 72  LGSPTGLTSSLNLSLEEKLEVDNRSIYVGNVDYGANAEELEQHFHGCGSINRVTILCNKY 131

Query: 129 DGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRGGPRGRGRG 188
           DGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTN+PG+ST+NR    GR RG
Sbjct: 132 DGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNKPGMSTSNRISRAGRYRG 191

Query: 189 RVSRGAAMYGGYRPVRRAR 207
           R  RG  +Y GYR  RR R
Sbjct: 192 RAGRGYPLY-GYRLPRRPR 209

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189239479|ref|XP_975440.2| PREDICTED: similar to polyadenylate binding protein 2 [Tribolium castaneum]

 Score =  268 bits (686), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 142/211 (67%), Positives = 162/211 (76%), Gaps = 15/211 (7%)

Query: 1   MSDQENSFIHEEENFE-----NGDH----IENGDMEADQSKCTDEAELAAMKARVREMEE 51
           M+D E+  +  E++ E     NG H    + + D++       D+ EL A+KARVREMEE
Sbjct: 1   MADNEDLGLGPEDHLESLDETNGMHDDALLNDTDLDGTGG---DDPELEAIKARVREMEE 57

Query: 52  EAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKEADLRSIYVGNVDYGATAEELESH 111
           EAEKLKQLQSEVDKQM+MGSPP   + LN+S+EEK E D RSIYVGNVDYGATAEELE H
Sbjct: 58  EAEKLKQLQSEVDKQMNMGSPPGLTSPLNMSLEEKMEVDNRSIYVGNVDYGATAEELEQH 117

Query: 112 FHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNR 171
           FHGCGS+NRVTILCNK+DGHPKGFAYIEF D+DSVQTAMAMDESLFRGR IKV PKRTNR
Sbjct: 118 FHGCGSINRVTILCNKYDGHPKGFAYIEFGDRDSVQTAMAMDESLFRGRPIKVMPKRTNR 177

Query: 172 PGISTTNRGGPRGRGRGRVSRGA--AMYGGY 200
           PG+STTNR  PRGRG  R +RG     Y GY
Sbjct: 178 PGLSTTNR-PPRGRGAFRGARGVGRGFYAGY 207

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

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	207
UNIPROTKB|Q7ZXB8	295	pabpn1-b "Polyadenylate-bindin	0.942	0.661	0.605	4.6e-57
UNIPROTKB|Q9DDY9	296	pabpn1-a "Polyadenylate-bindin	0.942	0.658	0.605	5.9e-57
UNIPROTKB|Q6NVP7	296	pabpn1 "Polyadenylate-binding	0.942	0.658	0.605	7.5e-57
UNIPROTKB|F1MTN4	275	PABPN1 "Polyadenylate-binding	0.758	0.570	0.715	2.3e-55
UNIPROTKB|Q28165	306	PABPN1 "Polyadenylate-binding	0.758	0.513	0.715	2.3e-55
MGI|MGI:1859158	302	Pabpn1 "poly(A) binding protei	0.758	0.519	0.715	2.9e-55
UNIPROTKB|E2R6I0	306	PABPN1 "Uncharacterized protei	0.758	0.513	0.715	4.8e-55
UNIPROTKB|Q86U42	306	PABPN1 "Polyadenylate-binding	0.758	0.513	0.715	4.8e-55
UNIPROTKB|F2Z5L8	306	PABPN1 "Uncharacterized protei	0.758	0.513	0.715	4.8e-55
UNIPROTKB|G3V7Z8	302	Pabpn1 "Protein Pabpn1" [Rattu	0.758	0.519	0.708	7.8e-55

UNIPROTKB|Q7ZXB8 pabpn1-b "Polyadenylate-binding protein 2-B" [Xenopus laevis (taxid:8355)]

 Score = 587 (211.7 bits), Expect = 4.6e-57, P = 4.6e-57
 Identities = 121/200 (60%), Positives = 143/200 (71%)

Query:    11 EEENFENGDHIENGDMEADQSKCTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMG 70
             EE   E  +  E G++  DQ+   ++ EL A+KARVREMEEEAEKLK+LQ+EV+KQM+M 
Sbjct:    83 EELEDEELEEEEPGELTGDQT--IEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMS 140

Query:    71 XXXXXXXXXXXXIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDG 130
                         +EEK EAD RSIYVGNVDYGATAEELE+HFHGCGSVNRVTILC+KF G
Sbjct:   141 PPPGNAGPVIMSVEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFTG 200

Query:   131 HPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNXX---XXXXXXX 187
             HPKGFAYIEF+DK+SV+T++A+DESLFRGRQIKV PKRTNRPGISTT+            
Sbjct:   201 HPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVVPKRTNRPGISTTDRGFPRARYRARA 260

Query:   188 XXXXXXAAMYGGYRPVRRAR 207
                   +  Y GY P  R R
Sbjct:   261 SSYSSRSRFYSGYTPRPRGR 280

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0006378 "mRNA polyadenylation" evidence=ISS

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

UNIPROTKB|Q9DDY9 pabpn1-a "Polyadenylate-binding protein 2-A" [Xenopus laevis (taxid:8355)]

 Score = 586 (211.3 bits), Expect = 5.9e-57, P = 5.9e-57
 Identities = 121/200 (60%), Positives = 142/200 (71%)

Query:    11 EEENFENGDHIENGDMEADQSKCTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMG 70
             EE   E  +  E G++  DQ+   ++ EL A+KARVREMEEEAEKLK+LQ+EV+KQM+M 
Sbjct:    84 EELEDEELEEEEPGELTGDQT--IEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMS 141

Query:    71 XXXXXXXXXXXXIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDG 130
                         +EEK EAD RSIYVGNVDYGATAEELE+HFHGCGSVNRVTILC+KF G
Sbjct:   142 PPPGNAGPVIMSVEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFTG 201

Query:   131 HPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNXX---XXXXXXX 187
             HPKGFAYIEF DK+SV+T++A+DESLFRGRQIKV PKRTNRPGISTT+            
Sbjct:   202 HPKGFAYIEFCDKESVRTSLALDESLFRGRQIKVVPKRTNRPGISTTDRGFPRARYRARA 261

Query:   188 XXXXXXAAMYGGYRPVRRAR 207
                   +  Y GY P  R R
Sbjct:   262 SSYSSRSRFYSGYTPRPRGR 281

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=ISS

GO:0006378 "mRNA polyadenylation" evidence=ISS

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

UNIPROTKB|Q6NVP7 pabpn1 "Polyadenylate-binding protein 2" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 585 (211.0 bits), Expect = 7.5e-57, P = 7.5e-57
 Identities = 121/200 (60%), Positives = 143/200 (71%)

Query:    11 EEENFENGDHIENGDMEADQSKCTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMG 70
             EE   E  +  E G++  DQ+   ++ EL A+KARVREMEEEAEKLK+LQ+EV+KQM+M 
Sbjct:    84 EELEDEELEEEEPGELTGDQT--IEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMS 141

Query:    71 XXXXXXXXXXXXIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDG 130
                         IEEK EAD RSIYVGNVDYGATAEELE+HFHGCGSVNRVTILC+K+ G
Sbjct:   142 PPPGNAGPVIMSIEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKYTG 201

Query:   131 HPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNXX---XXXXXXX 187
             HPKGFAYIEF+DK+SV+T++A+DESLFRGRQIKV PKRTNRPGISTT+            
Sbjct:   202 HPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVVPKRTNRPGISTTDRGFPRARYRARA 261

Query:   188 XXXXXXAAMYGGYRPVRRAR 207
                   +  Y GY P  R R
Sbjct:   262 SSYSSRSRFYSGYTPRPRGR 281

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0006378 "mRNA polyadenylation" evidence=ISS

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

UNIPROTKB|F1MTN4 PABPN1 "Polyadenylate-binding protein 2" [Bos taurus (taxid:9913)]

 Score = 571 (206.1 bits), Expect = 2.3e-55, P = 2.3e-55
 Identities = 113/158 (71%), Positives = 131/158 (82%)

Query:    22 ENGDMEADQSK-CTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGXXXXXXXXXX 80
             E+G +E D      ++ EL A+KARVREMEEEAEKLK+LQ+EV+KQM+M           
Sbjct:    70 ESGLVEGDPGDGAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVI 129

Query:    81 XXIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEF 140
               IEEK EAD RSIYVGNVDYGATAEELE+HFHGCGSVNRVTILC+KF GHPKGFAYIEF
Sbjct:   130 MSIEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF 189

Query:   141 ADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTN 178
             +DK+SV+T++A+DESLFRGRQIKV PKRTNRPGISTT+
Sbjct:   190 SDKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTD 227

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q28165 PABPN1 "Polyadenylate-binding protein 2" [Bos taurus (taxid:9913)]

 Score = 571 (206.1 bits), Expect = 2.3e-55, P = 2.3e-55
 Identities = 113/158 (71%), Positives = 131/158 (82%)

Query:    22 ENGDMEADQSK-CTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGXXXXXXXXXX 80
             E+G +E D      ++ EL A+KARVREMEEEAEKLK+LQ+EV+KQM+M           
Sbjct:   101 ESGLVEGDPGDGAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVI 160

Query:    81 XXIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEF 140
               IEEK EAD RSIYVGNVDYGATAEELE+HFHGCGSVNRVTILC+KF GHPKGFAYIEF
Sbjct:   161 MSIEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF 220

Query:   141 ADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTN 178
             +DK+SV+T++A+DESLFRGRQIKV PKRTNRPGISTT+
Sbjct:   221 SDKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTD 258

GO:0030529 "ribonucleoprotein complex" evidence=ISS

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:1859158 Pabpn1 "poly(A) binding protein, nuclear 1" [Mus musculus (taxid:10090)]

 Score = 570 (205.7 bits), Expect = 2.9e-55, P = 2.9e-55
 Identities = 113/158 (71%), Positives = 131/158 (82%)

Query:    22 ENGDMEADQSK-CTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGXXXXXXXXXX 80
             E G +EAD      ++ EL A+KARVREMEEEAEKLK+LQ+EV+KQM+M           
Sbjct:    97 EPGLVEADPGDGAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVI 156

Query:    81 XXIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEF 140
               +EEK EAD RSIYVGNVDYGATAEELE+HFHGCGSVNRVTILC+KF GHPKGFAYIEF
Sbjct:   157 MSLEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF 216

Query:   141 ADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTN 178
             +DK+SV+T++A+DESLFRGRQIKV PKRTNRPGISTT+
Sbjct:   217 SDKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTD 254

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0006378 "mRNA polyadenylation" evidence=TAS

GO:0006397 "mRNA processing" evidence=IEA

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

GO:0016973 "poly(A)+ mRNA export from nucleus" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=ISO

UNIPROTKB|E2R6I0 PABPN1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 568 (205.0 bits), Expect = 4.8e-55, P = 4.8e-55
 Identities = 113/158 (71%), Positives = 130/158 (82%)

Query:    22 ENGDMEADQSK-CTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGXXXXXXXXXX 80
             E G +E D      ++ EL A+KARVREMEEEAEKLK+LQ+EV+KQM+M           
Sbjct:   101 EPGLVEGDPGDGAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVI 160

Query:    81 XXIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEF 140
               IEEK EAD RSIYVGNVDYGATAEELE+HFHGCGSVNRVTILC+KF GHPKGFAYIEF
Sbjct:   161 MSIEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF 220

Query:   141 ADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTN 178
             +DK+SV+T++A+DESLFRGRQIKV PKRTNRPGISTT+
Sbjct:   221 SDKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTD 258

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q86U42 PABPN1 "Polyadenylate-binding protein 2" [Homo sapiens (taxid:9606)]

 Score = 568 (205.0 bits), Expect = 4.8e-55, P = 4.8e-55
 Identities = 113/158 (71%), Positives = 130/158 (82%)

Query:    22 ENGDMEADQSK-CTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGXXXXXXXXXX 80
             E G +E D      ++ EL A+KARVREMEEEAEKLK+LQ+EV+KQM+M           
Sbjct:   101 EPGLVEGDPGDGAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVI 160

Query:    81 XXIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEF 140
               IEEK EAD RSIYVGNVDYGATAEELE+HFHGCGSVNRVTILC+KF GHPKGFAYIEF
Sbjct:   161 MSIEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF 220

Query:   141 ADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTN 178
             +DK+SV+T++A+DESLFRGRQIKV PKRTNRPGISTT+
Sbjct:   221 SDKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTD 258

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0030529 "ribonucleoprotein complex" evidence=IDA

GO:0016973 "poly(A)+ mRNA export from nucleus" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0006396 "RNA processing" evidence=TAS

GO:0006936 "muscle contraction" evidence=TAS

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006369 "termination of RNA polymerase II transcription" evidence=TAS

GO:0006397 "mRNA processing" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

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

GO:0019054 "modulation by virus of host cellular process" evidence=TAS

GO:0019058 "viral infectious cycle" evidence=TAS

GO:0031124 "mRNA 3'-end processing" evidence=TAS

GO:0046778 "modification by virus of host mRNA processing" evidence=TAS

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|F2Z5L8 PABPN1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 568 (205.0 bits), Expect = 4.8e-55, P = 4.8e-55
 Identities = 113/158 (71%), Positives = 130/158 (82%)

Query:    22 ENGDMEADQSK-CTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGXXXXXXXXXX 80
             E G +E D      ++ EL A+KARVREMEEEAEKLK+LQ+EV+KQM+M           
Sbjct:   101 EPGLVEGDPGDGAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVI 160

Query:    81 XXIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEF 140
               IEEK EAD RSIYVGNVDYGATAEELE+HFHGCGSVNRVTILC+KF GHPKGFAYIEF
Sbjct:   161 MSIEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF 220

Query:   141 ADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTN 178
             +DK+SV+T++A+DESLFRGRQIKV PKRTNRPGISTT+
Sbjct:   221 SDKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTD 258

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|G3V7Z8 Pabpn1 "Protein Pabpn1" [Rattus norvegicus (taxid:10116)]

 Score = 566 (204.3 bits), Expect = 7.8e-55, P = 7.8e-55
 Identities = 112/158 (70%), Positives = 130/158 (82%)

Query:    22 ENGDMEADQSK-CTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGXXXXXXXXXX 80
             E G +E D      ++ EL A+KARVREMEEEAEKLK+LQ+EV+KQM+M           
Sbjct:    97 EPGLVETDPGDGAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVI 156

Query:    81 XXIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEF 140
               +EEK EAD RSIYVGNVDYGATAEELE+HFHGCGSVNRVTILC+KF GHPKGFAYIEF
Sbjct:   157 MSLEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF 216

Query:   141 ADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTN 178
             +DK+SV+T++A+DESLFRGRQIKV PKRTNRPGISTT+
Sbjct:   217 SDKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTD 254

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid 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)
O14327	PAB2_SCHPO	No assigned EC number	0.5211	0.6280	0.7831	yes	N/A
Q28165	PABP2_BOVIN	No assigned EC number	0.7176	0.8164	0.5522	yes	N/A
Q7KNF2	PABP2_DROME	No assigned EC number	0.6542	0.8454	0.7812	yes	N/A
Q8CCS6	PABP2_MOUSE	No assigned EC number	0.7218	0.8115	0.5562	yes	N/A
Q6NVP7	PABP2_XENTR	No assigned EC number	0.6648	0.7922	0.5540	yes	N/A
Q28ZX3	PABP2_DROPS	No assigned EC number	0.6860	0.8019	0.7377	yes	N/A
Q54ZS8	PABP2_DICDI	No assigned EC number	0.4413	0.6521	0.6081	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	207
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	9e-56
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	2e-46
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	3e-46
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	3e-20
smart00360	73	smart00360, RRM, RNA recognition motif	2e-19
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-17
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	3e-15
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	9e-15
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	1e-14
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-14
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-14
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	9e-14
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-13
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-13
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	3e-12
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-12
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	4e-12
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-11
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-11
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	2e-11
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-11
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-11
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	8e-11
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	1e-10
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	1e-10
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-10
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	3e-10
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	6e-10
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-09
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	1e-09
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	2e-09
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-09
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	1e-08
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	1e-08
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	1e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-08
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	2e-08
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	3e-08
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	4e-08
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	6e-08
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	7e-08
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	7e-08
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	8e-08
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-07
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	1e-07
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	1e-07
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-07
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	1e-07
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-07
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-07
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	3e-07
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	3e-07
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	4e-07
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	7e-07
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	7e-07
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	8e-07
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-06
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	1e-06
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-06
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	2e-06
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	2e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-06
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	3e-06
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	4e-06
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	5e-06
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	6e-06
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	6e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	6e-06
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	7e-06
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	7e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	1e-05
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	1e-05
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	1e-05
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	2e-05
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-05
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-05
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	2e-05
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-05
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	3e-05
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	3e-05
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	3e-05
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	5e-05
cd12460	82	cd12460, RRM2_CID8_like, RNA recognition motif 2 i	5e-05
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	5e-05
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	6e-05
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	6e-05
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	6e-05
cd12396	85	cd12396, RRM1_Nop13p_fungi, RNA recognition motif	8e-05
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	9e-05
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	1e-04
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	1e-04
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	1e-04
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	1e-04
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	1e-04
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-04
cd12503	77	cd12503, RRM1_hnRNPH_GRSF1_like, RNA recognition m	1e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	2e-04
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	2e-04
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-04
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	2e-04
cd12533	84	cd12533, RRM_EWS, RNA recognition motif in vertebr	2e-04
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	3e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-04
cd12730	79	cd12730, RRM1_GRSF1, RNA recognition motif 1 in G-	4e-04
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	4e-04
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	5e-04
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	5e-04
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	5e-04
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	6e-04
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	7e-04
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	7e-04
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	7e-04
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	8e-04
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	8e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	9e-04
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	0.001
cd12301	74	cd12301, RRM1_2_PAR10_like, RNA recognition motif	0.001
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	0.001
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	0.001
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	0.002
cd12643	77	cd12643, RRM_CFIm68, RNA recognition motif of pre-	0.002
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	0.002
cd12294	102	cd12294, RRM_Rrp7A, RNA recognition motif in ribos	0.002
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	0.002
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	0.002
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	0.002
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	0.002
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	0.003
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	0.003
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	0.003
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.003
cd12282	91	cd12282, RRM2_TatSF1_like, RNA recognition motif 2	0.003
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	0.004
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	0.004
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	0.004
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	0.004
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	0.004

>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score =  171 bits (434), Expect = 9e-56
 Identities = 66/76 (86%), Positives = 74/76 (97%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
           S+YVGNVDYGATAEELE+HFHGCGSVNRVTILC+KF GHPKGFAYIEF+DK+SV+TA+A+
Sbjct: 1   SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALAL 60

Query: 153 DESLFRGRQIKVNPKR 168
           DESLFRGRQIKV PKR
Sbjct: 61  DESLFRGRQIKVMPKR 76

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

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

 Score =  147 bits (372), Expect = 2e-46
 Identities = 59/77 (76%), Positives = 69/77 (89%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
           S+YVGNVDYG+TAEELE+HF GCG +NRVTILC+KF GHPKG+AYIEFA +DSV+ A+A+
Sbjct: 1   SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVAL 60

Query: 153 DESLFRGRQIKVNPKRT 169
           DES FRGR IKV PKRT
Sbjct: 61  DESSFRGRVIKVLPKRT 77

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

 Score =  147 bits (372), Expect = 3e-46
 Identities = 50/72 (69%), Positives = 60/72 (83%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
           SI+VGNVDYG T EEL+ HF  CG++NR+TILC+KF G PKGFAYIEF DK SV+ A+ +
Sbjct: 1   SIFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLL 60

Query: 153 DESLFRGRQIKV 164
           +ES FRGRQIKV
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|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 80.3 bits (199), Expect = 3e-20
 Identities = 29/72 (40%), Positives = 43/72 (59%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
           S++VGN+ +    EEL  HF  CG V  V I+ ++  G  KGF Y+ F  KDSV  A+ +
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL 60

Query: 153 DESLFRGRQIKV 164
           +    +GR+I+V
Sbjct: 61  NGIKLKGRKIRV 72

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

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

 Score = 78.4 bits (194), Expect = 2e-19
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-A 151
           +++VGN+    T EEL   F   G V  V ++ +K  G  KGFA++EF  ++  + A+ A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 152 MDESLFRGRQIKV 164
           ++     GR +KV
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 72.0 bits (177), Expect = 4e-17
 Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 2/73 (2%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           ++VGN+    T E+L   F   G +  V I+ +K DG  KGFA++EF   +  + A+ A+
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 153 DESLFRGRQIKVN 165
           +     GR++KV+
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|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 67.7 bits (166), Expect = 3e-15
 Identities = 28/74 (37%), Positives = 45/74 (60%), Gaps = 2/74 (2%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
           R+IYVGN+D   TA++L   F   G V  V  +    +  P  +A++EFA++ SV  A+ 
Sbjct: 5   RTIYVGNLDPTTTADQLLEFFSQAGEVKYVR-MAGD-ETQPTRYAFVEFAEQTSVINALK 62

Query: 152 MDESLFRGRQIKVN 165
           ++ ++F GR +KVN
Sbjct: 63  LNGAMFGGRPLKVN 76

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|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 = 66.2 bits (162), Expect = 9e-15
 Identities = 26/78 (33%), Positives = 46/78 (58%), Gaps = 2/78 (2%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
           R+I+VG +D   + ++L+  F  CG V RV +  +    H   FA++EFAD +S  +A+ 
Sbjct: 1   RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGD--RQHSARFAFVEFADAESALSALN 58

Query: 152 MDESLFRGRQIKVNPKRT 169
           +  +L  G  ++V+P +T
Sbjct: 59  LSGTLLGGHPLRVSPSKT 76

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

 Score = 65.8 bits (161), Expect = 1e-14
 Identities = 26/71 (36%), Positives = 44/71 (61%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           ++VGN+ Y  TAE+L +HF   G+   V +L +K  G  KG A++EF   +++  A+ + 
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 154 ESLFRGRQIKV 164
            +L +GR+I V
Sbjct: 63  HTLLKGRKINV 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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 64.6 bits (158), Expect = 3e-14
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           +YVGN+ Y  T E+L+  F   G V    ++ ++  G  +GF ++E    +    A+  +
Sbjct: 2   LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61

Query: 153 DESLFRGRQIKVN 165
           + + F GR + VN
Sbjct: 62  NGTDFGGRTLTVN 74

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 64.2 bits (157), Expect = 5e-14
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           ++VGN+    T E+L+  F   G +  + I      G  KGFA++EF D++  + A+ A+
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRI-VRDETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 153 DESLFRGRQIK 163
           +     GR+++
Sbjct: 60  NGKELGGRELR 70

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

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

 Score = 63.4 bits (155), Expect = 9e-14
 Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 3/78 (3%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILC---NKFDGHPKGFAYIEFADKDSVQT 148
           R IYV N+D+    ++L   F   G V  + I      K      GFA++ F D  S + 
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 149 AMAMDESLFRGRQIKVNP 166
           A+ ++ +   GR+I V+ 
Sbjct: 61  ALQLNGTELGGRKISVSL 78

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

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

 Score = 62.3 bits (152), Expect = 2e-13
 Identities = 26/72 (36%), Positives = 44/72 (61%), Gaps = 1/72 (1%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
           +++V N+DY    +EL   F  CG +  V ++   + G  KG+AY+EF +++SVQ A+ +
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLV-KNYKGKSKGYAYVEFENEESVQEALKL 59

Query: 153 DESLFRGRQIKV 164
           D  L +GR + V
Sbjct: 60  DRELIKGRPMFV 71

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

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

 Score = 61.8 bits (151), Expect = 4e-13
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM- 152
           +YV N+    T E+L   F   G V  V ++ NK    P+GFA++EFA  +  + A+   
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDR--PRGFAFVEFASPEDAEAALKKL 58

Query: 153 DESLFRGRQIK 163
           +  +  GR ++
Sbjct: 59  NGLVLDGRTLR 69

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

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

 Score = 59.7 bits (145), Expect = 3e-12
 Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFAD-KDSVQTAMAM 152
           ++V N+ Y    ++LE  F   G ++ V +  +K  G  KGFAY+ F D +D+V+    +
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 153 DESLFRGRQIKVNP 166
           D  +F+GR I + P
Sbjct: 65  DGKVFQGRLIHILP 78

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

>gnl|CDD|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 = 59.2 bits (144), Expect = 3e-12
 Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           ++VGN+ Y AT E+L   F   G V    ++ ++  G PKG+ + EF D ++  +A+  +
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 153 DESLFRGRQIKVNP 166
           +   F GR ++V+ 
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|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 58.9 bits (143), Expect = 4e-12
 Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
           +++VGN+ + A  ++LE  F  CG V  V I  +  DG  KGF ++EFA ++  Q A+  
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDD-DGRSKGFGHVEFATEEGAQKALEK 59

Query: 153 DESLFRGRQIKV 164
                 GR+I+V
Sbjct: 60  SGEELLGREIRV 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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 57.6 bits (140), Expect = 1e-11
 Identities = 19/74 (25%), Positives = 36/74 (48%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
             I+VG + Y  T + L  +F   G +    ++ ++  G  +G+ ++ F DK+S + A  
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 152 MDESLFRGRQIKVN 165
               +  GR+  VN
Sbjct: 61  DPNPIIDGRKANVN 74

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

 Score = 57.3 bits (139), Expect = 2e-11
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           ++V N+ +  T EEL   F   G ++ V +  +K     KGFA++ F   +    A   +
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 153 DESLFRGRQIKV 164
           D S+F+GR + V
Sbjct: 62  DGSIFQGRLLHV 73

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

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

 Score = 57.0 bits (138), Expect = 2e-11
 Identities = 20/73 (27%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
           ++Y+GN+ +  T +++   F     +  V +  +K  G  KGF +++FAD++S+  A+ +
Sbjct: 1   TVYIGNLAWDITEDDVREFF-KGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALKL 59

Query: 153 DESLFRGRQIKVN 165
           D ++  GR I++ 
Sbjct: 60  DGTVLCGRPIRIA 72

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

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

 Score = 57.0 bits (138), Expect = 2e-11
 Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 5/77 (6%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA-MAM 152
           ++V  + +  T EELE  F   G V  V ++ N+  G PKG AY+E+ ++ S   A + M
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVLKM 63

Query: 153 DESLFRGRQIKV---NP 166
           D +  + + I V   NP
Sbjct: 64  DGTEIKEKTISVAISNP 80

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

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

 Score = 61.1 bits (147), Expect = 3e-11
 Identities = 26/120 (21%), Positives = 56/120 (46%), Gaps = 1/120 (0%)

Query: 50  EEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKEADLRSIYVGNVDYGATAEELE 109
           EE   ++++                  +  +    +K + +  +++VGN+ Y  T E+L 
Sbjct: 74  EENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLR 133

Query: 110 SHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AMDESLFRGRQIKVNPKR 168
             F   G V RV ++ ++  G  +GFA++EF  ++S + A+  ++     GR ++V   +
Sbjct: 134 ELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ 193

Length = 306

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

 Score = 55.9 bits (135), Expect = 8e-11
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           ++VGN+ +    E L++ F   G+V    ++ ++  G  +GF Y++F   +  + A+ AM
Sbjct: 2   LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAM 61

Query: 153 DESLFRGRQIKVN 165
           D     GR I V+
Sbjct: 62  DGKELDGRPINVD 74

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

 Score = 55.4 bits (134), Expect = 1e-10
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           I+VG +    T EEL   F   GSV  V I+ ++  G  KG+ ++ F  ++  +  +AM 
Sbjct: 5   IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILAMG 63

Query: 154 ESLFRGRQIKVNP 166
              FRG+++ + P
Sbjct: 64  NLNFRGKKLNIGP 76

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|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 55.5 bits (134), Expect = 1e-10
 Identities = 24/62 (38%), Positives = 33/62 (53%)

Query: 105 AEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKV 164
              L  HF  CG + RV+I  ++  G  KGFAYIEF   D V+ A+ +D S   G  + V
Sbjct: 17  RRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALELDGSDLGGGNLVV 76

Query: 165 NP 166
           + 
Sbjct: 77  DE 78

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 54.5 bits (132), Expect = 2e-10
 Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 6/81 (7%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
           R++++ N+ + AT EEL+  F   G V    I+ +K  GH KG A+++F  K+S Q  + 
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 152 ------MDESLFRGRQIKVNP 166
                        GR++ V  
Sbjct: 61  AADNAEDSGLSLDGRRLIVTL 81

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

 Score = 54.3 bits (131), Expect = 3e-10
 Identities = 20/73 (27%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           ++VGN+ + A  + +   F   G ++ V +  +   G PKGF Y+EF+ +++ Q A+ A+
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 153 DESLFRGRQIKVN 165
             +   GR ++++
Sbjct: 61  GGTDLLGRPVRLD 73

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

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

 Score = 53.5 bits (129), Expect = 6e-10
 Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 4/75 (5%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
           R+++VGN+D   T E L   F   G +  V I     +G PK FA++ F  + SV  A+ 
Sbjct: 2   RTLFVGNLDARVTEEILYELFLQAGPLEGVKI-PKDPNGKPKSFAFVTFKHEVSVPYAIQ 60

Query: 152 MDE--SLFRGRQIKV 164
           +     LF GR++++
Sbjct: 61  LLNGIRLF-GRELRI 74

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

 Score = 52.6 bits (127), Expect = 1e-09
 Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           +++G + +  T E L  +F   G V    I+ +   G  +GF ++ FAD  SV   +A  
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 154 ESLFRGRQIKVNPK 167
             +  GR+I  +PK
Sbjct: 61  PHVLDGREI--DPK 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|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 52.4 bits (126), Expect = 1e-09
 Identities = 21/71 (29%), Positives = 39/71 (54%)

Query: 95  YVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDE 154
           Y+GN+ Y  T E+++  F G    +          G  +GF Y EF D+DS+  A+++++
Sbjct: 5   YLGNLPYDVTEEDIKEFFRGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSLND 64

Query: 155 SLFRGRQIKVN 165
              + R+I+V+
Sbjct: 65  ESLKNRRIRVD 75

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

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

 Score = 52.2 bits (125), Expect = 2e-09
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
            ++VGN+ +    E L   F  CG +  V I+ +      KGFAY++F D+++V+ A+ +
Sbjct: 1   CVFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLL 60

Query: 153 DESLF---RGRQIKV 164
           +E  F     R+++V
Sbjct: 61  NEKKFPPMLPRELRV 75

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

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

 Score = 52.0 bits (125), Expect = 2e-09
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-A 151
           S+YV NV      ++L   F   G +  V I  + +   P+GFAY++F D    + A+  
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 152 MDESLFRGRQIKV 164
           +D + F GR+I++
Sbjct: 62  LDRTRFLGREIEI 74

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

 Score = 49.9 bits (120), Expect = 1e-08
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 94  IYVGNVDYGATAEELESHFHGCG-SVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
           + +  + + AT E++   F G     + + I+ +  DG P G AY+EFA  +  + A+  
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDD-DGRPTGEAYVEFASPEDARRALRK 60

Query: 153 DESLFRGRQIKV 164
             +   GR I+V
Sbjct: 61  HNNKMGGRYIEV 72

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

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

 Score = 49.8 bits (119), Expect = 1e-08
 Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           ++VG + +  T E L  +F   G V    I+ +K     +GF +++F D + V T +A  
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGG 61

Query: 154 ESLFRGRQIKVNPKRTN 170
                GR I  +PK   
Sbjct: 62  PHTLDGRTI--DPKPCT 76

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

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

 Score = 49.9 bits (120), Expect = 1e-08
 Identities = 19/72 (26%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
           +YVGN+ +  T E++   F  CG + R+ +  ++F   P GF ++E+  ++  + A+  +
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 153 DESLFRGRQIKV 164
           + +    R I+V
Sbjct: 61  NGTKLDDRIIRV 72

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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 53.0 bits (127), Expect = 2e-08
 Identities = 29/100 (29%), Positives = 47/100 (47%), Gaps = 2/100 (2%)

Query: 84  EEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADK 143
             + E D R+++V  +   A   +L   F   G V  V  + ++     KG AY+EF D 
Sbjct: 82  LTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDV 141

Query: 144 DSVQTAMAMDESLFRGRQIKVNPKRT--NRPGISTTNRGG 181
           +SV  A+A+   +  GR I V   +   NR   + T++ G
Sbjct: 142 ESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPG 181

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|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 49.3 bits (118), Expect = 2e-08
 Identities = 22/78 (28%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
           R++YV ++D   T E+L + F  CG V    + C   +     FA+IEF D++  + A++
Sbjct: 3   RTVYVSDIDQQVTEEQLAALFSNCGQVVDCRV-CGDPN-SVLRFAFIEFTDEEGARAALS 60

Query: 152 MDESLFRGRQIKVNPKRT 169
           +  ++     ++V P +T
Sbjct: 61  LSGTMLGFYPVRVLPSKT 78

This subgroup corresponds to the RRM1 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 = 80

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

 Score = 48.8 bits (117), Expect = 3e-08
 Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA- 151
           +++V N+ Y  T E+LE  F   G + R  ++ +K     +GF Y+ FA ++  + A+  
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 152 MDESLFRGRQIKV 164
             ++ F GR+I V
Sbjct: 61  KKKTKFGGRKIHV 73

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

 Score = 50.4 bits (120), Expect = 4e-08
 Identities = 27/108 (25%), Positives = 45/108 (41%), Gaps = 1/108 (0%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
           +++G + +G     L   F   G V    ++ ++  G  +GF ++ F D+ +   A++ M
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 153 DESLFRGRQIKVNPKRTNRPGISTTNRGGPRGRGRGRVSRGAAMYGGY 200
           D     GR I+VNP             GG    G G    G    GG+
Sbjct: 97  DGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGGGGYGGGGDGGGGF 144

Length = 144

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

 Score = 48.1 bits (115), Expect = 6e-08
 Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 2/78 (2%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM- 152
           +YV  +   AT E L++ F   G+V  V++   K  G  KGFA+IEF   +  Q A    
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 153 -DESLFRGRQIKVNPKRT 169
            +       +    PK  
Sbjct: 62  NNPPETATDKPGKFPKTV 79

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

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

 Score = 47.6 bits (114), Expect = 7e-08
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQ-TAMAM 152
           +Y+G++ +G    EL  +F   G+V R+ +  +K  G  KG+A++EF   +  +  A  M
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 153 DESLFRGRQIKV 164
           +  L   R +K 
Sbjct: 62  NNYLLFERLLKC 73

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|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 47.6 bits (113), Expect = 7e-08
 Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
           R+++VGN+D   T E +   F   G V +V I  +K DG PK FA++ F  + SV  AM 
Sbjct: 2   RTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDK-DGKPKQFAFVNFKHEVSVPYAMN 60

Query: 152 MDESL-FRGRQIKV 164
           +   +   GR + +
Sbjct: 61  LLNGIKLYGRPLNI 74

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

 Score = 47.7 bits (114), Expect = 8e-08
 Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 95  YVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDE 154
           +VGN+ +     +L++ F    SV  V ++ +K     KGF Y+EF D +S++ A+  D 
Sbjct: 5   FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALEYDG 63

Query: 155 SLFRGRQIKVN 165
           +LF  R ++V+
Sbjct: 64  ALFDDRSLRVD 74

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

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

 Score = 47.4 bits (113), Expect = 1e-07
 Identities = 17/73 (23%), Positives = 34/73 (46%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           I+VG +    T EE + +F   G V    ++ +   G  +GF ++ F  + +V+   +  
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAG 61

Query: 154 ESLFRGRQIKVNP 166
                G+Q++V  
Sbjct: 62  MLELGGKQVEVKR 74

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

 Score = 47.0 bits (112), Expect = 1e-07
 Identities = 22/71 (30%), Positives = 41/71 (57%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           +YVG + Y +T +E+ S+F  CG +  + ++     G  +G A+I F  +++ + A+A+D
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALALD 60

Query: 154 ESLFRGRQIKV 164
                GR +KV
Sbjct: 61  GEDMGGRFLKV 71

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

 Score = 47.2 bits (113), Expect = 1e-07
 Identities = 21/78 (26%), Positives = 43/78 (55%), Gaps = 1/78 (1%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
           ++++V  ++Y  T  +L   F   G + R+ ++ +K  G P+G+A+IEF  +  ++ A  
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 151 AMDESLFRGRQIKVNPKR 168
             D     GR++ V+ +R
Sbjct: 62  YADGKKIDGRRVLVDVER 79

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

 Score = 46.9 bits (112), Expect = 1e-07
 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
           +YVGN+ +  T ++L   F   G +  V +  +   G  KG+ +I+FAD +  + A+  +
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 153 DESLFRGRQIKVN 165
           +     GR IKV 
Sbjct: 61  NGFELAGRPIKVG 73

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

 Score = 46.7 bits (111), Expect = 1e-07
 Identities = 23/73 (31%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
           ++VGN+ Y AT E+L+  F   G V    ++ ++  G PKG+ + E+ D+++  +AM  +
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 153 DESLFRGRQIKVN 165
           +     GRQ++V+
Sbjct: 61  NGYELNGRQLRVD 73

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

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

 Score = 46.4 bits (111), Expect = 2e-07
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           +YVG +      + L + F   G +  + I  +      +GFA++EF + +    A+  M
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 153 DESLFRGRQIKVN 165
           +ES   GR I+VN
Sbjct: 61  NESELFGRTIRVN 73

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

 Score = 46.4 bits (111), Expect = 2e-07
 Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 5/64 (7%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPK-----GFAYIEFADKDSV 146
            +++V N+++  T E L+ HF  CG V  VTI   K    P      G+ ++EF  K++ 
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 147 QTAM 150
           Q A+
Sbjct: 61  QKAL 64

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

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

 Score = 46.2 bits (110), Expect = 3e-07
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-A 151
           ++YV N+ +  T  +L   F   G V +VTI+ +K     KG A+I F D++     + A
Sbjct: 3   TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 152 MDESLFRGRQIKV 164
           ++     GR +K 
Sbjct: 63  LNNKELFGRTLKC 75

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

 Score = 45.9 bits (109), Expect = 3e-07
 Identities = 18/57 (31%), Positives = 34/57 (59%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
           ++VGN+ +  T +EL +HF   G + RV ++  +  G  KGFA+++F + +    A+
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57

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

 Score = 46.1 bits (110), Expect = 3e-07
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           +YVGN+   AT  ELE  F   G +  V +  N     P GFA++EF D    + A+ A+
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRAL 56

Query: 153 DESLFRGRQIKV 164
           D     G +++V
Sbjct: 57  DGRRICGNRVRV 68

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|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 = 45.7 bits (109), Expect = 4e-07
 Identities = 28/74 (37%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           + V NV + AT +EL   F   G V  V  L  KFDG  +GFA++EF  K   Q AM A+
Sbjct: 3   LIVRNVPFEATKKELRELFSPFGQVKSVR-LPKKFDGSHRGFAFVEFVTKQEAQNAMEAL 61

Query: 153 DESLFRGRQIKVNP 166
             +   GR + +  
Sbjct: 62  KSTHLYGRHLVLEY 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|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 44.9 bits (107), Expect = 7e-07
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           I+V N+ +  T ++L+  F  CG+V R  +  +  DG  KGF  + F   +  Q A+   
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTD-NDGRSKGFGTVLFESPEDAQRAIEMF 59

Query: 153 DESLFRGRQIKV 164
           +     GR+++V
Sbjct: 60  NGYDLEGRELEV 71

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

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

 Score = 44.9 bits (107), Expect = 7e-07
 Identities = 20/72 (27%), Positives = 34/72 (47%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
           +++V  +       +L   F   G V  V I+ ++     KG AY+EF D++SV  A+ +
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGL 60

Query: 153 DESLFRGRQIKV 164
                 G+ I V
Sbjct: 61  TGQRLLGQPIMV 72

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

>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 45.0 bits (106), Expect = 8e-07
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
           R+++VGN++     E L   F   G + +VTI C   +G PK F ++ F   +SV  A+A
Sbjct: 2   RTLFVGNLECRVREEILYELFLQAGPLTKVTI-CKDKEGKPKSFGFVCFKHSESVPYAIA 60

Query: 152 MDESL-FRGRQIKVN 165
           +   +   GR IKV+
Sbjct: 61  LLNGIRLYGRPIKVH 75

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|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 = 44.5 bits (106), Expect = 1e-06
 Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 7/73 (9%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-A 151
           ++YVGN+ +G T EEL+  F   G++  V +         KG+A++ F   ++  TA+ A
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVF------KDKGYAFVRFDTHEAAATAIVA 55

Query: 152 MDESLFRGRQIKV 164
           ++ +   G+ +K 
Sbjct: 56  VNGTSINGQTVKC 68

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

 Score = 44.3 bits (105), Expect = 1e-06
 Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA- 151
           ++Y G         +++  F  CG V +VT+L      H    A+I F + ++ Q A+  
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPH----AFITFENLEAAQLAIET 56

Query: 152 MDESLFRGRQIKV 164
           ++ +   G  IKV
Sbjct: 57  LNGASVDGNCIKV 69

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 43.7 bits (104), Expect = 1e-06
 Identities = 16/57 (28%), Positives = 33/57 (57%), Gaps = 6/57 (10%)

Query: 111 HFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AMDESLFRGRQIKVNP 166
            F   G+V ++ +L  K      GFA++EF+ +++ + A+  ++  LF GR ++V+ 
Sbjct: 4   LFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 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|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 43.9 bits (104), Expect = 2e-06
 Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 5/77 (6%)

Query: 91  LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
            RS++V     G + E+L  +F   G V  V +  +K  G    +A +EF  K+ V   +
Sbjct: 2   ERSVFVSGFKRGTSEEQLMDYFSAFGPVMNVIM--DKDKGV---YAIVEFDSKEGVDKVL 56

Query: 151 AMDESLFRGRQIKVNPK 167
           +  +    G +++V P+
Sbjct: 57  SEPQHTLNGHRLRVRPR 73

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

 Score = 43.8 bits (104), Expect = 2e-06
 Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 3/76 (3%)

Query: 94  IYVGNVDYGATAEELESHFHGCG--SVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
           +YVGN+ +  T E+LE      G   V  +    +K +G  KGFAY+EFA + +      
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 151 AMDESLFRGRQIKVNP 166
            ++   F G++  V  
Sbjct: 61  KLEGREFNGKKCVVTY 76

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

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

 Score = 43.8 bits (104), Expect = 2e-06
 Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 96  VGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AMDE 154
           V N+ Y  T ++L   F   G V  V I  +++    +GFA++ F DK   + AM AMD 
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 155 SLFRGRQIKV 164
               GR+++V
Sbjct: 63  KELDGRELRV 72

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

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 17/71 (23%), Positives = 40/71 (56%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           ++VGN+ +   ++EL+ +F   G V    +  +K  G  KG+ ++ F+ +D ++ A+   
Sbjct: 2   LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQKQ 61

Query: 154 ESLFRGRQIKV 164
           + +  G +++V
Sbjct: 62  KHILEGNKLQV 72

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

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

 Score = 43.3 bits (103), Expect = 3e-06
 Identities = 16/59 (27%), Positives = 31/59 (52%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
           +I V N+   A  ++L   F   G ++RV +  +K  G  +GFA++ F  ++  + A+ 
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIE 59

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

 Score = 43.3 bits (102), Expect = 4e-06
 Identities = 19/73 (26%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           +++G + +    + LE  F   G ++ V ++ ++     +GF ++ F + D  + AM AM
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 153 DESLFRGRQIKVN 165
           +     GRQI+V+
Sbjct: 63  NGKSVDGRQIRVD 75

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

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

 Score = 42.8 bits (101), Expect = 5e-06
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 1/80 (1%)

Query: 90  DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA 149
           D   ++VGN+ +  T +EL+  F   G+V  V I      G    F ++ F D ++VQ  
Sbjct: 2   DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKI 61

Query: 150 MAMDESLFRGRQ-IKVNPKR 168
           +A     FRG   + V  K+
Sbjct: 62  LANKPIYFRGDHRLNVEEKK 81

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

 Score = 42.8 bits (101), Expect = 6e-06
 Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
           +++ N+ Y  T E+LE  F   G ++ V +  +K    PKGFA++ +   +    A A +
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 153 DESLFRGRQIKVNP 166
           D ++F+GR + + P
Sbjct: 65  DGTVFQGRLLHLLP 78

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

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

 Score = 42.2 bits (100), Expect = 6e-06
 Identities = 18/73 (24%), Positives = 29/73 (39%), Gaps = 4/73 (5%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
           ++ V N+    T  ++   F  CG +  V I     +      A IEF  +D    A+  
Sbjct: 2   TVKVKNLPKDTTENKIRQFFKDCGEIREVKI----VESEGGLVAVIEFETEDEALAALTK 57

Query: 153 DESLFRGRQIKVN 165
           D     G +I V+
Sbjct: 58  DHKRLGGNEISVS 70

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

>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 42.6 bits (101), Expect = 6e-06
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 5/75 (6%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA---M 150
           +YVGN+D   T E L   F   G V  V I  ++     +G+ ++EF  ++    A   M
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 151 AMDESLFRGRQIKVN 165
            M   L+ G+ I+VN
Sbjct: 61  NM-IKLY-GKPIRVN 73

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 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 = 74

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

 Score = 42.5 bits (101), Expect = 7e-06
 Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEF--ADKDSVQTAMA 151
           ++VG +    T  +LE  F   G+V+ V I+  K  G  +GFAYI+   ++    +    
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 152 MDESLFRGRQIKV 164
           ++ + ++G  +K+
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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 42.3 bits (100), Expect = 7e-06
 Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 3/76 (3%)

Query: 90  DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA 149
           D  SI+VG +    T EEL   F   G +  V ++  K   H   FA+I+F  + +   A
Sbjct: 2   DKYSIFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARA 59

Query: 150 M-AMDESLFRGRQIKV 164
           + + + S+ + + + V
Sbjct: 60  VESENHSMLKNKTMHV 75

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

 Score = 41.5 bits (98), Expect = 1e-05
 Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
           IYV +V    + ++++S F   G +   ++  +   G  KG+ +IE+ +  S Q A+A M
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 153 DESLFRGRQIKVN 165
           +     G+Q++V 
Sbjct: 63  NLFDLGGQQLRVG 75

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|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 41.4 bits (97), Expect = 1e-05
 Identities = 17/54 (31%), Positives = 28/54 (51%)

Query: 96  VGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA 149
           V N+    T EE E      G++ R  ++ ++  GH KG+ ++E+  KDS   A
Sbjct: 4   VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKA 57

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct 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. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

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

 Score = 42.2 bits (99), Expect = 1e-05
 Identities = 18/59 (30%), Positives = 29/59 (49%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
           +++V N+ Y AT E L  HF   GSV     + +K  G  KG  ++ F D+ +    + 
Sbjct: 3   TLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLK 61

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

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

 Score = 41.4 bits (97), Expect = 2e-05
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           ++VG + +  T ++L+ +F   G V   TI  +   G  +GF ++ F D  SV+  +   
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 154 ESLFRGRQIKVNPKR 168
           E    GR I  +PKR
Sbjct: 61  EHKLDGRVI--DPKR 73

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

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

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 4/79 (5%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNK---FDGHPKGFAYIEFADKDSVQTAM 150
           +++GN+D   T   L   F   G + +   L +K     G P+G+ ++ F  K+  + A+
Sbjct: 2   LWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKAL 61

Query: 151 A-MDESLFRGRQIKVNPKR 168
             ++     G+++ V    
Sbjct: 62  KSLNGKTALGKKLVVRWAH 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|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 40.9 bits (96), Expect = 2e-05
 Identities = 20/72 (27%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           IY+G++ +G   +EL+ +F   G+V  V +  +K  G+ K + +I+F + +    A  +M
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 153 DESLFRGRQIKV 164
           +  L  G+ ++V
Sbjct: 62  NNYLLMGKVLQV 73

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

 Score = 40.9 bits (96), Expect = 2e-05
 Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           +YVG++ +    + +   F   G +  + +  +      KGFA++E+   ++ Q A+  M
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 153 DESLFRGRQIKVN 165
           +  +  GR IKV 
Sbjct: 63  NGVMLGGRNIKVG 75

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|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 40.6 bits (96), Expect = 2e-05
 Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           ++VG +      + L+  F   G+V  V +  ++    P+G+AY+EF   +  + A+  M
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 153 DESLFRGRQIKV 164
           D     G+++ V
Sbjct: 61  DGGQIDGQEVTV 72

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

 Score = 41.0 bits (96), Expect = 3e-05
 Identities = 15/74 (20%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA- 151
           +++V N+ +  T E+L   F     +    ++ +   G  +G+ ++ FA  +  Q A+A 
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 152 MDESLFRGRQIKVN 165
           +      GR ++++
Sbjct: 61  LKNKKLHGRILRLD 74

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

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

 Score = 40.7 bits (95), Expect = 3e-05
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           ++VG + +  + ++L+ +F   G V   TI  +   G  +GF +I F D  SV+  +   
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 154 ESLFRGRQIKVNPKR 168
           E    GR I  +PK+
Sbjct: 62  EHRLDGRLI--DPKK 74

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

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

 Score = 40.3 bits (95), Expect = 3e-05
 Identities = 21/71 (29%), Positives = 36/71 (50%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           ++VG +    T E+L  +F   G+V  V I+ +K  G  +GFA++ F D D V   +   
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQK 61

Query: 154 ESLFRGRQIKV 164
                G +++V
Sbjct: 62  YHTINGHRVEV 72

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|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 40.0 bits (94), Expect = 5e-05
 Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 10/80 (12%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNR--------VTILCNKFDGHPKGFAYIEFADKDS 145
           IY+  +    T + L   F G G + R        + I  +K +  PKG A + + D  +
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDK-ETEPKGEATVTYDDPSA 59

Query: 146 VQTAMAM-DESLFRGRQIKV 164
            Q A+   +   FRG +IKV
Sbjct: 60  AQAAIEWFNGYEFRGNKIKV 79

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

>gnl|CDD|240906 cd12460, RRM2_CID8_like, RNA recognition motif 2 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 40.2 bits (94), Expect = 5e-05
 Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 3/79 (3%)

Query: 92  RSIYVGNVDYGATAEELESHFHG-CGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
           R+IY  N+D   T  +++  F   CG V+R+ +L +    H    A++EFA  +S   A+
Sbjct: 5   RTIYCTNIDKKVTQSDVKLFFESLCGEVSRLRLLGDYH--HSTRIAFVEFAMAESAIAAL 62

Query: 151 AMDESLFRGRQIKVNPKRT 169
               ++     I+V+P +T
Sbjct: 63  NCSGAVLGSLPIRVSPSKT 81

This subgroup corresponds to the RRM2 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 = 82

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

 Score = 39.9 bits (94), Expect = 5e-05
 Identities = 15/50 (30%), Positives = 27/50 (54%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFAD 142
           ++++G+++       + S F  CG V  V I+ NK  G   G+ ++EFA 
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFAT 50

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

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

 Score = 40.0 bits (94), Expect = 6e-05
 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 93  SIYVGNVDYGATAEELESHFHG-CGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
           SI+VG++    T   L+  F     SV    ++ +   G  KG+ ++ F D+D    A+ 
Sbjct: 3   SIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALT 62

Query: 152 -MDESLFRGRQIKVNP 166
            M+      R ++V+P
Sbjct: 63  EMNGVYCSSRPMRVSP 78

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

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

 Score = 39.6 bits (93), Expect = 6e-05
 Identities = 16/56 (28%), Positives = 28/56 (50%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA 149
           + VGN+    T E+        G+V R  ++ ++  G  KG+ ++E+A K S   A
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKA 57

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

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

 Score = 39.8 bits (94), Expect = 6e-05
 Identities = 25/84 (29%), Positives = 38/84 (45%), Gaps = 17/84 (20%)

Query: 92  RSIYVGNVDYGATAEELESHFHGC-----------GSVNRVTILCNKFDGHPKGFAYIEF 140
           R +YVGN+  G T EEL   F+               V  V I         K FA++EF
Sbjct: 2   RRLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQI------NPEKNFAFVEF 55

Query: 141 ADKDSVQTAMAMDESLFRGRQIKV 164
              +    A+A+D  +F+G+ +K+
Sbjct: 56  RTVEEATAALALDGIIFKGQPLKI 79

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

>gnl|CDD|240842 cd12396, RRM1_Nop13p_fungi, RNA recognition motif 1 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 39.8 bits (93), Expect = 8e-05
 Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 11/80 (13%)

Query: 94  IYVGNVDYGATAEELESHF-------HGCGSVNRVTI--LCNKFDGHP--KGFAYIEFAD 142
           +++GN+ +  T E L   F            + RV +     K  G    KGFAY++F  
Sbjct: 1   VWIGNLSFTTTKEMLRQFFVSKSGDRITDEQITRVHMPDSKAKRKGVKQNKGFAYVDFTS 60

Query: 143 KDSVQTAMAMDESLFRGRQI 162
           +++ + A+A+ E +  GR++
Sbjct: 61  QEATKAAIALSEKILNGRKL 80

This subfamily corresponds to the RRM1 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 = 85

>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 39.2 bits (91), Expect = 9e-05
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFAD-KDSVQTAMAM 152
           +YVGN+  GA   ELE  F   G +  V I  N     P GFA++EF D +D+      +
Sbjct: 2   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 56

Query: 153 DESLFRGRQIKV 164
           D  +  G +++V
Sbjct: 57  DGKVICGSRVRV 68

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that 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. 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. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, 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 = 77

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

 Score = 39.2 bits (91), Expect = 1e-04
 Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           +++G + +  T ++L+ +F   G V   T+  +   G  +GF ++ F + +SV   M   
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 154 ESLFRGRQIKVNPKR 168
           E    G+ I  +PKR
Sbjct: 61  EHKLNGKVI--DPKR 73

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

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

 Score = 39.3 bits (91), Expect = 1e-04
 Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 2/78 (2%)

Query: 91  LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
           LR +++G + +  T E L SHF   G++    ++ +      +GF ++ ++  + V  AM
Sbjct: 2   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAM 61

Query: 151 AMDESLFRGRQIKVNPKR 168
                   GR   V PKR
Sbjct: 62  NARPHKVDGRV--VEPKR 77

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

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 21/93 (22%), Positives = 42/93 (45%), Gaps = 21/93 (22%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSV----------------NRVTILCNKFDGHPKG- 134
           R+++VGN+      ++L+  F   G +                 +V  +  KF  H K  
Sbjct: 1   RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKF--HDKKD 58

Query: 135 --FAYIEFADKDSVQTAMAMDESLFRGRQIKVN 165
              AY+ F +++S + A+ ++ + F G  I+V+
Sbjct: 59  NVNAYVVFKEEESAEKALKLNGTEFEGHHIRVD 91

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|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 = 38.9 bits (91), Expect = 1e-04
 Identities = 15/74 (20%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
            ++++G++    T E+L++ F   G +  + ++       P+G AY+    +     A+ 
Sbjct: 3   TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI------PPRGCAYVCMETRQDAHRALQ 56

Query: 151 AMDESLFRGRQIKV 164
            +      G++IKV
Sbjct: 57  KLRNVKLAGKKIKV 70

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

 Score = 38.8 bits (90), Expect = 1e-04
 Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 1/80 (1%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFAD-KDSVQTAMA 151
           S++V N+     +E+L   F   G +  V +  + +   P+GFAY++F D +D+      
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 152 MDESLFRGRQIKVNPKRTNR 171
           +D     GRQI++   + +R
Sbjct: 62  LDRKWICGRQIEIQFAQGDR 81

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

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

 Score = 38.8 bits (91), Expect = 1e-04
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
           + V N+ +  T  +L+  F   G V  VTI   K DG  KGFA+++F  K   + A+  +
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIP-RKPDGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 153 DESLFRGRQIKV 164
           +    +GR + V
Sbjct: 61  NGKKIKGRPVAV 72

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|240947 cd12503, RRM1_hnRNPH_GRSF1_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, G-rich sequence factor 1 (GRSF-1) and similar proteins

 Score = 38.5 bits (90), Expect = 1e-04
 Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 4/65 (6%)

Query: 103 ATAEELESHFHGC---GSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRG 159
           ATAE++ + F  C   G  N +    ++ +G P G A+IE   ++ V+ A+         
Sbjct: 11  ATAEDVLNFFSDCRIKGGENGIHFTYSR-EGRPSGEAFIELESEEDVEKALEKHNEHMGH 69

Query: 160 RQIKV 164
           R I+V
Sbjct: 70  RYIEV 74

This subfamily corresponds to the RRM1 of hnRNP H proteins and GRSF-1. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. These proteins have similar RNA binding affinities and specifically recognize the sequence GGGA. They can either stimulate or repress splicing upon binding to a GGG motif. hnRNP H binds to the RNA substrate in the presence or absence of these proteins, whereas hnRNP F binds to the nuclear mRNA only in the presence of cap-binding proteins. hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. hnRNP H3 may be involved in splicing arrest induced by heat shock. Most family members contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and play an important role in efficiently silencing the exon. Members in this family can regulate the alternative splicing of fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. Members in this family have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. They also include a cytoplasmic poly(A)+ mRNA binding protein, GRSF-1, which interacts with RNA in a G-rich element-dependent manner. They may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RRMs responsible for the RNA binding, and two auxiliary domains (an acidic alpha-helical domain and an N-terminal alanine-rich region) that may play a role in protein-protein interactions and provide binding specificity. . Length = 77

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

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 2/52 (3%)

Query: 103 ATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDE 154
            T E+L   F   G +  V+I+ +K  G  KGF Y++F  K S Q A+A++ 
Sbjct: 12  YTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFH-KPS-QAAVALEN 61

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

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 8/79 (10%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDG------HPKGFAYIEFADKDSV 146
            +Y+ N+ Y ++ E+LE  F        V I      G       P G AY EF+  +  
Sbjct: 1   RVYISNLSYSSSEEDLEE-FLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59

Query: 147 QTAM-AMDESLFRGRQIKV 164
           +  +  ++  +F+ R++ V
Sbjct: 60  EKVVKDLNGKVFKNRKLFV 78

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

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 4/73 (5%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA-MAM 152
           +YVGN+D   T + L   F   G +    ++    +     +A++E+ D  S   A   M
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLI---REHGNDPYAFVEYYDHRSAAAALQTM 57

Query: 153 DESLFRGRQIKVN 165
           +  L  G++IKVN
Sbjct: 58  NGRLILGQEIKVN 70

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 104 TAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA-MAMDESLFRGRQI 162
           T E+LE  F   G +    ++ +K  G    +A+IEF  K+  + A   MD  L   R+I
Sbjct: 16  TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRRI 75

Query: 163 KV 164
            V
Sbjct: 76  HV 77

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|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing Sarcoma Protein (EWS)

 Score = 38.3 bits (89), Expect = 2e-04
 Identities = 28/82 (34%), Positives = 41/82 (50%), Gaps = 9/82 (10%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSV--NR------VTILCNKFDGHPKGFAYIEFADKD 144
           +IYV  ++   T EEL   F  CG V  N+      V I  +K  G PKG A + + D  
Sbjct: 2   TIYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPP 61

Query: 145 SVQTAMAM-DESLFRGRQIKVN 165
           S + A+   D   F+G ++KV+
Sbjct: 62  SAKAAVEWFDGKDFQGSKLKVS 83

This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene. . Length = 84

>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 = 38.0 bits (89), Expect = 3e-04
 Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           ++V  +    T +ELE+ F   G V  V ++ +   G  +GF ++ F   +    A+  +
Sbjct: 4   LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63

Query: 153 DESLFRGRQIKV 164
           +     GR IKV
Sbjct: 64  NGKELEGRVIKV 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 40.9 bits (96), Expect = 3e-04
 Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 2/87 (2%)

Query: 80  NLSIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIE 139
            L  E K +A   ++YV N+D   T E+L   F  CG +    ++ ++  G  +GF ++ 
Sbjct: 274 ELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVC 332

Query: 140 FADKDSVQTAMA-MDESLFRGRQIKVN 165
           F++ +    A+  M   +  G+ + V 
Sbjct: 333 FSNPEEANRAVTEMHGRMLGGKPLYVA 359

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|241174 cd12730, RRM1_GRSF1, RNA recognition motif 1 in G-rich sequence factor 1 (GRSF-1) and similar proteins

 Score = 37.5 bits (87), Expect = 4e-04
 Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 4/67 (5%)

Query: 101 YGATAEELESHFHGC---GSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLF 157
           +  TAE++ + F  C      N V  L N+ DG P+G A IE   ++ VQ A+       
Sbjct: 11  WSCTAEDVMNFFDDCRIRNGENGVHFLLNR-DGKPRGDALIELESEEDVQKALEQHRHYM 69

Query: 158 RGRQIKV 164
             R ++V
Sbjct: 70  GQRYVEV 76

This subgroup corresponds to the RRM1 of GRSF-1, a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity. . Length = 79

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

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 19/84 (22%), Positives = 35/84 (41%), Gaps = 7/84 (8%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSV---NRVTILCNKFDGHPKGFAYIEFADKDSVQT 148
            +++VGN+  G + + +      CG V    RV    +   G  K F + EF D +    
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVK---DPSTGKLKAFGFCEFEDPEGALR 57

Query: 149 AM-AMDESLFRGRQIKVNPKRTNR 171
           A+  ++     G+++ V      R
Sbjct: 58  ALRLLNGLELGGKKLLVKVDAKTR 81

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

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

 Score = 37.5 bits (87), Expect = 5e-04
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 2/74 (2%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
           +++VG +D      E+ S F   GSV  V I+ ++  G  KG+ ++ F D   VQ  +  
Sbjct: 7   TVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKIVES 65

Query: 153 DESLFRGRQIKVNP 166
             + F G+++K+ P
Sbjct: 66  QIN-FHGKKLKLGP 78

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

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

 Score = 37.3 bits (87), Expect = 5e-04
 Identities = 19/71 (26%), Positives = 35/71 (49%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           I+VG +    T  +L  +F   G+V  V ++ +     P+GF +I F  +DSV   +   
Sbjct: 5   IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNEH 64

Query: 154 ESLFRGRQIKV 164
                G++++V
Sbjct: 65  FHDINGKKVEV 75

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

 Score = 37.0 bits (86), Expect = 5e-04
 Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
           I+VG++      E L + F   G ++   ++ +   G  KG+ ++ F  K+  + A+  M
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 153 DESLFRGRQIKVN 165
           +     GR I+ N
Sbjct: 62  NGQWLGGRAIRTN 74

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

 Score = 37.3 bits (86), Expect = 6e-04
 Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 1/80 (1%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFAD-KDSVQTAMA 151
           S++V NV      E+L   F   G +  V +  + +   P+GFAYI+F D +D+      
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 152 MDESLFRGRQIKVNPKRTNR 171
           ++     GRQI++   + +R
Sbjct: 62  LNRKWVCGRQIEIQFAQGDR 81

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

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

 Score = 37.2 bits (87), Expect = 7e-04
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 5/74 (6%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           IY+G + Y  T  ++   F   G +  + ++ +K  G  KGFA++ + D+ S  T +A+D
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRS--TILAVD 69

Query: 154 E---SLFRGRQIKV 164
                   GR I+V
Sbjct: 70  NLNGIKLLGRTIRV 83

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

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

 Score = 36.9 bits (86), Expect = 7e-04
 Identities = 18/80 (22%), Positives = 39/80 (48%), Gaps = 14/80 (17%)

Query: 91  LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
           + ++YVG +    T ++L  HF+  G +  +T++        +  A++ F  +++ + A 
Sbjct: 1   ITTLYVGGLGERVTEKDLRDHFYQFGEIRSITVV------PRQQCAFVTFTTREAAEKAA 54

Query: 151 AMDESLF-----RGRQIKVN 165
              E LF      GR++K+ 
Sbjct: 55  ---ERLFNKLIINGRRLKLK 71

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

 Score = 36.6 bits (85), Expect = 7e-04
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
           R++++GN++   T  +L   F   G +  + I   K  G    +A+I++AD  SV  AM 
Sbjct: 3   RTLFIGNLEKTTTYSDLREAFERFGEIIDIDI---KKQGGNPAYAFIQYADIASVVKAMR 59

Query: 151 AMDESLFRGRQIKV 164
            MD       ++K+
Sbjct: 60  KMDGEYLGNNRVKL 73

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

 Score = 36.8 bits (85), Expect = 8e-04
 Identities = 17/71 (23%), Positives = 33/71 (46%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           ++VG +       +L  HF   G V +  ++ +K  G  +GF ++ F + DS   A  + 
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVK 61

Query: 154 ESLFRGRQIKV 164
                G +++V
Sbjct: 62  FHPINGHRVEV 72

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

 Score = 36.5 bits (84), Expect = 8e-04
 Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           +++G + +  + ++L  +    G V   TI  +   G  +GF ++ F D  SV   + + 
Sbjct: 2   MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELK 61

Query: 154 ESLFRGRQIKVNPKR 168
           E    G+ I  +PKR
Sbjct: 62  EHKLDGKLI--DPKR 74

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

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

 Score = 36.4 bits (84), Expect = 9e-04
 Identities = 17/69 (24%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-A 151
           ++YV N+    T +EL   F   G++ +  +L +K  G P+G A++ +  ++  Q A+ +
Sbjct: 2   NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

Query: 152 MDESLFRGR 160
           ++ ++  G 
Sbjct: 62  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|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 36.2 bits (83), Expect = 0.001
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 91  LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
            R +++G + +  T E L +++   G +    ++ +      +GF ++ F+  + V  AM
Sbjct: 2   FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAM 61

Query: 151 AMDESLFRGRQIKVNPKR 168
           A       GR   V PKR
Sbjct: 62  AARPHTIDGRV--VEPKR 77

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

>gnl|CDD|240747 cd12301, RRM1_2_PAR10_like, RNA recognition motif 1 and 2 in poly [ADP-ribose] polymerase PARP-10, RNA recognition motif 2 in PARP-14, RNA recognition motif in N-myc-interactor (Nmi), interferon-induced 35 kDa protein (IFP 35), RNA-binding protein 43 (RBM43) and similar proteins

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 21/80 (26%), Positives = 32/80 (40%), Gaps = 11/80 (13%)

Query: 92  RSIYVGNVDYGATAEELESHF-----HGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSV 146
           R + V  +    + ++LE +F      G G V RV  L        KG A + FAD    
Sbjct: 1   RCVLVAGLPETVSDDKLELYFENKRRSGGGDVTRVQYL------REKGSALVTFADFKVA 54

Query: 147 QTAMAMDESLFRGRQIKVNP 166
           +  +   +    G Q+ V P
Sbjct: 55  ERVVKQKKHPLNGTQLSVRP 74

This subfamily corresponds to the RRM1 and RRM2 of PARP-10, RRM2 of PARP-14, RRM of N-myc-interactor (Nmi), interferon-induced 35 kDa protein (IFP 35) and RNA-binding protein 43 (RBM43). PARP-10 is a novel oncoprotein c-Myc-interacting protein with poly(ADP-ribose) polymerase activity. It is localized to the nuclear and cytoplasmic compartments. In addition to PARP activity, PARP-10 is also involved in the control of cell proliferation by inhibiting c-Myc- and E1A-mediated cotransformation of primary cells. PARP-10 may also play a role in nuclear processes including the regulation of chromatin, gene transcription, and nuclear/cytoplasmic transport. PARP-10 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two overlapping C-terminal domains composed of a glycine-rich region and a region with homology to catalytic domains of PARP enzymes (PARP domain). In addition, PARP-10 contains two ubiquitin-interacting motifs (UIM). PARP-14, also termed aggressive lymphoma protein 2, is a member of the B aggressive lymphoma (BAL) family of macrodomain-containing PARPs. Like PARP-10, PARP-14 also includes two RRMs at the N-terminus. Nmi, also termed N-myc and STAT interactor, is an interferon inducible protein that interacts with c-Myc, N-Myc, Max and c-Fos, and other transcription factors containing bHLH-ZIP, bHLH or ZIP domains. Besides binding Myc proteins, Nmi also associates with all the Stat family of transcription factors except Stat2. In response to cytokine (e.g. IL-2 and IFN-gamma) stimulation, Nmi can enhance Stat-mediated transcriptional activity through recruiting the Stat1 and Stat5 transcriptional coactivators, CREB-binding protein (CBP) and p300. IFP 35 is an interferon-induced leucine zipper protein that can specifically form homodimers. Distinct from known bZIP proteins, IFP 35 lacks a basic domain critical for DNA binding. In addition, IFP 35 may negatively regulate other bZIP transcription factors by protein-protein interaction. For instance, it can form heterodimers with B-ATF, a member of the AP1 transcription factor family. Both Nmi and IFP35 harbor one RRM. RBM43 is a putative RNA-binding protein containing one RRM, but its biological function remains unclear. . Length = 74

>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 38.5 bits (89), Expect = 0.001
 Identities = 31/138 (22%), Positives = 62/138 (44%), Gaps = 11/138 (7%)

Query: 31  SKCTDEAELAAMKARVREMEEEAEK--LKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKE 88
            K + E +    KA+   ME+  ++  LKQ ++   +Q+         N       ++  
Sbjct: 53  PKLSSEQKDDIQKAKKYAMEQSIKQVLLKQTKAHQQQQLE--------NQQRQQQRQQAL 104

Query: 89  ADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQT 148
           A +  +YVG++ +    + +   F   G +  + +  +   G  KGFA++E+   ++ Q 
Sbjct: 105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQL 164

Query: 149 AM-AMDESLFRGRQIKVN 165
           A+  M+  +  GR IKV 
Sbjct: 165 ALEQMNGQMLGGRNIKVG 182

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

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 11/65 (16%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPK---GFAYIEFADKDSVQT 148
           R ++VG +    T E+L  +F   G V  V I        PK    FA++ FAD +  Q+
Sbjct: 1   RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYI--------PKPFRAFAFVTFADPEVAQS 52

Query: 149 AMAMD 153
               D
Sbjct: 53  LCGED 57

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|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 35.6 bits (82), Expect = 0.002
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 7/72 (9%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
           ++VGN+    T EE+   F   G    +      F    KGF +I    +   + A A +
Sbjct: 4   LFVGNLPPDITEEEMRKLFEKYGKAGEI------FIHKDKGFGFIRLETRTLAEIAKAEL 57

Query: 153 DESLFRGRQIKV 164
           D    RG+Q++V
Sbjct: 58  DNMPLRGKQLRV 69

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|241087 cd12643, RRM_CFIm68, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 4/61 (6%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNR---VTILCNKFDGHPKGFAYIEFADKDSVQTA 149
           ++YVGN+ +  T ++L       G VN    +    N+ +G  KGFA I    + S +  
Sbjct: 1   ALYVGNLTWWTTDQDLTEAIQSIG-VNDLLEIKFFENRANGQSKGFALIVLGSESSSRKL 59

Query: 150 M 150
           M
Sbjct: 60  M 60

This subgroup corresponds to the RRM of CFIm68. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. The family includes CFIm68, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF6), or cleavage and polyadenylation specificity factor 68 kDa subunit (CPSF68), or protein HPBRII-4/7. CFIm68 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. The N-terminal RRM of CFIm68 mediates the interaction with CFIm25. It also serves to enhance RNA binding and facilitate RNA looping. . Length = 77

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

 Score = 35.7 bits (82), Expect = 0.002
 Identities = 16/55 (29%), Positives = 28/55 (50%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSV 146
           + I+VG +        L  +F   G +  + I+ ++  G  +GFA++ F D DSV
Sbjct: 1   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 55

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

>gnl|CDD|240740 cd12294, RRM_Rrp7A, RNA recognition motif in ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 20/76 (26%), Positives = 29/76 (38%), Gaps = 15/76 (19%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCN-------------KFDGHPKGF--A 136
           R+++V NV    T E L+  F  CG V  V +                      KGF  A
Sbjct: 1   RTLFVLNVPPYCTEESLKRLFSRCGKVESVELQEKPGPAESEDLTSKFFPPKPIKGFKVA 60

Query: 137 YIEFADKDSVQTAMAM 152
           Y+ F    S+  A+ +
Sbjct: 61  YVVFKKPSSLSRALKL 76

This subfamily corresponds to the RRM of Rrp7A, also termed gastric cancer antigen Zg14, a homolog of yeast ribosomal RNA-processing protein 7 (Rrp7p), and mainly found in Metazoa. Rrp7p is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. In contrast, the cellular function of Rrp7A remains unclear currently. Rrp7A harbors an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal Rrp7 domain. . Length = 102

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 9/74 (12%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
           + +YV N+    T E+L   F   G V RV           K +A++ F ++D    AM 
Sbjct: 2   KVLYVRNLPLSTTEEQLRELFSEYGEVERVKK--------IKDYAFVHFEERDDAVKAME 53

Query: 151 AMDESLFRGRQIKV 164
            M+     G  I+V
Sbjct: 54  EMNGKELEGSPIEV 67

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

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 3/66 (4%)

Query: 102 GATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AMDESLF--R 158
             T ++L   F   G +  + ++ +K     KG AY++FA   S   AM  M+       
Sbjct: 13  SVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGD 72

Query: 159 GRQIKV 164
            + +KV
Sbjct: 73  TKPLKV 78

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

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

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA- 151
           +I+VG++    T   L + F    S +   ++ +   G  +G+ ++ F  +   + A+  
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 152 MDESLFRGRQIKVN 165
           M+      R I+ N
Sbjct: 61  MNGKWLGSRPIRCN 74

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

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

 Score = 35.4 bits (82), Expect = 0.002
 Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           +++G + Y  T + L+++F   G +    ++ +      +GF ++ FA    V  AM   
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNAR 61

Query: 154 ESLFRGRQIKVNPKR 168
                GR+  V PKR
Sbjct: 62  PHKVDGRE--VEPKR 74

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

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

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           +++G +++  T + L  +F   G V   T++ +   G  +GF ++ F    SV   M   
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMK-K 59

Query: 154 ESLFRGRQIKVNPKR 168
           E +  G+ I  +PKR
Sbjct: 60  EHILDGKII--DPKR 72

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

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

 Score = 35.2 bits (81), Expect = 0.003
 Identities = 17/76 (22%), Positives = 31/76 (40%)

Query: 91  LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
           L  ++VG ++   +   L  HF   G +    ++ +      +GF +I F+  D    AM
Sbjct: 2   LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61

Query: 151 AMDESLFRGRQIKVNP 166
                   G QI++  
Sbjct: 62  EAQPHSIDGNQIELKR 77

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

 Score = 35.5 bits (81), Expect = 0.003
 Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 2/78 (2%)

Query: 91  LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
           LR +++G + +  T + L  HF   G++    ++ +      +GF ++ ++  + V  AM
Sbjct: 2   LRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM 61

Query: 151 AMDESLFRGRQIKVNPKR 168
           +       GR   V PKR
Sbjct: 62  SARPHKVDGRV--VEPKR 77

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

>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 34.8 bits (80), Expect = 0.003
 Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 7/78 (8%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNK-FDGHPKGFAYIEFADKDSVQTAMAM 152
           +YVGN+D   T + L+  F   G V  V I+ +K   G   GF  +E+      + A+  
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGF--VEYHQSHDAEIAL-- 56

Query: 153 DESLFRGRQIKVNPKRTN 170
                 GRQI+ N  R N
Sbjct: 57  --QTLNGRQIENNEIRVN 72

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|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 5/60 (8%)

Query: 106 EELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AMDESLFRGRQIKV 164
           ++L       G V +V +    FD HP G A ++F + +     + A++   F GRQ++ 
Sbjct: 27  DDLREECEKFGQVKKVVV----FDRHPDGVASVKFKEPEEADRCIEALNGRWFAGRQLEA 82

This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. . Length = 91

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

 Score = 34.5 bits (80), Expect = 0.004
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 6/73 (8%)

Query: 96  VGNVDYGATAEELESHFHGCGSVNRVTILCNKFD--GHPKGFAYIEFADKDSVQTAMA-M 152
           V N+ Y  T E+LE  F   G V +V I    +D  G  +G A + F  ++  + A+   
Sbjct: 5   VSNLHYDVTEEDLEELFGRVGEVKKVKI---NYDRSGRSEGTADVVFEKREDAERAIKQF 61

Query: 153 DESLFRGRQIKVN 165
           +  L  G+ ++V 
Sbjct: 62  NGVLLDGQPMQVE 74

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|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 = 35.1 bits (81), Expect = 0.004
 Identities = 21/84 (25%), Positives = 41/84 (48%), Gaps = 4/84 (4%)

Query: 87  KEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSV 146
           K+ D   ++VG +      ++L   F   G +  +T+L +K+ G  KG A++ +  ++S 
Sbjct: 1   KDDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESA 60

Query: 147 QTAMAM--DESLFRG--RQIKVNP 166
             A +   ++    G  R I+V P
Sbjct: 61  LKAQSALHEQKTLPGMNRPIQVKP 84

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

 Score = 34.4 bits (79), Expect = 0.004
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 4/72 (5%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFAD-KDSVQTAMAM 152
           +YVGN+       E+E  F+  G +  + +   K    P G+A+IEF D +D+       
Sbjct: 2   VYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAEDAIRGR 58

Query: 153 DESLFRGRQIKV 164
           D   F G++++V
Sbjct: 59  DGYDFDGQRLRV 70

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

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

 Score = 34.7 bits (79), Expect = 0.004
 Identities = 13/55 (23%), Positives = 27/55 (49%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSV 146
           + ++VG +        L  +F   G ++ + I+ ++  G  +GF ++ F D D V
Sbjct: 1   KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPV 55

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

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 34.4 bits (79), Expect = 0.004
 Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 5/77 (6%)

Query: 90  DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA 149
           D R+++V N+ Y  T +EL+  F     +   +      DG  KG AYIEF  +   + A
Sbjct: 2   DARTLFVKNLPYNITVDELKEVFEDAVDIRLPS----GKDGSSKGIAYIEFKTEAEAEKA 57

Query: 150 MA-MDESLFRGRQIKVN 165
           +     +   GR I V+
Sbjct: 58  LEEKQGAEVDGRSIVVD 74

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	207
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		7e-43
3ucg_A	89	Crystal Structure Of A Rna Binding Domain Of Hypoth		9e-43
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		3e-39
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		2e-09
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		3e-08
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		9e-07
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		2e-06
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		4e-06
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		2e-05
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		2e-05
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		4e-05
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-05
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		4e-05
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		5e-05
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		5e-05
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		5e-05
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		5e-05
2hzc_A	87	Crystal Structure Of The N-terminal Rrm Of The U2af		6e-05
1u2f_A	90	Solution Structure Of The First Rna-Binding Domain		6e-05
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		8e-05
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		8e-05
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		8e-05
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		1e-04
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		1e-04
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		1e-04
2hvz_A	101	Solution Structure Of The Rrm Domain Of Sr Rich Fac		2e-04
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		3e-04
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		4e-04
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		4e-04
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		5e-04
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		5e-04
2dng_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		6e-04

>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm Length = 96

Iteration: 1
 Score =  169 bits (429), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 76/87 (87%), Positives = 84/87 (96%)
Query: 88  EADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQ 147
           EAD RSIYVGNVDYGATAEELE+HFHGCGSVNRVTILC+KF GHPKGFAYIEF+DK+SV+
Sbjct: 2   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 61
Query: 148 TAMAMDESLFRGRQIKVNPKRTNRPGI 174
           T++A+DESLFRGRQIKV PKRTNRPGI
Sbjct: 62  TSLALDESLFRGRQIKVIPKRTNRPGI 88

>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens At 1.95 A Resolution Length = 89

Iteration: 1
 Score =  169 bits (428), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 76/87 (87%), Positives = 84/87 (96%)
Query: 88  EADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQ 147
           EAD RSIYVGNVDYGATAEELE+HFHGCGSVNRVTILC+KF GHPKGFAYIEF+DK+SV+
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 148 TAMAMDESLFRGRQIKVNPKRTNRPGI 174
           T++A+DESLFRGRQIKV PKRTNRPGI
Sbjct: 63  TSLALDESLFRGRQIKVIPKRTNRPGI 89

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score =  157 bits (398), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 68/95 (71%), Positives = 85/95 (89%)
Query: 84  EEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADK 143
           EEKKE D RS+YVGNVDYG+TA++LE+HF  CGS+NR+TILC+KF GHPKG+AYIEFA++
Sbjct: 29  EEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAER 88
Query: 144 DSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTN 178
           +SV  A+AMDE++FRGR IKV PKRTN PGIS+T+
Sbjct: 89  NSVDAAVAMDETVFRGRTIKVLPKRTNMPGISSTD 123

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 32/83 (38%), Positives = 53/83 (63%), Gaps = 5/83 (6%)
Query: 91  LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
           +R+IYVGN+ Y AT+E+++  F   G V  V ++ ++    PKGF ++E  + +SV  A+
Sbjct: 1   MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAI 59
Query: 151 A-MDESLFRGRQIKV---NPKRT 169
           A +D + F GR I+V   NPK++
Sbjct: 60  AKLDNTDFMGRTIRVTEANPKKS 82

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 54.7 bits (130), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 91  LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
           LRS++VGN+ Y AT E+L+  F   G V    ++ ++  G PKG+ + E+ D+++  +AM
Sbjct: 8   LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
Query: 151 A-MDESLFRGRQIKVN 165
             ++   F GR ++V+
Sbjct: 68  RNLNGREFSGRALRVD 83

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 50.1 bits (118), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 91  LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
           + S+ V N+ Y  + + L   F   G V  V I  +++    +GFA++ F DK   + AM
Sbjct: 70  MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 129
Query: 151 -AMDESLFRGRQIKVNPKRTNRP 172
            AMD ++  GR+++V   R  RP
Sbjct: 130 DAMDGAVLDGRELRVQMARYGRP 152

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 91  LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
           + S+ V N+ Y  + + L   F   G V  V I  +++    +GFA++ F DK   + AM
Sbjct: 47  MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 151 -AMDESLFRGRQIKVNPKRTNRP 172
            AMD ++  GR+++V   R  RP
Sbjct: 107 DAMDGAVLDGRELRVQMARYGRP 129

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 48.1 bits (113), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 36/73 (49%)
Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           ++VG +D+  T E L S+F   G V    I+ +K     +GF +++F D + V T +A  
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 154 ESLFRGRQIKVNP 166
                GR I   P
Sbjct: 79  PHTLDGRNIDPKP 91

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-A 151
           ++YV N+ +  T  +L   F   G V +VTI+ +K     KG A+I F DKDS Q    A
Sbjct: 18  TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 152 MDESLFRGRQIK 163
           ++     GR IK
Sbjct: 78  INNKQLFGRVIK 89

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/81 (34%), Positives = 45/81 (55%), Gaps = 3/81 (3%)
Query: 86  KKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDS 145
           ++EAD R+++VGN++     E L   F   G + +VTI C   +G PK F ++ F   +S
Sbjct: 12  QEEAD-RTVFVGNLEARVREEILYELFLQAGPLTKVTI-CKDREGKPKSFGFVCFKHPES 69
Query: 146 VQTAMAMDESL-FRGRQIKVN 165
           V  A+A+   +   GR I V+
Sbjct: 70  VSYAIALLNGIRLYGRPINVS 90

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/98 (27%), Positives = 44/98 (44%), Gaps = 8/98 (8%)
Query: 86  KKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDS 145
           K+   LR +++G + +  T E L SHF   G++    ++ +      +GF ++ +A  + 
Sbjct: 7   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 66
Query: 146 VQTAMAMDESLFRGRQIKVNPKR------TNRPGISTT 177
           V  AM        GR   V PKR      + RPG   T
Sbjct: 67  VDAAMNARPHKVDGRV--VEPKRAVSREDSQRPGAHLT 102

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/98 (27%), Positives = 44/98 (44%), Gaps = 8/98 (8%)
Query: 86  KKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDS 145
           K+   LR +++G + +  T E L SHF   G++    ++ +      +GF ++ +A  + 
Sbjct: 8   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 67
Query: 146 VQTAMAMDESLFRGRQIKVNPKR------TNRPGISTT 177
           V  AM        GR   V PKR      + RPG   T
Sbjct: 68  VDAAMNARPHKVDGRV--VEPKRAVSREDSQRPGAHLT 103

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/98 (27%), Positives = 44/98 (44%), Gaps = 8/98 (8%)
Query: 86  KKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDS 145
           K+   LR +++G + +  T E L SHF   G++    ++ +      +GF ++ +A  + 
Sbjct: 9   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 68
Query: 146 VQTAMAMDESLFRGRQIKVNPKR------TNRPGISTT 177
           V  AM        GR   V PKR      + RPG   T
Sbjct: 69  VDAAMNARPHKVDGRV--VEPKRAVSREDSQRPGAHLT 104

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 27/98 (27%), Positives = 44/98 (44%), Gaps = 8/98 (8%)
Query: 86  KKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDS 145
           K+   LR +++G + +  T E L SHF   G++    ++ +      +GF ++ +A  + 
Sbjct: 8   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 67
Query: 146 VQTAMAMDESLFRGRQIKVNPKR------TNRPGISTT 177
           V  AM        GR   V PKR      + RPG   T
Sbjct: 68  VDAAMNARPHKVDGRV--VEPKRAVSREDSQRPGAHLT 103

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 27/98 (27%), Positives = 44/98 (44%), Gaps = 8/98 (8%)
Query: 86  KKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDS 145
           K+   LR +++G + +  T E L SHF   G++    ++ +      +GF ++ +A  + 
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60
Query: 146 VQTAMAMDESLFRGRQIKVNPKR------TNRPGISTT 177
           V  AM        GR   V PKR      + RPG   T
Sbjct: 61  VDAAMNARPHKVDGRV--VEPKRAVSREDSQRPGAHLT 96

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 27/98 (27%), Positives = 44/98 (44%), Gaps = 8/98 (8%)
Query: 86  KKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDS 145
           K+   LR +++G + +  T E L SHF   G++    ++ +      +GF ++ +A  + 
Sbjct: 6   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 65
Query: 146 VQTAMAMDESLFRGRQIKVNPKR------TNRPGISTT 177
           V  AM        GR   V PKR      + RPG   T
Sbjct: 66  VDAAMNARPHKVDGRV--VEPKRAVSREDSQRPGAHLT 101

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
           ++V N+ Y ++ E+LE  F   G ++ +    +     PKGFA++ F   +    A A +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 153 DESLFRGRQIKVNPKRTNR 171
           D  +F+GR + V P    +
Sbjct: 71  DGQVFQGRMLHVLPSTIKK 89

>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large Subunit Length = 87

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 13/82 (15%)
Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHP---------KGFAYIEFAD 142
           R +YVGN+ +G T E +   F+    +  +T    +  G+P         K FA++EF  
Sbjct: 7   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLT----QAPGNPVLAVQINQDKNFAFLEFRS 62
Query: 143 KDSVQTAMAMDESLFRGRQIKV 164
            D    AMA D  +F+G+ +K+
Sbjct: 63  VDETTQAMAFDGIIFQGQSLKI 84

>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of Hu2af65 Length = 90

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 13/82 (15%)
Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHP---------KGFAYIEFAD 142
           R +YVGN+ +G T E +   F+    +  +T    +  G+P         K FA++EF  
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLT----QAPGNPVLAVQINQDKNFAFLEFRS 57
Query: 143 KDSVQTAMAMDESLFRGRQIKV 164
            D    AMA D  +F+G+ +K+
Sbjct: 58  VDETTQAMAFDGIIFQGQSLKI 79

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 43.5 bits (101), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 13/82 (15%)
Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHP---------KGFAYIEFAD 142
           R +YVGN+ +G T E +   F+    +  +T    +  G+P         K FA++EF  
Sbjct: 7   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLT----QAPGNPVLAVQINQDKNFAFLEFRS 62
Query: 143 KDSVQTAMAMDESLFRGRQIKV 164
            D    AMA D  +F+G+ +K+
Sbjct: 63  VDETTQAMAFDGIIFQGQSLKI 84

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 43.5 bits (101), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 13/82 (15%)
Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHP---------KGFAYIEFAD 142
           R +YVGN+ +G T E +   F+    +  +T    +  G+P         K FA++EF  
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLT----QAPGNPVLAVQINQDKNFAFLEFRS 60
Query: 143 KDSVQTAMAMDESLFRGRQIKV 164
            D    AMA D  +F+G+ +K+
Sbjct: 61  VDETTQAMAFDGIIFQGQSLKI 82

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 43.5 bits (101), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 13/82 (15%)
Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHP---------KGFAYIEFAD 142
           R +YVGN+ +G T E +   F+    +  +T    +  G+P         K FA++EF  
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLT----QAPGNPVLAVQINQDKNFAFLEFRS 60
Query: 143 KDSVQTAMAMDESLFRGRQIKV 164
            D    AMA D  +F+G+ +K+
Sbjct: 61  VDETTQAMAFDGIIFQGQSLKI 82

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/80 (23%), Positives = 38/80 (47%)
Query: 86  KKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDS 145
           +K+     I+VG + Y  T   L  +F G G +    ++ ++  G  +G+ ++  AD+ +
Sbjct: 12  QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA 71
Query: 146 VQTAMAMDESLFRGRQIKVN 165
            + A      +  GR+  VN
Sbjct: 72  AERACKDPNPIIDGRKANVN 91

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 91  LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
            ++++V  V+Y  T  +L   F   G + R+ ++ +K  G P+G+A+IE+  +  + +A 
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 151 A-MDESLFRGRQIKVNPKR 168
              D     GR++ V+ +R
Sbjct: 162 KHADGKKIDGRRVLVDVER 180

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 91  LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
            ++++V  V+Y  T  +L   F   G + R+ ++ +K  G P+G+A+IE+  +  + +A 
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 151 A-MDESLFRGRQIKVN 165
              D     GR++ V+
Sbjct: 162 KHADGKKIDGRRVLVD 177

>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8 Length = 101

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 6/72 (8%)
Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFAD-KDSVQTAMAM 152
           +YVGN+  GA   ELE  F   G +  V I  N     P GFA++EF D +D+      +
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 153 DESLFRGRQIKV 164
           D  +  G +++V
Sbjct: 58  DGKVICGSRVRV 69

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 3/86 (3%)
Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           I+VG + +     EL  +F   G V  V ++ +     P+GF +I F D+ SV  A+ M 
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 154 ESLFRGRQIKVN---PKRTNRPGIST 176
                G++++V    P+ +   G S+
Sbjct: 73  FHDIMGKKVEVKRAEPRDSKSSGPSS 98

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/87 (27%), Positives = 44/87 (50%), Gaps = 4/87 (4%)
Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA-MAM 152
           ++VG + +    + LE  F   G ++ V ++ ++     +GF ++ F + D  + A MAM
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 153 DESLFRGRQIKVN---PKRTNRPGIST 176
           +     GRQI+V+       NR G S+
Sbjct: 75  NGKSVDGRQIRVDQAGKSSDNRSGPSS 101

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           +++G + +  T ++L+ +F   G V   T+  +   G  +GF ++ F + +SV   M   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 154 ESLFRGRQIKVNPKR 168
           E    G+ I  +PKR
Sbjct: 62  EHKLNGKVI--DPKR 74

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 2/83 (2%)
Query: 86  KKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDS 145
           K E D    +VG + +  + ++L+ +F   G V   TI  +   G  +GF +I F D  S
Sbjct: 6   KNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAAS 65
Query: 146 VQTAMAMDESLFRGRQIKVNPKR 168
           V+  +   E    GR I  +PK+
Sbjct: 66  VEKVLDQKEHRLDGRVI--DPKK 86

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA-MA 151
           ++ V N+ Y  + + L   F   G V  V I        P+GFA++ F D+   Q A  A
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 152 MDESLFRGRQIKVNPKRTNRPGIS 175
           MD +   GR+++V   R  R  +S
Sbjct: 75  MDGAELDGRELRVQVARYGRRDLS 98

>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 4h Length = 103

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 95  YVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDE 154
           YVGN+ +     ++++ F    S+  V ++ +K     KGF Y+EF + DS++ A+  D 
Sbjct: 19  YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDG 77
Query: 155 SLFRGRQIKVN 165
           +L   R ++V+
Sbjct: 78  ALLGDRSLRVD 88

---

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	207
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-17
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	9e-17
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-16
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-16
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	7e-16
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-15
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-15
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-14
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-14
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	8e-14
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-13
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-13
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-13
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-13
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-13
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-13
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-13
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-13
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-13
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	6e-13
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	7e-13
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	7e-13
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	7e-13
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-12
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-12
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-12
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	4e-12
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-12
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	4e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	6e-12
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	6e-12
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	8e-10
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	7e-12
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-12
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	9e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-11
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-11
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-11
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-11
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	5e-11
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-11
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	8e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	9e-11
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-10
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-10
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-10
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-10
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-10
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-10
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	3e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	4e-10
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	4e-10
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	9e-10
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-09
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-09
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-09
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	8e-09
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	9e-09
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-08
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-08
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-08
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	4e-08
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	4e-08
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	6e-08
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-07
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-07
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-07
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-07
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	5e-07
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	6e-07
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	1e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-06
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	6e-06
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-06
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-05
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-05
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	3e-05
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	8e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.003
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	0.004
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	0.004

>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 = 70.8 bits (173), Expect = 4e-17
 Identities = 14/72 (19%), Positives = 29/72 (40%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           +++G + +  T E L  +F   G V    ++ +      +GF ++ F D+  V   +A  
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 154 ESLFRGRQIKVN 165
                 + I   
Sbjct: 63  RHELDSKTIDPK 74

>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 = 70.5 bits (172), Expect = 9e-17
 Identities = 15/83 (18%), Positives = 38/83 (45%)

Query: 84  EEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADK 143
           +++++   R +++G + +  T E L +++   G +    ++ +      +GF ++ F+  
Sbjct: 13  KKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSM 72

Query: 144 DSVQTAMAMDESLFRGRQIKVNP 166
             V  AMA       GR ++   
Sbjct: 73  AEVDAAMAARPHSIDGRVVEPKR 95

>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 = 69.6 bits (170), Expect = 1e-16
 Identities = 15/79 (18%), Positives = 35/79 (44%), Gaps = 1/79 (1%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-A 151
           S+YVG++    T   L   F   G +  + +  +       G+AY+ F      + A+  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 152 MDESLFRGRQIKVNPKRTN 170
           M+  + +G+ +++   + +
Sbjct: 62  MNFDVIKGKPVRIMWSQRD 80

>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 = 68.5 bits (167), Expect = 5e-16
 Identities = 24/89 (26%), Positives = 37/89 (41%), Gaps = 2/89 (2%)

Query: 85  EKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKD 144
             +E D R+++   +       +LE  F   G V  V I+ ++     KG AY+EF +  
Sbjct: 12  SPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQ 71

Query: 145 SVQTAMAMDESLFRGRQIKVNP--KRTNR 171
           SV  A+ +      G  I V       NR
Sbjct: 72  SVPLAIGLTGQRLLGVPIIVQASQAEKNR 100

>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 = 67.8 bits (165), Expect = 7e-16
 Identities = 19/80 (23%), Positives = 37/80 (46%)

Query: 86  KKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDS 145
           K+   LR +++G + +  T E L SHF   G++    ++ +      +GF ++ +A  + 
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 146 VQTAMAMDESLFRGRQIKVN 165
           V  AM        GR ++  
Sbjct: 61  VDAAMNARPHKVDGRVVEPK 80

>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 = 65.4 bits (159), Expect = 5e-15
 Identities = 14/72 (19%), Positives = 31/72 (43%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           I+VG +      E++  +F G G V  + +  +      +GF +I F +++ V+  M   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 154 ESLFRGRQIKVN 165
                  + ++ 
Sbjct: 62  YHNVGLSKCEIK 73

>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 = 65.2 bits (158), Expect = 7e-15
 Identities = 24/86 (27%), Positives = 39/86 (45%), Gaps = 5/86 (5%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTIL-----CNKFDGHPKGFAYIEFADKDSV 146
           R +YVGN+ +G T E +   F+    +  +T               K FA++EF   D  
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 147 QTAMAMDESLFRGRQIKVNPKRTNRP 172
             AMA D  +F+G+ +K+      +P
Sbjct: 62  TQAMAFDGIIFQGQSLKIRRPHDYQP 87

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.6 bits (157), Expect = 1e-14
 Identities = 19/90 (21%), Positives = 41/90 (45%), Gaps = 1/90 (1%)

Query: 85  EKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKD 144
           EK      ++YVGN+ +  T E++   F   G + ++ +  +K      GF ++E+  + 
Sbjct: 1   EKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRA 60

Query: 145 SVQTAM-AMDESLFRGRQIKVNPKRTNRPG 173
             + AM  ++ +    R I+ +     + G
Sbjct: 61  DAENAMRYINGTRLDDRIIRTDWDAGFKEG 90

>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 = 63.1 bits (153), Expect = 3e-14
 Identities = 17/72 (23%), Positives = 34/72 (47%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           +++G + +  T ++L+ +F   G V   T+  +   G  +GF ++ F + +SV   M   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61

Query: 154 ESLFRGRQIKVN 165
           E    G+ I   
Sbjct: 62  EHKLNGKVIDPK 73

>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 = 61.9 bits (150), Expect = 8e-14
 Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 4/82 (4%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-A 151
           ++ V  +    T  EL + F   G +N   I+ +   G+  G+A+++F  +   Q A+  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 152 MDESLFRGRQIKVNPKRTNRPG 173
           ++    R +++KV+     RPG
Sbjct: 64  LNGITVRNKRLKVSYA---RPG 82

>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 = 62.0 bits (150), Expect = 1e-13
 Identities = 18/84 (21%), Positives = 38/84 (45%), Gaps = 5/84 (5%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFD---GHPKGFAYIEFADKDSVQTAM 150
           +++ N+++  T E L+  F   G++   TI   K         GF ++E+   +  Q A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 151 -AMDESLFRGRQIKVNP-KRTNRP 172
             +      G +++V   +R  +P
Sbjct: 61  KQLQGHTVDGHKLEVRISERATKP 84

>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 = 61.7 bits (149), Expect = 1e-13
 Identities = 18/74 (24%), Positives = 32/74 (43%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
           + I+VG +        L  +F   G +  + I+ ++  G  +GFA++ F D DSV   + 
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 152 MDESLFRGRQIKVN 165
                  G   +V 
Sbjct: 63  QKYHTVNGHNCEVR 76

>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 = 62.1 bits (150), Expect = 2e-13
 Identities = 21/96 (21%), Positives = 43/96 (44%), Gaps = 6/96 (6%)

Query: 86  KKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDS 145
           +K+     I+VG + Y  T   L  +F G G +    ++ ++  G  +G+ ++  AD+ +
Sbjct: 5   QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA 64

Query: 146 VQTAMAMDESLFRGRQIKVNPK------RTNRPGIS 175
            + A      +  GR+  VN        R+ + G +
Sbjct: 65  AERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFA 100

>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 = 61.7 bits (149), Expect = 2e-13
 Identities = 22/88 (25%), Positives = 40/88 (45%), Gaps = 3/88 (3%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
            + ++GN+ Y  T E ++  F G                  KGF Y EF D DS+ +A++
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 152 MDESLFRGRQIKVN---PKRTNRPGIST 176
           ++E     ++I+V+     +    G S+
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKDSGPSS 103

>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 = 60.9 bits (147), Expect = 2e-13
 Identities = 14/72 (19%), Positives = 33/72 (45%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           I+VG +    T E+++ +F   G V+   ++ +K     +GF ++ F  +D V+    + 
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 154 ESLFRGRQIKVN 165
                 + ++  
Sbjct: 62  FHEINNKMVECK 73

>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 = 61.7 bits (149), Expect = 2e-13
 Identities = 29/100 (29%), Positives = 54/100 (54%), Gaps = 3/100 (3%)

Query: 86  KKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDS 145
             +  LRS++VGN+ Y AT E+L+  F   G V    ++ ++  G PKG+ + E+ D+++
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 146 VQTAM-AMDESLFRGRQIKVNP--KRTNRPGISTTNRGGP 182
             +AM  ++   F GR ++V+      N+  + +   G P
Sbjct: 63  ALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102

>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 = 60.9 bits (147), Expect = 2e-13
 Identities = 13/82 (15%), Positives = 30/82 (36%), Gaps = 1/82 (1%)

Query: 86  KKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDS 145
           K +   RS+Y+      AT ++++      G V     +        KG  ++ F   +S
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIES 59

Query: 146 VQTAMAMDESLFRGRQIKVNPK 167
            +  +      ++   + +  K
Sbjct: 60  AKKFVETPGQKYKETDLLILFK 81

>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 = 61.6 bits (149), Expect = 3e-13
 Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 4/82 (4%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
           R +Y+ N+ Y  TAEE+   F   G + ++           +G AY+ + D    + A  
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDAKNACD 64

Query: 151 AMDESLFRGRQIKVNPKRTNRP 172
            +       R + V     NR 
Sbjct: 65  HLSGFNVCNRYLVVLYYNANRA 86

>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 = 60.9 bits (147), Expect = 4e-13
 Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 5/93 (5%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
             ++V N+ Y ++ E+LE  F   G ++ +    +     PKGFA++ F   +    A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 151 AMDESLFRGRQIKVNPKRTNRPGISTTNRGGPR 183
            +D  +F+GR + V P    +      ++ GP 
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEA----SQSGPS 97

>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 = 60.4 bits (146), Expect = 4e-13
 Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 3/77 (3%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
            ++YV N+    T ++L++ F   GS+ +  IL +K  G P+G A++ +  ++  Q A+ 
Sbjct: 7   TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 66

Query: 151 AMDESLFRG--RQIKVN 165
           A++  +  G  + + V 
Sbjct: 67  ALNNVIPEGGSQPLSVR 83

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.7 bits (144), Expect = 6e-13
 Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 1/78 (1%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
            ++ V  +    T EE  S F   G +    ++ +K  G   G+ ++ + D    + A+ 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 151 AMDESLFRGRQIKVNPKR 168
            ++    + + IKV+  R
Sbjct: 63  TLNGLRLQTKTIKVSYAR 80

>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 = 60.0 bits (145), Expect = 7e-13
 Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 3/82 (3%)

Query: 87  KEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCN-KFDGHPKGFAYIEFADKDS 145
           K+     I V N+ + A   E+   F   G +  V +       G  +GF +++F  K  
Sbjct: 4   KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 63

Query: 146 VQTAMA--MDESLFRGRQIKVN 165
            + A       +   GR++ + 
Sbjct: 64  AKKAFNALCHSTHLYGRRLVLE 85

>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 = 59.7 bits (144), Expect = 7e-13
 Identities = 16/73 (21%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           I V N+ +  + +E+   F+G   +     L     G P G A + F  +D    A+  +
Sbjct: 12  IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 71

Query: 153 DESLFRGRQIKVN 165
           ++     R++K+ 
Sbjct: 72  NDRPIGSRKVKLV 84

>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 = 59.7 bits (144), Expect = 7e-13
 Identities = 15/81 (18%), Positives = 39/81 (48%), Gaps = 1/81 (1%)

Query: 86  KKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDS 145
           ++  +   ++V ++   A  +E++  F   G +  + +  ++  G  KG+A +E+     
Sbjct: 2   QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ 61

Query: 146 VQTAM-AMDESLFRGRQIKVN 165
              A  A++ +   G+ I+V+
Sbjct: 62  ALAAKEALNGAEIMGQTIQVD 82

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 2e-12
 Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
           R +YVG +      + L + F   G +  + I  +      +GFA++EF   +    A+ 
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

Query: 151 AMDESLFRGRQIKVNPKRTNRP 172
            M+ES   GR I+VN  +  R 
Sbjct: 66  NMNESELFGRTIRVNLAKPMRI 87

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 58.9 bits (142), Expect = 2e-12
 Identities = 23/100 (23%), Positives = 40/100 (40%), Gaps = 9/100 (9%)

Query: 76  NNLLNLSIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGF 135
           +++L      KK    R++   N+ +  T +EL+  F     +  V+      DG  KG 
Sbjct: 1   SHMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGI 55

Query: 136 AYIEFADKDSVQTAM-AMDESLFRGRQIKVN---PKRTNR 171
           AYIEF  +   +  +     +   GR + +     K   R
Sbjct: 56  AYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 2e-12
 Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 4/83 (4%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
            ++YVG +D   +   L   F   G V    +  ++  G  +G+ ++EF  ++    A+ 
Sbjct: 10  ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 69

Query: 151 AMDESLFRGRQIKVN---PKRTN 170
            MD     G+ I+VN       N
Sbjct: 70  IMDMIKLYGKPIRVNKASAHNKN 92

>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 = 58.3 bits (140), Expect = 4e-12
 Identities = 14/105 (13%), Positives = 34/105 (32%), Gaps = 2/105 (1%)

Query: 84  EEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADK 143
           E    +     ++ N+ +  T  ++     G         +    +G   G A ++F ++
Sbjct: 1   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 60

Query: 144 DSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRGGPRGRGRG 188
           D  + +  +      GR+  V+        +    +  P     G
Sbjct: 61  DDARKSERLHRKKLNGREAFVHV--VTLEDMREIEKNPPAQGKSG 103

>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 = 58.0 bits (140), Expect = 4e-12
 Identities = 16/90 (17%), Positives = 42/90 (46%), Gaps = 13/90 (14%)

Query: 92  RSIYVGNVD-YGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
             +++GN++       ++E+ F   G +   ++          GFA++++ ++ + + A+
Sbjct: 16  SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAFVQYVNERNARAAV 67

Query: 151 -AMDESLFRGRQIKVN---PKRTNRPGIST 176
              D  +  G+ + +N     + NR G S+
Sbjct: 68  AGEDGRMIAGQVLDINLAAEPKVNRSGPSS 97

>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 = 57.2 bits (138), Expect = 4e-12
 Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 2/73 (2%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           + V N+D+G +  +++  F   G++ +  +      G   G A + F  K     AM   
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAV-HYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 153 DESLFRGRQIKVN 165
           +     GR + + 
Sbjct: 62  NGVPLDGRPMNIQ 74

>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 = 57.4 bits (138), Expect = 6e-12
 Identities = 17/74 (22%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
             + V  +    T  +L   F   G +  V+I+ ++     +GFA++ F + D  + A  
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 151 AMDESLFRGRQIKV 164
             +     GR+I+V
Sbjct: 70  RANGMELDGRRIRV 83

>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 = 59.6 bits (143), Expect = 6e-12
 Identities = 18/75 (24%), Positives = 32/75 (42%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
           + I+VG +        L  +F   G +  + I+ ++  G  +GFA++ F D DSV   + 
Sbjct: 98  KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 157

Query: 152 MDESLFRGRQIKVNP 166
                  G   +V  
Sbjct: 158 QKYHTVNGHNCEVRK 172

>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 = 53.9 bits (128), Expect = 8e-10
 Identities = 17/67 (25%), Positives = 33/67 (49%)

Query: 86  KKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDS 145
           K+   LR +++G + +  T E L SHF   G++    ++ +      +GF ++ +A  + 
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 146 VQTAMAM 152
           V  AM  
Sbjct: 61  VDAAMNA 67

>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 = 57.4 bits (138), Expect = 7e-12
 Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 1/84 (1%)

Query: 86  KKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDS 145
           ++  D  +I V N+       +L+  F   GS++R+ +  +K  G  KGFA+I F  ++ 
Sbjct: 3   RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 62

Query: 146 VQTAM-AMDESLFRGRQIKVNPKR 168
              A+  +    +    + V   +
Sbjct: 63  AARAIAGVSGFGYDHLILNVEWAK 86

>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 = 56.9 bits (137), Expect = 8e-12
 Identities = 10/73 (13%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           +++G +      ++++      G +    ++ +   G  KG+A+ E+ D +    A+  +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 153 DESLFRGRQIKVN 165
           +      +++ V 
Sbjct: 64  NGMQLGDKKLLVQ 76

>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 = 56.9 bits (137), Expect = 9e-12
 Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 1/82 (1%)

Query: 85  EKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKD 144
           ++       + V  + +  T ++L+ +F   G V  V +  +   GH KGF ++ F + +
Sbjct: 2   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 61

Query: 145 SVQTAMAMDESLFRGRQIKVNP 166
           +    M+    +  GR      
Sbjct: 62  TQVKVMSQRHMI-DGRWCDCKL 82

>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 = 57.0 bits (137), Expect = 1e-11
 Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 4/80 (5%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           IYVGN+      +++E  F+  G++  +     K       FA++EF D    + A+   
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAIRDI---DLKNRRGGPPFAFVEFEDPRDAEDAVYGR 73

Query: 153 DESLFRGRQIKVNPKRTNRP 172
           D   + G +++V   R+ R 
Sbjct: 74  DGYDYDGYRLRVEFPRSGRG 93

>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 = 56.6 bits (136), Expect = 1e-11
 Identities = 18/77 (23%), Positives = 32/77 (41%), Gaps = 3/77 (3%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
            ++YV  +    T +ELE  F   G +    IL ++  G  +G  +I F  +   + A+ 
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 151 AMDESLFRGR--QIKVN 165
            ++     G    I V 
Sbjct: 67  GLNGQKPSGATEPITVK 83

>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 = 56.5 bits (136), Expect = 1e-11
 Identities = 21/82 (25%), Positives = 33/82 (40%), Gaps = 7/82 (8%)

Query: 85  EKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKD 144
           EK       ++VGN+    T EE+   F   G    V I  +K       F +I    + 
Sbjct: 2   EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRT 55

Query: 145 SVQTAM-AMDESLFRGRQIKVN 165
             + A   +D    RG+Q++V 
Sbjct: 56  LAEIAKVELDNMPLRGKQLRVR 77

>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 = 56.3 bits (135), Expect = 1e-11
 Identities = 23/88 (26%), Positives = 43/88 (48%), Gaps = 4/88 (4%)

Query: 88  EADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQ 147
            +D   ++VG + +    + LE  F   G ++ V ++ ++     +GF ++ F + D  +
Sbjct: 2   ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 61

Query: 148 TAM-AMDESLFRGRQIKVN---PKRTNR 171
            AM AM+     GRQI+V+       NR
Sbjct: 62  DAMMAMNGKSVDGRQIRVDQAGKSSDNR 89

>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 = 55.8 bits (134), Expect = 2e-11
 Identities = 20/87 (22%), Positives = 35/87 (40%), Gaps = 9/87 (10%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
             ++VG      T +EL   F   G V  V           + FA++ FAD    Q+   
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDV-----FIPKPFRAFAFVTFADDQIAQSLC- 59

Query: 152 MDESLFRGRQIKVN---PKRTNRPGIS 175
            ++ + +G  + ++   PK  +  G S
Sbjct: 60  GEDLIIKGISVHISNAEPKHNSNSGPS 86

>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 = 54.8 bits (131), Expect = 5e-11
 Identities = 20/76 (26%), Positives = 30/76 (39%), Gaps = 2/76 (2%)

Query: 92  RSIYVGNVDYGATAEE-LESHFHG-CGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA 149
           R I + N+      E  L   F G             K        A++ F +KDS + A
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 150 MAMDESLFRGRQIKVN 165
           + M+ SL   R+I V+
Sbjct: 65  LQMNRSLLGNREISVS 80

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.0 bits (132), Expect = 6e-11
 Identities = 14/100 (14%), Positives = 39/100 (39%), Gaps = 7/100 (7%)

Query: 74  NSNNLLNLSIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPK 133
           N+  L    +  +      ++Y G +  G T + +   F   G +  + +   K      
Sbjct: 1   NTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG----- 55

Query: 134 GFAYIEFADKDSVQTAM-AMDESLFRGRQIKVNPKRTNRP 172
            ++++ F+  +S   A+ +++ +   G  +K    + +  
Sbjct: 56  -YSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD 94

>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 = 55.7 bits (133), Expect = 8e-11
 Identities = 23/104 (22%), Positives = 43/104 (41%), Gaps = 8/104 (7%)

Query: 90  DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA 149
            LR++ V  +       +L   F   G +  V I+C++     +G+ +++F    S Q A
Sbjct: 41  VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA 100

Query: 150 M-AMDESLFRGRQIKVNP--KRTNRPGISTTNRGGPRGRGRGRV 190
           +  ++      +++KV        RPG       G  G G G +
Sbjct: 101 IAGLNGFNILNKRLKVALAASGHQRPG-----IAGAVGDGNGYL 139

>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 = 54.0 bits (129), Expect = 9e-11
 Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 2/74 (2%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGH-PKGFAYIEFADKDSVQTAM-A 151
           I++GN+D     + L   F   G + +   +    D    KG+A+I FA  D+   A+ A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 152 MDESLFRGRQIKVN 165
           M+      R I V+
Sbjct: 61  MNGQYLCNRPITVS 74

>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 = 53.7 bits (128), Expect = 1e-10
 Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
           ++ V N+       ++  +F  CG +  V +           FA IEFA  D    A+  
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALAAITK 59

Query: 153 DESLFRGRQIKVN 165
              +    +I V+
Sbjct: 60  THKVVGQNEIIVS 72

>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 = 53.9 bits (129), Expect = 2e-10
 Identities = 12/77 (15%), Positives = 25/77 (32%), Gaps = 5/77 (6%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNR--VTILCNKFDGHPKGFAYIEFADKDSVQTA-- 149
           +++G +      EE+              +           +GFA++E+    +   A  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 150 -MAMDESLFRGRQIKVN 165
            +        G QI V+
Sbjct: 64  KLMPGRIQLWGHQIAVD 80

>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 = 53.5 bits (128), Expect = 2e-10
 Identities = 20/90 (22%), Positives = 41/90 (45%), Gaps = 7/90 (7%)

Query: 86  KKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDS 145
           + ++  + ++V N+ +     +L   F   G +  V I+ N+     KGF ++ F +   
Sbjct: 6   ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSAD 63

Query: 146 VQTAM-AMDESLFRGRQIKVN---PK-RTN 170
              A   +  ++  GR+I+VN    +  TN
Sbjct: 64  ADRAREKLHGTVVEGRKIEVNNATARVMTN 93

>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 = 53.5 bits (128), Expect = 2e-10
 Identities = 15/80 (18%), Positives = 40/80 (50%), Gaps = 3/80 (3%)

Query: 93  SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-A 151
           +I++ N+D     + L   F   G++    ++C++     KG+ ++ F  +++ + A+  
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEK 67

Query: 152 MDESLFRGRQIKVNPKRTNR 171
           M+  L   R++ V   ++ +
Sbjct: 68  MNGMLLNDRKVFVGRFKSRK 87

>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 = 53.6 bits (128), Expect = 2e-10
 Identities = 20/92 (21%), Positives = 39/92 (42%), Gaps = 7/92 (7%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
             +++  + Y AT  ++ + F     +     +    DG   G A +EFA  +    AMA
Sbjct: 16  HCVHMRGLPYRATENDIYNFFSPLNPMRVHIEI--GPDGRVTGEADVEFATHEDAVAAMA 73

Query: 152 MDESLFRGRQIKVNPKRTNRPGISTTNRGGPR 183
            D++  + R +++    T     + T+  GP 
Sbjct: 74  KDKANMQHRYVELFLNST-----AGTSGSGPS 100

>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 = 53.2 bits (127), Expect = 2e-10
 Identities = 25/95 (26%), Positives = 43/95 (45%), Gaps = 9/95 (9%)

Query: 87  KEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILC--------NKFDGHPKGFAYI 138
           +++D  +IYV  ++   T ++L   F  CG V               +K  G PKG A +
Sbjct: 4   EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 63

Query: 139 EFADKDSVQTAM-AMDESLFRGRQIKVNPKRTNRP 172
            + D  + + A+   D   F+G ++KV+  R   P
Sbjct: 64  SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 98

>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 = 53.2 bits (127), Expect = 3e-10
 Identities = 15/81 (18%), Positives = 37/81 (45%), Gaps = 1/81 (1%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
            ++++ ++      ++L   F   G+V    +  +K     K F ++ + +  S Q A+ 
Sbjct: 19  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 78

Query: 151 AMDESLFRGRQIKVNPKRTNR 171
           +M+      +++KV  KR+  
Sbjct: 79  SMNGFQIGMKRLKVQLKRSKN 99

>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 = 52.5 bits (125), Expect = 4e-10
 Identities = 10/75 (13%), Positives = 24/75 (32%), Gaps = 1/75 (1%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
            ++++ N     T   +         V     L +      + FAYI+   K+  +  + 
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 151 AMDESLFRGRQIKVN 165
            ++     G  +   
Sbjct: 62  KLNGLKIEGYTLVTK 76

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.5 bits (125), Expect = 4e-10
 Identities = 17/84 (20%), Positives = 38/84 (45%), Gaps = 7/84 (8%)

Query: 90  DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA 149
           + +++++ N+ + +  E L       G +  V ++ +    H KG A+ +F  +++ Q  
Sbjct: 7   EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKC 66

Query: 150 MA-------MDESLFRGRQIKVNP 166
           +A              GRQ+KV+ 
Sbjct: 67  LAAASLEAEGGGLKLDGRQLKVDL 90

>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 = 51.6 bits (123), Expect = 9e-10
 Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 88  EADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQ 147
           +   R++YVGN+    T   +   F   G      ++       P  F  +EF +     
Sbjct: 5   DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCF--VEFYEHRDAA 62

Query: 148 TAM-AMDESLFRGRQIKVN 165
            A+ AM+     G+++KVN
Sbjct: 63  AALAAMNGRKILGKEVKVN 81

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.5 bits (120), Expect = 1e-09
 Identities = 14/71 (19%), Positives = 31/71 (43%), Gaps = 1/71 (1%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           +Y+  +  G T ++L       G +     + +K     KG+ +++F    + Q A+ A+
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 153 DESLFRGRQIK 163
             S  + +  K
Sbjct: 61  KASGVQAQMAK 71

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.2 bits (122), Expect = 1e-09
 Identities = 15/81 (18%), Positives = 34/81 (41%), Gaps = 2/81 (2%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCN-KFDGHPKGFAYIEFADKDSVQTAM 150
            +IY+ N++     +EL+   H   S     +          +G A++ F +  S   A+
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 151 -AMDESLFRGRQIKVNPKRTN 170
            +M    F  + +++   +T+
Sbjct: 64  RSMQGFPFYDKPMRIQYAKTD 84

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.4 bits (122), Expect = 1e-09
 Identities = 23/111 (20%), Positives = 42/111 (37%), Gaps = 7/111 (6%)

Query: 70  GSPPNSNNLLNLSIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFD 129
           GS  +S N           A+   + +  + +G + EE+   F G   V     L   F 
Sbjct: 1   GSSGSSGN-------SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQ 53

Query: 130 GHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRG 180
           G   G A+++FA ++  + A+   +     R I++          S  + G
Sbjct: 54  GRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTSGPSSG 104

>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 = 8e-09
 Identities = 15/81 (18%), Positives = 32/81 (39%), Gaps = 1/81 (1%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
           + +Y+ N+    T  +L S F          I      G  +G A+I F +K+    A+ 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 151 AMDESLFRGRQIKVNPKRTNR 171
            ++     G+ + +   +  +
Sbjct: 79  LVNGYKLYGKILVIEFGKNKK 99

>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 = 49.2 bits (117), Expect = 9e-09
 Identities = 22/102 (21%), Positives = 36/102 (35%), Gaps = 15/102 (14%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           I V N+ Y  T + L   F   G+V ++           +  A +++AD  S Q A  ++
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSL 65

Query: 153 D--ESLFRGRQIKV--------NPKRTNRPGISTTNRGGPRG 184
           D          +++        N K  N      T    P G
Sbjct: 66  DGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSG 107

>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 = 48.8 bits (115), Expect = 1e-08
 Identities = 14/88 (15%), Positives = 39/88 (44%), Gaps = 1/88 (1%)

Query: 82  SIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFA 141
            +E  +     ++++GN++   +  EL+       + N + +  +   G  + F Y++F 
Sbjct: 4   MVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFE 62

Query: 142 DKDSVQTAMAMDESLFRGRQIKVNPKRT 169
             + ++ A+ +      G +IK+   + 
Sbjct: 63  SAEDLEKALELTGLKVFGNEIKLEKPKG 90

>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 = 47.6 bits (113), Expect = 2e-08
 Identities = 12/74 (16%), Positives = 26/74 (35%), Gaps = 8/74 (10%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
           + V      + +  L   F   G++ +          +   + +I +  K   + A++ D
Sbjct: 7   VTVFGFPQASASYILL-QFAQYGNILKH------VMSNTGNWMHIRYQSKLQARKALSKD 59

Query: 154 ESLFRGRQ-IKVNP 166
             +F     I V P
Sbjct: 60  GRIFGESIMIGVKP 73

>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 = 47.7 bits (113), Expect = 2e-08
 Identities = 15/83 (18%), Positives = 37/83 (44%), Gaps = 7/83 (8%)

Query: 84  EEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADK 143
           +E   + ++ +YV N+    + E +E  F+         +         + +A++ F+++
Sbjct: 1   DEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNR 54

Query: 144 DSVQTAM-AMDESLFRGRQIKVN 165
           +    AM A++  +  G  I+V 
Sbjct: 55  EDAVEAMKALNGKVLDGSPIEVT 77

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.6 bits (112), Expect = 4e-08
 Identities = 13/75 (17%), Positives = 30/75 (40%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
             +Y+  + + A  + +   F     V     +    +G   G  ++EF ++   + A+ 
Sbjct: 19  FCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC 78

Query: 152 MDESLFRGRQIKVNP 166
             +     R I+V+P
Sbjct: 79  RHKQYMGNRFIQVHP 93

>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 = 47.1 bits (111), Expect = 4e-08
 Identities = 12/86 (13%), Positives = 29/86 (33%), Gaps = 2/86 (2%)

Query: 84  EEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADK 143
            +++E D  ++Y+ N+      +ELE+     G     T +     G  +G  +      
Sbjct: 11  AKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQ-VISTRILRDSSGTSRGVGFARMEST 69

Query: 144 DSVQTAM-AMDESLFRGRQIKVNPKR 168
           +  +  +   +    +       P  
Sbjct: 70  EKCEAVIGHFNGKFIKTPPGVSAPTE 95

>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 = 46.7 bits (110), Expect = 6e-08
 Identities = 13/81 (16%), Positives = 32/81 (39%), Gaps = 6/81 (7%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
            ++++ N+    + E+L+  F   G V    +   KF    +  A I+    +    A+ 
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQALI 66

Query: 152 M--DESLFRGRQIKVNPKRTN 170
              +  L     ++V+  ++ 
Sbjct: 67  DLHNHDLGENHHLRVSFSKST 87

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (107), Expect = 1e-07
 Identities = 13/81 (16%), Positives = 35/81 (43%), Gaps = 8/81 (9%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           +Y+GN+    TA++L   F          +          G+A++++ D++    A+  +
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLAGQV------LLKSGYAFVDYPDQNWAIRAIETL 57

Query: 153 DESL-FRGRQIKVNPKRTNRP 172
              +   G+ ++V+   + + 
Sbjct: 58  SGKVELHGKIMEVDYSVSKKL 78

>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 = 45.4 bits (107), Expect = 1e-07
 Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 9/78 (11%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
            ++YV   D   T   L   F   G++  +          P+  A++ +   +S   A+ 
Sbjct: 6   NTLYVYGED--MTPTLLRGAFSPFGNIIDL------SMDPPRNCAFVTYEKMESADQAVA 57

Query: 151 AMDESLFRGRQIKVNPKR 168
            ++ +     Q+KVN  R
Sbjct: 58  ELNGTQVESVQLKVNIAR 75

>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 = 45.6 bits (107), Expect = 2e-07
 Identities = 21/95 (22%), Positives = 34/95 (35%), Gaps = 12/95 (12%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA-- 149
             ++V  +       +L       G++  V ++  K        A +EF + DS +    
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFENIDSAKECVT 69

Query: 150 -MAMDESLFRGRQIKVN---PKRTNRPGISTTNRG 180
             A       G+Q   N    KR  RPG S  + G
Sbjct: 70  FAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSSG 104

>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 = 45.2 bits (106), Expect = 2e-07
 Identities = 11/80 (13%), Positives = 23/80 (28%), Gaps = 7/80 (8%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCG------SVNRVTILCNKFDGHPKGFAYIEFADKDS 145
             ++V  +       E+       G       V             P   AY+ +   + 
Sbjct: 9   NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 146 VQTAM-AMDESLFRGRQIKV 164
              A+  ++  +  GR +K 
Sbjct: 69  ALRAIQCVNNVVVDGRTLKA 88

>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 = 44.7 bits (105), Expect = 2e-07
 Identities = 15/90 (16%), Positives = 31/90 (34%), Gaps = 8/90 (8%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
             I V N+   +  +E+                   +    K  A++   + +  Q A+ 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 151 AMDESLFRGRQIKVNPKRTNRPGISTTNRG 180
              +  FRG+ + V  + T+    S  + G
Sbjct: 59  MFHQYSFRGKDLIVQLQPTDALLCSGPSSG 88

>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 = 44.4 bits (104), Expect = 5e-07
 Identities = 14/90 (15%), Positives = 33/90 (36%), Gaps = 8/90 (8%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
             + V  +    + ++L+ H                 D    G   +E+  K+ ++ A+ 
Sbjct: 16  FRVLVSGLPPSGSWQDLKDHMREA-------GDVCYADVQKDGMGMVEYLRKEDMEYALR 68

Query: 151 AMDESLFRGRQIKVNPKRTNRPGISTTNRG 180
            +D++ FR  + + +  R      S  + G
Sbjct: 69  KLDDTKFRSHEGETSYIRVYPERSSGPSSG 98

>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 = 44.0 bits (103), Expect = 6e-07
 Identities = 13/87 (14%), Positives = 26/87 (29%), Gaps = 12/87 (13%)

Query: 93  SIYVGNVD-----YGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQ 147
            +     +        T  + ES F                         I F++  S  
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF------KSFKRVRINFSNPLSAA 60

Query: 148 TAM-AMDESLFRGRQIKVNPKRTNRPG 173
            A   + ++ F G+++K+   +T   G
Sbjct: 61  DARLRLHKTEFLGKEMKLYFAQTLHIG 87

>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 = 43.0 bits (100), Expect = 1e-06
 Identities = 17/95 (17%), Positives = 32/95 (33%), Gaps = 12/95 (12%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           + V  +    + ++L+ H                 D +  G   +EF  K+ +  A+  +
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREA-------GDVCYADVYRDGTGVVEFVRKEDMTYAVRKL 55

Query: 153 DESLFRGRQIKVNPKRTNRPGISTTNRGGPRGRGR 187
           D + FR  + +    R          R    GR R
Sbjct: 56  DNTKFRSHEGETAYIRVKVD----GPRSPSYGRSR 86

>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 = 42.7 bits (100), Expect = 2e-06
 Identities = 17/83 (20%), Positives = 33/83 (39%), Gaps = 9/83 (10%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
             ++VG +    +   L   F   GS+  +  +          FAYI++   D+ Q A  
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESLDAAQAACA 71

Query: 151 AMDESLFRG--RQIKVNPKRTNR 171
            M      G  R+++V+  ++  
Sbjct: 72  KMRGFPLGGPDRRLRVDFAKSGP 94

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.7 bits (97), Expect = 6e-06
 Identities = 24/106 (22%), Positives = 42/106 (39%), Gaps = 10/106 (9%)

Query: 92  RSIYVGNVD-YGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
             + V N++    T + L   F   G V RV IL      + K  A ++ AD +  Q AM
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF-----NKKENALVQMADGNQAQLAM 57

Query: 151 -AMDESLFRGRQIKVN---PKRTNRPGISTTNRGGPRGRGRGRVSR 192
             ++     G+ I++     +    P     ++G  +  G   + R
Sbjct: 58  SHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHR 103

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.5 bits (97), Expect = 6e-06
 Identities = 13/73 (17%), Positives = 25/73 (34%), Gaps = 3/73 (4%)

Query: 96  VGNVDYGATAEELESHFHGCGSVNRVTIL--CNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           + + +Y    E++       G V  + I    +  +    G  ++EF      Q AM  +
Sbjct: 19  LDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGL 78

Query: 153 DESLFRGRQIKVN 165
               F  R +   
Sbjct: 79  TGRKFANRVVVTK 91

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.7 bits (95), Expect = 1e-05
 Identities = 16/60 (26%), Positives = 21/60 (35%), Gaps = 1/60 (1%)

Query: 106 EELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AMDESLFRGRQIKV 164
            E+        S          FD HP G A + F D +     +  +D   F GRQI  
Sbjct: 30  NEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 89

>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 = 39.6 bits (92), Expect = 2e-05
 Identities = 12/78 (15%), Positives = 27/78 (34%), Gaps = 2/78 (2%)

Query: 89  ADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQT 148
           + +  + +         E         G V  + +  N    H  G  Y++F  ++  + 
Sbjct: 25  SAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEK 83

Query: 149 AM-AMDESLFRGRQIKVN 165
           A+  ++   F G+ I   
Sbjct: 84  AVIDLNNRWFNGQPIHAE 101

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.7 bits (89), Expect = 3e-05
 Identities = 12/78 (15%), Positives = 27/78 (34%), Gaps = 8/78 (10%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           I +  +    T +E+                        KG A++   + +  + A+   
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKYCFV-------DKYKGTAFVTLLNGEQAEAAINTF 53

Query: 153 DESLFRGRQIKVNPKRTN 170
            +S  R R++ V  + T+
Sbjct: 54  HQSRLRERELSVQLQPTD 71

>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 = 37.9 bits (87), Expect = 8e-05
 Identities = 11/77 (14%), Positives = 26/77 (33%), Gaps = 9/77 (11%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA-- 149
           R +++  +    T  E+ +             + N      K  A++E A +++  T   
Sbjct: 9   RVLHIRKLPGEVTETEVIALGLPF------GKVTNILMLKGKNQAFLELATEEAAITMVN 62

Query: 150 -MAMDESLFRGRQIKVN 165
             +      R + I + 
Sbjct: 63  YYSAVTPHLRNQPIYIQ 79

>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 = 33.8 bits (76), Expect = 0.003
 Identities = 16/82 (19%), Positives = 26/82 (31%), Gaps = 7/82 (8%)

Query: 92  RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
             I   N+  G  A E++  F   GS+ RV              A +EF +    + A  
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRV------LLPEGGITAIVEFLEPLEARKAFR 64

Query: 151 AMDESLFRGRQIKVNPKRTNRP 172
            +  S F    + +        
Sbjct: 65  HLAYSKFHHVPLYLEWAPIGVF 86

>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 = 33.5 bits (76), Expect = 0.004
 Identities = 10/74 (13%), Positives = 27/74 (36%), Gaps = 8/74 (10%)

Query: 94  IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
           +  G +  G +  +L      CG V+ + +  NK       +++  +   +  + A   +
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKRAYVTL 76

Query: 153 DES-LFRGRQIKVN 165
           +   +      K+ 
Sbjct: 77  NGKEVVDDLGQKIT 90

>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 = 33.6 bits (76), Expect = 0.004
 Identities = 20/118 (16%), Positives = 39/118 (33%), Gaps = 18/118 (15%)

Query: 82  SIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFA 141
           S+EEK        + G++D     E+L   F   G +  +  +             I F 
Sbjct: 4   SLEEKIGC--LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFK 55

Query: 142 DK--DSVQTAMAMDESLFRGRQIKVN--------PKRTNRPGISTTNRGGPRGRGRGR 189
           +K  +++  A   +    + R  +V          K   +  I        + + +GR
Sbjct: 56  EKAKEALGKAKDANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQESLNKWKSKGR 113

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	207
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.89
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.88
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.88
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.88
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.88
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.88
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.88
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.88
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.88
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.88
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.88
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.88
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.87
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.87
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.87
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.87
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.87
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.87
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.87
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.86
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.86
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.86
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.86
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.86
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.86
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.86
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.85
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.85
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.85
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.85
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.85
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.85
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.84
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.84
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.84
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.83
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.83
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.83
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.83
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.82
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.82
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.82
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.81
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.81
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.81
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.81
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.8
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.8
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.8
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.8
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.79
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.79
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.79
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.79
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.78
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.78
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.78
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.78
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.78
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.78
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.78
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.78
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.77
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.77
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.77
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.77
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.76
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.76
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.75
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.74
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.73
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.73
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.72
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.72
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.72
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.71
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.68
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.68
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.6
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.56
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.54
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.54
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.5
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.46
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.37
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	98.03
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.61
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.23
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	93.04

>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=99.89  E-value=6.6e-23  Score=136.81  Aligned_cols=79  Identities=23%  Similarity=0.515  Sum_probs=75.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a~  168 (207)
                      ..++|||+|||+++|+++|+.+|++||.|..+.|+.|+.++.++|||||+|.+.+.|.+||+++++.|.|+.|.|..|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            3469999999999999999999999999999999999999999999999999999999999999999999999999885

>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=99.88  E-value=1e-22  Score=139.98  Aligned_cols=83  Identities=27%  Similarity=0.541  Sum_probs=78.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      ..++|||+|||+.+++++|+.+|.+||.|..|.|+.++.++.++|||||+|.+.++|..||. ||++.|.|+.|+|.+|+
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~   86 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            45689999999999999999999999999999999999999999999999999999999996 99999999999999998


Q ss_pred             CCCC
Q psy13533        169 TNRP  172 (207)
Q Consensus       169 ~~~~  172 (207)
                      .++.
T Consensus        87 ~~~~   90 (99)
T d1whwa_          87 IKKE   90 (99)
T ss_dssp             CCST
T ss_pred             CCCc
Confidence            7553

>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=99.88  E-value=3.1e-23  Score=139.91  Aligned_cols=83  Identities=28%  Similarity=0.444  Sum_probs=78.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      ..++|||+|||+++|+++|+.+|++||.|..|.++.++.++.++|||||+|.+.++|.+||. ||+..|.|+.|.|.+|+
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            45799999999999999999999999999999999999999999999999999999999995 99999999999999998


Q ss_pred             CCCC
Q psy13533        169 TNRP  172 (207)
Q Consensus       169 ~~~~  172 (207)
                      +++.
T Consensus        84 p~~~   87 (89)
T d2cqba1          84 PMRI   87 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.88  E-value=5.4e-23  Score=136.58  Aligned_cols=79  Identities=23%  Similarity=0.390  Sum_probs=76.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecCC
Q psy13533         91 LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKRT  169 (207)
Q Consensus        91 ~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~~  169 (207)
                      .++|||+|||+.+|+++|+.+|++||.|..+.++.++.++.++|||||+|.+.++|.+||. ||+..|.|+.|+|.+|+|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4689999999999999999999999999999999999999999999999999999999996 999999999999999975

>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=99.88  E-value=1.5e-22  Score=137.57  Aligned_cols=83  Identities=19%  Similarity=0.422  Sum_probs=78.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeec
Q psy13533         89 ADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPK  167 (207)
Q Consensus        89 ~~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a  167 (207)
                      ..+++|||+|||+++|+++|+.+|++||.|..|.++.++.++.++|||||+|.+.++|..||. ||+..|.|+.|+|.++
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            356799999999999999999999999999999999999999999999999999999999996 9999999999999999


Q ss_pred             CCCC
Q psy13533        168 RTNR  171 (207)
Q Consensus       168 ~~~~  171 (207)
                      ...+
T Consensus        85 ~~~~   88 (93)
T d1h2vz_          85 AGFK   88 (93)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7543

>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=99.88  E-value=1.9e-22  Score=146.93  Aligned_cols=82  Identities=21%  Similarity=0.433  Sum_probs=77.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      ..++|||+|||+++|+++|+.+|++||.|..|.|+.++.++.++|||||+|.+.++|..||. ||++.|.|+.|+|.+|+
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~  120 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45789999999999999999999999999999999999999999999999999999999996 99999999999999998


Q ss_pred             CCC
Q psy13533        169 TNR  171 (207)
Q Consensus       169 ~~~  171 (207)
                      ++.
T Consensus       121 ~~~  123 (139)
T d1u6fa1         121 SGH  123 (139)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.88  E-value=6.5e-23  Score=141.94  Aligned_cols=81  Identities=19%  Similarity=0.458  Sum_probs=77.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeecCCC
Q psy13533         91 LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTN  170 (207)
Q Consensus        91 ~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a~~~  170 (207)
                      .++|||+|||+++|+++|+.+|++||.|..+.|+.++.++.++|||||+|.+.++|.+||+++++.|.|+.|.|.+|.++
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECccc
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999999875


Q ss_pred             C
Q psy13533        171 R  171 (207)
Q Consensus       171 ~  171 (207)
                      .
T Consensus       100 e  100 (103)
T d1x4ba1         100 E  100 (103)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=2.3e-22  Score=133.40  Aligned_cols=78  Identities=21%  Similarity=0.437  Sum_probs=75.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecCC
Q psy13533         92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKRT  169 (207)
Q Consensus        92 ~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~~  169 (207)
                      ++|||+|||+++++++|+.+|++||.|..|+++.+..++.++|||||+|.+.++|..|+. ||++.|.|+.|+|.+|+|
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            579999999999999999999999999999999999999999999999999999999996 999999999999999986

>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=99.88  E-value=1.3e-22  Score=136.57  Aligned_cols=82  Identities=17%  Similarity=0.357  Sum_probs=77.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeec
Q psy13533         89 ADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPK  167 (207)
Q Consensus        89 ~~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a  167 (207)
                      ..+++|||+|||+++|+++|..+|++||.|..|+|+.++.++.++|||||+|.+.++|..|+. ||+..|.|+.|+|.+|
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            356799999999999999999999999999999999999999999999999999999999996 9999999999999999


Q ss_pred             CCC
Q psy13533        168 RTN  170 (207)
Q Consensus       168 ~~~  170 (207)
                      .++
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            763

>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=99.88  E-value=1.8e-22  Score=133.45  Aligned_cols=76  Identities=20%  Similarity=0.449  Sum_probs=74.1

Q ss_pred             eEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        93 ~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      +|||+|||+.+|+++|+.+|++||.|..|+|+.++.++.++|||||+|.++++|..||. |++..|.|+.|+|.+|+
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999999999999999999999999999996 99999999999999995

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=1.9e-22  Score=136.27  Aligned_cols=81  Identities=25%  Similarity=0.407  Sum_probs=77.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      ...+|||+|||+++++++|+.+|++||.|..|.|+.++.++.++|||||+|.+.++|.+||. ||+..|.|+.|+|.+|+
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~~ak   86 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAK   86 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            45689999999999999999999999999999999999999999999999999999999996 99999999999999998


Q ss_pred             CC
Q psy13533        169 TN  170 (207)
Q Consensus       169 ~~  170 (207)
                      ++
T Consensus        87 p~   88 (90)
T d2cq0a1          87 PS   88 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=1.8e-22  Score=137.18  Aligned_cols=82  Identities=23%  Similarity=0.436  Sum_probs=77.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      ..++|||+|||+.+|+++|+.+|++||.|..|+|+.++.++.++|||||+|.+.++|.+||. ||++.|.|+.|+|.+|+
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~   87 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   87 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            34699999999999999999999999999999999999999999999999999999999995 99999999999999998


Q ss_pred             CCC
Q psy13533        169 TNR  171 (207)
Q Consensus       169 ~~~  171 (207)
                      ++.
T Consensus        88 ~~~   90 (93)
T d1x5ua1          88 AHN   90 (93)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            754

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=2.9e-22  Score=135.34  Aligned_cols=82  Identities=20%  Similarity=0.381  Sum_probs=76.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeecCC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRT  169 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a~~  169 (207)
                      ..++|||+|||+++|+++|+.+|++||.|..|.|+.|+.++.++|||||+|.+.++|.+||+ +.+.|.|+.|.|.+|.+
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~-~~~~l~Gr~i~v~~a~~   85 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCKLPNS   85 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEECCCT
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh-cCCccCCEEeEEEeCCC
Confidence            45789999999999999999999999999999999999999999999999999999999997 34589999999999987


Q ss_pred             CCC
Q psy13533        170 NRP  172 (207)
Q Consensus       170 ~~~  172 (207)
                      ++.
T Consensus        86 k~~   88 (90)
T d2cqga1          86 KQS   88 (90)
T ss_dssp             TCC
T ss_pred             CCC
Confidence            654

>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=99.87  E-value=5.2e-23  Score=135.08  Aligned_cols=76  Identities=18%  Similarity=0.441  Sum_probs=73.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeec
Q psy13533         92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPK  167 (207)
Q Consensus        92 ~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a  167 (207)
                      ++|||+|||+++|+++|+.+|++||.|..+.|+.|+.++.++|||||+|.+.++|.+||+++++.|.|+.|.|..|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            4799999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.87  E-value=1.7e-22  Score=131.96  Aligned_cols=75  Identities=23%  Similarity=0.521  Sum_probs=72.4

Q ss_pred             eEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeec
Q psy13533         93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPK  167 (207)
Q Consensus        93 ~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a  167 (207)
                      +|||+|||+++|+++|+.+|++||.|..|.|+.++.+++++|||||+|.+.++|.+||.++++.|.|+.|.|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            589999999999999999999999999999999999999999999999999999999999999999999999765

>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=99.87  E-value=5e-22  Score=130.89  Aligned_cols=77  Identities=23%  Similarity=0.504  Sum_probs=74.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeec
Q psy13533         91 LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPK  167 (207)
Q Consensus        91 ~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a  167 (207)
                      .++|||+|||+++|+++|+.+|++||.|..+.++.++.++.++|||||+|.+.+++.+|+.++++.|.|+.|.|..|
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 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999876

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=2.8e-22  Score=134.03  Aligned_cols=79  Identities=14%  Similarity=0.378  Sum_probs=76.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecCCC
Q psy13533         92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKRTN  170 (207)
Q Consensus        92 ~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~~~  170 (207)
                      .+|||+|||+++|+++|+.+|++||.|..|+|+.|+.+|.++|||||+|.++++|..|+. ||++.|.|+.|.|.+|.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            479999999999999999999999999999999999999999999999999999999997 9999999999999999764

>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=99.87  E-value=8.3e-23  Score=140.93  Aligned_cols=80  Identities=25%  Similarity=0.454  Sum_probs=76.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeecCCC
Q psy13533         91 LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTN  170 (207)
Q Consensus        91 ~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a~~~  170 (207)
                      .++|||+|||+++++++|+.+|+.||.|..|+|+.++.++.++|||||+|.+.++|.+||+||++.|.|+.|.|.+|.++
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~~a~~~   97 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAE   97 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECCCC
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999998653

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=6.4e-22  Score=136.71  Aligned_cols=82  Identities=18%  Similarity=0.307  Sum_probs=78.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      +.++|||+|||+++++++|+.+|++||.|..+.++.++.++.++|||||+|.+.++|..||. ||++.|.|+.|.|.+|+
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            45689999999999999999999999999999999999999999999999999999999995 99999999999999998


Q ss_pred             CCC
Q psy13533        169 TNR  171 (207)
Q Consensus       169 ~~~  171 (207)
                      ++.
T Consensus        97 ~k~   99 (102)
T d2cpza1          97 SKN   99 (102)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            754

>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=99.86  E-value=1.2e-21  Score=135.52  Aligned_cols=82  Identities=22%  Similarity=0.545  Sum_probs=75.8

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEee
Q psy13533         88 EADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNP  166 (207)
Q Consensus        88 ~~~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~  166 (207)
                      +...++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||+ ++ ..|.|+.|.|.+
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~l~Gr~l~V~~   85 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN-PIIDGRKANVNL   85 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSS-CEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCC-CcCCCEEEEEEE
Confidence            3455789999999999999999999999999999999999999999999999999999999998 55 589999999999


Q ss_pred             cCCC
Q psy13533        167 KRTN  170 (207)
Q Consensus       167 a~~~  170 (207)
                      |...
T Consensus        86 a~~~   89 (103)
T d2cqda1          86 AYLG   89 (103)
T ss_dssp             STTT
T ss_pred             cCCC
Confidence            9764

>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=99.86  E-value=1.6e-22  Score=131.99  Aligned_cols=75  Identities=19%  Similarity=0.398  Sum_probs=72.4

Q ss_pred             eEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeec
Q psy13533         93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPK  167 (207)
Q Consensus        93 ~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a  167 (207)
                      +|||+|||+++|+++|+.+|++||.|..|.|+.++.++.++|||||+|.+.++|.+||+++++.|.|+.|.|..|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEEC
Confidence            599999999999999999999999999999999999999999999999999999999998889999999999876

>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=99.86  E-value=1.2e-21  Score=130.85  Aligned_cols=78  Identities=24%  Similarity=0.522  Sum_probs=73.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCC--eeeEEee
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRG--RQIKVNP  166 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g--~~i~V~~  166 (207)
                      ..++|||+|||+++++++|+.+|++||.|..++++.++.++.++|||||+|.+.++|..||+ ||+..+.|  ++|.|.+
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            45689999999999999999999999999999999999999999999999999999999996 99999876  8899998


Q ss_pred             c
Q psy13533        167 K  167 (207)
Q Consensus       167 a  167 (207)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            7

>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=99.86  E-value=7.4e-22  Score=133.27  Aligned_cols=82  Identities=24%  Similarity=0.539  Sum_probs=77.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      ..++|||+|||+++++++|+.+|++||.|..+.++.++.++.++|||||+|.++++|..||. |+++.|.|+.|.|.+|.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            45789999999999999999999999999999999999999999999999999999999995 99999999999999997


Q ss_pred             CCC
Q psy13533        169 TNR  171 (207)
Q Consensus       169 ~~~  171 (207)
                      ++.
T Consensus        84 ~~~   86 (90)
T d1x5sa1          84 KSS   86 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            644

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=8.8e-22  Score=130.94  Aligned_cols=75  Identities=23%  Similarity=0.382  Sum_probs=72.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEE
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKV  164 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V  164 (207)
                      +.++|||+|||+.+|+++|+.+|++||.|..|.|+.++.++.++|||||+|.+.++|..||. ||++.|.|+.|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            45799999999999999999999999999999999999999999999999999999999995 9999999999987

>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=99.86  E-value=1e-21  Score=130.60  Aligned_cols=79  Identities=27%  Similarity=0.442  Sum_probs=73.6

Q ss_pred             EEEcCCCCCCCHHHHHHhhccCCCeeE-EEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecCCCC
Q psy13533         94 IYVGNVDYGATAEELESHFHGCGSVNR-VTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKRTNR  171 (207)
Q Consensus        94 lfV~nL~~~~t~~~l~~~f~~~G~i~~-v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~~~~  171 (207)
                      |||+|||+++|+++|+.+|++||.|.. +.++.++.+++++|||||+|.+.++|..||. |++..|.|++|+|.+|.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            799999999999999999999999866 4788999999999999999999999999996 99999999999999998654


Q ss_pred             C
Q psy13533        172 P  172 (207)
Q Consensus       172 ~  172 (207)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.86  E-value=1.9e-21  Score=129.89  Aligned_cols=78  Identities=23%  Similarity=0.384  Sum_probs=73.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCC--eeeEEee
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRG--RQIKVNP  166 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g--~~i~V~~  166 (207)
                      ..++|||+|||+.+|+++|+.+|++||.|..++++.++.++.++|||||+|.+.++|..|+. ||++.|.|  ++|.|.+
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            34689999999999999999999999999999999999999999999999999999999996 99999998  5599988


Q ss_pred             c
Q psy13533        167 K  167 (207)
Q Consensus       167 a  167 (207)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=9.6e-22  Score=136.24  Aligned_cols=82  Identities=32%  Similarity=0.684  Sum_probs=77.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      ..++|||+|||+++++++|+.+|++||.|..|+|+.++.++.++|||||+|.+.++|..||. ||++.|.|+.|.|.+|.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            34689999999999999999999999999999999999999999999999999999999996 99999999999999997


Q ss_pred             CCC
Q psy13533        169 TNR  171 (207)
Q Consensus       169 ~~~  171 (207)
                      +.+
T Consensus        87 ~~~   89 (104)
T d1p1ta_          87 SEK   89 (104)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            643

>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=99.85  E-value=1.8e-21  Score=132.39  Aligned_cols=82  Identities=20%  Similarity=0.391  Sum_probs=75.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHH-h-CCCccCCeeeEEee
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNK-FDGHPKGFAYIEFADKDSVQTAMA-M-DESLFRGRQIKVNP  166 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~-~~~~~kG~afV~f~~~~~a~~al~-l-~~~~l~g~~i~V~~  166 (207)
                      ...+|||+|||+.+++++|+.+|++||.|..|+|+.++ .+|.++|||||+|.+.++|.+||. | |+..|.|++|.|.+
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~   86 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW   86 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEE
Confidence            45789999999999999999999999999999998886 479999999999999999999996 7 89999999999999


Q ss_pred             cCCCC
Q psy13533        167 KRTNR  171 (207)
Q Consensus       167 a~~~~  171 (207)
                      |.+..
T Consensus        87 A~~~~   91 (94)
T d2cpha1          87 ADSEV   91 (94)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98643

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.85  E-value=1.1e-21  Score=129.89  Aligned_cols=78  Identities=13%  Similarity=0.186  Sum_probs=68.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecCC
Q psy13533         92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKRT  169 (207)
Q Consensus        92 ~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~~  169 (207)
                      ++|||+|||+++|+++|+.+|++||.|..+.++.++.++.++|||||+|.+.+.|.+|+. ||++.|.|++|.|.+++|
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 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            589999999999999999999999999998888888899999999999999999999996 999999999999999986

>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=99.85  E-value=1.2e-21  Score=127.68  Aligned_cols=75  Identities=19%  Similarity=0.449  Sum_probs=72.7

Q ss_pred             eEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeec
Q psy13533         93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPK  167 (207)
Q Consensus        93 ~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a  167 (207)
                      +|||+|||+++|+++|+.+|++||.|..+.++.++.++.++|||||+|.+.++|.+|+++|++.|.|+.|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEEC
Confidence            599999999999999999999999999999999999999999999999999999999999999999999999986

>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=99.85  E-value=2.1e-21  Score=127.65  Aligned_cols=76  Identities=20%  Similarity=0.455  Sum_probs=72.6

Q ss_pred             eEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecCC
Q psy13533         93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKRT  169 (207)
Q Consensus        93 ~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~~  169 (207)
                      +|||+|||+++++++|+.+|++||.|..+.|+.++ ++.++|||||+|.+.++|..|+. ||++.|.|++|+|.+|.+
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 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            69999999999999999999999999999999986 89999999999999999999996 999999999999999863

>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=99.85  E-value=2.5e-21  Score=133.30  Aligned_cols=86  Identities=30%  Similarity=0.548  Sum_probs=78.0

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHHHhhccCCCee--------EEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccC
Q psy13533         88 EADLRSIYVGNVDYGATAEELESHFHGCGSVN--------RVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFR  158 (207)
Q Consensus        88 ~~~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~--------~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~  158 (207)
                      +...++|||+|||+.+|+++|+++|.+||.|.        .+.++.++.++.++|||||+|.+.++|.+||. ||++.|.
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            34567999999999999999999999999874        56777888899999999999999999999996 9999999


Q ss_pred             CeeeEEeecCCCCCC
Q psy13533        159 GRQIKVNPKRTNRPG  173 (207)
Q Consensus       159 g~~i~V~~a~~~~~~  173 (207)
                      |+.|+|.+|+++.++
T Consensus        85 gr~i~V~~a~~~~p~   99 (101)
T d2cpea1          85 GSKLKVSLARKKPPM   99 (101)
T ss_dssp             TEECEEECSSCCCCS
T ss_pred             CEEEEEEEcCCCCCC
Confidence            999999999987664

>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=99.85  E-value=3.2e-21  Score=128.71  Aligned_cols=76  Identities=21%  Similarity=0.472  Sum_probs=71.2

Q ss_pred             EEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCC---CcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecCC
Q psy13533         94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDG---HPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKRT  169 (207)
Q Consensus        94 lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~---~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~~  169 (207)
                      |||+|||+++|+++|+.+|++||.|..|.|+.++.++   .++|||||+|.+.++|.+|+. ||++.|.|+.|.|.+|+.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            7999999999999999999999999999999887665   468999999999999999995 999999999999999864

>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=99.85  E-value=1.4e-21  Score=130.85  Aligned_cols=81  Identities=27%  Similarity=0.436  Sum_probs=71.5

Q ss_pred             CCCeEEEcCCCCCCC-HHHHHHhhccCCCeeEEEEeec-CCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeec
Q psy13533         90 DLRSIYVGNVDYGAT-AEELESHFHGCGSVNRVTILCN-KFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPK  167 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t-~~~l~~~f~~~G~i~~v~~~~d-~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a  167 (207)
                      ..++|||+|||+++| ++.|+.+|++||.|..|.|+.+ +.++.++|||||+|.+.++|.+||+||++.|.|+.|+|.+|
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEEc
Confidence            467999999999976 5679999999999999998764 46889999999999999999999999999999999999999


Q ss_pred             CCC
Q psy13533        168 RTN  170 (207)
Q Consensus       168 ~~~  170 (207)
                      +++
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            864

>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=99.84  E-value=4.9e-21  Score=129.23  Aligned_cols=81  Identities=22%  Similarity=0.404  Sum_probs=74.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeec
Q psy13533         89 ADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPK  167 (207)
Q Consensus        89 ~~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a  167 (207)
                      ...++|||+|||+++|+++|+.+|++||.|..|.++.++.+  .+|||||+|.+.++|..|+. |+++.|.|+.|+|.+|
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            35579999999999999999999999999999999998654  48999999999999999996 9999999999999999


Q ss_pred             CCCC
Q psy13533        168 RTNR  171 (207)
Q Consensus       168 ~~~~  171 (207)
                      ++..
T Consensus        84 ~~~~   87 (90)
T d2cqia1          84 TTPS   87 (90)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            8644

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=9e-21  Score=128.68  Aligned_cols=81  Identities=22%  Similarity=0.439  Sum_probs=74.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeec
Q psy13533         89 ADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPK  167 (207)
Q Consensus        89 ~~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a  167 (207)
                      ...++|||+|||+.+++++|+.+|++||.|..|.++.++  ..++|||||+|.+.++|.+||. ||++.|.|+.|.|.+|
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            356789999999999999999999999999999999886  3479999999999999999996 9999999999999999


Q ss_pred             CCCC
Q psy13533        168 RTNR  171 (207)
Q Consensus       168 ~~~~  171 (207)
                      +++.
T Consensus        87 ~~r~   90 (93)
T d2cq3a1          87 TARV   90 (93)
T ss_dssp             CSSC
T ss_pred             CcCC
Confidence            8753

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=9.4e-21  Score=131.13  Aligned_cols=82  Identities=26%  Similarity=0.487  Sum_probs=73.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNK-FDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~-~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a~  168 (207)
                      +.++|||+|||+.+|+++|+.+|+.|| |..+.++.++ .++.++|||||+|.+.++|++|+.||++.|.|+.|+|.+|.
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~a~   92 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVAD   92 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            457999999999999999999999998 7777777665 57889999999999999999888999999999999999998


Q ss_pred             CCCC
Q psy13533        169 TNRP  172 (207)
Q Consensus       169 ~~~~  172 (207)
                      +++.
T Consensus        93 ~~~~   96 (104)
T d1wi8a_          93 QAQD   96 (104)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7554

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=5.8e-21  Score=128.58  Aligned_cols=79  Identities=19%  Similarity=0.518  Sum_probs=73.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecCC
Q psy13533         91 LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKRT  169 (207)
Q Consensus        91 ~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~~  169 (207)
                      ..+|||+|||+++++++|+.+|++||.|..+.|+.++  +.++|||||+|.+.++|.+||. ||++.|.|+.|.|.+|++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4589999999999999999999999999999999886  4478999999999999999996 999999999999999987


Q ss_pred             CC
Q psy13533        170 NR  171 (207)
Q Consensus       170 ~~  171 (207)
                      ++
T Consensus        86 ~~   87 (89)
T d1cvja2          86 RK   87 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.83  E-value=1.4e-20  Score=128.74  Aligned_cols=82  Identities=22%  Similarity=0.429  Sum_probs=75.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hC------CCccCCeee
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MD------ESLFRGRQI  162 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~------~~~l~g~~i  162 (207)
                      ..++|||+|||+++|+++|+.+|.+||.|..+.++.++.++.++|||||+|.+.++|.+||. |+      +..|.|+.|
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l   86 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQL   86 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEE
Confidence            45799999999999999999999999999999999999999999999999999999999996 75      567899999


Q ss_pred             EEeecCCCC
Q psy13533        163 KVNPKRTNR  171 (207)
Q Consensus       163 ~V~~a~~~~  171 (207)
                      +|.+|.++.
T Consensus        87 ~v~~a~~k~   95 (98)
T d1x4ha1          87 KVDLAVTRD   95 (98)
T ss_dssp             EEECCCCCC
T ss_pred             EEEECCCCC
Confidence            999998754

>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=99.83  E-value=2e-20  Score=124.79  Aligned_cols=78  Identities=15%  Similarity=0.243  Sum_probs=73.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a~  168 (207)
                      ..++|||+|||+++|+++|+.+|+.||.|..|.|+.++ ++.++|||||+|.+.++|.+||++++..|.|+.|.|.++.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            45799999999999999999999999999999998875 8999999999999999999999999999999999999864

>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=99.83  E-value=3.2e-20  Score=128.48  Aligned_cols=84  Identities=19%  Similarity=0.308  Sum_probs=76.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeecCC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRT  169 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a~~  169 (207)
                      ...+|||+|||+++|+++|+++|..||.|..+.++.+..++.++|||||+|.++++|.+|+++|++.|.||.|.|.++.+
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~~~   93 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSR   93 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEECT
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEECCH
Confidence            45689999999999999999999999988887777777899999999999999999999999999999999999999987


Q ss_pred             CCCC
Q psy13533        170 NRPG  173 (207)
Q Consensus       170 ~~~~  173 (207)
                      .+..
T Consensus        94 ~~~~   97 (104)
T d1wg5a_          94 AEVR   97 (104)
T ss_dssp             TTSC
T ss_pred             HHhc
Confidence            6654

>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=99.82  E-value=3.8e-20  Score=130.10  Aligned_cols=78  Identities=23%  Similarity=0.303  Sum_probs=72.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      ..++|||+|||+.+++++|..+|++||.|..|+++.+   +.++|||||+|.+.++|..||. ||++.|.|+.|.|.++.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            5679999999999999999999999999999998754   5679999999999999999995 99999999999999987


Q ss_pred             CC
Q psy13533        169 TN  170 (207)
Q Consensus       169 ~~  170 (207)
                      +.
T Consensus        83 ~~   84 (114)
T d2f9da1          83 AN   84 (114)
T ss_dssp             HH
T ss_pred             CC
Confidence            53

>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=99.82  E-value=3.9e-20  Score=127.59  Aligned_cols=82  Identities=24%  Similarity=0.305  Sum_probs=73.8

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeec
Q psy13533         88 EADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPK  167 (207)
Q Consensus        88 ~~~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a  167 (207)
                      .....+|||+|||+++|+++|+.+|..|| |..|.++.+. ++.++|||||+|.+.++|++||++|++.|.||.|.|.++
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34567999999999999999999999998 5578788775 689999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13533        168 RTNR  171 (207)
Q Consensus       168 ~~~~  171 (207)
                      .+..
T Consensus        90 ~~~~   93 (102)
T d1weza_          90 STAG   93 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.82  E-value=1.1e-21  Score=132.64  Aligned_cols=82  Identities=16%  Similarity=0.339  Sum_probs=75.1

Q ss_pred             cCCCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeec
Q psy13533         88 EADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPK  167 (207)
Q Consensus        88 ~~~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a  167 (207)
                      +...++|||+|||+.+|+++|+.+|++||.|..+.|+.+ .+++++|||||+|.+.++|.+||+||++.|.|+.|.|.+|
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEec
Confidence            335679999999999999999999999999998887654 5899999999999999999999999999999999999999


Q ss_pred             CCC
Q psy13533        168 RTN  170 (207)
Q Consensus       168 ~~~  170 (207)
                      +.+
T Consensus        89 k~k   91 (91)
T d1fjeb1          89 KGR   91 (91)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            853

>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=99.81  E-value=7.3e-20  Score=124.57  Aligned_cols=78  Identities=23%  Similarity=0.401  Sum_probs=70.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      ..++|||+|||+++|+++|+++|++||.|..+.+..+   ..++|||||+|.+.++|..||. ||++.|.|+.|+|.+|+
T Consensus        13 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~   89 (95)
T d1x4aa1          13 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   89 (95)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecc
Confidence            4568999999999999999999999999999887544   5578999999999999999996 99999999999999997


Q ss_pred             CC
Q psy13533        169 TN  170 (207)
Q Consensus       169 ~~  170 (207)
                      +.
T Consensus        90 ~~   91 (95)
T d1x4aa1          90 SG   91 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.81  E-value=6.5e-21  Score=131.46  Aligned_cols=83  Identities=18%  Similarity=0.295  Sum_probs=77.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      +.++|||+|||.++++++|+.+|++||.|..+.++.+..++.++|||||.|.+.++|..||. ||+..|.|+.|.|.+|+
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            46799999999999999999999999999999888888889999999999999999999996 99999999999999998


Q ss_pred             CCCC
Q psy13533        169 TNRP  172 (207)
Q Consensus       169 ~~~~  172 (207)
                      ++..
T Consensus        97 ~k~~  100 (102)
T d2cpxa1          97 NKKQ  100 (102)
T ss_dssp             CCSC
T ss_pred             Cccc
Confidence            7553

>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=99.81  E-value=4.7e-20  Score=126.93  Aligned_cols=80  Identities=16%  Similarity=0.372  Sum_probs=73.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeec
Q psy13533         89 ADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPK  167 (207)
Q Consensus        89 ~~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a  167 (207)
                      ...++|||+|||+++++++|+.+|++||.|..+.++.+. ++.++|||||+|.+.++|.+||. |||+.|.|+++.|.++
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            345799999999999999999999999999999988874 88999999999999999999996 9999999999999887


Q ss_pred             CC
Q psy13533        168 RT  169 (207)
Q Consensus       168 ~~  169 (207)
                      +|
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=99.81  E-value=7.8e-20  Score=124.67  Aligned_cols=76  Identities=17%  Similarity=0.431  Sum_probs=71.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      ..++|||+|||..+++++|+.+|++||.|..|+++.+      +|||||+|.+.++|.+||. ||++.|.|+.|+|.|++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4568999999999999999999999999999999876      7899999999999999995 99999999999999998


Q ss_pred             CCC
Q psy13533        169 TNR  171 (207)
Q Consensus       169 ~~~  171 (207)
                      +++
T Consensus        91 ~~p   93 (96)
T d1x4ga1          91 ESP   93 (96)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.80  E-value=1.1e-19  Score=118.40  Aligned_cols=74  Identities=22%  Similarity=0.279  Sum_probs=68.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeec
Q psy13533         92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPK  167 (207)
Q Consensus        92 ~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a  167 (207)
                      .+|||+|||+++++++|+++|+.||.|..|+++.++.  ..++||||+|.+.++|.+||.++++.|.|+.|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            4899999999999999999999999999999998864  3468999999999999999999999999999999875

>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=99.80  E-value=1.5e-19  Score=123.67  Aligned_cols=75  Identities=19%  Similarity=0.474  Sum_probs=67.6

Q ss_pred             CCCCeEEEcCCC-CCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEee
Q psy13533         89 ADLRSIYVGNVD-YGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNP  166 (207)
Q Consensus        89 ~~~~~lfV~nL~-~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~  166 (207)
                      ....+|||+||| +.+++.+|+.+|++||.|..|.|        ++|||||+|.+.++|.+||. ||++.|.|+.|+|.+
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345689999997 57889999999999999999988        37899999999999999996 999999999999999


Q ss_pred             cCCCC
Q psy13533        167 KRTNR  171 (207)
Q Consensus       167 a~~~~  171 (207)
                      +++.+
T Consensus        85 a~~~~   89 (98)
T d1wf2a_          85 AAEPK   89 (98)
T ss_dssp             TTSCC
T ss_pred             CCCCC
Confidence            97643

>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=99.80  E-value=1.8e-20  Score=125.61  Aligned_cols=72  Identities=19%  Similarity=0.347  Sum_probs=66.6

Q ss_pred             eEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecCCCC
Q psy13533         93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKRTNR  171 (207)
Q Consensus        93 ~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~~~~  171 (207)
                      +|||+|||+.+++++|+.+|++||.|..+.++.+       |||||+|.+.++|.+||. ||+..|.|+.|.|.+++.+.
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            6999999999999999999999999999988643       799999999999999995 99999999999999887644

>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=99.80  E-value=1.1e-19  Score=123.90  Aligned_cols=79  Identities=23%  Similarity=0.413  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeec
Q psy13533         89 ADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPK  167 (207)
Q Consensus        89 ~~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a  167 (207)
                      ...++|||+|||+++|+++|+.+|.+||.|..+..     ++.++|||||+|.+.++|.+|+. ||++.|.|+.|.|.++
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a   88 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            35679999999999999999999999998876643     67889999999999999999996 9999999999999999


Q ss_pred             CCCCC
Q psy13533        168 RTNRP  172 (207)
Q Consensus       168 ~~~~~  172 (207)
                      .++..
T Consensus        89 ~~k~~   93 (96)
T d1fjca_          89 GEKGG   93 (96)
T ss_dssp             SSSCC
T ss_pred             CCCCC
Confidence            87553

>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=99.79  E-value=8.4e-20  Score=122.54  Aligned_cols=76  Identities=22%  Similarity=0.411  Sum_probs=68.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeecCC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRT  169 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a~~  169 (207)
                      ..++|||+|||+.+|+++|+.+|++||.|..|+++.     .++|||||+|.+.+.|++||. +++.|.|+.|.|.+|++
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~~a~~   77 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG-EDLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEECCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh-CCCEECCEEeEEEeCCC
Confidence            457999999999999999999999999999997654     368999999999999999986 77899999999999976


Q ss_pred             CC
Q psy13533        170 NR  171 (207)
Q Consensus       170 ~~  171 (207)
                      +.
T Consensus        78 k~   79 (88)
T d1wf0a_          78 KH   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.79  E-value=1.2e-20  Score=130.44  Aligned_cols=80  Identities=14%  Similarity=0.209  Sum_probs=72.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeecCC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRT  169 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a~~  169 (207)
                      ...+|||+|||+++|+++|..+|..||.|..+.++....+|.++|||||+|.+.++|.+||.||++.|.|+.|.|.++..
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~~~   86 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVTL   86 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEECH
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEECCH
Confidence            45689999999999999999999999988775455555689999999999999999999999999999999999999865

>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=99.79  E-value=2.9e-19  Score=118.58  Aligned_cols=74  Identities=14%  Similarity=0.210  Sum_probs=68.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccC-CeeeEEeec
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFR-GRQIKVNPK  167 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~-g~~i~V~~a  167 (207)
                      +.++|||+|||+++|+++|..+|+.||.|..|+++.+     .+|||||+|.+.++|..|+. |+++.|. |+.|+|.||
T Consensus         7 P~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~a   81 (83)
T d2b0ga1           7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFA   81 (83)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEe
Confidence            4579999999999999999999999999999999765     37899999999999999996 9999885 689999999


Q ss_pred             C
Q psy13533        168 R  168 (207)
Q Consensus       168 ~  168 (207)
                      +
T Consensus        82 k   82 (83)
T d2b0ga1          82 K   82 (83)
T ss_dssp             C
T ss_pred             c
Confidence            6

>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=99.79  E-value=2.6e-19  Score=119.61  Aligned_cols=75  Identities=27%  Similarity=0.459  Sum_probs=69.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      ..++|||+|||+++++++|+.+|++||.|..|.++.+      +|||||+|.+.++|..|+. ||+..|.|+.|+|.+|.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3468999999999999999999999999999999765      6899999999999999996 99999999999999997


Q ss_pred             CC
Q psy13533        169 TN  170 (207)
Q Consensus       169 ~~  170 (207)
                      ..
T Consensus        81 ~~   82 (86)
T d2cpja1          81 HS   82 (86)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>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=99.78  E-value=7.2e-20  Score=118.25  Aligned_cols=70  Identities=19%  Similarity=0.393  Sum_probs=67.4

Q ss_pred             EEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeE
Q psy13533         94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIK  163 (207)
Q Consensus        94 lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~  163 (207)
                      |||+|||+++|+++|+.+|++||.|..+.++.++.++.++|||||+|.+.++|.+|+. ||++.|.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            7999999999999999999999999999999999999999999999999999999996 999999999874

>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=99.78  E-value=1.5e-19  Score=121.49  Aligned_cols=76  Identities=16%  Similarity=0.294  Sum_probs=68.8

Q ss_pred             CCCeEEEcCCCCCCCHHHH---HHhhccCCCeeEEEEeecCCCCCc---ceEEEEEecCHHHHHHHHH-hCCCccCCeee
Q psy13533         90 DLRSIYVGNVDYGATAEEL---ESHFHGCGSVNRVTILCNKFDGHP---KGFAYIEFADKDSVQTAMA-MDESLFRGRQI  162 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l---~~~f~~~G~i~~v~~~~d~~~~~~---kG~afV~f~~~~~a~~al~-l~~~~l~g~~i  162 (207)
                      ..++|||+|||+.+++++|   .++|++||.|..|.++.++.++.+   +|||||+|.+.++|..||. ||++.|.|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            3468999999999999999   678999999999999999866654   5999999999999999996 99999999999


Q ss_pred             EEe
Q psy13533        163 KVN  165 (207)
Q Consensus       163 ~V~  165 (207)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            984

>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=99.78  E-value=6e-19  Score=117.74  Aligned_cols=76  Identities=17%  Similarity=0.375  Sum_probs=68.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      ..++|||+|||+++|+++|+.+|++||.|..+.+..      ++|||||+|.+.++|..||. ||++.|.|+.|.|.+|+
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            346899999999999999999999999988877643      48999999999999999996 99999999999999998


Q ss_pred             CCC
Q psy13533        169 TNR  171 (207)
Q Consensus       169 ~~~  171 (207)
                      |..
T Consensus        81 P~~   83 (86)
T d2cpda1          81 PVD   83 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=8.4e-19  Score=122.05  Aligned_cols=75  Identities=29%  Similarity=0.416  Sum_probs=69.1

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         91 LRSIYVGNVDY-GATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        91 ~~~lfV~nL~~-~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      ..+|||+|||+ .+|+++|+.+|+.||.|..|.|+.++     +|||||+|.+.++|.+||. ||+..|.|+.|+|.+++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            36999999965 59999999999999999999998874     7999999999999999996 99999999999999997


Q ss_pred             CC
Q psy13533        169 TN  170 (207)
Q Consensus       169 ~~  170 (207)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.78  E-value=1.5e-19  Score=119.19  Aligned_cols=75  Identities=19%  Similarity=0.398  Sum_probs=67.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCC-ccCCeeeEEeecCC
Q psy13533         92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDES-LFRGRQIKVNPKRT  169 (207)
Q Consensus        92 ~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~-~l~g~~i~V~~a~~  169 (207)
                      .+|||+|||+++|+++|+.+|++||.|..+.++.      ++|||||+|.+.++|..|++ |||. .|.|+.|.|.+|.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            4799999999999999999999999887776654      37899999999999999996 9986 59999999999998


Q ss_pred             CCC
Q psy13533        170 NRP  172 (207)
Q Consensus       170 ~~~  172 (207)
                      ++.
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            654

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=2.5e-19  Score=119.64  Aligned_cols=78  Identities=21%  Similarity=0.325  Sum_probs=69.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeec
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPK  167 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a  167 (207)
                      ...+|||+|||+++++++|+++|..||.|....++....++.++|||||+|.+.++|.+||. ||++.|.|+.|+|.++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34579999999999999999999999988764334444689999999999999999999996 9999999999999875

>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=99.78  E-value=5.6e-19  Score=116.05  Aligned_cols=75  Identities=21%  Similarity=0.327  Sum_probs=68.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeec
Q psy13533         89 ADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPK  167 (207)
Q Consensus        89 ~~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a  167 (207)
                      ..+++|||+||+  +|+++|+.+|++||.|..|.+..+      +|||||+|.+.++|..|+. ||+..|.|+.|+|.+|
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            356799999996  899999999999999999998654      6899999999999999995 9999999999999999


Q ss_pred             CCCC
Q psy13533        168 RTNR  171 (207)
Q Consensus       168 ~~~~  171 (207)
                      ++++
T Consensus        75 ~~~P   78 (79)
T d2bz2a1          75 RKQP   78 (79)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            8654

>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=99.78  E-value=4.4e-19  Score=120.87  Aligned_cols=81  Identities=17%  Similarity=0.256  Sum_probs=72.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhccCCC-eeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHH-hCC--CccCCeeeEEee
Q psy13533         92 RSIYVGNVDYGATAEELESHFHGCGS-VNRVTILCNK-FDGHPKGFAYIEFADKDSVQTAMA-MDE--SLFRGRQIKVNP  166 (207)
Q Consensus        92 ~~lfV~nL~~~~t~~~l~~~f~~~G~-i~~v~~~~d~-~~~~~kG~afV~f~~~~~a~~al~-l~~--~~l~g~~i~V~~  166 (207)
                      ++|||+|||..+++++|+.+|++||. |..+.++.+. .++.++|||||+|.+.++|..|+. |++  ..+.|+.|.|.+
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            58999999999999999999999995 9999998875 468999999999999999999996 764  456799999999


Q ss_pred             cCCCCC
Q psy13533        167 KRTNRP  172 (207)
Q Consensus       167 a~~~~~  172 (207)
                      |+++..
T Consensus        82 A~p~~~   87 (96)
T d2disa1          82 AEPEID   87 (96)
T ss_dssp             SCSSCS
T ss_pred             cCCCCC
Confidence            987553

>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=99.77  E-value=1.8e-19  Score=126.23  Aligned_cols=81  Identities=16%  Similarity=0.310  Sum_probs=73.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeecC
Q psy13533         89 ADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKR  168 (207)
Q Consensus        89 ~~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a~  168 (207)
                      ....+|||+|||+.+|+++|..||+.||.|..+.++.+..+|.++|||||+|.+.++|.+||.||++.|+|+.|.|.++.
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEEC
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEcC
Confidence            35679999999999999999999999998877656666679999999999999999999999999999999999999875


Q ss_pred             C
Q psy13533        169 T  169 (207)
Q Consensus       169 ~  169 (207)
                      .
T Consensus        96 ~   96 (112)
T d1wela1          96 K   96 (112)
T ss_dssp             H
T ss_pred             h
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=99.77  E-value=6.3e-19  Score=123.03  Aligned_cols=76  Identities=21%  Similarity=0.206  Sum_probs=69.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      ..++|||+|||+.+++++|+.+|+.||.|..|.|..      .+|||||+|.+.++|.+||. ||++.|.|+.|.|.+|.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            446999999999999999999999999999998743      47999999999999999996 99999999999999997


Q ss_pred             CCC
Q psy13533        169 TNR  171 (207)
Q Consensus       169 ~~~  171 (207)
                      ...
T Consensus        83 ~~~   85 (111)
T d1whxa_          83 IGV   85 (111)
T ss_dssp             TTT
T ss_pred             CCc
Confidence            643

>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=99.77  E-value=1.5e-18  Score=116.26  Aligned_cols=77  Identities=13%  Similarity=0.255  Sum_probs=68.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCcc-CCeeeEEeec
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLF-RGRQIKVNPK  167 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l-~g~~i~V~~a  167 (207)
                      +.++|||+|||+.+++++|+.+|++||.|..+.+...    ..+|||||+|.+.++|.+|+. ||+..| .|+.|+|.++
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            4679999999999999999999999999988876543    357899999999999999995 999988 5899999999


Q ss_pred             CCC
Q psy13533        168 RTN  170 (207)
Q Consensus       168 ~~~  170 (207)
                      ++.
T Consensus        85 k~~   87 (88)
T d2adca2          85 KST   87 (88)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            863

>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=99.77  E-value=1.2e-18  Score=116.75  Aligned_cols=74  Identities=18%  Similarity=0.326  Sum_probs=64.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecCC
Q psy13533         91 LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKRT  169 (207)
Q Consensus        91 ~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~~  169 (207)
                      .++|||+|||+.+++++|+.+|.+|| +..+.+      +.++|||||+|.+.++|.+||. ||++.|.|++|.|.+++.
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999 333433      3468999999999999999995 999999999999999976


Q ss_pred             CC
Q psy13533        170 NR  171 (207)
Q Consensus       170 ~~  171 (207)
                      +.
T Consensus        78 ~~   79 (88)
T d1wg1a_          78 DA   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.76  E-value=8.1e-19  Score=119.96  Aligned_cols=75  Identities=17%  Similarity=0.319  Sum_probs=69.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      ...+|||+|||+.+++++|+.+|++||.|..+.+..       +|||||+|.+.++|.+||+ ||+..|.|+.|.|.+++
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEe
Confidence            557899999999999999999999999999998853       5899999999999999996 99999999999999997


Q ss_pred             CCC
Q psy13533        169 TNR  171 (207)
Q Consensus       169 ~~~  171 (207)
                      ...
T Consensus        87 ~~~   89 (98)
T d1wg4a_          87 VYP   89 (98)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            644

>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=99.76  E-value=7.1e-19  Score=118.63  Aligned_cols=78  Identities=19%  Similarity=0.354  Sum_probs=69.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHH----hhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEE
Q psy13533         90 DLRSIYVGNVDYGATAEELES----HFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKV  164 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~----~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V  164 (207)
                      +.++|||+|||+.+++++|+.    +|++||.|..|.+..   ++.++|||||+|.+.++|..|+. ||++.|.|+.|.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            457999999999999998864    689999999998754   46789999999999999999996 9999999999999


Q ss_pred             eecCCC
Q psy13533        165 NPKRTN  170 (207)
Q Consensus       165 ~~a~~~  170 (207)
                      .+|+++
T Consensus        79 ~~ak~~   84 (91)
T d1nu4a_          79 QYAKTD   84 (91)
T ss_dssp             EECSSC
T ss_pred             EEeCCC
Confidence            999864

>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=99.75  E-value=4.5e-18  Score=115.96  Aligned_cols=77  Identities=23%  Similarity=0.433  Sum_probs=69.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCC--eeeEEe
Q psy13533         89 ADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRG--RQIKVN  165 (207)
Q Consensus        89 ~~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g--~~i~V~  165 (207)
                      .+.++|||+|||+++++++|+++|++||.|..|.++.+      ++||||+|.+.++|..|+. ||+..|.|  ++|+|.
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            35689999999999999999999999999999998754      6899999999999999996 99999986  589999


Q ss_pred             ecCCCC
Q psy13533        166 PKRTNR  171 (207)
Q Consensus       166 ~a~~~~  171 (207)
                      +|++.+
T Consensus        89 ~ak~~~   94 (97)
T d1whya_          89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             eCCCCC
Confidence            998644

>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=99.74  E-value=5.1e-18  Score=117.93  Aligned_cols=78  Identities=21%  Similarity=0.255  Sum_probs=70.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCcc--CCeeeEEee
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLF--RGRQIKVNP  166 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l--~g~~i~V~~  166 (207)
                      ...+|||+|||+.+|+++|+++|++||.|..|.++.++    .+|||||+|.+.++|..||. ||++.|  .++.|.|.+
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            44689999999999999999999999999999998764    58999999999999999996 999988  578999999


Q ss_pred             cCCCC
Q psy13533        167 KRTNR  171 (207)
Q Consensus       167 a~~~~  171 (207)
                      ++++.
T Consensus        82 s~~~~   86 (108)
T d2adba1          82 SKLTS   86 (108)
T ss_dssp             CSSCS
T ss_pred             cCCcc
Confidence            97654

>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=99.73  E-value=1.9e-17  Score=110.84  Aligned_cols=77  Identities=18%  Similarity=0.207  Sum_probs=69.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH---hCCCccCCeeeEEe
Q psy13533         89 ADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA---MDESLFRGRQIKVN  165 (207)
Q Consensus        89 ~~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~---l~~~~l~g~~i~V~  165 (207)
                      .+.++|||+|||+.+++++|..+|++||.|..+.++.+      ++||||+|.+.++|.+|+.   +++..|.|++|.|.
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~   79 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   79 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEE
Confidence            46789999999999999999999999999999998765      5899999999999999994   47789999999999


Q ss_pred             ecCCCC
Q psy13533        166 PKRTNR  171 (207)
Q Consensus       166 ~a~~~~  171 (207)
                      +++.+.
T Consensus        80 ~sk~~~   85 (88)
T d2cq1a1          80 YSNHKE   85 (88)
T ss_dssp             ECSCSS
T ss_pred             ECCCCC
Confidence            998654

>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=99.73  E-value=1.3e-17  Score=108.39  Aligned_cols=69  Identities=17%  Similarity=0.319  Sum_probs=62.7

Q ss_pred             EEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecCC
Q psy13533         94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKRT  169 (207)
Q Consensus        94 lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~~  169 (207)
                      |||+|||+++++++|+.+|.+|| +..+.+      +.++|||||+|.+.++|.+|+. ||+..|.|++|.|.+++.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~   70 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPT   70 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCS
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCC
Confidence            79999999999999999999999 555544      3468999999999999999995 999999999999999975

>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=99.72  E-value=4.2e-17  Score=112.46  Aligned_cols=77  Identities=18%  Similarity=0.197  Sum_probs=69.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-h--CCCccCCeeeEEe
Q psy13533         89 ADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M--DESLFRGRQIKVN  165 (207)
Q Consensus        89 ~~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l--~~~~l~g~~i~V~  165 (207)
                      .+.++|||+|||+.+|+++|..+|.+||.|..|.++.+      +|+|||+|.+.++|..|+. |  ++..+.|++|.|.
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~   86 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEE
Confidence            45679999999999999999999999999999998754      7899999999999999995 5  6778999999999


Q ss_pred             ecCCCC
Q psy13533        166 PKRTNR  171 (207)
Q Consensus       166 ~a~~~~  171 (207)
                      +++.+.
T Consensus        87 ~s~~~~   92 (104)
T d1wexa_          87 YSTSKR   92 (104)
T ss_dssp             ECSSSS
T ss_pred             EcCCCc
Confidence            997643

>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=99.72  E-value=1.4e-17  Score=125.54  Aligned_cols=84  Identities=21%  Similarity=0.458  Sum_probs=78.7

Q ss_pred             ccCCCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEee
Q psy13533         87 KEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNP  166 (207)
Q Consensus        87 ~~~~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~  166 (207)
                      .....++|||+|||+.+|+++|+.+|+.||.|..+.++.++.++.++|||||+|.+.++|.+||.++++.|.|+.|.|.+
T Consensus        93 ~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~~~~~~G~~i~V~~  172 (183)
T d1u1qa_          93 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK  172 (183)
T ss_dssp             TTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSSCEEETTEEEEEEE
T ss_pred             cccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHHhCCCeECCEEEEEEe
Confidence            34466899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q psy13533        167 KRTN  170 (207)
Q Consensus       167 a~~~  170 (207)
                      |.++
T Consensus       173 A~~k  176 (183)
T d1u1qa_         173 ALSK  176 (183)
T ss_dssp             CCCH
T ss_pred             cCCc
Confidence            9764

>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=99.72  E-value=1.1e-19  Score=122.34  Aligned_cols=78  Identities=29%  Similarity=0.518  Sum_probs=68.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEe-----ecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEee
Q psy13533         92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTIL-----CNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNP  166 (207)
Q Consensus        92 ~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~-----~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~  166 (207)
                      ++|||+|||+++|+++|+++|++||.|..+.++     .+..++.++|||||+|.+.++|.+|++||++.|.|+.|+|..
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V~r   81 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR   81 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCCBC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEECC
Confidence            689999999999999999999999977665443     344677899999999999999999999999999999999976


Q ss_pred             cCC
Q psy13533        167 KRT  169 (207)
Q Consensus       167 a~~  169 (207)
                      ++.
T Consensus        82 ~k~   84 (90)
T d1u2fa_          82 PHD   84 (90)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            543

>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=99.71  E-value=1.6e-17  Score=113.59  Aligned_cols=77  Identities=17%  Similarity=0.237  Sum_probs=69.2

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH---hCCCccCCeeeEE
Q psy13533         89 ADLRSIYVGNVDYG-ATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA---MDESLFRGRQIKV  164 (207)
Q Consensus        89 ~~~~~lfV~nL~~~-~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~---l~~~~l~g~~i~V  164 (207)
                      ..+++|||+|||.. +|+++|..+|++||.|..|.++.+      +|||||+|.+.++|..|+.   +++..|.|+.|.|
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V   89 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   89 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEE
Confidence            45689999999985 899999999999999999998765      6899999999999999983   7888999999999


Q ss_pred             eecCCCC
Q psy13533        165 NPKRTNR  171 (207)
Q Consensus       165 ~~a~~~~  171 (207)
                      .+|+.++
T Consensus        90 ~~s~~~~   96 (99)
T d1x4fa1          90 DLSEKYK   96 (99)
T ss_dssp             EEECSCS
T ss_pred             EEcCCcc
Confidence            9997543

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.68  E-value=5.3e-17  Score=111.91  Aligned_cols=78  Identities=15%  Similarity=0.158  Sum_probs=68.3

Q ss_pred             CCCeEEEcCCCCCC-CH----HHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeE
Q psy13533         90 DLRSIYVGNVDYGA-TA----EELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIK  163 (207)
Q Consensus        90 ~~~~lfV~nL~~~~-t~----~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~  163 (207)
                      ...+|||+||+..+ ++    ++|+.+|++||.|..+.++.      +++||||.|.+.++|.+|+. ||++.|.|+.|+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            45689999999986 33    56999999999999999875      37899999999999999996 999999999999


Q ss_pred             EeecCCCCCC
Q psy13533        164 VNPKRTNRPG  173 (207)
Q Consensus       164 V~~a~~~~~~  173 (207)
                      |.+|++....
T Consensus        78 v~~a~~~~~~   87 (104)
T d1weya_          78 LYFAQTLHIG   87 (104)
T ss_dssp             EECCCCSSCC
T ss_pred             EeecccCCCC
Confidence            9999876543

>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=99.68  E-value=7.1e-17  Score=108.20  Aligned_cols=77  Identities=19%  Similarity=0.254  Sum_probs=68.5

Q ss_pred             cCCCCeEEEcCCCCC-CCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH---hCCCccCCeeeE
Q psy13533         88 EADLRSIYVGNVDYG-ATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA---MDESLFRGRQIK  163 (207)
Q Consensus        88 ~~~~~~lfV~nL~~~-~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~---l~~~~l~g~~i~  163 (207)
                      ....++|||+|||.. +|+++|..+|++||.|..|.++.+      +++|||.|.+.++|..|+.   +++..+.|++|.
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            346689999999996 889999999999999999999765      5799999999999999995   478889999999


Q ss_pred             EeecCCC
Q psy13533        164 VNPKRTN  170 (207)
Q Consensus       164 V~~a~~~  170 (207)
                      |.+|+..
T Consensus        79 V~~s~~~   85 (89)
T d1x4da1          79 VHLSQKY   85 (89)
T ss_dssp             EEEECCC
T ss_pred             EEECCCc
Confidence            9999753

>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=99.60  E-value=3.8e-15  Score=111.98  Aligned_cols=80  Identities=21%  Similarity=0.497  Sum_probs=75.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeecCCCC
Q psy13533         92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTNR  171 (207)
Q Consensus        92 ~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a~~~~  171 (207)
                      ++|||+|||+.+|+++|+.+|++||.|..+.++.+..++.++|||||+|.+.++|.+|+.+++..+.++.+.+....+..
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~~   86 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSRE   86 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCTT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhcc
Confidence            69999999999999999999999999999999999999999999999999999999999988999999999888776543

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=2.3e-16  Score=108.62  Aligned_cols=75  Identities=16%  Similarity=0.275  Sum_probs=69.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeec
Q psy13533         92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPK  167 (207)
Q Consensus        92 ~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a  167 (207)
                      ..++|.+++..+++++|+.+|++||.|..|.|+.+ .++.++|||||+|.+.++|.+|+. |||+.|.|++|.|.+.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            46888899999999999999999999999999876 589999999999999999999996 9999999999999875

>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=99.54  E-value=4.3e-15  Score=103.68  Aligned_cols=73  Identities=15%  Similarity=0.176  Sum_probs=62.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCH-HHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533         91 LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADK-DSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus        91 ~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~-~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      ...+||||||+.+|+++|+.+|++||.|.+|.|+.+      +|||||.|.++ +.|..|+. +++..|.++.+.|.++.
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            346799999999999999999999999999999754      79999999985 67878885 99998887777776664


Q ss_pred             C
Q psy13533        169 T  169 (207)
Q Consensus       169 ~  169 (207)
                      .
T Consensus        85 ~   85 (113)
T d1owxa_          85 L   85 (113)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.54  E-value=6.7e-15  Score=96.51  Aligned_cols=72  Identities=17%  Similarity=0.180  Sum_probs=62.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCe-eeEEeecCC
Q psy13533         91 LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGR-QIKVNPKRT  169 (207)
Q Consensus        91 ~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~-~i~V~~a~~  169 (207)
                      .+.|||+++|++++++.| .+|++||.|..+++..      .+|||||.|.++++|.+||.+||..|+|+ .|.|.++..
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCCC
Confidence            357999999999986655 5799999999998743      47999999999999999999999999998 567988764

>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=99.50  E-value=2.1e-14  Score=98.13  Aligned_cols=63  Identities=16%  Similarity=0.342  Sum_probs=56.1

Q ss_pred             CCCeEEEc--CCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccC
Q psy13533         90 DLRSIYVG--NVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFR  158 (207)
Q Consensus        90 ~~~~lfV~--nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~  158 (207)
                      +..+|||.  |||+.+|+++|+.+|++||.|..|.++.+      ++||||+|.+.++|..|+. |||+.|.
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            44688885  59999999999999999999999988765      6799999999999999995 9999873

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=1.1e-13  Score=94.02  Aligned_cols=78  Identities=22%  Similarity=0.410  Sum_probs=66.5

Q ss_pred             CCCCeEEEcCC--CCCCC---------HHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCc
Q psy13533         89 ADLRSIYVGNV--DYGAT---------AEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESL  156 (207)
Q Consensus        89 ~~~~~lfV~nL--~~~~t---------~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~  156 (207)
                      ...++|+|.||  |..+.         .++|+..|++||.|..|.++.+    ..+|||||.|.+.++|.+|+. |||..
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            45689999999  54321         2578999999999999988655    367999999999999999995 99999


Q ss_pred             cCCeeeEEeecCCC
Q psy13533        157 FRGRQIKVNPKRTN  170 (207)
Q Consensus       157 l~g~~i~V~~a~~~  170 (207)
                      |.|++|.|.++.++
T Consensus        82 ~~gr~i~v~~~~g~   95 (99)
T d2dita1          82 FGGRQITAQAWDGT   95 (99)
T ss_dssp             ETTEECEEEECCSC
T ss_pred             ECCEEEEEEEeCCc
Confidence            99999999998754

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=4.8e-13  Score=91.69  Aligned_cols=80  Identities=16%  Similarity=0.130  Sum_probs=67.2

Q ss_pred             CCCeEEEcCC--CCCCC--------HHHHHHhhccCCCeeEEEEeecCCC--CCcceEEEEEecCHHHHHHHHH-hCCCc
Q psy13533         90 DLRSIYVGNV--DYGAT--------AEELESHFHGCGSVNRVTILCNKFD--GHPKGFAYIEFADKDSVQTAMA-MDESL  156 (207)
Q Consensus        90 ~~~~lfV~nL--~~~~t--------~~~l~~~f~~~G~i~~v~~~~d~~~--~~~kG~afV~f~~~~~a~~al~-l~~~~  156 (207)
                      ++++|+|.||  |..+.        .++|+..|++||.|..|.|+.+..+  ....|++||.|.+.++|.+|+. |||..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            4578999999  44432        3578999999999999999876544  3456899999999999999996 99999


Q ss_pred             cCCeeeEEeecCC
Q psy13533        157 FRGRQIKVNPKRT  169 (207)
Q Consensus       157 l~g~~i~V~~a~~  169 (207)
                      +.||.|.|.++..
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            9999999999864

>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=98.03  E-value=4.7e-06  Score=53.65  Aligned_cols=55  Identities=24%  Similarity=0.352  Sum_probs=49.7

Q ss_pred             HHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHhCCCccCCeeeEEeecC
Q psy13533        106 EELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKR  168 (207)
Q Consensus       106 ~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~l~~~~l~g~~i~V~~a~  168 (207)
                      ..|.+.|..||.|.-|+++.+        ..+|+|.+-.+|.+|+.+++..++|+.|+|....
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDVDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHGGGSEETTEEEEEECCC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhccCCeEEcceEEEEecCC
Confidence            367788999999999999877        7999999999999999999999999999998653

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.61  E-value=0.00014  Score=47.11  Aligned_cols=77  Identities=16%  Similarity=0.174  Sum_probs=61.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCC--cceEEEEEecCHHHHHHHHH-hCCCccCCe-----eeE
Q psy13533         92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGH--PKGFAYIEFADKDSVQTAMA-MDESLFRGR-----QIK  163 (207)
Q Consensus        92 ~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~--~kG~afV~f~~~~~a~~al~-l~~~~l~g~-----~i~  163 (207)
                      ++|.|.+||+.+|++++...+...|.+........+.+.+  .-.-|||.|.+.+++..... .+|+.+.+.     .-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            4799999999999999999999999999888877765443  33569999999999888885 999986542     345


Q ss_pred             EeecC
Q psy13533        164 VNPKR  168 (207)
Q Consensus       164 V~~a~  168 (207)
                      |.+|-
T Consensus        82 VE~AP   86 (91)
T d1uw4a_          82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            66653

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.23  E-value=0.00061  Score=41.41  Aligned_cols=59  Identities=15%  Similarity=0.158  Sum_probs=49.4

Q ss_pred             HHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH-hCCCccCCeeeEEeecC
Q psy13533        107 ELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR  168 (207)
Q Consensus       107 ~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~-l~~~~l~g~~i~V~~a~  168 (207)
                      .|...|.+++.|..+.+....   ...-.|-|...+..+|.-|+. |+...|++++|.|.++.
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 LLQEAFARHGKVKSVELSPHT---DYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCC---STTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEecc---CCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            455668899999999886542   224478999999999999996 99999999999999985

>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=93.04  E-value=0.14  Score=32.69  Aligned_cols=54  Identities=13%  Similarity=0.188  Sum_probs=43.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH
Q psy13533         90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA  151 (207)
Q Consensus        90 ~~~~lfV~nL~~~~t~~~l~~~f~~~G~i~~v~~~~d~~~~~~kG~afV~f~~~~~a~~al~  151 (207)
                      ...-||.-..|..-...+|.++|+.||.|.=- .+-+.       .|||.....++|..++.
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~Vs-wIddT-------Sa~V~L~~~e~~~~v~~   67 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQIS-WIDDT-------SAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCCCE-EEETT-------EEEEECSCHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceEEE-EecCc-------eEEEEecCHHHHHHHHH
Confidence            34468888999999999999999999966433 33442       89999999999998885