Citrus Sinensis ID: 030488

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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------
Protein Sequence
MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPYY
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccEEEEccccccccHHHHHHHHHccccEEEEEEEEccccccccEEEEEEccHHHHHHHHHccccccccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHcccEEEEEcccccccHHHHHHHHHccccEEEEEEEEccccccccEEEEEEccHHHHHHHHHHccccEcccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MKIRLKEMEEEATALRQMHAKVgnemaskqdpaaggsslanreevdsrsvfvgnvdysctpeEVQQHFQScgtvnrvtirtdkfgqpkgyaYVEFLQSEAVQEALHLNESELHGRQLKVTVkrtnvpgmkqhrprrpnpfmvyqsrgaiippflyspygygkiprfrmpmryspyy
Flexible Loop (DISEMBL)
mkirlkemEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNeselhgrqlkvtvkrtnvpgmkqhrprrpnpFMVYQSRGAIIPpflyspygygkiprfrmpmryspyy
Low Complexity Region (SEG)
MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPYY
Disordered region (IsUnstruct)
*************************************************VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLN*******************************FMVYQSRGAIIPPFLYSPYGYGKIPRFRM********
Disordered Region (DISOPRED)
*KIRLKE******************************************VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV*********************************************************
Disordered Region (DISEMBL)
*************ALRQMHAKVGN*******************EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPYY
Disordered Region (DISPRO)
*****KEMEEEATALRQMHAKVGNE*******************VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRTN***MKQ****RPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPYY
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKIRxxxxxxxxxxxxxxxxxxxxxMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPYY
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	176	2.2.26 [Sep-21-2011]
O14327	166	Polyadenylate-binding pro	yes	no	0.681	0.722	0.553	5e-32
Q28ZX3	225	Polyadenylate-binding pro	yes	no	0.732	0.573	0.515	5e-31
Q7KNF2	224	Polyadenylate-binding pro	yes	no	0.732	0.575	0.507	2e-30
Q54ZS8	222	Polyadenylate-binding pro	yes	no	0.778	0.617	0.412	2e-25
Q8CCS6	302	Polyadenylate-binding pro	yes	no	0.767	0.447	0.452	4e-25
Q28165	306	Polyadenylate-binding pro	yes	no	0.767	0.441	0.445	4e-25
Q86U42	306	Polyadenylate-binding pro	no	no	0.767	0.441	0.445	5e-25
Q9DDY9	296	Polyadenylate-binding pro	N/A	no	0.522	0.310	0.559	7e-25
Q7ZXB8	295	Polyadenylate-binding pro	N/A	no	0.522	0.311	0.559	1e-24
Q6TY21	218	Embryonic polyadenylate-b	N/A	no	0.732	0.591	0.397	1e-24

>sp|O14327|PAB2_SCHPO Polyadenylate-binding protein 2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=pab2 PE=3 SV=1

 Score =  137 bits (344), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 72/130 (55%), Positives = 89/130 (68%), Gaps = 10/130 (7%)

Query: 1   MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCT 60
           MK R+ EME EA  LR M  ++ NE  + ++         ++E +D++SV+VGNVDYS T
Sbjct: 17  MKERVAEMEAEAAKLRAMQEQLDNETEALRN---------DKESIDAQSVYVGNVDYSVT 67

Query: 61  PEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV 119
           PEE+Q HF SCG+VNRVTI  DKF G PKG+AY+EF +   V  AL LN S LH R LKV
Sbjct: 68  PEELQSHFASCGSVNRVTILCDKFTGHPKGFAYIEFSEPSLVPNALLLNGSMLHERPLKV 127

Query: 120 TVKRTNVPGM 129
           T KRTNVPGM
Sbjct: 128 TPKRTNVPGM 137

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

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

 Score =  133 bits (335), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 68/132 (51%), Positives = 92/132 (69%), Gaps = 3/132 (2%)

Query: 1   MKIRLKEMEEEATALRQMHAKVGNEMA--SKQDPAAGGSSLANREEVDSRSVFVGNVDYS 58
           +K R+KEMEEEA  ++QM ++V  +MA  S    AA   SL  ++E+D+RSV+VGNVDY 
Sbjct: 47  IKARVKEMEEEAEKIKQMQSEVDKQMAGGSTTGLAAVPLSLEEKQEIDTRSVYVGNVDYG 106

Query: 59  CTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLNESELHGRQL 117
            + EE++ HF  CGT+NRVTI  +K  G PKG+AY+EF   E V+ AL +NE+   GRQ+
Sbjct: 107 ASAEELEAHFHGCGTINRVTILCNKADGHPKGFAYIEFGSKEFVETALAMNETLFRGRQI 166

Query: 118 KVTVKRTNVPGM 129
           KV  KRTN PG+
Sbjct: 167 KVMSKRTNRPGL 178

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

 Score =  131 bits (329), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 67/132 (50%), Positives = 91/132 (68%), Gaps = 3/132 (2%)

Query: 1   MKIRLKEMEEEATALRQMHAKVGNEMA--SKQDPAAGGSSLANREEVDSRSVFVGNVDYS 58
           +K R+KEMEEEA  ++QM ++V  +MA  S    A    SL  ++E+D+RSV+VGNVDY 
Sbjct: 47  IKARVKEMEEEAEKIKQMQSEVDKQMAGGSTTGLATVPLSLEEKQEIDTRSVYVGNVDYG 106

Query: 59  CTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLNESELHGRQL 117
            + EE++ HF  CGT+NRVTI  +K  G PKG+AY+EF   E V+ AL +NE+   GRQ+
Sbjct: 107 ASAEELEAHFHGCGTINRVTILCNKADGHPKGFAYIEFGSKEFVETALAMNETLFRGRQI 166

Query: 118 KVTVKRTNVPGM 129
           KV  KRTN PG+
Sbjct: 167 KVMSKRTNRPGL 178

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|Q54ZS8|PABP2_DICDI Polyadenylate-binding protein 2 OS=Dictyostelium discoideum GN=pabpn1 PE=3 SV=1

 Score =  115 bits (288), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 66/160 (41%), Positives = 93/160 (58%), Gaps = 23/160 (14%)

Query: 1   MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSL-------ANREEVDSRSVFVG 53
           MK R +EMEEEA  L ++   + + +        GG+          ++EE+DSRSV+VG
Sbjct: 47  MKKRFREMEEEAKKLTELQNNLESNITGNNGVGIGGNIGGGGGLMNTDQEEIDSRSVYVG 106

Query: 54  NVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESEL 112
           NVDY  T +++  +FQSCGTVNR+TI +DK  G PKG  YVEF+  E++  A+ LN+S  
Sbjct: 107 NVDYKSTHDQILAYFQSCGTVNRITILSDKTTGHPKGCCYVEFVNKESIINAMALNDSFF 166

Query: 113 HGRQLKVTVKRTNVPGMKQHRPRRPNPFMVYQSRGAIIPP 152
           + RQLK+T KRTN+P               Y  R  ++PP
Sbjct: 167 NERQLKITPKRTNLP---------------YYMRQGVLPP 191

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.

Dictyostelium discoideum (taxid: 44689)

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

 Score =  114 bits (284), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 67/148 (45%), Positives = 84/148 (56%), Gaps = 13/148 (8%)

Query: 38  SLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFL 96
           SL  + E D+RS++VGNVDY  T EE++ HF  CG+VNRVTI  DKF G PKG+AY+EF 
Sbjct: 158 SLEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFS 217

Query: 97  QSEAVQEALHLNESELHGRQLKVTVKRTNVPGM---------KQHRPRRPNPFMVYQSRG 147
             E+V+ +L L+ES   GRQ+KV  KRTN PG+          ++R R  N      SR 
Sbjct: 218 DKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTDRGFPRSRYRARTTN---YNSSRS 274

Query: 148 AIIPPFLYSPYGYGKIPRFRMPMRYSPY 175
                F   P G     R R    YSPY
Sbjct: 275 RFYSGFNSRPRGRIYRGRARATSWYSPY 302

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

 Score =  114 bits (284), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 66/148 (44%), Positives = 84/148 (56%), Gaps = 13/148 (8%)

Query: 38  SLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFL 96
           S+  + E D+RS++VGNVDY  T EE++ HF  CG+VNRVTI  DKF G PKG+AY+EF 
Sbjct: 162 SIEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFS 221

Query: 97  QSEAVQEALHLNESELHGRQLKVTVKRTNVPGMK---------QHRPRRPNPFMVYQSRG 147
             E+V+ +L L+ES   GRQ+KV  KRTN PG+          ++R R  N      SR 
Sbjct: 222 DKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTDRGFPRARYRARTTN---YNSSRS 278

Query: 148 AIIPPFLYSPYGYGKIPRFRMPMRYSPY 175
                F   P G     R R    YSPY
Sbjct: 279 RFYSGFNSRPRGRVYRGRARATSWYSPY 306

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

 Score =  113 bits (283), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 66/148 (44%), Positives = 84/148 (56%), Gaps = 13/148 (8%)

Query: 38  SLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFL 96
           S+  + E D+RS++VGNVDY  T EE++ HF  CG+VNRVTI  DKF G PKG+AY+EF 
Sbjct: 162 SIEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFS 221

Query: 97  QSEAVQEALHLNESELHGRQLKVTVKRTNVPGMK---------QHRPRRPNPFMVYQSRG 147
             E+V+ +L L+ES   GRQ+KV  KRTN PG+          ++R R  N      SR 
Sbjct: 222 DKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTDRGFPRARYRARTTN---YNSSRS 278

Query: 148 AIIPPFLYSPYGYGKIPRFRMPMRYSPY 175
                F   P G     R R    YSPY
Sbjct: 279 RFYSGFNSRPRGRVYRGRARATSWYSPY 306

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

 Score =  113 bits (282), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 52/93 (55%), Positives = 68/93 (73%), Gaps = 1/93 (1%)

Query: 38  SLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFL 96
           S+  + E D+RS++VGNVDY  T EE++ HF  CG+VNRVTI  DKF G PKG+AY+EF 
Sbjct: 153 SVEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFTGHPKGFAYIEFC 212

Query: 97  QSEAVQEALHLNESELHGRQLKVTVKRTNVPGM 129
             E+V+ +L L+ES   GRQ+KV  KRTN PG+
Sbjct: 213 DKESVRTSLALDESLFRGRQIKVVPKRTNRPGI 245

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

 Score =  112 bits (280), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 52/93 (55%), Positives = 68/93 (73%), Gaps = 1/93 (1%)

Query: 38  SLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFL 96
           S+  + E D+RS++VGNVDY  T EE++ HF  CG+VNRVTI  DKF G PKG+AY+EF 
Sbjct: 152 SVEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFTGHPKGFAYIEFS 211

Query: 97  QSEAVQEALHLNESELHGRQLKVTVKRTNVPGM 129
             E+V+ +L L+ES   GRQ+KV  KRTN PG+
Sbjct: 212 DKESVRTSLALDESLFRGRQIKVVPKRTNRPGI 244

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 =  112 bits (280), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 58/146 (39%), Positives = 90/146 (61%), Gaps = 17/146 (11%)

Query: 1   MKIRLKEMEEEATALRQMHAK---VGNE----MASKQDPAAGGS---------SLANREE 44
           +++R++EMEEEA  L+ +  +   +G      M +       G+         S   ++E
Sbjct: 30  IRMRVREMEEEAERLKGLSGQDKSIGVSTRPCMQTTHSKMTAGAYTEGPPQPLSAEEKKE 89

Query: 45  VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQE 103
           +D RSV+VGNVDY  T ++++ HF SCG++NR+TI  DKF G PKGYAY+EF +  +V  
Sbjct: 90  IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDA 149

Query: 104 ALHLNESELHGRQLKVTVKRTNVPGM 129
           A+ ++E+   GR +KV  KRTN+PG+
Sbjct: 150 AVAMDETVFRGRTIKVLPKRTNMPGI 175

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	176
255569758	198	poly-A binding protein, putative [Ricinu	0.988	0.878	0.817	1e-79
449438769	196	PREDICTED: polyadenylate-binding protein	1.0	0.897	0.784	2e-78
449523199	196	PREDICTED: polyadenylate-binding protein	1.0	0.897	0.778	1e-77
358248734	197	uncharacterized protein LOC100791351 [Gl	1.0	0.893	0.792	6e-77
224140775	199	predicted protein [Populus trichocarpa]	0.994	0.879	0.772	2e-75
358248311	197	uncharacterized protein LOC100784473 [Gl	1.0	0.893	0.775	7e-75
224081120	218	predicted protein [Populus trichocarpa]	1.0	0.807	0.772	2e-74
255581746	218	poly-A binding protein, putative [Ricinu	1.0	0.807	0.767	3e-74
356512681	215	PREDICTED: polyadenylate-binding protein	1.0	0.818	0.761	5e-73
224060413	199	predicted protein [Populus trichocarpa]	0.994	0.879	0.761	2e-72

>gi|255569758|ref|XP_002525843.1| poly-A binding protein, putative [Ricinus communis] gi|223534848|gb|EEF36537.1| poly-A binding protein, putative [Ricinus communis]

 Score =  300 bits (768), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 143/175 (81%), Positives = 154/175 (88%), Gaps = 1/175 (0%)

Query: 1   MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCT 60
           MK RLKEME+EA ALR+M AKV  EM S QDP A  S  ANREEVDSRSVFVGNVDYSCT
Sbjct: 24  MKKRLKEMEDEAAALREMQAKVEKEMGSSQDPTAAASQ-ANREEVDSRSVFVGNVDYSCT 82

Query: 61  PEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVT 120
           PEEVQQHFQSCGTVNR+TIRTDK+GQPKGYAYVEFL+ EAVQEAL LNESELHGRQLKVT
Sbjct: 83  PEEVQQHFQSCGTVNRITIRTDKYGQPKGYAYVEFLEPEAVQEALLLNESELHGRQLKVT 142

Query: 121 VKRTNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPY 175
            KRTNVPGMKQ RPRRPNP+M +  RG+ +PP+ YSPYGYGK+PRFRMPMRYSPY
Sbjct: 143 AKRTNVPGMKQFRPRRPNPYMGFAPRGSQLPPYFYSPYGYGKVPRFRMPMRYSPY 197

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449438769|ref|XP_004137160.1| PREDICTED: polyadenylate-binding protein 2-like [Cucumis sativus]

 Score =  296 bits (758), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 138/176 (78%), Positives = 154/176 (87%)

Query: 1   MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCT 60
           MK RLK+ME+EA ALR+M AKV  EM+S QDPA+  +S ANREEVDSRSVFVGNVDYSCT
Sbjct: 21  MKKRLKDMEDEAAALREMQAKVEKEMSSVQDPASAAASQANREEVDSRSVFVGNVDYSCT 80

Query: 61  PEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVT 120
           PEEVQQHFQSCGTVNR+TIRTDKFGQPKGYAYVEF++ EAVQEAL LNESELHGRQLKVT
Sbjct: 81  PEEVQQHFQSCGTVNRITIRTDKFGQPKGYAYVEFVEPEAVQEALLLNESELHGRQLKVT 140

Query: 121 VKRTNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPYY 176
            KRTN+PGMKQ+RPRR NPFM  +SR   + P+ +SPYGYGK+PRFRMP RY PYY
Sbjct: 141 AKRTNIPGMKQYRPRRSNPFMGARSRSPYVAPYFFSPYGYGKVPRFRMPTRYGPYY 196

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449523199|ref|XP_004168611.1| PREDICTED: polyadenylate-binding protein 2-like [Cucumis sativus]

 Score =  294 bits (752), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 137/176 (77%), Positives = 153/176 (86%)

Query: 1   MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCT 60
           MK RLK+ME+EA ALR+M AKV  EM+S QDPA+  +S ANREEVDSRSVFVGNVDYSCT
Sbjct: 21  MKKRLKDMEDEAAALREMQAKVEKEMSSVQDPASAAASQANREEVDSRSVFVGNVDYSCT 80

Query: 61  PEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVT 120
           PEEVQQHFQSCGTVNR+TIRTDKFGQPKGYAYVEF++ EAVQEAL LNESELHGRQLKVT
Sbjct: 81  PEEVQQHFQSCGTVNRITIRTDKFGQPKGYAYVEFVEPEAVQEALLLNESELHGRQLKVT 140

Query: 121 VKRTNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPYY 176
             RTN+PGMKQ+RPRR NPFM  +SR   + P+ +SPYGYGK+PRFRMP RY PYY
Sbjct: 141 AMRTNIPGMKQYRPRRSNPFMGARSRSPYVAPYFFSPYGYGKVPRFRMPTRYGPYY 196

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358248734|ref|NP_001239931.1| uncharacterized protein LOC100791351 [Glycine max] gi|255647673|gb|ACU24298.1| unknown [Glycine max]

 Score =  291 bits (746), Expect = 6e-77,   Method: Compositional matrix adjust.
 Identities = 141/178 (79%), Positives = 154/178 (86%), Gaps = 2/178 (1%)

Query: 1   MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCT 60
           MK RLKEME+EA ALR+M AKV  EM S QDPA   +S AN+EE+DSRSVFVGNVDYSCT
Sbjct: 20  MKKRLKEMEDEAAALREMQAKVEKEMGSAQDPANASASQANKEEIDSRSVFVGNVDYSCT 79

Query: 61  PEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVT 120
           PEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFL+ EAVQEAL LNESELHGRQLKVT
Sbjct: 80  PEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLEVEAVQEALLLNESELHGRQLKVT 139

Query: 121 VKRTNVPGMKQHRPRRP-NPFM-VYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPYY 176
            KRTN+PGMKQ+RPRR  NP+M  ++ R    PPF+YSPYGYGK+PRFRM MRYSPYY
Sbjct: 140 AKRTNIPGMKQYRPRRTINPYMGGFRGRTPYAPPFIYSPYGYGKVPRFRMAMRYSPYY 197

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224140775|ref|XP_002323754.1| predicted protein [Populus trichocarpa] gi|222866756|gb|EEF03887.1| predicted protein [Populus trichocarpa]

 Score =  286 bits (733), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 136/176 (77%), Positives = 155/176 (88%), Gaps = 1/176 (0%)

Query: 1   MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGS-SLANREEVDSRSVFVGNVDYSC 59
           MK RLKEME+EA ALR+M AKV  EM S QDP+A  + S AN+EEVDSRSVFVGNVDY+C
Sbjct: 23  MKKRLKEMEDEAAALREMQAKVEKEMGSVQDPSASATASQANKEEVDSRSVFVGNVDYAC 82

Query: 60  TPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV 119
           TPEEVQQHFQ+CGTVNRVTIR+DK+GQPKGYAYVEF++ EAVQEAL LNESELHGRQLKV
Sbjct: 83  TPEEVQQHFQACGTVNRVTIRSDKYGQPKGYAYVEFVEPEAVQEALLLNESELHGRQLKV 142

Query: 120 TVKRTNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPY 175
           T KRTNVPGMKQ R RRP+P+M +  R AI+PP+L+SPYGYGK+ R+RMPMRYSPY
Sbjct: 143 TAKRTNVPGMKQFRARRPSPYMGFPPRAAIMPPYLFSPYGYGKVMRYRMPMRYSPY 198

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358248311|ref|NP_001240115.1| uncharacterized protein LOC100784473 [Glycine max] gi|255635956|gb|ACU18324.1| unknown [Glycine max]

 Score =  285 bits (728), Expect = 7e-75,   Method: Compositional matrix adjust.
 Identities = 138/178 (77%), Positives = 152/178 (85%), Gaps = 2/178 (1%)

Query: 1   MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCT 60
           MK RLKEME+EA ALR+M AKV  EM S QDPA   +S AN+EE+DSRSVFVGNVDYSCT
Sbjct: 20  MKKRLKEMEDEAAALREMQAKVEKEMGSVQDPANASASQANKEEIDSRSVFVGNVDYSCT 79

Query: 61  PEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVT 120
           PEEVQQHFQSCGTVNR+TIRTDKFGQPKGYAYVEFL+ EAVQEAL LNESELHGRQLKVT
Sbjct: 80  PEEVQQHFQSCGTVNRITIRTDKFGQPKGYAYVEFLEVEAVQEALLLNESELHGRQLKVT 139

Query: 121 VKRTNVPGMKQHRPRRP-NPFM-VYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPYY 176
            KRTN+PGMKQ+RPRR  NP+M   + R     PF+YSPYGYGK+PRFRM MR+SPYY
Sbjct: 140 AKRTNIPGMKQYRPRRSTNPYMGGLRGRTPYAAPFIYSPYGYGKVPRFRMAMRHSPYY 197

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224081120|ref|XP_002306300.1| predicted protein [Populus trichocarpa] gi|222855749|gb|EEE93296.1| predicted protein [Populus trichocarpa]

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 136/176 (77%), Positives = 149/176 (84%)

Query: 1   MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCT 60
           MK RLKEMEEEA ALR+M AKV  EM + QDPA   ++ ANREE DSRSVFVGNVDY+CT
Sbjct: 43  MKKRLKEMEEEAAALREMQAKVEKEMGAVQDPATAAANQANREEADSRSVFVGNVDYACT 102

Query: 61  PEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVT 120
           PEEVQQHFQSCGTVNRVTI TDKFGQPKG+AYVEFL+ EAVQEAL LNESELHGRQLKV+
Sbjct: 103 PEEVQQHFQSCGTVNRVTILTDKFGQPKGFAYVEFLEVEAVQEALALNESELHGRQLKVS 162

Query: 121 VKRTNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPYY 176
            KRTNVPGMKQ+RPRR NP+M Y+ R    PP+ YSPYGYGK+PRFR  MRY PYY
Sbjct: 163 PKRTNVPGMKQYRPRRINPYMGYRFRRPYAPPYFYSPYGYGKVPRFRRSMRYMPYY 218

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255581746|ref|XP_002531675.1| poly-A binding protein, putative [Ricinus communis] gi|223528706|gb|EEF30719.1| poly-A binding protein, putative [Ricinus communis]

 Score =  282 bits (722), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 135/176 (76%), Positives = 150/176 (85%)

Query: 1   MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCT 60
           MK RLKEMEEEA ALR+M AKV  EM + QDPA+  ++ AN+EE DSRSVFVGNVDY+CT
Sbjct: 43  MKKRLKEMEEEAAALREMQAKVEKEMGAVQDPASAAANQANKEETDSRSVFVGNVDYACT 102

Query: 61  PEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVT 120
           PEEVQQHFQSCGTVNRVTI TDKFGQPKG+AYVEFL+ EA+QEAL LNESELHGRQLKV 
Sbjct: 103 PEEVQQHFQSCGTVNRVTILTDKFGQPKGFAYVEFLEVEAIQEALLLNESELHGRQLKVL 162

Query: 121 VKRTNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPYY 176
            KRTNVPGMKQ+RPRR NP+M Y+ R   +PP+ YSPYGYGK PRFR PMRY PYY
Sbjct: 163 PKRTNVPGMKQYRPRRFNPYMGYRFRRPYVPPYFYSPYGYGKAPRFRRPMRYMPYY 218

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356512681|ref|XP_003525045.1| PREDICTED: polyadenylate-binding protein 2-like [Glycine max]

 Score =  278 bits (712), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 134/176 (76%), Positives = 148/176 (84%)

Query: 1   MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCT 60
           MK RLKEMEEEA ALR+M AKV  E+ S QDPA   +S AN+EE DSRSVFVGNVDY+CT
Sbjct: 40  MKRRLKEMEEEAAALREMQAKVDKEIGSVQDPANSAASQANKEEADSRSVFVGNVDYACT 99

Query: 61  PEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVT 120
           PEEVQQHFQSCGTVNRVTI TDKFGQPKG+AYVEF+++EAVQEAL LNESELHGRQLKV 
Sbjct: 100 PEEVQQHFQSCGTVNRVTILTDKFGQPKGFAYVEFVEAEAVQEALLLNESELHGRQLKVL 159

Query: 121 VKRTNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPYY 176
            KRTNVPGMKQ+RPRR NP+M Y  R    PP+ YSPYGYGK+PRFR P RY PY+
Sbjct: 160 PKRTNVPGMKQYRPRRFNPYMAYGFRRPYTPPYFYSPYGYGKVPRFRRPNRYMPYH 215

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224060413|ref|XP_002300187.1| predicted protein [Populus trichocarpa] gi|222847445|gb|EEE84992.1| predicted protein [Populus trichocarpa]

 Score =  276 bits (707), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 134/176 (76%), Positives = 153/176 (86%), Gaps = 1/176 (0%)

Query: 1   MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLA-NREEVDSRSVFVGNVDYSC 59
           MK RLKEME+EA AL +M AKV  EM S QDP+A  ++   NREEVDSRSVFVGNVDYSC
Sbjct: 23  MKKRLKEMEDEAAALLEMQAKVEKEMGSVQDPSASAAASQANREEVDSRSVFVGNVDYSC 82

Query: 60  TPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV 119
           TPEEVQQHFQ+CGT+NR+TIR+DK+GQPKGYAYVEFL+ E VQEAL LNESELHGRQLKV
Sbjct: 83  TPEEVQQHFQACGTINRITIRSDKYGQPKGYAYVEFLEPETVQEALLLNESELHGRQLKV 142

Query: 120 TVKRTNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPY 175
           TVKRTN+PGMKQ R RRPNP+M +  RGA +PP+L+SPYGYGK+ R+RMPMRYSPY
Sbjct: 143 TVKRTNLPGMKQFRARRPNPYMGFPPRGAPMPPYLFSPYGYGKVLRYRMPMRYSPY 198

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	176
TAIR|locus:2142519	217	AT5G10350 [Arabidopsis thalian	0.994	0.806	0.72	2e-65
TAIR|locus:2171780	220	AT5G65260 [Arabidopsis thalian	0.988	0.790	0.725	5.2e-65
UNIPROTKB|G4MUH3	193	MGG_07252 "Polyadenylate-bindi	0.721	0.658	0.566	2e-33
ASPGD|ASPL0000053752	187	AN1340 [Emericella nidulans (t	0.681	0.641	0.553	4.7e-32
POMBASE|SPBC16E9.12c	166	pab2 "poly(A) binding protein	0.715	0.759	0.544	6.9e-31
UNIPROTKB|Q9DDY9	296	pabpn1-a "Polyadenylate-bindin	0.994	0.591	0.418	3.8e-30
MGI|MGI:1859158	302	Pabpn1 "poly(A) binding protei	0.994	0.579	0.437	3.8e-30
UNIPROTKB|G3V7Z8	302	Pabpn1 "Protein Pabpn1" [Rattu	0.994	0.579	0.437	3.8e-30
UNIPROTKB|F1MTN4	275	PABPN1 "Polyadenylate-binding	0.994	0.636	0.432	4.9e-30
UNIPROTKB|Q28165	306	PABPN1 "Polyadenylate-binding	0.994	0.571	0.432	4.9e-30

TAIR|locus:2142519 AT5G10350 [Arabidopsis thaliana (taxid:3702)]

 Score = 666 (239.5 bits), Expect = 2.0e-65, P = 2.0e-65
 Identities = 126/175 (72%), Positives = 144/175 (82%)

Query:     1 MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCT 60
             MK RLKEMEEEA ALR+M AKV  EM + QDPA+  ++   +EEVD+RSV+VGNVDY+CT
Sbjct:    42 MKRRLKEMEEEAAALREMQAKVEKEMGATQDPASMAANQEGKEEVDARSVYVGNVDYACT 101

Query:    61 PEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVT 120
             PEEVQ HFQ+CGTVNRVTI  DKFGQPKG+AYVEF++ EAVQEAL LNESELHGRQLKV+
Sbjct:   102 PEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVS 161

Query:   121 VKRTNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPY 175
              KRTNVPGMKQ+ P R NP M Y+ R   +PP+ YSPYGYGK PRFR PMRY PY
Sbjct:   162 PKRTNVPGMKQYHPGRFNPSMGYRFRRPFVPPYFYSPYGYGKAPRFRRPMRYMPY 216

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0005515 "protein binding" evidence=IPI

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

GO:0005774 "vacuolar membrane" evidence=IDA

TAIR|locus:2171780 AT5G65260 [Arabidopsis thaliana (taxid:3702)]

 Score = 662 (238.1 bits), Expect = 5.2e-65, P = 5.2e-65
 Identities = 127/175 (72%), Positives = 147/175 (84%)

Query:     1 MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCT 60
             MK RLKEME+EA ALR+M AKV  EM + QDPA+  ++ A +EEVD+RSVFVGNVDY+CT
Sbjct:    46 MKKRLKEMEDEAAALREMQAKVEKEMGA-QDPASIAANQAGKEEVDARSVFVGNVDYACT 104

Query:    61 PEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVT 120
             PEEVQQHFQ+CGTV+RVTI TDKFGQPKG+AYVEF++ EAVQEAL LNESELHGRQLKV 
Sbjct:   105 PEEVQQHFQTCGTVHRVTILTDKFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVL 164

Query:   121 VKRTNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPY 175
              KRTNVPG+KQ R RR NP+M Y+ R   + P++YSPYGYGK PRFR PMRY PY
Sbjct:   165 QKRTNVPGLKQFRGRRFNPYMGYRFRRPFMSPYMYSPYGYGKAPRFRRPMRYMPY 219

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|G4MUH3 MGG_07252 "Polyadenylate-binding protein 2" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 364 (133.2 bits), Expect = 2.0e-33, P = 2.0e-33
 Identities = 77/136 (56%), Positives = 97/136 (71%)

Query:     1 MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCT 60
             MK R+ EMEEEA  LR+M A + ++    Q+      S  +R++VDSRS+FVGNVDYS +
Sbjct:    34 MKKRVAEMEEEAAKLREMQASLDSQ---SQE-----LSTESRDDVDSRSIFVGNVDYSAS 85

Query:    61 PEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV 119
             PEE+Q HFQSCG++NRVTI  DKF GQPKG+AYVEF +   V +AL LNES   GR +KV
Sbjct:    86 PEEIQAHFQSCGSINRVTILLDKFTGQPKGFAYVEFTEPSLVAQALVLNESVFKGRNIKV 145

Query:   120 TVKRTNVPGMKQHRPR 135
             + KRTN PGM + R R
Sbjct:   146 SPKRTNYPGMSRGRGR 161

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

ASPGD|ASPL0000053752 AN1340 [Emericella nidulans (taxid:162425)]

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 72/130 (55%), Positives = 91/130 (70%)

Query:     1 MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCT 60
             MK R+ EME EA  LR+M A +  +  S ++         ++E++D+RS+FVGNVDY  +
Sbjct:    30 MKRRVAEMESEAAKLREMQATLDQQSESLKE---------DKEDIDARSIFVGNVDYGAS 80

Query:    61 PEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV 119
             PEE+Q HFQSCG++NRVTI  DKF GQPKGYAYVEF +   V +AL LNES   GR LKV
Sbjct:    81 PEEIQAHFQSCGSINRVTILLDKFTGQPKGYAYVEFAEPSLVAQALVLNESVFRGRNLKV 140

Query:   120 TVKRTNVPGM 129
               KRTN+PGM
Sbjct:   141 VPKRTNLPGM 150

GO:0005634 "nucleus" evidence=IEA

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

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000289 "nuclear-transcribed mRNA poly(A) tail shortening" evidence=IEA

GO:0010972 "negative regulation of G2/M transition of mitotic cell cycle" evidence=IEA

POMBASE|SPBC16E9.12c pab2 "poly(A) binding protein Pab2" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 340 (124.7 bits), Expect = 6.9e-31, P = 6.9e-31
 Identities = 74/136 (54%), Positives = 92/136 (67%)

Query:     1 MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCT 60
             MK R+ EME EA  LR M  ++ NE  + ++         ++E +D++SV+VGNVDYS T
Sbjct:    17 MKERVAEMEAEAAKLRAMQEQLDNETEALRN---------DKESIDAQSVYVGNVDYSVT 67

Query:    61 PEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV 119
             PEE+Q HF SCG+VNRVTI  DKF G PKG+AY+EF +   V  AL LN S LH R LKV
Sbjct:    68 PEELQSHFASCGSVNRVTILCDKFTGHPKGFAYIEFSEPSLVPNALLLNGSMLHERPLKV 127

Query:   120 TVKRTNVPGMKQHRPR 135
             T KRTNVPGM + R R
Sbjct:   128 TPKRTNVPGMSRGRGR 143

GO:0000289 "nuclear-transcribed mRNA poly(A) tail shortening" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

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

GO:0010972 "negative regulation of G2/M transition of mitotic cell cycle" evidence=IMP

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

 Score = 333 (122.3 bits), Expect = 3.8e-30, P = 3.8e-30
 Identities = 77/184 (41%), Positives = 103/184 (55%)

Query:     1 MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGS---SLANREEVDSRSVFVGNVDY 57
             +K R++EMEEEA  L+++  +V  +M     P   G    S+  + E D+RS++VGNVDY
Sbjct:   113 IKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMSVEEKMEADARSIYVGNVDY 172

Query:    58 SCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLNESELHGRQ 116
               T EE++ HF  CG+VNRVTI  DKF G PKG+AY+EF   E+V+ +L L+ES   GRQ
Sbjct:   173 GATAEELEAHFHGCGSVNRVTILCDKFTGHPKGFAYIEFCDKESVRTSLALDESLFRGRQ 232

Query:   117 LKVTVKRTNVPGMKQH-----RPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMR 171
             +KV  KRTN PG+        R R       Y SR      +   P G     R R    
Sbjct:   233 IKVVPKRTNRPGISTTDRGFPRARYRARASSYSSRSRFYSGYTPRPRGRVYRGRARATSW 292

Query:   172 YSPY 175
             Y+PY
Sbjct:   293 YTPY 296

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

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

 Score = 333 (122.3 bits), Expect = 3.8e-30, P = 3.8e-30
 Identities = 81/185 (43%), Positives = 104/185 (56%)

Query:     1 MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGS---SLANREEVDSRSVFVGNVDY 57
             +K R++EMEEEA  L+++  +V  +M     P   G    SL  + E D+RS++VGNVDY
Sbjct:   118 IKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMSLEEKMEADARSIYVGNVDY 177

Query:    58 SCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLNESELHGRQ 116
               T EE++ HF  CG+VNRVTI  DKF G PKG+AY+EF   E+V+ +L L+ES   GRQ
Sbjct:   178 GATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQ 237

Query:   117 LKVTVKRTNVPGMKQ-HR--PR---RPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPM 170
             +KV  KRTN PG+    R  PR   R        SR      F   P G     R R   
Sbjct:   238 IKVIPKRTNRPGISTTDRGFPRSRYRARTTNYNSSRSRFYSGFNSRPRGRIYRGRARATS 297

Query:   171 RYSPY 175
              YSPY
Sbjct:   298 WYSPY 302

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

 Score = 333 (122.3 bits), Expect = 3.8e-30, P = 3.8e-30
 Identities = 81/185 (43%), Positives = 104/185 (56%)

Query:     1 MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGS---SLANREEVDSRSVFVGNVDY 57
             +K R++EMEEEA  L+++  +V  +M     P   G    SL  + E D+RS++VGNVDY
Sbjct:   118 IKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMSLEEKMEADARSIYVGNVDY 177

Query:    58 SCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLNESELHGRQ 116
               T EE++ HF  CG+VNRVTI  DKF G PKG+AY+EF   E+V+ +L L+ES   GRQ
Sbjct:   178 GATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQ 237

Query:   117 LKVTVKRTNVPGMKQ-HR--PR---RPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPM 170
             +KV  KRTN PG+    R  PR   R        SR      F   P G     R R   
Sbjct:   238 IKVIPKRTNRPGISTTDRGFPRARYRARTTNYNSSRSRFYSGFNSRPRGRIYRGRARATS 297

Query:   171 RYSPY 175
              YSPY
Sbjct:   298 WYSPY 302

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

 Score = 332 (121.9 bits), Expect = 4.9e-30, P = 4.9e-30
 Identities = 80/185 (43%), Positives = 104/185 (56%)

Query:     1 MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGS---SLANREEVDSRSVFVGNVDY 57
             +K R++EMEEEA  L+++  +V  +M     P   G    S+  + E D+RS++VGNVDY
Sbjct:    91 IKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMSIEEKMEADARSIYVGNVDY 150

Query:    58 SCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLNESELHGRQ 116
               T EE++ HF  CG+VNRVTI  DKF G PKG+AY+EF   E+V+ +L L+ES   GRQ
Sbjct:   151 GATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQ 210

Query:   117 LKVTVKRTNVPGMKQ-HR--PR---RPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPM 170
             +KV  KRTN PG+    R  PR   R        SR      F   P G     R R   
Sbjct:   211 IKVIPKRTNRPGISTTDRGFPRARYRARTTNYNSSRSRFYSGFNSRPRGRVYRGRARATS 270

Query:   171 RYSPY 175
              YSPY
Sbjct:   271 WYSPY 275

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 = 332 (121.9 bits), Expect = 4.9e-30, P = 4.9e-30
 Identities = 80/185 (43%), Positives = 104/185 (56%)

Query:     1 MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGS---SLANREEVDSRSVFVGNVDY 57
             +K R++EMEEEA  L+++  +V  +M     P   G    S+  + E D+RS++VGNVDY
Sbjct:   122 IKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMSIEEKMEADARSIYVGNVDY 181

Query:    58 SCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLNESELHGRQ 116
               T EE++ HF  CG+VNRVTI  DKF G PKG+AY+EF   E+V+ +L L+ES   GRQ
Sbjct:   182 GATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQ 241

Query:   117 LKVTVKRTNVPGMKQ-HR--PR---RPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPM 170
             +KV  KRTN PG+    R  PR   R        SR      F   P G     R R   
Sbjct:   242 IKVIPKRTNRPGISTTDRGFPRARYRARTTNYNSSRSRFYSGFNSRPRGRVYRGRARATS 301

Query:   171 RYSPY 175
              YSPY
Sbjct:   302 WYSPY 306

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

---

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	0.5538	0.6818	0.7228	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	eugene3.00170125	hypothetical protein (199 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	eugene3.00030485	hypothetical protein (164 aa)			•						0.467
	grail3.0067008905	hypothetical protein (142 aa)			•						0.435
	gw1.VII.3426.1	hypothetical protein (184 aa)			•						0.433
	grail3.1445000102	annotation not avaliable (101 aa)			•						0.421
	estExt_Genewise1_v1.C_LG_II0296	SubName- Full=Putative uncharacterized protein; (178 aa)			•						0.417
	eugene3.00050727	hypothetical protein (101 aa)			•						0.415
	eugene3.00120066	hypothetical protein (181 aa)			•						0.412
	gw1.IX.3509.1	hypothetical protein (282 aa)			•						0.410
	estExt_fgenesh4_pg.C_LG_VI1354	hypothetical protein (140 aa)			•						0.409
	estExt_fgenesh4_pg.C_280167	hypothetical protein (287 aa)			•						0.406

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	176
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	1e-45
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	4e-33
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	7e-29
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	8e-22
smart00360	73	smart00360, RRM, RNA recognition motif	1e-20
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-20
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-18
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-18
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	4e-18
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	5e-16
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	1e-15
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	8e-15
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	1e-14
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-14
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	3e-14
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	9e-14
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-13
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	5e-13
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	8e-13
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	1e-12
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	1e-11
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	1e-11
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-11
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	4e-11
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	5e-11
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	6e-11
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	6e-11
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	7e-11
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	9e-11
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-10
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	4e-10
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	4e-10
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	4e-10
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	1e-09
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	2e-09
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	2e-09
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	3e-09
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	3e-09
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	4e-09
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	4e-09
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	4e-09
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	6e-09
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	6e-09
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	7e-09
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	8e-09
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-08
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-08
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	1e-08
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	2e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-08
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	3e-08
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	3e-08
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	3e-08
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	4e-08
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	7e-08
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	8e-08
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	9e-08
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-07
cd12281	92	cd12281, RRM1_TatSF1_like, RNA recognition motif 1	2e-07
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-07
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-07
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	2e-07
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-07
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-07
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	3e-07
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	3e-07
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	3e-07
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	4e-07
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	4e-07
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	4e-07
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	5e-07
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	6e-07
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	6e-07
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	8e-07
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	8e-07
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	8e-07
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-06
cd12396	85	cd12396, RRM1_Nop13p_fungi, RNA recognition motif	1e-06
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	1e-06
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-06
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	1e-06
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	2e-06
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	2e-06
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-06
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-06
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-06
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	3e-06
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	3e-06
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	5e-06
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	5e-06
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	6e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-05
cd12730	79	cd12730, RRM1_GRSF1, RNA recognition motif 1 in G-	1e-05
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	1e-05
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	1e-05
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	1e-05
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	1e-05
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	1e-05
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	2e-05
cd12503	77	cd12503, RRM1_hnRNPH_GRSF1_like, RNA recognition m	2e-05
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	2e-05
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	2e-05
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	2e-05
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-05
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	2e-05
cd12504	77	cd12504, RRM2_hnRNPH_like, RNA recognition motif 2	2e-05
cd12403	75	cd12403, RRM1_NCL, RNA recognition motif 1 in vert	3e-05
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	3e-05
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	3e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-05
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	4e-05
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	4e-05
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	5e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	5e-05
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	6e-05
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	6e-05
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	8e-05
cd12228	84	cd12228, RRM_ENOX, RNA recognition motif (RRM) in	8e-05
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	9e-05
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	9e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-04
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	1e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	1e-04
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	1e-04
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	1e-04
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-04
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	1e-04
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-04
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-04
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	2e-04
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	2e-04
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	2e-04
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	2e-04
cd12514	73	cd12514, RRM4_RBM12_like, RNA recognition motif 4	3e-04
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	3e-04
cd12460	82	cd12460, RRM2_CID8_like, RNA recognition motif 2 i	3e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	3e-04
cd12294	102	cd12294, RRM_Rrp7A, RNA recognition motif in ribos	3e-04
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	4e-04
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	4e-04
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	5e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	5e-04
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	5e-04
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	5e-04
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	6e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	6e-04
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	7e-04
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	8e-04
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	0.001
cd12268	68	cd12268, RRM_Vip1, RNA recognition motif in fissio	0.001
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	0.001
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	0.001
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	0.001
cd12537	85	cd12537, RRM1_RBM23, RNA recognition motif 1 in ve	0.001
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	0.001
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	0.001
cd12536	85	cd12536, RRM1_RBM39, RNA recognition motif 1 in ve	0.001
cd12505	75	cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-	0.001
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	0.002
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	0.002
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	0.002
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	0.002
cd12533	84	cd12533, RRM_EWS, RNA recognition motif in vertebr	0.002
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	0.002
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	0.002
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	0.002
cd12508	80	cd12508, RRM2_ESRPs_Fusilli, RNA recognition motif	0.002
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.002
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	0.003
cd12643	77	cd12643, RRM_CFIm68, RNA recognition motif of pre-	0.003
cd12502	72	cd12502, RRM2_RMB19, RNA recognition motif 2 in RN	0.003
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	0.003
cd12520	74	cd12520, RRM1_MRN1, RNA recognition motif 1 of RNA	0.003
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	0.003
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	0.003
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	0.004
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	0.004

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

 Score =  144 bits (365), Expect = 1e-45
 Identities = 50/73 (68%), Positives = 61/73 (83%), Gaps = 1/73 (1%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHL 107
           S+FVGNVDY  TPEE+Q+HF+SCGT+NR+TI  DKF GQPKG+AY+EFL   +V+ AL L
Sbjct: 1   SIFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLL 60

Query: 108 NESELHGRQLKVT 120
           NESE  GRQ+KVT
Sbjct: 61  NESEFRGRQIKVT 73

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

 Score =  112 bits (282), Expect = 4e-33
 Identities = 46/76 (60%), Positives = 56/76 (73%), Gaps = 1/76 (1%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHL 107
           SV+VGNVDY  T EE++ HF  CG+VNRVTI  DKF G PKG+AY+EF   E+V+ AL L
Sbjct: 1   SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALAL 60

Query: 108 NESELHGRQLKVTVKR 123
           +ES   GRQ+KV  KR
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 =  101 bits (254), Expect = 7e-29
 Identities = 44/77 (57%), Positives = 55/77 (71%), Gaps = 1/77 (1%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHL 107
           SV+VGNVDY  T EE++ HF  CG +NRVTI  DKF G PKGYAY+EF   ++V+ A+ L
Sbjct: 1   SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVAL 60

Query: 108 NESELHGRQLKVTVKRT 124
           +ES   GR +KV  KRT
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|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 83.4 bits (207), Expect = 8e-22
 Identities = 31/73 (42%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRV-TIRTDKFGQPKGYAYVEFLQSEAVQEALHL 107
           SVFVGN+ +    EE+++HF+ CG V  V  +R  K G  KG+ YV F   ++V  AL L
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL 60

Query: 108 NESELHGRQLKVT 120
           N  +L GR+++V 
Sbjct: 61  NGIKLKGRKIRVK 73

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

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

 Score = 80.3 bits (199), Expect = 1e-20
 Identities = 32/73 (43%), Positives = 44/73 (60%), Gaps = 2/73 (2%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL-H 106
           ++FVGN+    T EE+++ F   G V  V +  DK  G+ KG+A+VEF   E  ++AL  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 107 LNESELHGRQLKV 119
           LN  EL GR LKV
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 79.7 bits (197), Expect = 2e-20
 Identities = 31/71 (43%), Positives = 44/71 (61%), Gaps = 1/71 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 108
           +FVGN+    T E++++ F   G +  V I  DK G+ KG+A+VEF   E  ++AL  LN
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 109 ESELHGRQLKV 119
             EL GR+LKV
Sbjct: 61  GKELDGRKLKV 71

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

 Score = 74.7 bits (184), Expect = 2e-18
 Identities = 27/71 (38%), Positives = 45/71 (63%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLN 108
           ++FVGN+ +S   +++++ F+ CG V  V I  D  G+ KG+ +VEF   E  Q+AL  +
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEKS 60

Query: 109 ESELHGRQLKV 119
             EL GR+++V
Sbjct: 61  GEELLGREIRV 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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 74.2 bits (183), Expect = 3e-18
 Identities = 27/70 (38%), Positives = 42/70 (60%), Gaps = 1/70 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 108
           +FVGN+    T E+++  F   G +  + I  D+ G+ KG+A+VEF   E  ++AL  LN
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 109 ESELHGRQLK 118
             EL GR+L+
Sbjct: 61  GKELGGRELR 70

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

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

 Score = 73.9 bits (182), Expect = 4e-18
 Identities = 30/71 (42%), Positives = 46/71 (64%), Gaps = 1/71 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLN 108
           +FVGN+ Y  T E++  HF++ G    V + TDK  G+ KG A+VEF  +EA+ +AL L+
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 109 ESELHGRQLKV 119
            + L GR++ 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|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 69.0 bits (169), Expect = 5e-16
 Identities = 30/76 (39%), Positives = 47/76 (61%), Gaps = 5/76 (6%)

Query: 49  SVFVGNVDYSCTPEEVQ----QHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQE 103
           ++FV   D S   ++++    +HF SCG + RV+I TD+  G  KG+AY+EF   + V++
Sbjct: 1   TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 104 ALHLNESELHGRQLKV 119
           AL L+ S+L G  L V
Sbjct: 61  ALELDGSDLGGGNLVV 76

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

 Score = 67.7 bits (166), Expect = 1e-15
 Identities = 30/67 (44%), Positives = 43/67 (64%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLN 108
           +VFV N+DYS   +E+++ F  CG +  V +  +  G+ KGYAYVEF   E+VQEAL L+
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKLD 60

Query: 109 ESELHGR 115
              + GR
Sbjct: 61  RELIKGR 67

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

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

 Score = 70.4 bits (171), Expect = 8e-15
 Identities = 37/172 (21%), Positives = 71/172 (41%), Gaps = 9/172 (5%)

Query: 6   KEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQ 65
           +EMEE+    R        E   +   ++       + + ++ ++FVGN+ Y  T E+++
Sbjct: 78  REMEEQNDGERGYT----KEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLR 133

Query: 66  QHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR 123
           + F+  G V RV +  D+  G+ +G+A+VEF   E+ ++A+  LN  EL GR L+V   +
Sbjct: 134 ELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ 193

Query: 124 TNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPY 175
                  +        F     + +     L        +    +       
Sbjct: 194 PASQPRSELSNNLDASFA---KKLSRGKALLLEKSDNLYVGNLPLKTAEEEL 242

Length = 306

>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 65.4 bits (160), Expect = 1e-14
 Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHL 107
           R+++VGN+D + T +++ + F   G V  V +  D+  QP  YA+VEF +  +V  AL L
Sbjct: 5   RTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDE-TQPTRYAFVEFAEQTSVINALKL 63

Query: 108 NESELHGRQLKVT 120
           N +   GR LKV 
Sbjct: 64  NGAMFGGRPLKVN 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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 65.3 bits (160), Expect = 1e-14
 Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 51  FVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL-HLN 108
           +VGN+ Y+ T E+++  F   G V    + TD+  G+ +G+ +VE   +E    A+  LN
Sbjct: 3   YVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKLN 62

Query: 109 ESELHGRQLKVTVKR 123
            ++  GR L V   R
Sbjct: 63  GTDFGGRTLTVNEAR 77

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

 Score = 63.8 bits (156), Expect = 3e-14
 Identities = 23/77 (29%), Positives = 43/77 (55%), Gaps = 4/77 (5%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTI---RTDKFG-QPKGYAYVEFLQSEAVQE 103
           R ++V N+D+    ++++  F   G V  + I   + +K G    G+A+V F  + + + 
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 104 ALHLNESELHGRQLKVT 120
           AL LN +EL GR++ V+
Sbjct: 61  ALQLNGTELGGRKISVS 77

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

 Score = 62.7 bits (153), Expect = 9e-14
 Identities = 23/70 (32%), Positives = 36/70 (51%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNE 109
           +FVG +    T EE++  F   G+V  V I TD+ G  KGY +V F   E  ++ L +  
Sbjct: 5   IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAMGN 64

Query: 110 SELHGRQLKV 119
               G++L +
Sbjct: 65  LNFRGKKLNI 74

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|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 = 62.3 bits (152), Expect = 1e-13
 Identities = 29/72 (40%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HL 107
           VFVGN+ Y  T E++ + F   G V    + TD+  G+PKGY + EF   E    A+ +L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 108 NESELHGRQLKV 119
           N  E +GR L+V
Sbjct: 61  NGYEFNGRALRV 72

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

 Score = 60.5 bits (147), Expect = 5e-13
 Identities = 26/72 (36%), Positives = 42/72 (58%), Gaps = 2/72 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALH-L 107
           +FVGN+ +    + + + F   G ++ V + TD   G+PKG+ YVEF   EA Q AL  L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 108 NESELHGRQLKV 119
             ++L GR +++
Sbjct: 61  GGTDLLGRPVRL 72

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

 Score = 60.5 bits (147), Expect = 8e-13
 Identities = 25/73 (34%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQ-SEAVQEALHLN 108
           +FV  + +S T EE+++ F+  G V  V + T++ G+PKG AYVE+   S A Q  L ++
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMD 64

Query: 109 ESELHGRQLKVTV 121
            +E+  + + V +
Sbjct: 65  GTEIKEKTISVAI 77

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|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 = 60.1 bits (146), Expect = 1e-12
 Identities = 25/77 (32%), Positives = 48/77 (62%), Gaps = 1/77 (1%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHL 107
           R++ VG +D S + +++++ F +CG V RV +  D+    + +A+VEF  +E+   AL+L
Sbjct: 1   RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR-FAFVEFADAESALSALNL 59

Query: 108 NESELHGRQLKVTVKRT 124
           + + L G  L+V+  +T
Sbjct: 60  SGTLLGGHPLRVSPSKT 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|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 = 56.8 bits (138), Expect = 1e-11
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCG-TVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLN 108
           V +  + +S T E+++  F       + + I  D  G+P G AYVEF   E  + AL  +
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKH 61

Query: 109 ESELHGRQLKV 119
            +++ GR ++V
Sbjct: 62  NNKMGGRYIEV 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|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 = 57.1 bits (138), Expect = 1e-11
 Identities = 29/72 (40%), Positives = 42/72 (58%), Gaps = 2/72 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HL 107
           VFVGN+ Y  T E+++  F   G V    +  D+  G+PKGY + E+   E    A+ +L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 108 NESELHGRQLKV 119
           N  EL+GRQL+V
Sbjct: 61  NGYELNGRQLRV 72

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 56.0 bits (136), Expect = 2e-11
 Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 2/70 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 108
           ++V N+  S T E++++ F   G V  V +  +K  +P+G+A+VEF   E  + AL  LN
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK-DRPRGFAFVEFASPEDAEAALKKLN 59

Query: 109 ESELHGRQLK 118
              L GR L+
Sbjct: 60  GLVLDGRTLR 69

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

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

 Score = 55.9 bits (135), Expect = 4e-11
 Identities = 22/72 (30%), Positives = 44/72 (61%), Gaps = 2/72 (2%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHL 107
           +V++GN+ +  T ++V++ F     +  V + TDK  G+ KG+ +V+F   E++  AL L
Sbjct: 1   TVYIGNLAWDITEDDVREFF-KGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALKL 59

Query: 108 NESELHGRQLKV 119
           + + L GR +++
Sbjct: 60  DGTVLCGRPIRI 71

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

 Score = 55.7 bits (135), Expect = 5e-11
 Identities = 28/80 (35%), Positives = 42/80 (52%), Gaps = 7/80 (8%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ-PKGYAYVEFLQSEAVQEAL- 105
           R+VF+ N+ +  T EE+++ F   G V    I  DK     KG A+V+F   E+ Q+ L 
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 106 ---HLNESE--LHGRQLKVT 120
              +  +S   L GR+L VT
Sbjct: 61  AADNAEDSGLSLDGRRLIVT 80

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|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 55.5 bits (134), Expect = 6e-11
 Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQS-EAVQEALHLN 108
           +FV N+DY    +++++ F+  G V R  I+ DK G+ +G   V+F    EAVQ     N
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60

Query: 109 ESELHGRQLKV 119
              L  R ++V
Sbjct: 61  GQMLFDRPMRV 71

This subfamily corresponds to the RRM2 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. It 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 = 74

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

 Score = 55.4 bits (134), Expect = 6e-11
 Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHL 107
           R++FVGN+D   T E + + F   G +  V I  D  G+PK +A+V F    +V  A+ L
Sbjct: 2   RTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQL 61

Query: 108 -NESELHGRQLKV 119
            N   L GR+L++
Sbjct: 62  LNGIRLFGRELRI 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|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 55.3 bits (133), Expect = 7e-11
 Identities = 29/73 (39%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH- 106
           R++FVGN+D   T E + + F   G V +V I  DK G+PK +A+V F    +V  A++ 
Sbjct: 2   RTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNL 61

Query: 107 LNESELHGRQLKV 119
           LN  +L+GR L +
Sbjct: 62  LNGIKLYGRPLNI 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|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 54.9 bits (133), Expect = 9e-11
 Identities = 30/77 (38%), Positives = 43/77 (55%), Gaps = 7/77 (9%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTI--RTDKFGQPK----GYAYVEFLQSEAV 101
            ++FV N+++  T E +++HF+ CG V  VTI  + D  G  K    GY +VEF   EA 
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 102 QEALH-LNESELHGRQL 117
           Q+AL  L  + L G  L
Sbjct: 61  QKALKRLQGTVLDGHAL 77

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

 Score = 53.9 bits (130), Expect = 2e-10
 Identities = 24/72 (33%), Positives = 42/72 (58%), Gaps = 2/72 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALH-L 107
           +FVGN+ +S   E ++  F+  GTV    + TD+  G+ +G+ YV+F   E  ++A+  +
Sbjct: 2   LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAM 61

Query: 108 NESELHGRQLKV 119
           +  EL GR + V
Sbjct: 62  DGKELDGRPINV 73

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

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

 Score = 53.0 bits (128), Expect = 4e-10
 Identities = 24/71 (33%), Positives = 44/71 (61%), Gaps = 2/71 (2%)

Query: 51  FVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALH-LN 108
           +VGN+ ++ T ++++  F+  G +  V ++ D   G+ KGY +++F  +E  ++AL  LN
Sbjct: 2   YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61

Query: 109 ESELHGRQLKV 119
             EL GR +KV
Sbjct: 62  GFELAGRPIKV 72

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

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

 Score = 53.1 bits (128), Expect = 4e-10
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 2/75 (2%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG-QPKGYAYVEFLQSEAVQEALH- 106
           +V+V N+ +S T  ++ + F   G V +VTI  DK   + KG A++ FL  E   + +  
Sbjct: 3   TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 107 LNESELHGRQLKVTV 121
           LN  EL GR LK ++
Sbjct: 63  LNNKELFGRTLKCSI 77

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

 Score = 53.3 bits (128), Expect = 4e-10
 Identities = 29/76 (38%), Positives = 43/76 (56%), Gaps = 4/76 (5%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTI-RTDKFGQPKGYAYVEFLQSEAVQEALHL 107
            VFVGN+ +    E + + F  CG +  V I R  K    KG+AYV+F    AV++AL L
Sbjct: 1   CVFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLL 60

Query: 108 NESE---LHGRQLKVT 120
           NE +   +  R+L+V+
Sbjct: 61  NEKKFPPMLPRELRVS 76

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

 Score = 51.9 bits (124), Expect = 1e-09
 Identities = 29/73 (39%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH- 106
           R++FVGN++     E + + F   G + +VTI  DK G+PK + +V F  SE+V  A+  
Sbjct: 2   RTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIAL 61

Query: 107 LNESELHGRQLKV 119
           LN   L+GR +KV
Sbjct: 62  LNGIRLYGRPIKV 74

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

 Score = 51.3 bits (123), Expect = 2e-09
 Identities = 21/57 (36%), Positives = 35/57 (61%), Gaps = 1/57 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRT-DKFGQPKGYAYVEFLQSEAVQEAL 105
           +FVGN+ +  T +E++ HF   G + RV + T +  G+ KG+A+V+F + E    AL
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|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp

 Score = 50.9 bits (122), Expect = 2e-09
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 4/72 (5%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH-L 107
           +V+ G    S    +V++ F++CG V +VT+ +      + +A++ F   EA Q A+  L
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTV---QPHAFITFENLEAAQLAIETL 57

Query: 108 NESELHGRQLKV 119
           N + + G  +KV
Sbjct: 58  NGASVDGNCIKV 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|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 51.5 bits (124), Expect = 3e-09
 Identities = 24/91 (26%), Positives = 42/91 (46%), Gaps = 18/91 (19%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTV----------------NRVTIRTDKFGQPKGY- 90
           R+VFVGN+  +   +++++ F+  G +                 +V     KF   K   
Sbjct: 1   RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60

Query: 91  -AYVEFLQSEAVQEALHLNESELHGRQLKVT 120
            AYV F + E+ ++AL LN +E  G  ++V 
Sbjct: 61  NAYVVFKEEESAEKALKLNGTEFEGHHIRVD 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|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 50.8 bits (122), Expect = 3e-09
 Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 3/75 (4%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLN 108
           +FVG +    T EE +++F   G V    +  D   G+ +G+ +V F    AV+      
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAG 61

Query: 109 ESELHGRQLKVTVKR 123
             EL G+Q  V VKR
Sbjct: 62  MLELGGKQ--VEVKR 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|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 50.4 bits (121), Expect = 4e-09
 Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 51  FVGNVDYSCTPEEVQQHFQSCGTVNRVTIR---TDKFGQPKGYAYVEFLQSEAVQEALHL 107
           FVGN+ ++    ++   F+     +   +R   TDKF   KG+ YVEF   E+++EAL  
Sbjct: 5   FVGNLPFNTVQGDLDAIFKDLSVKSVRLVRDKETDKF---KGFCYVEFEDVESLKEALEY 61

Query: 108 NESELHGRQLKVTV 121
           + +    R L+V +
Sbjct: 62  DGALFDDRSLRVDI 75

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

 Score = 50.3 bits (121), Expect = 4e-09
 Identities = 24/72 (33%), Positives = 33/72 (45%), Gaps = 1/72 (1%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEALHL 107
           +VFV  +       ++ + F   G V  V I  D    + KG AYVEF   E+V  AL L
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGL 60

Query: 108 NESELHGRQLKV 119
               L G+ + 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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 50.3 bits (121), Expect = 4e-09
 Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALH 106
             +FVG + Y  T + ++++F   G +    + TD+  G+ +GY +V F   E+ + A  
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 107 LNESELHGRQLKV 119
                + GR+  V
Sbjct: 61  DPNPIIDGRKANV 73

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

 Score = 50.3 bits (121), Expect = 6e-09
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPK--GYAYVEFLQSEAVQEAL- 105
           ++FV N+ Y  T E++++ F   G + R  +  DK G  K  G+ YV F   E  + AL 
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDK-GSKKCRGFGYVTFALEEDAKRALE 59

Query: 106 HLNESELHGRQLKVTV 121
              +++  GR++ V  
Sbjct: 60  EKKKTKFGGRKIHVEF 75

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|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 50.0 bits (120), Expect = 6e-09
 Identities = 26/72 (36%), Positives = 42/72 (58%), Gaps = 1/72 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH-LN 108
           +FV N+ +S T ++++  F+ CG V R  ++TD  G+ KG+  V F   E  Q A+   N
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 109 ESELHGRQLKVT 120
             +L GR+L+V 
Sbjct: 61  GYDLEGRELEVR 72

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

 Score = 50.3 bits (121), Expect = 7e-09
 Identities = 26/91 (28%), Positives = 53/91 (58%), Gaps = 4/91 (4%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL- 105
           +++FV  ++Y  T  ++++ F+  G + R+ +  DK  G+P+GYA++EF     ++ A  
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 106 HLNESELHGRQLKVTVKRTNVPGMKQHRPRR 136
           + +  ++ GR++ V V+R     +K   PRR
Sbjct: 62  YADGKKIDGRRVLVDVERGRT--VKGWLPRR 90

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

 Score = 49.5 bits (119), Expect = 8e-09
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 4/69 (5%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNE 109
           + V N+ Y  T E++++ F   G V +V I  D+ G+ +G A V F + E  + A+    
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAI---- 58

Query: 110 SELHGRQLK 118
            + +G  L 
Sbjct: 59  KQFNGVLLD 67

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

 Score = 49.6 bits (119), Expect = 1e-08
 Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 6/81 (7%)

Query: 45  VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTI--RTDKFGQPKGYAYVEFLQSEAVQ 102
           +D  S+FVG +    T EE+ + F   G +  V +  R +       +A+++F + +A  
Sbjct: 1   IDKYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANH---TNAFAFIKFEREQAAA 57

Query: 103 EAL-HLNESELHGRQLKVTVK 122
            A+   N S L  + + V  K
Sbjct: 58  RAVESENHSMLKNKTMHVQYK 78

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

 Score = 49.6 bits (119), Expect = 1e-08
 Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG----QPKGYAYVEFLQSEAVQEAL 105
           +++GN+D   T   + + F   G + +      K G    QP+GY +V F   E  ++AL
Sbjct: 2   LWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKAL 61

Query: 106 H-LNESELHGRQLKVT 120
             LN     G++L V 
Sbjct: 62  KSLNGKTALGKKLVVR 77

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|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 = 49.2 bits (118), Expect = 1e-08
 Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 10/78 (12%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF------GQPKGYAYVEFLQSEAVQE 103
           ++VGN+ +  T E+++      G V+  +I   KF      G+ KG+AYVEF    A   
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSI---KFFEHKANGKSKGFAYVEFASEAAAAA 57

Query: 104 AL-HLNESELHGRQLKVT 120
               L   E +G++  VT
Sbjct: 58  VKEKLEGREFNGKKCVVT 75

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

 Score = 49.0 bits (117), Expect = 2e-08
 Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLN 108
           +VFVG +D      E++  F   G+V  V I TD+ G  KGY +V F     VQ+ +  +
Sbjct: 7   TVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYDDVDVQKIVE-S 65

Query: 109 ESELHGRQLKV 119
           +   HG++LK+
Sbjct: 66  QINFHGKKLKL 76

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|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 = 48.1 bits (115), Expect = 3e-08
 Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 51  FVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLN 108
           FV N+ ++ T EE+++ F++ G ++ V +  DK   + KG+A+V F+  E   +A   L+
Sbjct: 3   FVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELD 62

Query: 109 ESELHGRQLKVT 120
            S   GR L V 
Sbjct: 63  GSIFQGRLLHVL 74

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

 Score = 48.4 bits (116), Expect = 3e-08
 Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALH-L 107
           V+VGN+D   T E + + F   G V  V I  D+     +GY +VEFL  E    A+  +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 108 NESELHGRQLKV 119
           N  +L+G+ ++V
Sbjct: 61  NMIKLYGKPIRV 72

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

 Score = 48.2 bits (115), Expect = 3e-08
 Identities = 24/76 (31%), Positives = 45/76 (59%), Gaps = 2/76 (2%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG-QPKGYAYVEFLQSE-AVQE 103
           +S  +F+ N+ Y+CT E++++ F   G ++ V +  DK   +PKG+A+V ++  E AV+ 
Sbjct: 1   ESGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKA 60

Query: 104 ALHLNESELHGRQLKV 119
              L+ +   GR L +
Sbjct: 61  FAELDGTVFQGRLLHL 76

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

 Score = 48.2 bits (115), Expect = 3e-08
 Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 2/76 (2%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSE-AVQE 103
           ++  +FV N+ YSC  +++++ F   G ++ V +  DK  G+ KG+AYV FL  E AV+ 
Sbjct: 1   ETGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKA 60

Query: 104 ALHLNESELHGRQLKV 119
              L+     GR + +
Sbjct: 61  YKELDGKVFQGRLIHI 76

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

 Score = 48.0 bits (115), Expect = 4e-08
 Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 108
           V+V N+      E++++ F   G +    +  D  G+ KG+ +V F   EA Q+A+  LN
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELN 63

Query: 109 ESELHGRQLKV 119
             E++G++L V
Sbjct: 64  GKEVNGKKLYV 74

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

>gnl|CDD|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 = 7e-08
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRT-DKFGQPKGYAYVEFLQSEAVQEALHLN 108
           V+VG + Y  T +E++ +F  CG +  + + T    G+ +G A++ F   EA + AL L+
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALALD 60

Query: 109 ESELHGRQLKV 119
             ++ GR LKV
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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 46.8 bits (112), Expect = 8e-08
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 8/71 (11%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH-LN 108
           +FVGN+  + T EE++  F+  GTV    +        K Y +V   + E  ++A+  LN
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVV-------KNYGFVHMEEEEDAEDAIKALN 54

Query: 109 ESELHGRQLKV 119
             E  G+++ V
Sbjct: 55  GYEFMGKRINV 65

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

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

 Score = 46.8 bits (112), Expect = 9e-08
 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQP-KGYAYVEFLQSEAVQEAL-HL 107
           ++VG +      + +   F   G +  + I  D   Q  +G+A+VEF + E    A+ ++
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 108 NESELHGRQLKVT 120
           NESEL GR ++V 
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|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 47.0 bits (112), Expect = 1e-07
 Identities = 21/73 (28%), Positives = 44/73 (60%), Gaps = 2/73 (2%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALH- 106
           S++V NV  +  P+++++ F   G +  V I  D +  +P+G+AYV+F      ++AL+ 
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 107 LNESELHGRQLKV 119
           L+ +   GR++++
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|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 46.8 bits (112), Expect = 2e-07
 Identities = 24/84 (28%), Positives = 43/84 (51%), Gaps = 10/84 (11%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVN--------RVTIRTDKFGQPKGYAYVEFLQSEA 100
           +V+V  +    T EE  + F  CG +         ++ +  D+ G  KG A   +L+ E+
Sbjct: 3   NVYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKIKLYRDENGNLKGDALCCYLKEES 62

Query: 101 VQEALH-LNESELHGRQLKVTVKR 123
           V+ A+  L+ +E+ GR  K+ V+R
Sbjct: 63  VELAIQLLDGTEI-GRGYKMKVER 85

This subfamily corresponds to the RRM1 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 = 92

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

 Score = 49.5 bits (118), Expect = 2e-07
 Identities = 27/78 (34%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 43  EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAV 101
            E D R+VFV  +       ++ + F   G V  V    D+   + KG AYVEF   E+V
Sbjct: 85  AERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESV 144

Query: 102 QEALHLNESELHGRQLKV 119
            +AL L    L GR + V
Sbjct: 145 IKALALTGQMLLGRPIIV 162

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

 Score = 46.0 bits (110), Expect = 2e-07
 Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 51  FVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLNE 109
           F+G + +  T E ++++F   G V    I  D   G+ +G+ +V F    +V + L    
Sbjct: 2   FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKP 61

Query: 110 SELHGRQ 116
             L GR+
Sbjct: 62  HVLDGRE 68

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

 Score = 46.0 bits (110), Expect = 2e-07
 Identities = 22/72 (30%), Positives = 43/72 (59%), Gaps = 2/72 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL-HL 107
           ++VGN+ +  T E++ + F  CG + R+ +  D+F   P G+ +VE+   E  + A+ +L
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 108 NESELHGRQLKV 119
           N ++L  R ++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|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score = 45.6 bits (109), Expect = 2e-07
 Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 108
           +F+ N+D S   + +   F + G +    + TD+ G  KGY +V F   EA   A+  +N
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVN 64

Query: 109 ESELHGRQLKV 119
              L+ +++ V
Sbjct: 65  GMLLNDKKVFV 75

This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 77

>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 = 45.7 bits (109), Expect = 3e-07
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 6/72 (8%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEA-LHL 107
           +V+VGN+ +  T EE+Q+ F   G +  V +  D     KGYA+V F   EA   A + +
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAAATAIVAV 56

Query: 108 NESELHGRQLKV 119
           N + ++G+ +K 
Sbjct: 57  NGTSINGQTVKC 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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 45.6 bits (108), Expect = 3e-07
 Identities = 20/57 (35%), Positives = 30/57 (52%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH 106
           +FVG +D+     ++++ F   GTV  V I  D+ G  KGY +V F   E  Q+ L 
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQ 61

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 45.2 bits (107), Expect = 3e-07
 Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 8/71 (11%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 108
           +FVGNV  +CT +E++  F+  G V    +  DK    K YA+V   + E    A+  LN
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRV----VECDKV---KDYAFVHMEREEEALAAIEALN 55

Query: 109 ESELHGRQLKV 119
             E+ GR++ V
Sbjct: 56  GKEVKGRRINV 66

This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 68

>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 45.4 bits (107), Expect = 3e-07
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQS-EAVQEALHL 107
           ++FV N+D+    +++++ F   GTV R  I+ DK G+ +G   V F Q  EAVQ     
Sbjct: 2   TIFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMF 61

Query: 108 NESELHGRQLKV 119
           N   L  R + V
Sbjct: 62  NGQFLFDRPMHV 73

This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, 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 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 45.3 bits (108), Expect = 4e-07
 Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL-HL 107
           +FV  +    T +E++  F   G V  V +  D   G+ +G+ +V F   E    A+  L
Sbjct: 4   LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63

Query: 108 NESELHGRQLKVTVKRT 124
           N  EL GR +KV   + 
Sbjct: 64  NGKELEGRVIKVEKAKR 80

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

 Score = 45.3 bits (108), Expect = 4e-07
 Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 51  FVGNVDYSCTPEEVQQHFQSCGTVNRV-TIRTDKFGQPKGYAYVEF-LQSEAVQEALHLN 108
            VGN+    T E+ ++     G V R   + ++  G+ KGY +VE+  ++ A++    L+
Sbjct: 3   CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62

Query: 109 ESELHGRQLKV 119
             ++ GR+L+V
Sbjct: 63  GKQIGGRKLQV 73

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

 Score = 45.1 bits (107), Expect = 4e-07
 Identities = 19/72 (26%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 51  FVGNVDYSCTPEEVQQHFQSCGTVN-RVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNE 109
           ++GN+ Y  T E++++ F+     + R+       G+ +G+ Y EF   +++ +AL LN+
Sbjct: 5   YLGNLPYDVTEEDIKEFFRGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSLND 64

Query: 110 SELHGRQLKVTV 121
             L  R+++V +
Sbjct: 65  ESLKNRRIRVDI 76

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

 Score = 45.0 bits (107), Expect = 5e-07
 Identities = 18/72 (25%), Positives = 44/72 (61%), Gaps = 2/72 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEALH-L 107
           ++V +V    + ++++  F++ G +   ++  D + G+ KGY ++E+   ++ Q+A+  +
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 108 NESELHGRQLKV 119
           N  +L G+QL+V
Sbjct: 63  NLFDLGGQQLRV 74

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|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 44.5 bits (105), Expect = 6e-07
 Identities = 26/75 (34%), Positives = 46/75 (61%), Gaps = 7/75 (9%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL 105
           S+ + V N+ YS + + +Q+ F+        +IR  +  G+PKGYA+VEF  +E  +EAL
Sbjct: 1   SKVLVVNNLSYSASEDSLQEVFEKA-----TSIRIPQNNGRPKGYAFVEFESAEDAKEAL 55

Query: 106 H-LNESELHGRQLKV 119
           +  N +E+ GR +++
Sbjct: 56  NSCNNTEIEGRSIRL 70

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is 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. . Length = 72

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 44.7 bits (106), Expect = 6e-07
 Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQS-CGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH-L 107
           VF+ N+ Y    ++++  F+   G V  V +  D+ G+ +G   VEF   E+VQ+AL  +
Sbjct: 2   VFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALETM 61

Query: 108 NESELHGRQLKV 119
           N  EL GR+L V
Sbjct: 62  NRYELKGRKLVV 73

This subfamily corresponds to the RRM1 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. Moreover, 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 = 76

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

 Score = 44.5 bits (105), Expect = 8e-07
 Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNE 109
           ++VGN+D   T + ++Q FQ  G V  V I  DK  +   Y +VE+ QS   + AL    
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQ--- 57

Query: 110 SELHGRQLKVTVKRTN 125
             L+GRQ++    R N
Sbjct: 58  -TLNGRQIENNEIRVN 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|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 44.4 bits (105), Expect = 8e-07
 Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 2/73 (2%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL-H 106
           ++FV N+ +S T E++   F     +    + TD + G+ +GY +V F   E  QEAL  
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 107 LNESELHGRQLKV 119
           L   +LHGR L++
Sbjct: 61  LKNKKLHGRILRL 73

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

 Score = 44.6 bits (106), Expect = 8e-07
 Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 2/59 (3%)

Query: 52  VGNVDYSCTPEEVQQHFQSCGTVNRVT-IRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 108
           +G+++       +   F  CG V  V  IR  + G+  GY +VEF   EA ++AL  LN
Sbjct: 4   MGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLN 62

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

 Score = 46.8 bits (111), Expect = 1e-06
 Identities = 25/74 (33%), Positives = 45/74 (60%), Gaps = 2/74 (2%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL- 105
             ++VGN+ ++ T +E++Q F+  G +  V +  D   G+ KG+ +++F  +E  +EAL 
Sbjct: 187 LKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALE 246

Query: 106 HLNESELHGRQLKV 119
            +N  EL GR +KV
Sbjct: 247 VMNGFELAGRPIKV 260

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

 Score = 44.5 bits (105), Expect = 1e-06
 Identities = 27/83 (32%), Positives = 44/83 (53%), Gaps = 12/83 (14%)

Query: 50  VFVGNVDYSCTPEEVQQHFQS-------CGTVNRVTIRTDK-----FGQPKGYAYVEFLQ 97
           V++GN+ ++ T E ++Q F S          + RV +   K       Q KG+AYV+F  
Sbjct: 1   VWIGNLSFTTTKEMLRQFFVSKSGDRITDEQITRVHMPDSKAKRKGVKQNKGFAYVDFTS 60

Query: 98  SEAVQEALHLNESELHGRQLKVT 120
            EA + A+ L+E  L+GR+L + 
Sbjct: 61  QEATKAAIALSEKILNGRKLLIK 83

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

 Score = 44.1 bits (105), Expect = 1e-06
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 9/76 (11%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALH-- 106
           +FVG +  S T  ++++ F   GTV+ V I   K  G  +G+AY++   SEA    L   
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEA---QLKKC 58

Query: 107 ---LNESELHGRQLKV 119
              LN ++  G  LK+
Sbjct: 59  KSTLNGTKWKGSVLKI 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|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 43.8 bits (104), Expect = 1e-06
 Identities = 21/71 (29%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFL-QSEAVQEALHLN 108
           + V N+ + CT  ++++ F   G V  VTI     G+ KG+A+V+F  +++A +    +N
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVN 61

Query: 109 ESELHGRQLKV 119
             ++ GR + V
Sbjct: 62  GKKIKGRPVAV 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|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 43.7 bits (103), Expect = 1e-06
 Identities = 26/77 (33%), Positives = 45/77 (58%), Gaps = 8/77 (10%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIR--TDKFGQPKGYAYVEFLQSEAVQE 103
           D+R++FV N+ Y+ T +E+++ F+     + V IR  + K G  KG AY+EF      ++
Sbjct: 2   DARTLFVKNLPYNITVDELKEVFE-----DAVDIRLPSGKDGSSKGIAYIEFKTEAEAEK 56

Query: 104 ALHLNE-SELHGRQLKV 119
           AL   + +E+ GR + V
Sbjct: 57  ALEEKQGAEVDGRSIVV 73

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

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

 Score = 43.6 bits (103), Expect = 2e-06
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQP-KGYAYVEFLQSEAVQEAL-HL 107
           V+VG++ +    + ++Q F   G +  + +  D      KG+A+VE+   EA Q AL  +
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 108 NESELHGRQLKV 119
           N   L GR +KV
Sbjct: 63  NGVMLGGRNIKV 74

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

 Score = 43.8 bits (104), Expect = 2e-06
 Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 9/80 (11%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNR--------VTIRTDKFGQPKGYAYVEFLQSEAV 101
           +++  +    T + + + F   G + R        + I TDK  +PKG A V +    A 
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60

Query: 102 QEAL-HLNESELHGRQLKVT 120
           Q A+   N  E  G ++KV+
Sbjct: 61  QAAIEWFNGYEFRGNKIKVS 80

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

 Score = 43.3 bits (103), Expect = 2e-06
 Identities = 21/73 (28%), Positives = 42/73 (57%), Gaps = 2/73 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HL 107
           + VG +  +   + +++ F + GTV  V +  D+    P+GYAYVEF   E  ++A+ H+
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 108 NESELHGRQLKVT 120
           +  ++ G+++ V 
Sbjct: 61  DGGQIDGQEVTVE 73

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

 Score = 43.5 bits (103), Expect = 2e-06
 Identities = 19/78 (24%), Positives = 46/78 (58%), Gaps = 3/78 (3%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ-PKGYAYVEFLQSEAVQEAL 105
           ++ +FVG +  + T  +++++F   GTV  V +  D   + P+G+ ++ F   ++V + +
Sbjct: 2   TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVV 61

Query: 106 HLNESELHGRQLKVTVKR 123
           + +  +++G++  V VKR
Sbjct: 62  NEHFHDINGKK--VEVKR 77

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

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 52  VGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNES 110
           V NV +  T +E+++ F   G V  V +     G  +G+A+VEF+  +  Q A+  L  +
Sbjct: 5   VRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKST 64

Query: 111 ELHGRQLKV 119
            L+GR L +
Sbjct: 65  HLYGRHLVL 73

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

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

 Score = 46.3 bits (110), Expect = 2e-06
 Identities = 25/95 (26%), Positives = 48/95 (50%), Gaps = 9/95 (9%)

Query: 26  MASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG 85
           M S++DP+   S + N        +FV N+D S   + +   F   G +    + TD+ G
Sbjct: 75  MWSQRDPSLRRSGVGN--------IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENG 126

Query: 86  QPKGYAYVEFLQSEAVQEALH-LNESELHGRQLKV 119
           + +GY +V F + E+ + A+  +N   L+ +++ V
Sbjct: 127 KSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYV 161

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

 Score = 43.8 bits (103), Expect = 3e-06
 Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 1/58 (1%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL 105
           ++FV N+ Y  T E +  HF   G+V       DK  G+ KG  +V F         L
Sbjct: 3   TLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

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 = 42.9 bits (101), Expect = 3e-06
 Identities = 20/67 (29%), Positives = 39/67 (58%), Gaps = 1/67 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLN 108
           +FVG + +  T ++++++F   G V   TI+ D   G+ +G+ +V F  + +V++ L   
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 109 ESELHGR 115
           E +L GR
Sbjct: 61  EHKLDGR 67

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

 Score = 42.4 bits (100), Expect = 5e-06
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEA 104
           DS  +FVGN+ +  T +E+++ F+  G V  V I +    G+   + +V F   EAVQ+ 
Sbjct: 2   DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKI 61

Query: 105 L 105
           L
Sbjct: 62  L 62

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

 Score = 42.2 bits (100), Expect = 5e-06
 Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 6/78 (7%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTV---NRVTIRTDKFGQPKGYAYVEFLQSEAVQEA 104
            +VFVGN+    + + +++  + CG V    RV       G+ K + + EF   E    A
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVK--DPSTGKLKAFGFCEFEDPEGALRA 58

Query: 105 LH-LNESELHGRQLKVTV 121
           L  LN  EL G++L V V
Sbjct: 59  LRLLNGLELGGKKLLVKV 76

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|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 41.9 bits (98), Expect = 6e-06
 Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQS-EAVQEALHL 107
           +VFV N+DY    +++++ F   G V R  I  DK G+ +G   V F Q  EAVQ     
Sbjct: 2   TVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISMF 61

Query: 108 NESELHGRQLKV 119
           N   L  R + V
Sbjct: 62  NGQLLFDRPMHV 73

This subgroup corresponds to the RRM2 of hnRNP M, a 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. It 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). . Length = 76

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

 Score = 41.5 bits (98), Expect = 1e-05
 Identities = 22/71 (30%), Positives = 42/71 (59%), Gaps = 2/71 (2%)

Query: 52  VGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG-QPKGYAYVEFLQSEAVQEALH-LNE 109
           V N+ Y  TP+++++ F+  G V  V I  D++  + +G+A+V F      ++A+  ++ 
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 110 SELHGRQLKVT 120
            EL GR+L+V 
Sbjct: 63  KELDGRELRVQ 73

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

 Score = 41.3 bits (97), Expect = 1e-05
 Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 3/66 (4%)

Query: 57  YSCTPEEVQQHFQSC---GTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELH 113
           +SCT E+V   F  C      N V    ++ G+P+G A +E    E VQ+AL  +   + 
Sbjct: 11  WSCTAEDVMNFFDDCRIRNGENGVHFLLNRDGKPRGDALIELESEEDVQKALEQHRHYMG 70

Query: 114 GRQLKV 119
            R ++V
Sbjct: 71  QRYVEV 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|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 41.5 bits (98), Expect = 1e-05
 Identities = 17/71 (23%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFL-QSEAVQEALHLN 108
           + V N+D+  + +++++ F   G + +  +  D+ G+  G A V F  +++A++     N
Sbjct: 3   LLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQYN 62

Query: 109 ESELHGRQLKV 119
              L GR +K+
Sbjct: 63  GVPLDGRPMKI 73

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

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

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 18/67 (26%), Positives = 40/67 (59%), Gaps = 1/67 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLN 108
           +F+G + +  T ++++ +F   G V   T++ D   G+ +G+ +V F +SE+V + +   
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 109 ESELHGR 115
           E +L+G+
Sbjct: 61  EHKLNGK 67

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

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 18/67 (26%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLN 108
           +F+G + +  + +++ ++    G V   TI+TD   G+ +G+ +V F  + +V + L L 
Sbjct: 2   MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELK 61

Query: 109 ESELHGR 115
           E +L G+
Sbjct: 62  EHKLDGK 68

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|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 41.4 bits (97), Expect = 1e-05
 Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 2/68 (2%)

Query: 54  NVDYSC-TPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH-LNESE 111
           N+ +S   P ++++ F   G V   TI   + G+  G+A+V   + +  + AL   N  E
Sbjct: 7   NLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLE 66

Query: 112 LHGRQLKV 119
           + GR + V
Sbjct: 67  IDGRPVAV 74

This subgroup corresponds to the RRM2 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 = 83

>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 41.1 bits (96), Expect = 1e-05
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH-LN 108
           +FV N+ +  T + ++  F  CG V    I+ +  G+ KG   V F   E  + A   +N
Sbjct: 2   IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVRFESPEVAERACRMMN 60

Query: 109 ESELHGRQLKVTVKR 123
             +L+GR++ V + R
Sbjct: 61  GYKLNGREIDVRIDR 75

This subgroup corresponds to the RRM3 of hnRNP M, a 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. Moreover, 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). . Length = 77

>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 = 41.3 bits (97), Expect = 2e-05
 Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 7/80 (8%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKG---YAYVEFLQSEAVQEA 104
           R+V+V ++D   T E++   F +CG V  V  R    G P     +A++EF   E  + A
Sbjct: 3   RTVYVSDIDQQVTEEQLAALFSNCGQV--VDCRV--CGDPNSVLRFAFIEFTDEEGARAA 58

Query: 105 LHLNESELHGRQLKVTVKRT 124
           L L+ + L    ++V   +T
Sbjct: 59  LSLSGTMLGFYPVRVLPSKT 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|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 = 40.8 bits (96), Expect = 2e-05
 Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 3/66 (4%)

Query: 57  YSCTPEEVQQHFQSC---GTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELH 113
           +S T E+V   F  C   G  N +     + G+P G A++E    E V++AL  +   + 
Sbjct: 9   WSATAEDVLNFFSDCRIKGGENGIHFTYSREGRPSGEAFIELESEEDVEKALEKHNEHMG 68

Query: 114 GRQLKV 119
            R ++V
Sbjct: 69  HRYIEV 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|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 = 2e-05
 Identities = 18/69 (26%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEALHLN 108
           +FVG + +  + ++++ +F   G V   TI+ D   G+ +G+ ++ F  + +V++ L   
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 109 ESELHGRQL 117
           E  L GR +
Sbjct: 62  EHRLDGRLI 70

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

 Score = 40.6 bits (95), Expect = 2e-05
 Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 8/71 (11%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH-LN 108
           +FVGNVD   + EE++  F++ G V    +        + +A+V      A   A+  LN
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVM-------RQFAFVHLRGEAAADRAIEELN 55

Query: 109 ESELHGRQLKV 119
             ELHGR+L V
Sbjct: 56  GRELHGRKLVV 66

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

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

 Score = 40.9 bits (96), Expect = 2e-05
 Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 4/69 (5%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHL 107
           R +FVG +    T ++V++ F+  GT+   TI     G  KG A+V+F      Q A+  
Sbjct: 2   RKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAI-- 59

Query: 108 NESELHGRQ 116
             + LHG Q
Sbjct: 60  --NALHGSQ 66

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

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

 Score = 40.6 bits (96), Expect = 2e-05
 Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 2/62 (3%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL-H 106
           ++ V N+      +++++ F+  G ++RV +  DK  GQ +G+A+V F   E  + A+  
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 107 LN 108
           LN
Sbjct: 61  LN 62

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|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 40.5 bits (95), Expect = 2e-05
 Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHL 107
           RSVFV       + E++  +F + G V  V +  DK      YA VEF   E V + L  
Sbjct: 3   RSVFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKDK----GVYAIVEFDSKEGVDKVLSE 58

Query: 108 NESELHGRQLKV 119
            +  L+G +L+V
Sbjct: 59  PQHTLNGHRLRV 70

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|240948 cd12504, RRM2_hnRNPH_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family

 Score = 40.4 bits (95), Expect = 2e-05
 Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 57  YSCTPEEVQQHFQSCGTV-NRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
           + C+ EE+ Q F     V N +T+  D  G+  G AYV+F   E+ + AL
Sbjct: 10  FGCSKEEIAQFFSGLEIVPNGITLPMDYRGRSTGEAYVQFASQESAERAL 59

This subfamily corresponds to the RRM2 of hnRNP H protein family which 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). They represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing, having similar RNA binding affinities and specifically recognizing 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. Furthermore, 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 the 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 they play an important role in efficiently silencing the exon. Members in this family can regulate the alternative splicing of the 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. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. . Length = 77

>gnl|CDD|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin

 Score = 40.2 bits (94), Expect = 3e-05
 Identities = 18/71 (25%), Positives = 40/71 (56%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLN 108
           S+FVGN++ +   +E++       +   + ++  + G  K + YV+F  +E +++AL L 
Sbjct: 2   SLFVGNLNPNKDFDELKTAISEFFSKKNLAVQDVRIGSSKKFGYVDFESAEDLEKALELT 61

Query: 109 ESELHGRQLKV 119
             +L G ++K+
Sbjct: 62  GKKLLGNEIKL 72

This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin is 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. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 75

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

 Score = 39.9 bits (94), Expect = 3e-05
 Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 3/73 (4%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLN 108
           +V V N+    T  +++Q F+ CG +  V I   + G     A +EF   +    AL  +
Sbjct: 2   TVKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGL---VAVIEFETEDEALAALTKD 58

Query: 109 ESELHGRQLKVTV 121
              L G ++ V+ 
Sbjct: 59  HKRLGGNEISVSR 71

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

 Score = 40.0 bits (94), Expect = 3e-05
 Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLN 108
           +FVGN+ ++   +E++++F   G V    +  DK  G  KGY +V F   + ++ AL   
Sbjct: 2   LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQKQ 61

Query: 109 ESELHGRQLKV 119
           +  L G +L+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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 42.5 bits (100), Expect = 4e-05
 Identities = 29/143 (20%), Positives = 53/143 (37%), Gaps = 24/143 (16%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 108
           ++V N+D + T E++++ F  CG +    +  D+ G  +G+ +V F   E    A+  ++
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMH 347

Query: 109 ESELHGRQLKVTVKR--------------TNVPGMKQHRPRRPN------PFMVYQSRGA 148
              L G+ L V + +                 P M+Q     P       P    Q    
Sbjct: 348 GRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPRMRQLPMGSPMGGAMGQPPYYGQGPQQ 407

Query: 149 IIPPFLYSPYGYGKIPRFRMPMR 171
                   P G+ ++     PM 
Sbjct: 408 QFNGQ---PLGWPRMSMMPTPMG 427

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|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 = 40.0 bits (94), Expect = 4e-05
 Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH 106
           S ++++G++    T E+++  F+  G +  +         P+G AYV     +    AL 
Sbjct: 2   STTLWIGHLSKKVTEEDLKNLFEEYGEIQSI-----DMIPPRGCAYVCMETRQDAHRALQ 56

Query: 107 -LNESELHGRQLKV 119
            L   +L G+++KV
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|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 39.5 bits (93), Expect = 4e-05
 Identities = 26/75 (34%), Positives = 40/75 (53%), Gaps = 6/75 (8%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRV-TIRTDKFGQPKGYAYVEFLQSEA---VQEAL 105
           V++G++ +     E++++F   GTV R+   R+ K G+ KGYA+VEF   E    V E  
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAET- 60

Query: 106 HLNESELHGRQLKVT 120
            +N   L  R LK  
Sbjct: 61  -MNNYLLFERLLKCK 74

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

 Score = 39.6 bits (93), Expect = 5e-05
 Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 108
           ++VGN+D + T + + + F   G +    +  +    P  YA+VE+    +   AL  +N
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP--YAFVEYYDHRSAAAALQTMN 58

Query: 109 ESELHGRQLKV 119
              + G+++KV
Sbjct: 59  GRLILGQEIKV 69

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 39.0 bits (92), Expect = 5e-05
 Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 5/57 (8%)

Query: 64  VQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV 119
           + + F   G V ++ +   K     G+A+VEF   EA ++A+ +LN     GR L+V
Sbjct: 1   LYKLFSPFGNVEKIKLLKKK----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRV 53

(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|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 39.3 bits (92), Expect = 6e-05
 Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 2/73 (2%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKG-YAYVEFLQSEAVQEAL-H 106
           +++V  +  +    +++Q F   G V    I T+        + +V     E   + + H
Sbjct: 1   NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQH 60

Query: 107 LNESELHGRQLKV 119
           L+ +ELHGR + V
Sbjct: 61  LHRTELHGRVISV 73

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

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

 Score = 39.6 bits (92), Expect = 6e-05
 Identities = 22/73 (30%), Positives = 42/73 (57%), Gaps = 2/73 (2%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ-PKGYAYVEFLQSEAVQEALH- 106
           S+FV N+      E++++ F   G +  V +  D + + P+G+AYV+F      ++ALH 
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 107 LNESELHGRQLKV 119
           L+   + GRQ+++
Sbjct: 62  LDRKWICGRQIEI 74

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|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 39.2 bits (92), Expect = 8e-05
 Identities = 24/75 (32%), Positives = 31/75 (41%), Gaps = 2/75 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRV-TIRTDKFGQPKGYAYVEFLQ-SEAVQEALHL 107
           +FV N+        + Q F   G V  V  IR     + KGY +V      EA      L
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 108 NESELHGRQLKVTVK 122
           N   L GR L+V+ K
Sbjct: 64  NGYRLGGRVLQVSFK 78

This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell surface Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX) proteins

 Score = 39.3 bits (92), Expect = 8e-05
 Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 6/60 (10%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHL 107
           ++VFVG +  + T E +++ F+ CG +  + IR  K    K + ++ F +  AV +A++L
Sbjct: 7   KTVFVGGLPENATEEIIREVFEQCGEI--IAIRMSK----KNFCHIRFAEEFAVDKAIYL 60

This subgroup corresponds to the conserved RNA recognition motif (RRM) in ECTO-NOX proteins (also termed ENOX), comprising a family of plant and animal NAD(P)H oxidases exhibiting both, oxidative and protein disulfide isomerase-like, activities. They are growth-related and drive cell enlargement, and may play roles in aging and neurodegenerative diseases. ENOX proteins function as terminal oxidases of plasma membrane electron transport (PMET) through catalyzing electron transport from plasma membrane quinones to extracellular oxygen, forming water as a product. They are also hydroquinone oxidases that oxidize externally supplied NADH, hence NOX. ENOX proteins harbor a di-copper center that lack flavin. ENOX proteins display protein disulfide interchange activity that is also possessed by protein disulfide isomerase. In contrast to the classic protein disulfide isomerases, ENOX proteins lack the double CXXC motif. This family includes two ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed candidate growth-related and time keeping constitutive hydroquinone [NADH] oxidase (cCNOX), or cell proliferation-inducing gene 38 protein, or Constitutive Ecto-NOX (cNOX), is the constitutively expressed cell surface NADH (ubiquinone) oxidase that is ubiquitous and refractory to drugs. ENOX2, also termed APK1 antigen, or cytosolic ovarian carcinoma antigen 1, or tumor-associated hydroquinone oxidase (tNOX), is a cancer-specific variant of ENOX1 and plays a key role in cell proliferation and tumor progression. In contrast to ENOX1, ENOX2 is drug-responsive and harbors a drug binding site to which the cancer-specific S-peptide tagged pan-ENOX2 recombinant (scFv) is directed. Moreover, ENOX2 is specifically inhibited by a variety of quinone site inhibitors that have anticancer activity and is unique to the surface of cancer cells. ENOX proteins contain many functional motifs. Length = 84

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 38.9 bits (91), Expect = 9e-05
 Identities = 20/50 (40%), Positives = 33/50 (66%)

Query: 47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFL 96
          +R++FVGN++ + T EE+++ F+  G V  V I+    GQ   YA+V+FL
Sbjct: 2  TRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFL 51

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

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

 Score = 39.1 bits (91), Expect = 9e-05
 Identities = 17/72 (23%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ-PKGYAYVEFLQSEAVQEALH-L 107
           +F+G + +    + ++Q F   G ++ V +  D+  Q  +G+ +V F   +  ++A+  +
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 108 NESELHGRQLKV 119
           N   + GRQ++V
Sbjct: 63  NGKSVDGRQIRV 74

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

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 23/91 (25%), Positives = 41/91 (45%), Gaps = 4/91 (4%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL- 105
            ++FVG +    T E +++ F   G + R+ +  D   G  KGYA+VE+        A  
Sbjct: 4   LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYR 63

Query: 106 HLNESELHGRQLKVTVKRTNVPGMKQHRPRR 136
             ++  + G ++ V  +R     +    PRR
Sbjct: 64  DAHKLVIDGSEIFVDFERERT--LPGWIPRR 92

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

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

 Score = 38.8 bits (91), Expect = 1e-04
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 7/75 (9%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG-QPKGYAYVEFLQSEAVQEAL 105
           SR++FV N++ +   EE++  F+  G      IRT     + +G+  V +    A + A 
Sbjct: 1   SRTLFVRNINSNVEDEELRALFEQFG-----DIRTLYTACKHRGFIMVSYYDIRAARRAK 55

Query: 106 H-LNESELHGRQLKV 119
             L  +EL GR+L +
Sbjct: 56  RALQGTELGGRKLDI 70

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

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 38.7 bits (91), Expect = 1e-04
 Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 4/71 (5%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNE 109
           VFVG +      +E+   F+  G +  + +  D  G  +GYA+V +   EA Q A+    
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQ-- 61

Query: 110 SELHGRQLKVT 120
             LH  +++  
Sbjct: 62  --LHNYEIRPG 70

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It 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. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

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

 Score = 38.7 bits (91), Expect = 1e-04
 Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 7/68 (10%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNE 109
           V + N+ Y  T + + Q F   G V ++ I   K    +  A V+F   E+ + A     
Sbjct: 4   VTISNLLYPVTVDVLHQVFSPYGAVEKILIFE-KNTGVQ--ALVQFDSVESAENAKKA-- 58

Query: 110 SELHGRQL 117
             L+GR +
Sbjct: 59  --LNGRNI 64

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

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

 Score = 38.8 bits (90), Expect = 1e-04
 Identities = 23/73 (31%), Positives = 44/73 (60%), Gaps = 2/73 (2%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ-PKGYAYVEFLQSEAVQEALH- 106
           S+FV NV  +  PE++++ F   G +  V +  D + + P+G+AY++F      ++AL+ 
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 107 LNESELHGRQLKV 119
           LN   + GRQ+++
Sbjct: 62  LNRKWVCGRQIEI 74

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

 Score = 38.3 bits (90), Expect = 1e-04
 Identities = 24/61 (39%), Positives = 36/61 (59%), Gaps = 4/61 (6%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEF---LQSEAVQEAL 105
           +FVG +  + T E+V+  F+  G +  VTI  DK  GQ KG A+V+F    +++   EAL
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 106 H 106
           H
Sbjct: 62  H 62

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

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 38.5 bits (89), Expect = 1e-04
 Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 2/75 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHL-N 108
           +FV N+ +  T +++++ F  CG V    I+ +  G+ KG   V F   E+ ++A  L N
Sbjct: 2   IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKMEN-GKSKGCGTVRFDSPESAEKACRLMN 60

Query: 109 ESELHGRQLKVTVKR 123
             +++GR++ V + R
Sbjct: 61  GIKINGREIDVRLDR 75

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, 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 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 4/65 (6%)

Query: 51  FVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNES 110
           +V N+D S   E +++ F   GT+    + TD+ G+ KG+ +V F   E   +A+    +
Sbjct: 5   YVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAV----T 60

Query: 111 ELHGR 115
           E++GR
Sbjct: 61  EMNGR 65

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

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

 Score = 38.0 bits (89), Expect = 2e-04
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 8/75 (10%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH- 106
           + ++V N+  S T E++++ F   G V RV          K YA+V F + +   +A+  
Sbjct: 2   KVLYVRNLPLSTTEEQLRELFSEYGEVERVKK-------IKDYAFVHFEERDDAVKAMEE 54

Query: 107 LNESELHGRQLKVTV 121
           +N  EL G  ++V++
Sbjct: 55  MNGKELEGSPIEVSL 69

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|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 38.4 bits (89), Expect = 2e-04
 Identities = 15/49 (30%), Positives = 31/49 (63%)

Query: 47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF 95
          +R++F+GN+D++ +  E+++ F   G +  V I+    GQ   YA+++F
Sbjct: 8  TRNLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKF 56

This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 85

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 38.2 bits (89), Expect = 2e-04
 Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 10/83 (12%)

Query: 50  VFVGNVDYSCTPEE----VQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
           VFV ++  S + +E    V +HF   GT+  V +  D   +P  YA+V+F   +  + AL
Sbjct: 5   VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRP--YAFVQFTNDDDAKNAL 62

Query: 106 HLNE-SELHGRQLK---VTVKRT 124
              + + L GR ++     V RT
Sbjct: 63  AKGQGTILDGRHIRCERAKVNRT 85

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

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

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 2/53 (3%)

Query: 60  TPEEVQQHFQSCGTVNRVTI-RTDKFGQPKGYAYVEFLQSEAVQEAL-HLNES 110
           T E ++  F   GTV  V++ R    G  KG+A++EF   E  Q+A  HLN  
Sbjct: 12  THEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHLNNP 64

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|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 38.0 bits (88), Expect = 2e-04
 Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 3/80 (3%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
           DS  +FVGN+ +     E+++ FQ  G V  V +R +  G+   + +V F  SE VQ+ L
Sbjct: 2   DSHQLFVGNLPHDVDKSELKEFFQQYGNV--VELRINSGGKLPNFGFVVFDDSEPVQKIL 59

Query: 106 HLNESELHGR-QLKVTVKRT 124
                   G  +L V  K+T
Sbjct: 60  SNRPIMFRGDVRLNVEEKKT 79

This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. Length = 80

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

 Score = 37.7 bits (88), Expect = 3e-04
 Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 1/68 (1%)

Query: 54  NVDYSCTPEEVQQHFQSCGTVNR-VTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESEL 112
           N+ +  T  EV   F       + + I  DK G+  G AYVEF+  E    A  L+  +L
Sbjct: 6   NIPFDVTKGEVLAFFAGIAIAEQGIHILYDKTGKTLGEAYVEFVSEEDAMRAERLHRKKL 65

Query: 113 HGRQLKVT 120
            GR++ + 
Sbjct: 66  KGREILLR 73

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

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

 Score = 37.7 bits (87), Expect = 3e-04
 Identities = 18/69 (26%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNR-VTIRTDKFGQPKGYAYVEFLQSEAVQEALH 106
           R +F+G + +  T E ++ HF+  GT+   V +R     + +G+ +V +   E V  A++
Sbjct: 3   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMN 62

Query: 107 LNESELHGR 115
               ++ GR
Sbjct: 63  ARPHKVDGR 71

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|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 = 37.5 bits (87), Expect = 3e-04
 Identities = 23/82 (28%), Positives = 46/82 (56%), Gaps = 2/82 (2%)

Query: 44  EVDSRSVFVGNVDYSCTPEEVQQHFQS-CGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQ 102
           E+ +R+++  N+D   T  +V+  F+S CG V+R+ +  D     +  A+VEF  +E+  
Sbjct: 1   EMCARTIYCTNIDKKVTQSDVKLFFESLCGEVSRLRLLGDYHHSTR-IAFVEFAMAESAI 59

Query: 103 EALHLNESELHGRQLKVTVKRT 124
            AL+ + + L    ++V+  +T
Sbjct: 60  AALNCSGAVLGSLPIRVSPSKT 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|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 37.6 bits (87), Expect = 3e-04
 Identities = 20/76 (26%), Positives = 43/76 (56%), Gaps = 2/76 (2%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL-H 106
           +++V N+    T +E+++ F++ G + +  +  DK  G P+G A+V + + E  Q A+  
Sbjct: 2   NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

Query: 107 LNESELHGRQLKVTVK 122
           LN +   G  + ++V+
Sbjct: 62  LNGTIPPGSTMPLSVR 77

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

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 27/81 (33%), Positives = 39/81 (48%), Gaps = 16/81 (19%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIR-----------TDKFGQP---KGY--A 91
           R++FV NV   CT E +++ F  CG V  V ++           T KF  P   KG+  A
Sbjct: 1   RTLFVLNVPPYCTEESLKRLFSRCGKVESVELQEKPGPAESEDLTSKFFPPKPIKGFKVA 60

Query: 92  YVEFLQSEAVQEALHLNESEL 112
           YV F +  ++  AL L  +E 
Sbjct: 61  YVVFKKPSSLSRALKLKSTEP 81

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

 Score = 37.4 bits (87), Expect = 4e-04
 Identities = 23/86 (26%), Positives = 41/86 (47%), Gaps = 10/86 (11%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRV----TIRTDKFG--QPKGYAYVEFLQSE-AV 101
            V++ N+ YS + E++++  +    V+ +    T+R  +    +P G AY EF   E A 
Sbjct: 1   RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60

Query: 102 QEALHLNESELHGRQLKVTVKRTNVP 127
           +    LN      R+L V   + +VP
Sbjct: 61  KVVKDLNGKVFKNRKLFV---KLHVP 83

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

 Score = 37.2 bits (86), Expect = 4e-04
 Identities = 20/67 (29%), Positives = 37/67 (55%), Gaps = 5/67 (7%)

Query: 52  VGNVDYSCTPEEVQQHFQSCGTVNR-VTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNES 110
           V N+  S T EE ++  ++ G + R   + ++  G  KGY +VE+++ ++  +A      
Sbjct: 4   VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKA----RL 59

Query: 111 ELHGRQL 117
           EL G+QL
Sbjct: 60  ELLGKQL 66

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

 Score = 37.1 bits (86), Expect = 5e-04
 Identities = 16/48 (33%), Positives = 26/48 (54%)

Query: 48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF 95
          R +FVG +   C   +V+  F   G++   T+  D+ GQ +G A+V F
Sbjct: 2  RKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTF 49

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

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

 Score = 36.9 bits (86), Expect = 5e-04
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 10/73 (13%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF---LQSEAVQEALH 106
           +FVGN+    T EE ++ F   G V+ V +  +     KG+ ++       +E  +    
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-----KGFGFIRLDTRTNAEKAKAE-- 56

Query: 107 LNESELHGRQLKV 119
           L+     GRQL+V
Sbjct: 57  LDGIMRKGRQLRV 69

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

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

 Score = 36.9 bits (86), Expect = 5e-04
 Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL 105
           +FVG +    T E+++++F   G V  V I TDK  G+ +G+A+V F   + V + +
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIV 58

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|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 = 37.0 bits (86), Expect = 5e-04
 Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 4/67 (5%)

Query: 44  EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQ---SE 99
           + D+  +FVG +  +   ++++  F+  G +  +T+  DK+ G  KG A++ +     + 
Sbjct: 2   DDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESAL 61

Query: 100 AVQEALH 106
             Q ALH
Sbjct: 62  KAQSALH 68

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|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 36.9 bits (85), Expect = 6e-04
 Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLN 108
           VFVG +      +E+   F+  G +  + +  D   GQ +GYA++ F   EA QEA+ L 
Sbjct: 4   VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLC 63

Query: 109 ES 110
           ++
Sbjct: 64  DN 65

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. . Length = 79

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

 Score = 36.4 bits (85), Expect = 6e-04
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 7/72 (9%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTI-RTDKFGQPKGYAYVEFLQSEAVQEALH-L 107
           V+VGN+    T  E++  F+  G +  V + R      P G+A+VEF      ++A+  L
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVAR-----NPPGFAFVEFEDPRDAEDAVRAL 56

Query: 108 NESELHGRQLKV 119
           +   + 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|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 36.3 bits (84), Expect = 7e-04
 Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 9/73 (12%)

Query: 49  SVFVGNVDYSCTPEE-VQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH- 106
           ++FV   D   T EE +++ F+  G + R  IR       K +A+VEF  SE   +AL  
Sbjct: 1   TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDIR-------KTFAFVEFEDSEDATKALEA 53

Query: 107 LNESELHGRQLKV 119
           L+ S + G  L V
Sbjct: 54  LHGSRIDGSVLTV 66

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

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

 Score = 36.5 bits (85), Expect = 8e-04
 Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGT-VNRVTIRTDKFGQPKGYAYVEFL-QSEAVQE 103
           DS  +++G + Y  T  ++   F   G  V+   +R  K G+ KG+A++ +  Q   +  
Sbjct: 8   DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILA 67

Query: 104 ALHLNESELHGRQLKV 119
             +LN  +L GR ++V
Sbjct: 68  VDNLNGIKLLGRTIRV 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|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 36.1 bits (84), Expect = 0.001
 Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 8/78 (10%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLN 108
           +F+G +    + ++V++  +S G +    +  D   G  KGYA+ E+L      +A+   
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAI--- 59

Query: 109 ESELHGRQL---KVTVKR 123
            + L+G QL   K+TV+R
Sbjct: 60  -AGLNGMQLGDKKLTVQR 76

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

>gnl|CDD|240714 cd12268, RRM_Vip1, RNA recognition motif in fission yeast protein Vip1 and similar proteins

 Score = 36.0 bits (83), Expect = 0.001
 Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNE 109
           V+V N+    T +++   F  CG ++ + +  D   Q    A + F +  A + AL L+ 
Sbjct: 1   VYVSNISPKTTEKQISDFFSFCGKISNLDLTNDGESQT---ATITFEKPSAAKTALLLDN 57

Query: 110 SELHGRQLKVT 120
           + L G+ ++VT
Sbjct: 58  ALLGGKVIQVT 68

This subfamily corresponds to Vip1, an RNA-binding protein encoded by gene vip1 from fission yeast Schizosaccharomyces pombe. Its biological role remains unclear. Vip1 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 68

>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 = 18/55 (32%), Positives = 26/55 (47%), Gaps = 4/55 (7%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQ 102
           R VFVG +    T E+++Q+F   G V  V I        + +A+V F   E  Q
Sbjct: 1   RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP----FRAFAFVTFADPEVAQ 51

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|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 35.6 bits (83), Expect = 0.001
 Identities = 19/71 (26%), Positives = 36/71 (50%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLN 108
           +V+V       T +++Q+ F+  G VN + +R D   + KG  +VEF   E  ++ L   
Sbjct: 1   TVYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAKKFLEKE 60

Query: 109 ESELHGRQLKV 119
           + +   ++L V
Sbjct: 61  KLKYKEKELTV 71

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 35.8 bits (82), Expect = 0.001
 Identities = 17/70 (24%), Positives = 40/70 (57%), Gaps = 1/70 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLN 108
           +FVG +  + T E+V+Q+F+  G V+   +  DK   + +G+ +V F   + V++   ++
Sbjct: 2   IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 109 ESELHGRQLK 118
             E++ + ++
Sbjct: 62  FHEINNKMVE 71

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 36.2 bits (83), Expect = 0.001
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ-PKGYAYVEFLQSEAVQEAL 105
           +R+VF   +     P +++  F + G V  V I +D+  +  KG AYVEF + ++V  A+
Sbjct: 1   ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 60

Query: 106 HLNESELHG 114
            L    L G
Sbjct: 61  GLTGQRLLG 69

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

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

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 58  SCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL 105
           S T E++++ F+  G +  V+I  DK  G+ KG+ YV+F +      AL
Sbjct: 11  SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59

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

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 60  TPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQL 117
           T +++ Q F   G V    +  DK  GQ K + +V +   E+ Q A+  +N  ++ G++L
Sbjct: 11  TDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRL 70

Query: 118 KVT 120
           KV 
Sbjct: 71  KVQ 73

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

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

 Score = 35.8 bits (82), Expect = 0.001
 Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ-PKGYAYVEFLQSEAVQEAL 105
           +R+VF   +     P ++++ F + G V  V + +D+  +  KG AYVEF+   +V  A+
Sbjct: 1   ARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAI 60

Query: 106 HLNESELHG 114
            L    + G
Sbjct: 61  GLTGQRVLG 69

This subgroup corresponds to the RRM1 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

>gnl|CDD|240949 cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-rich sequence factor 1 (GRSF-1) and similar proteins

 Score = 35.5 bits (82), Expect = 0.001
 Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 57  YSCTPEEVQQHFQSCGTVNR-VTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGR 115
           YSCT +++   F+    V+  V I  ++ G+  G AYV+F   E   +AL  +  E+  R
Sbjct: 11  YSCTEDDIIDFFRGLDIVDDGVVIVLNRRGRKTGEAYVQFATPEMANKALLKHREEIGNR 70

Query: 116 QLKV 119
            ++V
Sbjct: 71  YIEV 74

This subfamily corresponds to the RRM2 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 = 75

>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 8/69 (11%)

Query: 52  VGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH-LNES 110
           VGN+  SCT +E++  F+  G V    I  D       YA+V   ++E   EA+  L+ +
Sbjct: 5   VGNISSSCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGLDNT 57

Query: 111 ELHGRQLKV 119
           E  G+++ V
Sbjct: 58  EFQGKRMHV 66

This subgroup corresponds to the RRM2 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 11/75 (14%)

Query: 47  SRSVFVGNVDYSC--TPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEA 104
           ++ + V N       + EE+ + F+  GTV  + +        K Y +V +   E    A
Sbjct: 1   TQHLVVANGGLGNGVSREELLRVFEKYGTVEDLVMPPG-----KPYCFVSYSSIEDAAAA 55

Query: 105 LHLNESELHGRQLKV 119
                  L+G++L++
Sbjct: 56  YDA----LNGKELEL 66

This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) 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 = 35.4 bits (82), Expect = 0.002
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 7/78 (8%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL-HL 107
           +FVG++      E ++  F   G ++   +  D + G+ KGY +V F++ E  + A+  +
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 108 NESELHGRQLKVTVKRTN 125
           N   L GR +     RTN
Sbjct: 62  NGQWLGGRAI-----RTN 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|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 35.7 bits (82), Expect = 0.002
 Identities = 14/49 (28%), Positives = 29/49 (59%)

Query: 47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF 95
          +R++F+GN+D + T  ++++ F   G +  V I+    GQ   Y +++F
Sbjct: 7  NRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKF 55

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

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

 Score = 35.6 bits (82), Expect = 0.002
 Identities = 25/83 (30%), Positives = 44/83 (53%), Gaps = 10/83 (12%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTV--NR------VTIRTDK-FGQPKGYAYVEFLQSE 99
           +++V  ++ + T EE+   F+ CG V  N+      V I TDK  G+PKG A V +    
Sbjct: 2   TIYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPP 61

Query: 100 AVQEALHL-NESELHGRQLKVTV 121
           + + A+   +  +  G +LKV++
Sbjct: 62  SAKAAVEWFDGKDFQGSKLKVSL 84

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

 Score = 35.2 bits (82), Expect = 0.002
 Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 2/74 (2%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALH- 106
           S++VG++    T   + + F   G V  + +  D    +  GYAYV F      + AL  
Sbjct: 1   SLYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDT 60

Query: 107 LNESELHGRQLKVT 120
           LN   + G+ +++ 
Sbjct: 61  LNFDVIKGKPIRIM 74

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

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHL- 107
           +FVG +      +E+   F+  G +  + +  D   G  +GYA+V F   EA QEA+ L 
Sbjct: 4   IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLY 63

Query: 108 NESELH-GRQLKVTV 121
           N  E+  G+ + V +
Sbjct: 64  NNHEIRPGKHIGVCI 78

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

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

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 17/56 (30%), Positives = 31/56 (55%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
           +FVG ++   T +EV++ F   G V  + +  D+  Q +G A+V++   E  Q A+
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAI 57

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

>gnl|CDD|240952 cd12508, RRM2_ESRPs_Fusilli, RNA recognition motif 2 in epithelial splicing regulatory protein ESRP1, ESRP2, Drosophila RNA-binding protein Fusilli and similar proteins

 Score = 35.4 bits (82), Expect = 0.002
 Identities = 19/66 (28%), Positives = 26/66 (39%), Gaps = 10/66 (15%)

Query: 57  YSCTPEEVQQHFQSCGTVNRVTIRTDKF-------GQPKGYAYVEFLQSEAVQEALHLNE 109
           YS T  ++   F   G +  V    D         G+P G A+V F   E  Q AL  ++
Sbjct: 11  YSATAADILAFF---GGLCPVVGGPDGILFVTGPDGRPTGDAFVLFETEEDAQRALGKHK 67

Query: 110 SELHGR 115
             L  R
Sbjct: 68  ENLGSR 73

This subfamily corresponds to the RRM2 of ESRPs and Fusilli. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. They are highly conserved paralogs and specifically bind to GU-rich binding site. ESRP1 and ESRP2 contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes Drosophila fusilli (fus) gene encoding RNA-binding protein Fusilli.Loss of fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous FGFR2 splicing and functions as a splicing factor. It shows high sequence homology to ESRPs and contains three RRMs as well. It also has an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine. . Length = 80

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

 Score = 35.0 bits (81), Expect = 0.002
 Identities = 20/64 (31%), Positives = 37/64 (57%), Gaps = 2/64 (3%)

Query: 60  TPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALH-LNESELHGRQL 117
           T EE++  F++ G +    I  D+  GQ  GY +V+++     Q+A++ LN  E+  ++L
Sbjct: 13  TQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRL 72

Query: 118 KVTV 121
           KV+ 
Sbjct: 73  KVSY 76

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

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

 Score = 35.1 bits (80), Expect = 0.003
 Identities = 17/69 (24%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNR-VTIRTDKFGQPKGYAYVEFLQSEAVQEALH 106
           R +F+G + +  T + +++HF+  GT+   V +R  +  + +G+ +V +   E V  A+ 
Sbjct: 3   RKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMS 62

Query: 107 LNESELHGR 115
               ++ GR
Sbjct: 63  ARPHKVDGR 71

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

 Score = 34.7 bits (80), Expect = 0.003
 Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 12/80 (15%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF------GQPKGYAYVEFLQSEAVQ 102
           +++VGN+ +  T +++ +  QS G  + + I   KF      GQ KG+A +  L SE+  
Sbjct: 1   ALYVGNLTWWTTDQDLTEAIQSIGVNDLLEI---KFFENRANGQSKGFALIV-LGSESSS 56

Query: 103 EAL--HLNESELHGRQLKVT 120
             L   L + ELHG+   VT
Sbjct: 57  RKLMDKLPKKELHGQNPVVT 76

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|240946 cd12502, RRM2_RMB19, RNA recognition motif 2 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 34.6 bits (80), Expect = 0.003
 Identities = 13/63 (20%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 57  YSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQ 116
           ++   + +++ F     V  + I  +  G+  G+A+V+    E +++AL  N+  + GR 
Sbjct: 10  FNVKEKHIREFFSPLKPVA-IRIVKNDHGRKTGFAFVDLKSEEDLKKALKRNKDYMGGRY 68

Query: 117 LKV 119
           +++
Sbjct: 69  IEL 71

This subfamily corresponds to the RRM2 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is also 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 = 72

>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 35.1 bits (81), Expect = 0.003
 Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 10/82 (12%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNR--------VTIRTDK-FGQPKGYAYVEFLQSEA 100
           VFV N+  + T +++ +HF S G +          + +  DK  G+PKG A V +    A
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 101 VQEALH-LNESELHGRQLKVTV 121
              A+   N  +  G  +KV++
Sbjct: 61  ASAAIEWFNNKDFMGNTIKVSL 82

This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the 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 nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

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

 Score = 34.7 bits (80), Expect = 0.003
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 11/77 (14%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH 106
           SR+V++GN+  + T +E+  H +S G +  V I  +K       A++ FL   A   A H
Sbjct: 1   SRTVYLGNLPPNTTVKELLSHVRS-GPIENVRILPEKN-----CAFISFLDPSAAT-AFH 53

Query: 107 ----LNESELHGRQLKV 119
               L    + G +LK+
Sbjct: 54  SDAILKRLSIKGVELKI 70

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

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

 Score = 34.7 bits (80), Expect = 0.003
 Identities = 15/50 (30%), Positives = 30/50 (60%), Gaps = 5/50 (10%)

Query: 47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFL 96
          SR+V++GN+  S + EE+++  +  G ++++ I  +     K  A+V FL
Sbjct: 3  SRNVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE-----KNIAFVHFL 47

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

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

 Score = 34.4 bits (79), Expect = 0.003
 Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 2/74 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTI-RTDKFGQPKGYAYVEFLQSE-AVQEALHL 107
           +++G++ +    +E++++F   GTV  V + R+ K G  K Y +++FL  E A   A  +
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 108 NESELHGRQLKVTV 121
           N   L G+ L+V V
Sbjct: 62  NNYLLMGKVLQVHV 75

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

 Score = 34.4 bits (79), Expect = 0.004
 Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCG-TVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLN 108
           +FVG + +  T E ++++F   G  V+ V ++     + +G+ +V+F     V   L   
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGG 61

Query: 109 ESELHGR 115
              L GR
Sbjct: 62  PHTLDGR 68

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|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 34.3 bits (79), Expect = 0.004
 Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQP-KGYAYVEFLQSEAVQEALHLN 108
           +FVG +  + T ++V+++F   G V    +  DK     +G+ +V F   + V +   ++
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEIH 61

Query: 109 ESELHGRQLKVTVKR 123
             E++ +   V  K+
Sbjct: 62  FHEINNK--MVECKK 74

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	176
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.9
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.87
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.8
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.8
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.78
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.78
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.76
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.76
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.76
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.75
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.74
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.74
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.73
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.72
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.71
KOG0122	270	consensus Translation initiation factor 3, subunit	99.7
PLN03120	260	nucleic acid binding protein; Provisional	99.7
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.69
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.69
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.68
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.68
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.67
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.66
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.64
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.64
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.64
PLN03121	243	nucleic acid binding protein; Provisional	99.64
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.63
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.62
smart00362	72	RRM_2 RNA recognition motif.	99.62
PLN03213	759	repressor of silencing 3; Provisional	99.6
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.59
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.59
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.58
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.58
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	99.58
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.57
smart00360	71	RRM RNA recognition motif.	99.56
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.56
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.54
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.54
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.54
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.53
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.52
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.52
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.51
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.51
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.51
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.49
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.49
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.49
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.47
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.46
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.45
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.41
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.4
smart00361	70	RRM_1 RNA recognition motif.	99.4
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.39
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.39
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.39
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.35
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.34
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.32
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.31
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.27
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.25
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.23
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.23
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.22
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.22
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.21
KOG0533	243	consensus RRM motif-containing protein [RNA proces	99.2
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.19
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.18
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.14
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.12
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.1
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.06
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.0
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.99
KOG0151	877	consensus Predicted splicing regulator, contains R	98.95
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.95
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.82
KOG0226	290	consensus RNA-binding proteins [General function p	98.82
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.79
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.77
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.75
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.72
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.5
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.47
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.47
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.42
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.41
KOG4210	285	consensus Nuclear localization sequence binding pr	98.36
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.27
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.24
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.23
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.23
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.18
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.14
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.12
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.08
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.04
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.91
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	97.91
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.88
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.84
KOG2314	698	consensus Translation initiation factor 3, subunit	97.82
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.78
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.7
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.6
KOG3152	278	consensus TBP-binding protein, activator of basal	97.55
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.53
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.53
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.44
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.42
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.34
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.31
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.3
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.28
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.22
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.81
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.69
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.68
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.68
KOG2068	327	consensus MOT2 transcription factor [Transcription	96.67
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.59
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.42
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.36
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.34
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	96.18
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.15
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.6
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.41
KOG2135	526	consensus Proteins containing the RNA recognition	95.31
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	95.25
KOG2591	684	consensus c-Mpl binding protein, contains La domai	95.07
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.02
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	94.91
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	94.67
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	94.17
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	93.29
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	93.15
KOG4210	285	consensus Nuclear localization sequence binding pr	91.85
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	91.59
KOG2318	650	consensus Uncharacterized conserved protein [Funct	90.55
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	90.27
KOG4660	549	consensus Protein Mei2, essential for commitment t	89.96
KOG4483	528	consensus Uncharacterized conserved protein [Funct	87.09
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	83.81
KOG4019	193	consensus Calcineurin-mediated signaling pathway i	83.77
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	83.59
PF07530	68	PRE_C2HC: Associated with zinc fingers; InterPro:	81.45

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

Probab=99.90  E-value=3.2e-22  Score=142.17  Aligned_cols=83  Identities=22%  Similarity=0.505  Sum_probs=77.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ....++|||+|||+++|+++|+++|++||.|.+|.|+.++ +++++|||||+|.+.++|++|| .||++.|+|+.|+|++
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4457899999999999999999999999999999999998 7999999999999999999999 6999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      +....
T Consensus       111 a~~~~  115 (144)
T PLN03134        111 ANDRP  115 (144)
T ss_pred             CCcCC
Confidence            97543

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.87  E-value=6.5e-21  Score=152.98  Aligned_cols=116  Identities=22%  Similarity=0.367  Sum_probs=87.8

Q ss_pred             HHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCcccccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-
Q 030488            5 LKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-   83 (176)
Q Consensus         5 ~~e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-   83 (176)
                      |.+.+++..|+++++.............     ...........+|||+|||+++|+++|+++|++||.|+.|.|+.++ 
T Consensus       156 F~~~e~A~~Ai~~LnG~~l~gr~i~V~~-----a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~  230 (346)
T TIGR01659       156 FGSEADSQRAIKNLNGITVRNKRLKVSY-----ARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKL  230 (346)
T ss_pred             EccHHHHHHHHHHcCCCccCCceeeeec-----ccccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCC
Confidence            4555666666666654332111111110     0111123346789999999999999999999999999999999988 


Q ss_pred             CCCceeEEEEEecCHHHHHHHH-HhCCCeeCC--eeeEEEeccCC
Q 030488           84 FGQPKGYAYVEFLQSEAVQEAL-HLNESELHG--RQLKVTVKRTN  125 (176)
Q Consensus        84 ~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g--~~i~v~~a~~~  125 (176)
                      ++++++||||+|.+.++|++|| .||++.+.+  +.|+|.++...
T Consensus       231 tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~  275 (346)
T TIGR01659       231 TGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEH  275 (346)
T ss_pred             CCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCcc
Confidence            8999999999999999999999 799999876  68999988754

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

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

Probab=99.80  E-value=2.3e-19  Score=121.46  Aligned_cols=114  Identities=25%  Similarity=0.463  Sum_probs=93.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ...+++||||||++.++|+.|.++|+++|+|..|.|-.|+ +...+|||||+|.+.++|+.|+ -++++.++.+.|.|.+
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~  112 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDW  112 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeec
Confidence            4568999999999999999999999999999999999999 6788999999999999999999 5999999999999999


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 030488          122 KRTNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGK  162 (176)
Q Consensus       122 a~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~g~g~  162 (176)
                      ...-..+++..|+..     |++-+.-++..+|...+||+.
T Consensus       113 D~GF~eGRQyGRG~s-----GGqVrde~r~d~D~~rggy~k  148 (153)
T KOG0121|consen  113 DAGFVEGRQYGRGKS-----GGQVRDEYRTDYDPGRGGYGK  148 (153)
T ss_pred             cccchhhhhhcCCCC-----CCeechhhhhhcCcccCccch
Confidence            866555555555443     223344555566666666653

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

Probab=99.80  E-value=3.4e-18  Score=130.56  Aligned_cols=98  Identities=24%  Similarity=0.502  Sum_probs=88.1

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      ...+-++|||+.|+++++|.+|+..|+.||+|+.|.|+.|. ||+++|||||+|+++.++.+|. ..++..|+|+.|.|.
T Consensus        97 ~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VD  176 (335)
T KOG0113|consen   97 IGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVD  176 (335)
T ss_pred             cCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEE
Confidence            34567999999999999999999999999999999999998 9999999999999999999999 699999999999999


Q ss_pred             eccCCCCCCCCCCCCCCCCCCC
Q 030488          121 VKRTNVPGMKQHRPRRPNPFMV  142 (176)
Q Consensus       121 ~a~~~~~~~~~~~~~~~~~~~g  142 (176)
                      +-+...  .+.|.+++.+++-|
T Consensus       177 vERgRT--vkgW~PRRLGGGLG  196 (335)
T KOG0113|consen  177 VERGRT--VKGWLPRRLGGGLG  196 (335)
T ss_pred             eccccc--ccccccccccCCcC
Confidence            987644  46888888765544

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

Probab=99.78  E-value=5.1e-18  Score=120.69  Aligned_cols=77  Identities=23%  Similarity=0.503  Sum_probs=71.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      -.++||||||+..+++.||+..|..||+|..|.|-.++    .|||||+|++..+|+.|+ .|++..|+|..|+|+++..
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            46899999999999999999999999999999988765    899999999999999999 7999999999999999976


Q ss_pred             CC
Q 030488          125 NV  126 (176)
Q Consensus       125 ~~  126 (176)
                      ..
T Consensus        85 ~~   86 (195)
T KOG0107|consen   85 RP   86 (195)
T ss_pred             Cc
Confidence            44

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

Probab=99.78  E-value=7.7e-18  Score=142.18  Aligned_cols=73  Identities=30%  Similarity=0.514  Sum_probs=68.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhC--CCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSC--GTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~--G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ..++|||+|||+++|+++|+++|++|  |.|++|.++       ++||||+|.+.++|++|| .||+.+|+|+.|+|.++
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~-------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~A  304 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI-------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLA  304 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee-------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45789999999999999999999999  999999886       569999999999999999 79999999999999999


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      ++.
T Consensus       305 kp~  307 (578)
T TIGR01648       305 KPV  307 (578)
T ss_pred             cCC
Confidence            764

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.76  E-value=5.8e-18  Score=105.39  Aligned_cols=69  Identities=33%  Similarity=0.688  Sum_probs=66.1

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeE
Q 030488           50 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLK  118 (176)
Q Consensus        50 i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~  118 (176)
                      |||+|||+++|+++|+++|++||.|..+.+..+.++..+++|||+|.+.++|+.|+ .+++..+.|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            79999999999999999999999999999998878899999999999999999999 6999999999885

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.76  E-value=6.5e-18  Score=136.22  Aligned_cols=79  Identities=29%  Similarity=0.375  Sum_probs=74.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      ..+|||+|||+++++++|+++|++||.|.+|+|+.|. ++.++|||||+|.+.++|.+|| .||+..|+|+.|+|.++..
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~  348 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTN  348 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccC
Confidence            3479999999999999999999999999999999998 8999999999999999999999 7999999999999999865


Q ss_pred             C
Q 030488          125 N  125 (176)
Q Consensus       125 ~  125 (176)
                      .
T Consensus       349 ~  349 (352)
T TIGR01661       349 K  349 (352)
T ss_pred             C
Confidence            3

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.76  E-value=6e-18  Score=135.88  Aligned_cols=82  Identities=27%  Similarity=0.412  Sum_probs=76.6

Q ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEE
Q 030488           42 REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV  119 (176)
Q Consensus        42 ~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v  119 (176)
                      ......++|||+|||+++|+++|+++|+.||.|++|+|+.|. +++++|||||+|.++++|++|| .|++..|.++.|+|
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V  181 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKV  181 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeee
Confidence            345568999999999999999999999999999999999997 7999999999999999999999 79999999999999


Q ss_pred             Eecc
Q 030488          120 TVKR  123 (176)
Q Consensus       120 ~~a~  123 (176)
                      .+++
T Consensus       182 ~~a~  185 (346)
T TIGR01659       182 SYAR  185 (346)
T ss_pred             eccc
Confidence            8764

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.75  E-value=1.2e-17  Score=134.78  Aligned_cols=78  Identities=28%  Similarity=0.522  Sum_probs=74.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      ..+|||+|||..+|+++|+++|++||+|.+|+|++++ +|+++|||||+|.+.++|++|| .||+..|.|+.|+|+++++
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~   82 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP   82 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc
Confidence            5789999999999999999999999999999999998 7999999999999999999999 7999999999999998864

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

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

Probab=99.74  E-value=5.7e-18  Score=125.62  Aligned_cols=79  Identities=25%  Similarity=0.481  Sum_probs=73.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEecc
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKR  123 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~  123 (176)
                      ..-++||||+|+|.++.++|+++|++||+|++..|+.|+ +++++||+||+|.+.++|.+|++-.+-.|+|++..|.+|.
T Consensus        10 T~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   10 TTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLAS   89 (247)
T ss_pred             ceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchhh
Confidence            345789999999999999999999999999999999999 8999999999999999999999777789999999999874

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

Probab=99.74  E-value=1.7e-17  Score=119.17  Aligned_cols=79  Identities=23%  Similarity=0.479  Sum_probs=70.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      ...++|||+|||.++.+.+|+++|.+||.|..|.|...  .....||||+|++..+|+.|| .-++..++|+.|+|++++
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r--~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR--PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC--CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            35689999999999999999999999999999988532  223679999999999999999 699999999999999997


Q ss_pred             CC
Q 030488          124 TN  125 (176)
Q Consensus       124 ~~  125 (176)
                      .-
T Consensus        82 gg   83 (241)
T KOG0105|consen   82 GG   83 (241)
T ss_pred             CC
Confidence            53

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

Probab=99.73  E-value=3.7e-17  Score=119.20  Aligned_cols=81  Identities=30%  Similarity=0.569  Sum_probs=76.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      .....|-|-||.+-|+.++|..+|++||.|-+|.|++|+ |..++|||||-|.+..+|+.|+ +|++.+|+|+.|.|.+|
T Consensus        11 ~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~a   90 (256)
T KOG4207|consen   11 EGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMA   90 (256)
T ss_pred             ccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhh
Confidence            446789999999999999999999999999999999999 8999999999999999999999 79999999999999999


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      +-.
T Consensus        91 ryg   93 (256)
T KOG4207|consen   91 RYG   93 (256)
T ss_pred             hcC
Confidence            743

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

Probab=99.72  E-value=6.1e-17  Score=137.13  Aligned_cols=80  Identities=20%  Similarity=0.361  Sum_probs=75.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      ..++|||+|||+++++++|+++|+.||.|.+|+|.+++ +++++|||||+|.+.++|.+|| .||+..|+|+.|+|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            45799999999999999999999999999999999998 6889999999999999999999 799999999999999987


Q ss_pred             CC
Q 030488          124 TN  125 (176)
Q Consensus       124 ~~  125 (176)
                      ..
T Consensus       283 ~p  284 (612)
T TIGR01645       283 TP  284 (612)
T ss_pred             CC
Confidence            53

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.71  E-value=1.7e-16  Score=99.18  Aligned_cols=69  Identities=38%  Similarity=0.673  Sum_probs=63.2

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeE
Q 030488           50 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLK  118 (176)
Q Consensus        50 i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~  118 (176)
                      |||+|||+++++++|.++|+.||.|..+.+..++.+.++++|||+|.+.++|..|+ .+++..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999888899999999999999999999 5777999999875

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

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

Probab=99.70  E-value=7.3e-17  Score=120.29  Aligned_cols=83  Identities=27%  Similarity=0.437  Sum_probs=78.0

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      .-.+..+|-|.||+.++++++|+++|.+||.|.+|.|.+|+ ||.++|||||.|.+.++|++|| .||++-++...|+|+
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvE  264 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVE  264 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEE
Confidence            33467889999999999999999999999999999999999 8999999999999999999999 799999999999999


Q ss_pred             eccCC
Q 030488          121 VKRTN  125 (176)
Q Consensus       121 ~a~~~  125 (176)
                      ++++.
T Consensus       265 wskP~  269 (270)
T KOG0122|consen  265 WSKPS  269 (270)
T ss_pred             ecCCC
Confidence            99863

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.70  E-value=1.3e-16  Score=121.66  Aligned_cols=76  Identities=22%  Similarity=0.393  Sum_probs=71.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~  124 (176)
                      .++|||+|||+.+|+++|+++|+.||.|.+|.|+.++.  .++||||+|.+.++|+.||.|++..|.|+.|.|..+..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~--~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE--RSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC--CCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccC
Confidence            57999999999999999999999999999999998763  46899999999999999999999999999999999864

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

Probab=99.69  E-value=3e-16  Score=132.64  Aligned_cols=79  Identities=32%  Similarity=0.509  Sum_probs=71.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeC-CeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELH-GRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~-g~~i~v~~  121 (176)
                      ....++|||+|||+++++++|+++|++||.|.+|+|++|.+++++|||||+|.+.++|++|| .||+..|. ++.|.|..
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~  134 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCI  134 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccc
Confidence            34568999999999999999999999999999999999988999999999999999999999 69999885 67666654


Q ss_pred             c
Q 030488          122 K  122 (176)
Q Consensus       122 a  122 (176)
                      +
T Consensus       135 S  135 (578)
T TIGR01648       135 S  135 (578)
T ss_pred             c
Confidence            4

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

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

Probab=99.69  E-value=1e-15  Score=115.78  Aligned_cols=116  Identities=26%  Similarity=0.484  Sum_probs=90.8

Q ss_pred             HHHHHHHHHHHHHHHHhhccc---cccCCC--CCC-CCC--C---cccccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCC
Q 030488            5 LKEMEEEATALRQMHAKVGNE---MASKQD--PAA-GGS--S---LANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGT   73 (176)
Q Consensus         5 ~~e~e~~~~~~~~~~~~~~~~---~~~~~~--~~~-~~~--~---~~~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~   73 (176)
                      |-..++++.|+.+|..+....   ..+|..  |.. ...  .   .-.+...++++||||||+..+|+++|++.|+.||.
T Consensus       111 f~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~  190 (321)
T KOG0148|consen  111 FPNKEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGP  190 (321)
T ss_pred             ccchHHHHHHHHHhCCeeeccceeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCc
Confidence            345678889999998864422   112221  110 000  0   01234566899999999999999999999999999


Q ss_pred             eeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccCC
Q 030488           74 VNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTN  125 (176)
Q Consensus        74 i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~~  125 (176)
                      |.+|++.++     +||+||.|++.|+|..|| .+|+.+|.|+.++|.+-+..
T Consensus       191 I~EVRvFk~-----qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~  238 (321)
T KOG0148|consen  191 IQEVRVFKD-----QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEG  238 (321)
T ss_pred             ceEEEEecc-----cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccC
Confidence            999999988     899999999999999999 89999999999999998764

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

Probab=99.68  E-value=1.2e-16  Score=109.35  Aligned_cols=87  Identities=29%  Similarity=0.474  Sum_probs=80.0

Q ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeE
Q 030488           41 NREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLK  118 (176)
Q Consensus        41 ~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~  118 (176)
                      ++.......|||.++...+|+++|.+.|..||+|+++.|..|+ ||..+|||+|+|++.++|++|+ ++|+..|-|+.|.
T Consensus        66 PqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~  145 (170)
T KOG0130|consen   66 PQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVS  145 (170)
T ss_pred             CccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCcee
Confidence            3445667889999999999999999999999999999999998 9999999999999999999999 7999999999999


Q ss_pred             EEeccCCCC
Q 030488          119 VTVKRTNVP  127 (176)
Q Consensus       119 v~~a~~~~~  127 (176)
                      |.++....|
T Consensus       146 VDw~Fv~gp  154 (170)
T KOG0130|consen  146 VDWCFVKGP  154 (170)
T ss_pred             EEEEEecCC
Confidence            999965443

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

Probab=99.68  E-value=1.8e-16  Score=134.25  Aligned_cols=79  Identities=29%  Similarity=0.524  Sum_probs=74.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ...++|||+|||+++++++|+++|.+||.|.+|.|++|+ +++++|||||+|.+.++|+.|| .||+..|+|+.|+|...
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            356899999999999999999999999999999999997 8999999999999999999999 79999999999999865


Q ss_pred             c
Q 030488          123 R  123 (176)
Q Consensus       123 ~  123 (176)
                      .
T Consensus       185 ~  185 (612)
T TIGR01645       185 S  185 (612)
T ss_pred             c
Confidence            3

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.

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

Probab=99.67  E-value=3.5e-16  Score=133.56  Aligned_cols=81  Identities=23%  Similarity=0.510  Sum_probs=76.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      .....+|||+||+.++|+++|+++|++||.|.+|+++.+.++.++|||||+|.+.++|.+|+ +||+..|+|+.|.|.++
T Consensus       282 ~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a  361 (562)
T TIGR01628       282 KAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA  361 (562)
T ss_pred             ccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEec
Confidence            34567899999999999999999999999999999999988999999999999999999999 79999999999999998


Q ss_pred             cC
Q 030488          123 RT  124 (176)
Q Consensus       123 ~~  124 (176)
                      ..
T Consensus       362 ~~  363 (562)
T TIGR01628       362 QR  363 (562)
T ss_pred             cC
Confidence            64

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

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

Probab=99.66  E-value=1e-15  Score=129.09  Aligned_cols=79  Identities=20%  Similarity=0.408  Sum_probs=74.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      ..++|||+|||+.+|+++|+++|+.||.|..+.|+.+. +|.++|||||+|.+.++|+.|| .|++..|.|+.|.|.++.
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~  373 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAC  373 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECc
Confidence            45799999999999999999999999999999999987 7999999999999999999999 799999999999999986


Q ss_pred             C
Q 030488          124 T  124 (176)
Q Consensus       124 ~  124 (176)
                      .
T Consensus       374 ~  374 (509)
T TIGR01642       374 V  374 (509)
T ss_pred             c
Confidence            4

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

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

Probab=99.64  E-value=1.4e-15  Score=121.87  Aligned_cols=77  Identities=30%  Similarity=0.457  Sum_probs=70.5

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      .....+.|||.||+.+||++.|+++|++||.|++|+.++|       ||||+|.+.++|.+|+ .+|+++|+|..|.|.+
T Consensus       255 ~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtL  327 (506)
T KOG0117|consen  255 TMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTL  327 (506)
T ss_pred             hhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-------eeEEeecchHHHHHHHHHhcCceecCceEEEEe
Confidence            3345688999999999999999999999999999988844       9999999999999999 7999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      |++..
T Consensus       328 AKP~~  332 (506)
T KOG0117|consen  328 AKPVD  332 (506)
T ss_pred             cCChh
Confidence            98753

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

Probab=99.64  E-value=1.4e-15  Score=126.79  Aligned_cols=78  Identities=32%  Similarity=0.618  Sum_probs=74.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      ..+|||+|||.++|+++|+++|++||.|..|.|+.+. +|+++|||||+|.+.++|..|+ .|++..|.|+.|.|.++..
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            6899999999999999999999999999999999988 6799999999999999999999 7999999999999999753

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

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

Probab=99.64  E-value=3e-15  Score=119.89  Aligned_cols=81  Identities=31%  Similarity=0.508  Sum_probs=75.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCee-CCeeeEEE
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESEL-HGRQLKVT  120 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~-~g~~i~v~  120 (176)
                      ....+.||||.||.++.|++|.-+|++.|+|-+++|++|+ +|.++|||||.|.+.++|+.|| .||+++| .|+.|.|+
T Consensus        80 p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc  159 (506)
T KOG0117|consen   80 PPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVC  159 (506)
T ss_pred             CCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEE
Confidence            3568999999999999999999999999999999999997 8999999999999999999999 7999999 68999998


Q ss_pred             eccC
Q 030488          121 VKRT  124 (176)
Q Consensus       121 ~a~~  124 (176)
                      .+..
T Consensus       160 ~Sva  163 (506)
T KOG0117|consen  160 VSVA  163 (506)
T ss_pred             Eeee
Confidence            7744

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.64  E-value=2.1e-15  Score=113.42  Aligned_cols=76  Identities=22%  Similarity=0.319  Sum_probs=70.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEecc
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKR  123 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~  123 (176)
                      ...+|||+||++.+|+++|++||+.||.|.+|.|+++.  ...+||||+|.++++++.|+.|++..|.++.|.|....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~--et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG--EYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC--CcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCc
Confidence            46799999999999999999999999999999999874  44689999999999999999999999999999998764

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

Probab=99.63  E-value=2.6e-15  Score=125.16  Aligned_cols=81  Identities=33%  Similarity=0.488  Sum_probs=75.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      +...++|||+|||..+++++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|++||.|++..|.|+.|.|..+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~  165 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSS  165 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeec
Confidence            4457899999999999999999999999999999999998 799999999999999999999999999999999999876


Q ss_pred             cC
Q 030488          123 RT  124 (176)
Q Consensus       123 ~~  124 (176)
                      ..
T Consensus       166 ~~  167 (457)
T TIGR01622       166 QA  167 (457)
T ss_pred             ch
Confidence            53

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

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

Probab=99.62  E-value=2.5e-15  Score=116.31  Aligned_cols=79  Identities=19%  Similarity=0.374  Sum_probs=72.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      ...++|+|+|||+...+-||+..|.+||+|.+|.|+.+. .-+|||+||+|++.++|++|- +||+..+.|++|.|..+.
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE-RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~AT  172 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE-RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNAT  172 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc-CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccc
Confidence            446899999999999999999999999999999999875 335999999999999999999 799999999999999874


Q ss_pred             C
Q 030488          124 T  124 (176)
Q Consensus       124 ~  124 (176)
                      .
T Consensus       173 a  173 (376)
T KOG0125|consen  173 A  173 (376)
T ss_pred             h
Confidence            4

>smart00362 RRM_2 RNA recognition motif

Probab=99.62  E-value=6.3e-15  Score=91.08  Aligned_cols=71  Identities=38%  Similarity=0.700  Sum_probs=65.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           49 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        49 ~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      +|||+|||.++++++|+++|.+||.|..+.+..+. +.++++|||+|.+.++|+.|+ .+++..+.|+.|.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT-GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999998776 778899999999999999999 699999999998874

>PLN03213 repressor of silencing 3; Provisional

Probab=99.60  E-value=4.6e-15  Score=120.41  Aligned_cols=77  Identities=21%  Similarity=0.396  Sum_probs=70.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCH--HHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQS--EAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~--~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ....+||||||++.+++++|..+|..||.|.+|.|++. +|  +|||||+|.+.  .++.+|| .||+..+.|+.|+|..
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE-TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT-KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc-cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            44689999999999999999999999999999999932 56  99999999987  6799999 7999999999999999


Q ss_pred             ccC
Q 030488          122 KRT  124 (176)
Q Consensus       122 a~~  124 (176)
                      |++
T Consensus        85 AKP   87 (759)
T PLN03213         85 AKE   87 (759)
T ss_pred             ccH
Confidence            875

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

Probab=99.59  E-value=1.9e-16  Score=113.45  Aligned_cols=79  Identities=24%  Similarity=0.463  Sum_probs=74.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      =.++.-|||||||++.||.||--+|++||.|..|.|++|+ ||+++||||+.|++..+-.-|+ .||+..|.|+.|+|..
T Consensus        32 YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDH  111 (219)
T KOG0126|consen   32 YKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDH  111 (219)
T ss_pred             cccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeee
Confidence            3457789999999999999999999999999999999999 8999999999999999988899 8999999999999986


Q ss_pred             c
Q 030488          122 K  122 (176)
Q Consensus       122 a  122 (176)
                      .
T Consensus       112 v  112 (219)
T KOG0126|consen  112 V  112 (219)
T ss_pred             c
Confidence            5

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

Probab=99.59  E-value=9e-15  Score=124.89  Aligned_cols=80  Identities=23%  Similarity=0.461  Sum_probs=74.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeC----CeeeE
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELH----GRQLK  118 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~----g~~i~  118 (176)
                      ....++|||+|||.++|+++|+++|+.||.|.++.+..+.+++++|||||+|.+.++|.+|+ .+++..|.    |..|.
T Consensus       175 ~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~  254 (562)
T TIGR01628       175 LKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLY  254 (562)
T ss_pred             ccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeE
Confidence            34467899999999999999999999999999999999989999999999999999999999 79999999    99999


Q ss_pred             EEecc
Q 030488          119 VTVKR  123 (176)
Q Consensus       119 v~~a~  123 (176)
                      |..+.
T Consensus       255 v~~a~  259 (562)
T TIGR01628       255 VGRAQ  259 (562)
T ss_pred             eeccc
Confidence            98764

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

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

Probab=99.58  E-value=3.8e-15  Score=118.93  Aligned_cols=121  Identities=25%  Similarity=0.382  Sum_probs=92.4

Q ss_pred             HHHHHHHHHHHHHHHHhhccccccCCCCCCCC-CCcccccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC
Q 030488            5 LKEMEEEATALRQMHAKVGNEMASKQDPAAGG-SSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK   83 (176)
Q Consensus         5 ~~e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~   83 (176)
                      |...+++.+++.+++....-  .....|...+ +..+.....+.++||||-|+..+||.+|+++|++||.|++|.|.++.
T Consensus        83 ~~trk~a~~a~~Alhn~ktl--pG~~~pvqvk~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~  160 (510)
T KOG0144|consen   83 YYTRKEADEAINALHNQKTL--PGMHHPVQVKYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP  160 (510)
T ss_pred             eccHHHHHHHHHHhhccccc--CCCCcceeecccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecc
Confidence            44567777888887765432  2222222111 12222222457899999999999999999999999999999999999


Q ss_pred             CCCceeEEEEEecCHHHHHHHH-HhCCC-eeCC--eeeEEEeccCCCC
Q 030488           84 FGQPKGYAYVEFLQSEAVQEAL-HLNES-ELHG--RQLKVTVKRTNVP  127 (176)
Q Consensus        84 ~g~~~g~afv~f~~~~~a~~a~-~l~~~-~~~g--~~i~v~~a~~~~~  127 (176)
                      .+.++|||||.|.+.+.|..|| +||+. ++.|  .+|.|++|.+.++
T Consensus       161 ~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkd  208 (510)
T KOG0144|consen  161 DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKD  208 (510)
T ss_pred             cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCC
Confidence            9999999999999999999999 79985 4555  6899999987654

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

Probab=99.58  E-value=3.6e-14  Score=115.56  Aligned_cols=85  Identities=29%  Similarity=0.477  Sum_probs=72.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccCC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRTN  125 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~~  125 (176)
                      ...|||.|||++++.++|+++|.+||.|+...|.... .++..+||||+|.+.++++.||..+...|++++|.|+..+..
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEecccc
Confidence            4569999999999999999999999999988776543 455559999999999999999976789999999999999876


Q ss_pred             CCCCCC
Q 030488          126 VPGMKQ  131 (176)
Q Consensus       126 ~~~~~~  131 (176)
                      ..+...
T Consensus       368 ~~g~~~  373 (419)
T KOG0116|consen  368 FRGNGN  373 (419)
T ss_pred             cccccc
Confidence            655443

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

Probab=99.58  E-value=1.7e-14  Score=109.57  Aligned_cols=134  Identities=45%  Similarity=0.648  Sum_probs=108.2

Q ss_pred             hhHHHHHHHHHHHHHHHHhhccccccCCCCCC---CCCCcccccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEE
Q 030488            3 IRLKEMEEEATALRQMHAKVGNEMASKQDPAA---GGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTI   79 (176)
Q Consensus         3 ~~~~e~e~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~   79 (176)
                      .+..++|.+...++.|+......+........   ...........+...+||+|+.+.+|.++++..|+.||.|..+.|
T Consensus        54 ~~~~e~e~~i~~le~m~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti  133 (231)
T KOG4209|consen   54 NRSSEKEWEITKLERMCPATVKPLMDLSLKAAVVVKEKFPERQKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTV  133 (231)
T ss_pred             cccccchhhhHHHHhhchhhhhhhhhcccccchhhhhcchhhhhccCCceEEEeccccccccchhhheeeccCCccceee
Confidence            34457788888999988877764333222211   112233456778899999999999999999999999999999999


Q ss_pred             eeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccCCCCCCCCCCCCC
Q 030488           80 RTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRR  136 (176)
Q Consensus        80 ~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~  136 (176)
                      +.++ .+.+++|+||+|.+.+.++.++.|++..|.++.|.|.+.+.+.++.....+.+
T Consensus       134 ~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt~~r~~~pg~~~~~~~~  191 (231)
T KOG4209|consen  134 PKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVTLKRTNVPGMGRSSPPR  191 (231)
T ss_pred             eccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceeeeeeeecCCcCCCCCCc
Confidence            9999 47899999999999999999999999999999999999988877766555444

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

Probab=99.57  E-value=2.9e-15  Score=110.45  Aligned_cols=83  Identities=27%  Similarity=0.527  Sum_probs=78.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ....++||||+|..++|+.-|...|-.||.|..|.++.|- +++++||+||+|...++|.+|| .||..+|.|+.|+|.+
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~   86 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNL   86 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEee
Confidence            4557899999999999999999999999999999999998 7999999999999999999999 7999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      |++.+
T Consensus        87 AkP~k   91 (298)
T KOG0111|consen   87 AKPEK   91 (298)
T ss_pred             cCCcc
Confidence            98753

>smart00360 RRM RNA recognition motif

Probab=99.56  E-value=3e-14  Score=87.64  Aligned_cols=69  Identities=43%  Similarity=0.688  Sum_probs=64.3

Q ss_pred             EcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           52 VGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        52 v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      |+|||..+++++|+++|++||.|..+.+..++ ++.++++|||+|.+.++|..|+ .+++..+.|+.|.|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            67999999999999999999999999999887 5889999999999999999999 699999999998874

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.56  E-value=7.2e-14  Score=86.71  Aligned_cols=73  Identities=41%  Similarity=0.647  Sum_probs=67.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           49 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        49 ~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      +|+|+|||..+++++|+++|+.+|.|..+.+..+..+..+++|||+|.+.++|..|+ .+++..+.|+.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            489999999999999999999999999999998876678999999999999999999 7999999999998863

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).

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

Probab=99.54  E-value=3.4e-14  Score=107.20  Aligned_cols=84  Identities=24%  Similarity=0.468  Sum_probs=78.3

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      .+.....|.|--||++.|+++|+.+|...|+|++|++++|+ +|.+.||+||.|.++++|++|| .||+..+..+.|+|+
T Consensus        37 t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVS  116 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVS  116 (360)
T ss_pred             cCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEE
Confidence            34556788899999999999999999999999999999999 8999999999999999999999 799999999999999


Q ss_pred             eccCCC
Q 030488          121 VKRTNV  126 (176)
Q Consensus       121 ~a~~~~  126 (176)
                      +|++..
T Consensus       117 yARPSs  122 (360)
T KOG0145|consen  117 YARPSS  122 (360)
T ss_pred             eccCCh
Confidence            998643

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

Probab=99.54  E-value=2.9e-14  Score=111.60  Aligned_cols=83  Identities=19%  Similarity=0.386  Sum_probs=77.6

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      ...+.+.|||..|.+.+|.++|.-+|+.||.|.+|.+++|+ ||.+..||||+|.+.+++++|. +|++..|++++|+|.
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVD  314 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVD  314 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEee
Confidence            34556889999999999999999999999999999999998 8999999999999999999999 899999999999999


Q ss_pred             eccCC
Q 030488          121 VKRTN  125 (176)
Q Consensus       121 ~a~~~  125 (176)
                      ++.+.
T Consensus       315 FSQSV  319 (479)
T KOG0415|consen  315 FSQSV  319 (479)
T ss_pred             hhhhh
Confidence            88653

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

Probab=99.54  E-value=5.1e-14  Score=108.11  Aligned_cols=77  Identities=38%  Similarity=0.734  Sum_probs=74.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      ..+|||+|||.++|+++|.++|..||.|..+.+..++ ++.++|||||+|.+.++|..|+ .+++..|.|+.|.|..+.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            6999999999999999999999999999999999997 8999999999999999999999 799999999999999964

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

Probab=99.53  E-value=7.7e-14  Score=117.16  Aligned_cols=76  Identities=26%  Similarity=0.357  Sum_probs=70.4

Q ss_pred             CCCCEEEEcCCCC-CCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDY-SCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ..+.+|||+|||+ .+|+++|+++|+.||.|.+|+|+.++    +|||||+|.+.++|+.|| .||+..|.|+.|+|.++
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s  348 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPS  348 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            3568999999998 69999999999999999999998874    799999999999999999 79999999999999998


Q ss_pred             cC
Q 030488          123 RT  124 (176)
Q Consensus       123 ~~  124 (176)
                      +.
T Consensus       349 ~~  350 (481)
T TIGR01649       349 KQ  350 (481)
T ss_pred             cc
Confidence            64

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

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

Probab=99.52  E-value=1.7e-14  Score=103.47  Aligned_cols=79  Identities=28%  Similarity=0.467  Sum_probs=74.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ....+|||+||+..++++.|.++|-+.|+|.++++++|+ +...+|||||+|.++++|+-|+ -||...|.|++|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            446899999999999999999999999999999999999 7889999999999999999999 59999999999999988


Q ss_pred             c
Q 030488          123 R  123 (176)
Q Consensus       123 ~  123 (176)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            6

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

Probab=99.52  E-value=1.8e-13  Score=109.71  Aligned_cols=81  Identities=35%  Similarity=0.542  Sum_probs=75.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhh-hCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQ-SCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~-~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ....+.+||+|||+++.|.+|+++|. +-|+|+.|.|..|.+|+++|||.|+|+++|.+++|+ .||.+++.|++|.|+.
T Consensus        41 ~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKE  120 (608)
T KOG4212|consen   41 AARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKE  120 (608)
T ss_pred             ccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEec
Confidence            34456799999999999999999997 578999999999999999999999999999999999 6999999999999998


Q ss_pred             ccC
Q 030488          122 KRT  124 (176)
Q Consensus       122 a~~  124 (176)
                      .+.
T Consensus       121 d~d  123 (608)
T KOG4212|consen  121 DHD  123 (608)
T ss_pred             cCc
Confidence            764

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

Probab=99.51  E-value=1.6e-13  Score=89.98  Aligned_cols=78  Identities=24%  Similarity=0.393  Sum_probs=69.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      ..++.|||.|||+++|.+++.++|.+||.|..|+|-..+  ..+|.|||.|++..+|.+|+ .|++..++++.|.|-+-.
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k--~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK--ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc--CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            457889999999999999999999999999999986443  34889999999999999999 799999999999998764


Q ss_pred             C
Q 030488          124 T  124 (176)
Q Consensus       124 ~  124 (176)
                      +
T Consensus        94 ~   94 (124)
T KOG0114|consen   94 P   94 (124)
T ss_pred             H
Confidence            3

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

Probab=99.51  E-value=5e-14  Score=106.70  Aligned_cols=78  Identities=26%  Similarity=0.467  Sum_probs=74.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      .-..|||+.|...++-++|++.|.+||+|.+++|++|. |+++|||+||.|.+.++|+.|| .||+..|.++.|+..+|.
T Consensus        61 ~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWAT  140 (321)
T KOG0148|consen   61 QHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWAT  140 (321)
T ss_pred             cceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccc
Confidence            35679999999999999999999999999999999998 8999999999999999999999 799999999999999883

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

Probab=99.51  E-value=1.1e-13  Score=116.21  Aligned_cols=73  Identities=19%  Similarity=0.218  Sum_probs=67.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-H--hCCCeeCCeeeEEEecc
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-H--LNESELHGRQLKVTVKR  123 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~--l~~~~~~g~~i~v~~a~  123 (176)
                      +++|||+|||+++++++|+++|++||.|.+|.|+.+     ++||||+|.+.++|++|| .  +++..|.|+.|.|.++.
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~-----k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~   76 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG-----KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYST   76 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC-----CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecC
Confidence            578999999999999999999999999999999865     689999999999999999 4  47899999999999985


Q ss_pred             C
Q 030488          124 T  124 (176)
Q Consensus       124 ~  124 (176)
                      .
T Consensus        77 ~   77 (481)
T TIGR01649        77 S   77 (481)
T ss_pred             C
Confidence            3

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

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

Probab=99.49  E-value=7.6e-14  Score=114.27  Aligned_cols=78  Identities=35%  Similarity=0.660  Sum_probs=75.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccCC
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTN  125 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~~  125 (176)
                      +.|||||||+++++++|..+|+..|.|.+++++.|+ +|+++||+|++|.+.++++.|+ .||+.++.|++|+|.++...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            899999999999999999999999999999999999 7999999999999999999999 69999999999999998654

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

Probab=99.49  E-value=1e-13  Score=110.84  Aligned_cols=85  Identities=22%  Similarity=0.487  Sum_probs=74.6

Q ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCC-eeCC--e
Q 030488           41 NREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNES-ELHG--R  115 (176)
Q Consensus        41 ~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~-~~~g--~  115 (176)
                      +..+.+.-++||+.||..++|.||+++|++||.|.+|-|++|+ |+.++|||||.|.+.++|.+|+ +||+. +|-|  .
T Consensus        28 d~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~  107 (510)
T KOG0144|consen   28 DNPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHH  107 (510)
T ss_pred             CCCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCc
Confidence            3445667889999999999999999999999999999999999 8999999999999999999999 78775 5655  5


Q ss_pred             eeEEEeccCC
Q 030488          116 QLKVTVKRTN  125 (176)
Q Consensus       116 ~i~v~~a~~~  125 (176)
                      .|.|++|...
T Consensus       108 pvqvk~Ad~E  117 (510)
T KOG0144|consen  108 PVQVKYADGE  117 (510)
T ss_pred             ceeecccchh
Confidence            7888888643

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

Probab=99.49  E-value=3.1e-13  Score=110.92  Aligned_cols=77  Identities=23%  Similarity=0.497  Sum_probs=73.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      ..+|.|.||||.+...+|+.+|+.||.|..|.|++...|+-+|||||.|....+|..|| .+|+.+|+|++|-|.||-
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            67899999999999999999999999999999998888888899999999999999999 699999999999999984

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

Probab=99.47  E-value=8.2e-14  Score=106.48  Aligned_cols=71  Identities=27%  Similarity=0.518  Sum_probs=66.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccCC
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTN  125 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~~  125 (176)
                      .+|||||||..+++.+|+.+|++||+|.+|.|+       |.|+||..++...++.|| .||+.+|+|..|+|+.++..
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv-------KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIV-------KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeee-------cccceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            469999999999999999999999999999999       669999999999999999 69999999999999987654

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

Probab=99.46  E-value=3e-13  Score=111.00  Aligned_cols=80  Identities=38%  Similarity=0.574  Sum_probs=72.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-Hh-----CC-CeeCCee
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HL-----NE-SELHGRQ  116 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l-----~~-~~~~g~~  116 (176)
                      ....+|||.|||+++|+++|.++|++||+|..+.|+.++ |+.++|.|||.|.+..+++.|| ..     .+ ..|+|+.
T Consensus       290 ~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~  369 (678)
T KOG0127|consen  290 TEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRL  369 (678)
T ss_pred             cccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccE
Confidence            346899999999999999999999999999999999999 8999999999999999999999 33     23 6789999


Q ss_pred             eEEEeccC
Q 030488          117 LKVTVKRT  124 (176)
Q Consensus       117 i~v~~a~~  124 (176)
                      |+|..+-+
T Consensus       370 Lkv~~Av~  377 (678)
T KOG0127|consen  370 LKVTLAVT  377 (678)
T ss_pred             Eeeeeccc
Confidence            99998844

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

Probab=99.45  E-value=4.2e-13  Score=108.66  Aligned_cols=108  Identities=25%  Similarity=0.386  Sum_probs=84.8

Q ss_pred             HHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCcccccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCC
Q 030488            5 LKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF   84 (176)
Q Consensus         5 ~~e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~   84 (176)
                      |...+++.+|+.++...............          ..+...|||.||+++++..+|.++|+.||.|.+|++.++.+
T Consensus        44 f~~~~da~~A~~~~n~~~~~~~~~rim~s----------~rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~  113 (369)
T KOG0123|consen   44 FQQPADAERALDTMNFDVLKGKPIRIMWS----------QRDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN  113 (369)
T ss_pred             cCCHHHHHHHHHHcCCcccCCcEEEeehh----------ccCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC
Confidence            45567777777777765442221111000          01111299999999999999999999999999999999998


Q ss_pred             CCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           85 GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        85 g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      | ++|| ||+|.++++|++|| .+|+..+.++.|.|.....
T Consensus       114 g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~  152 (369)
T KOG0123|consen  114 G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFER  152 (369)
T ss_pred             C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccc
Confidence            8 8999 99999999999999 7999999999999987643

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

Probab=99.41  E-value=1.7e-13  Score=107.77  Aligned_cols=78  Identities=29%  Similarity=0.532  Sum_probs=73.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      .-.++||||.|.+++.|+.|+..|..||+|++|.+.+|. |++++|||||+|+-++.|+-|+ .||+..++|+.|+|...
T Consensus       111 aiMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  111 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             HHhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCC
Confidence            346899999999999999999999999999999999999 8999999999999999999999 69999999999999744

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

Probab=99.40  E-value=2.9e-13  Score=102.59  Aligned_cols=85  Identities=24%  Similarity=0.377  Sum_probs=80.5

Q ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeE
Q 030488           41 NREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLK  118 (176)
Q Consensus        41 ~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~  118 (176)
                      ..+..+.++|||=.||.+..+.+|...|-.||.|.+.++..|+ |+.+|+|+||.|.+..++++|| +||++.|+-++|+
T Consensus       279 qreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLK  358 (371)
T KOG0146|consen  279 QREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLK  358 (371)
T ss_pred             hhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhh
Confidence            4567789999999999999999999999999999999999999 8999999999999999999999 8999999999999


Q ss_pred             EEeccCC
Q 030488          119 VTVKRTN  125 (176)
Q Consensus       119 v~~a~~~  125 (176)
                      |.+.++.
T Consensus       359 VQLKRPk  365 (371)
T KOG0146|consen  359 VQLKRPK  365 (371)
T ss_pred             hhhcCcc
Confidence            9998864

>smart00361 RRM_1 RNA recognition motif

Probab=99.40  E-value=2.6e-12  Score=80.34  Aligned_cols=60  Identities=28%  Similarity=0.512  Sum_probs=53.3

Q ss_pred             HHHHHHHhh----hCCCeeEEE-EeeCC-C--CCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           61 PEEVQQHFQ----SCGTVNRVT-IRTDK-F--GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        61 ~~~l~~~f~----~~G~i~~~~-~~~~~-~--g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      +++|+++|+    +||.|.+|. ++.++ +  +.++|||||+|.+.++|.+|+ .||+..+.|+.|++.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            578899998    999999985 66665 4  889999999999999999999 799999999999873

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

Probab=99.39  E-value=1.5e-13  Score=105.14  Aligned_cols=75  Identities=31%  Similarity=0.586  Sum_probs=69.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      .....+|+|+||.+.++..+|+..|++||+|.+|+|+       ++|+||.|.-.++|..|+ .|+++++.|++++|.++
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv-------kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~s  147 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV-------KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLS  147 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeee-------cceeEEEEeeccchHHHHhcccccccccceeeeeee
Confidence            3457889999999999999999999999999999999       669999999999999999 79999999999999998


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      .++
T Consensus       148 tsr  150 (346)
T KOG0109|consen  148 TSR  150 (346)
T ss_pred             ccc
Confidence            543

>PF13893 RRM_5: RNA recognition motif

Probab=99.39  E-value=2.7e-12  Score=76.63  Aligned_cols=55  Identities=36%  Similarity=0.657  Sum_probs=49.5

Q ss_pred             HHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           64 VQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        64 l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      |.++|++||.|.++.+..+.    +++|||+|.+.++|+.|+ .||+..+.|+.|+|++|
T Consensus         1 L~~~f~~fG~V~~i~~~~~~----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999997653    589999999999999999 69999999999999985

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

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

Probab=99.39  E-value=2.2e-12  Score=108.95  Aligned_cols=76  Identities=24%  Similarity=0.352  Sum_probs=64.0

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhC------------CCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCC
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSC------------GTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNES  110 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~------------G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~  110 (176)
                      .....++|||+|||+++|+++|+++|.++            +.|..+.+.     +.++||||+|.+.++|+.||+|++.
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~-----~~kg~afVeF~~~e~A~~Al~l~g~  245 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNIN-----KEKNFAFLEFRTVEEATFAMALDSI  245 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEEC-----CCCCEEEEEeCCHHHHhhhhcCCCe
Confidence            44567899999999999999999999975            234445443     3489999999999999999999999


Q ss_pred             eeCCeeeEEEecc
Q 030488          111 ELHGRQLKVTVKR  123 (176)
Q Consensus       111 ~~~g~~i~v~~a~  123 (176)
                      .|.|..|+|....
T Consensus       246 ~~~g~~l~v~r~~  258 (509)
T TIGR01642       246 IYSNVFLKIRRPH  258 (509)
T ss_pred             EeeCceeEecCcc
Confidence            9999999997553

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

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

Probab=99.35  E-value=1.3e-12  Score=107.30  Aligned_cols=76  Identities=33%  Similarity=0.660  Sum_probs=71.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ...||||||.+++++++|+..|+.||.|+.|.+.+|. ||.++||+||+|.+.++|.+|+ .||+.+|.|+.|+|...
T Consensus       278 ~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v  355 (549)
T KOG0147|consen  278 MRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVV  355 (549)
T ss_pred             hhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEe
Confidence            3449999999999999999999999999999999998 9999999999999999999999 79999999999999865

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

Probab=99.34  E-value=8.6e-12  Score=94.33  Aligned_cols=78  Identities=26%  Similarity=0.353  Sum_probs=73.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      ...|||=||.++++|.-|.++|.+||.|..|++++|. |.+++||+||...+-++|..|| .||+..+.++.|.|.+...
T Consensus       278 g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtn  357 (360)
T KOG0145|consen  278 GWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTN  357 (360)
T ss_pred             eeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecC
Confidence            6789999999999999999999999999999999999 5999999999999999999999 7999999999999998753

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

Probab=99.32  E-value=6.7e-12  Score=90.20  Aligned_cols=85  Identities=24%  Similarity=0.398  Sum_probs=74.7

Q ss_pred             ccccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeE-EEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCee
Q 030488           40 ANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNR-VTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQ  116 (176)
Q Consensus        40 ~~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~-~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  116 (176)
                      .......+.+|||+||.+++++..|.+.|+.||.+.. ..++++. ||.+++|+||.|.+.+.+.+|+ .+|+..++.+.
T Consensus        89 ~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~  168 (203)
T KOG0131|consen   89 HQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRP  168 (203)
T ss_pred             ccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCc
Confidence            3334455689999999999999999999999999854 4677777 7999999999999999999999 79999999999


Q ss_pred             eEEEeccC
Q 030488          117 LKVTVKRT  124 (176)
Q Consensus       117 i~v~~a~~  124 (176)
                      |.|+++..
T Consensus       169 itv~ya~k  176 (203)
T KOG0131|consen  169 ITVSYAFK  176 (203)
T ss_pred             eEEEEEEe
Confidence            99999864

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

Probab=99.31  E-value=7.3e-12  Score=98.72  Aligned_cols=80  Identities=24%  Similarity=0.480  Sum_probs=74.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccC
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~  124 (176)
                      ...+|||++||.++++++|+++|.+||.|..+.++.|. +.+.++|+||.|.+++++++++...-+.|+++.+.|..|.+
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~~f~~~~gk~vevkrA~p  175 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQKFHDFNGKKVEVKRAIP  175 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecccceeeecCceeeEeeccc
Confidence            46799999999999999999999999999999999998 68999999999999999999998888999999999998865


Q ss_pred             C
Q 030488          125 N  125 (176)
Q Consensus       125 ~  125 (176)
                      .
T Consensus       176 k  176 (311)
T KOG4205|consen  176 K  176 (311)
T ss_pred             h
Confidence            3

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

Probab=99.27  E-value=2.1e-11  Score=89.22  Aligned_cols=82  Identities=29%  Similarity=0.409  Sum_probs=73.0

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhC-CCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSC-GTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV  119 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~-G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v  119 (176)
                      .......++|..+|..+.+.++..+|.++ |.|..+++.+++ ||.++|||||+|++.+.|..|- .||++.|.++.|.|
T Consensus        45 ~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c  124 (214)
T KOG4208|consen   45 EQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLEC  124 (214)
T ss_pred             ccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeee
Confidence            34456779999999999999999999998 778888997887 9999999999999999999999 79999999999999


Q ss_pred             EeccC
Q 030488          120 TVKRT  124 (176)
Q Consensus       120 ~~a~~  124 (176)
                      .+-.+
T Consensus       125 ~vmpp  129 (214)
T KOG4208|consen  125 HVMPP  129 (214)
T ss_pred             EEeCc
Confidence            87643

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

Probab=99.25  E-value=2.6e-11  Score=94.89  Aligned_cols=78  Identities=24%  Similarity=0.513  Sum_probs=70.9

Q ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-H-hCCCeeCCeeeEE
Q 030488           42 REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-H-LNESELHGRQLKV  119 (176)
Q Consensus        42 ~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~-l~~~~~~g~~i~v  119 (176)
                      .++..-.+|||++|-..+++.+|+++|.+||+|.++.+...     +++|||+|.+.++|+.|. + ++...|+|.+|+|
T Consensus       223 PeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-----~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i  297 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-----KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKI  297 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-----cccceeeehhhHHHHHHHHhhcceeeecceEEEE
Confidence            34566789999999989999999999999999999998866     679999999999999999 5 8888899999999


Q ss_pred             EeccC
Q 030488          120 TVKRT  124 (176)
Q Consensus       120 ~~a~~  124 (176)
                      .|.++
T Consensus       298 ~Wg~~  302 (377)
T KOG0153|consen  298 KWGRP  302 (377)
T ss_pred             EeCCC
Confidence            99987

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

Probab=99.23  E-value=1.1e-11  Score=97.70  Aligned_cols=80  Identities=24%  Similarity=0.516  Sum_probs=74.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccC
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~  124 (176)
                      +.++|||++|+|+++++.|+++|.+||.|.+|.+++|+ ++++++|+||+|.+.+...++|....+.|+|+.|.+..|.+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~   84 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVS   84 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccC
Confidence            67899999999999999999999999999999999999 79999999999999999999997788999999999988865


Q ss_pred             C
Q 030488          125 N  125 (176)
Q Consensus       125 ~  125 (176)
                      .
T Consensus        85 r   85 (311)
T KOG4205|consen   85 R   85 (311)
T ss_pred             c
Confidence            4

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

Probab=99.23  E-value=1.4e-11  Score=103.83  Aligned_cols=120  Identities=21%  Similarity=0.424  Sum_probs=90.9

Q ss_pred             HHHHHHHHHHHHHHHHhhccc----cccCC-CCCCCCCCcccccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEE
Q 030488            5 LKEMEEEATALRQMHAKVGNE----MASKQ-DPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTI   79 (176)
Q Consensus         5 ~~e~e~~~~~~~~~~~~~~~~----~~~~~-~~~~~~~~~~~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~   79 (176)
                      |...+++.+|++.|+.+....    +.... .+..... ...........|+|.|||+..+..+|+++|..||.|.+|+|
T Consensus       567 F~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~g-K~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRl  645 (725)
T KOG0110|consen  567 FAKPESAQAALKALQGTVLDGHKLELKISENKPASTVG-KKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRL  645 (725)
T ss_pred             ecCHHHHHHHHHHhcCceecCceEEEEeccCccccccc-cccccccccceeeeeccchHHHHHHHHHHHhcccceeeecc
Confidence            567788899999988543211    11110 1111111 11111222578999999999999999999999999999999


Q ss_pred             eeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccCC
Q 030488           80 RTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTN  125 (176)
Q Consensus        80 ~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~~  125 (176)
                      +... .+.++|||||+|.++.+|..|+ +|..+.|.|++|.++||...
T Consensus       646 PKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d  693 (725)
T KOG0110|consen  646 PKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSD  693 (725)
T ss_pred             chhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccc
Confidence            8773 4678999999999999999999 79999999999999999753

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

Probab=99.22  E-value=5.2e-11  Score=88.36  Aligned_cols=79  Identities=19%  Similarity=0.401  Sum_probs=71.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHH----HhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQ----HFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~----~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      ...+|||.||+..+..++|++    +|++||.|..|...  ++.+.+|-|||.|.+.+.|..|+ +|+|..+-|+.++|.
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~--kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriq   85 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF--KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQ   85 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec--CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhhee
Confidence            344999999999999999988    99999999888665  57788999999999999999999 799999999999999


Q ss_pred             eccCCC
Q 030488          121 VKRTNV  126 (176)
Q Consensus       121 ~a~~~~  126 (176)
                      +|++..
T Consensus        86 yA~s~s   91 (221)
T KOG4206|consen   86 YAKSDS   91 (221)
T ss_pred             cccCcc
Confidence            997653

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

Probab=99.22  E-value=5.3e-11  Score=98.56  Aligned_cols=79  Identities=22%  Similarity=0.444  Sum_probs=73.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      .++|||.+|...+...+|+.+|++||.|...+++++. +.-.++|+||++.+.++|.+|| .||.++|.|+.|.|+.++.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            5789999999999999999999999999999999886 6566999999999999999999 7999999999999998865


Q ss_pred             C
Q 030488          125 N  125 (176)
Q Consensus       125 ~  125 (176)
                      .
T Consensus       485 E  485 (940)
T KOG4661|consen  485 E  485 (940)
T ss_pred             C
Confidence            4

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

Probab=99.21  E-value=6.3e-11  Score=99.95  Aligned_cols=75  Identities=31%  Similarity=0.541  Sum_probs=69.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCC----CceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           49 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG----QPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        49 ~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g----~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      +|||.||++++|.++|..+|...|.|.++.|...+.+    .+.|||||+|.+.++|+.|+ .|+++.|+|+.|.|+++.
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            3999999999999999999999999999998876643    35699999999999999999 799999999999999997

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

Probab=99.20  E-value=4.9e-10  Score=85.36  Aligned_cols=82  Identities=27%  Similarity=0.468  Sum_probs=75.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      +....+|+|.|||+.+++++|+++|..||.++.+.|..++.|.+.|.|-|.|...++|.+|+ .+++..++|..|++.+.
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i  159 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEII  159 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEe
Confidence            44457899999999999999999999999999999999999999999999999999999999 79999999999999987


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      .++
T Consensus       160 ~~~  162 (243)
T KOG0533|consen  160 SSP  162 (243)
T ss_pred             cCc
Confidence            543

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

Probab=99.19  E-value=8.4e-11  Score=92.80  Aligned_cols=118  Identities=19%  Similarity=0.296  Sum_probs=89.8

Q ss_pred             HHHHHHHHHHHHHhhccccc-cCCCCCCCCCCcc-----cccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEee
Q 030488            8 MEEEATALRQMHAKVGNEMA-SKQDPAAGGSSLA-----NREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRT   81 (176)
Q Consensus         8 ~e~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~-----~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~   81 (176)
                      .|.++.+++.|+........ ....|........     ..+...-.+|||..+.++.+++||+.+|+.||+|..|.+-+
T Consensus       165 PEaAqLAlEqMNg~mlGGRNiKVgrPsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr  244 (544)
T KOG0124|consen  165 PEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLAR  244 (544)
T ss_pred             cHHHHHHHHHhccccccCccccccCCCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeec
Confidence            35666777787765432211 1112222222111     11233468899999999999999999999999999999999


Q ss_pred             CCC-CCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccCC
Q 030488           82 DKF-GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTN  125 (176)
Q Consensus        82 ~~~-g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~~  125 (176)
                      +.| +.++||+||+|.+..+...|| .||-+.++|+.|+|-.+-.+
T Consensus       245 ~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTP  290 (544)
T KOG0124|consen  245 APTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTP  290 (544)
T ss_pred             cCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccCC
Confidence            985 789999999999999999999 69999999999999877543

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

Probab=99.18  E-value=5.5e-11  Score=101.19  Aligned_cols=73  Identities=18%  Similarity=0.470  Sum_probs=69.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      +++||||+|+.++++.+|..+|+.||.|.+|.++.+     ++||||......+|.+|+ +|++..+.++.|+|.|+..
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~-----R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP-----RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC-----CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            689999999999999999999999999999999876     899999999999999999 8999999999999999853

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

Probab=99.14  E-value=1.3e-10  Score=88.38  Aligned_cols=81  Identities=30%  Similarity=0.496  Sum_probs=73.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCC-eeCC--eeeEEEe
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNES-ELHG--RQLKVTV  121 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~-~~~g--~~i~v~~  121 (176)
                      +.++||||.|...-.|+|++.+|..||.|++|.+.+...|.+||||||.|.+..+|+.|| .||+. ++-|  ..|.|++
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~   97 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKF   97 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEe
Confidence            578999999999999999999999999999999999889999999999999999999999 79975 4444  6799999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      +...+
T Consensus        98 ADTdk  102 (371)
T KOG0146|consen   98 ADTDK  102 (371)
T ss_pred             ccchH
Confidence            87643

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

Probab=99.12  E-value=7.9e-10  Score=86.64  Aligned_cols=82  Identities=28%  Similarity=0.478  Sum_probs=74.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCee--------EEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCC
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVN--------RVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHG  114 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~--------~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  114 (176)
                      ...+..|||+|||.++|.+++.++|++||.|.        .|+|.++..|+.+|-|.|.|...++++-|+ -|++..|.|
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            44567899999999999999999999999875        488998889999999999999999999999 699999999


Q ss_pred             eeeEEEeccCC
Q 030488          115 RQLKVTVKRTN  125 (176)
Q Consensus       115 ~~i~v~~a~~~  125 (176)
                      +.|+|+.|+-.
T Consensus       211 ~~~rVerAkfq  221 (382)
T KOG1548|consen  211 KKLRVERAKFQ  221 (382)
T ss_pred             cEEEEehhhhh
Confidence            99999998643

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

Probab=99.10  E-value=1.4e-10  Score=86.57  Aligned_cols=71  Identities=25%  Similarity=0.586  Sum_probs=66.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccCC
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTN  125 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~~  125 (176)
                      ..|||++||+.+.+.+|+.||..||.|..+.+.       .+|+||+|.+..+|..|| .+|+..|.+..+.|++++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk-------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK-------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee-------cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            469999999999999999999999999999886       789999999999999999 89999999999999998754

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

Probab=99.06  E-value=6.3e-10  Score=90.30  Aligned_cols=72  Identities=28%  Similarity=0.482  Sum_probs=68.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      ..||||   +++|+..|.++|+.+|+|.++++++|. + +.|||||.|.++++|++|| ++|...+.|+.|+|.++..
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t-slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~r   74 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T-SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQR   74 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C-ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhcc
Confidence            468998   899999999999999999999999999 6 9999999999999999999 7999999999999999854

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

Probab=99.00  E-value=1.1e-09  Score=88.41  Aligned_cols=75  Identities=28%  Similarity=0.427  Sum_probs=66.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ..+.++|||.|||+++||..|++-|..||.|..+.|+  ..|+++|  .|.|.++++|+.|+ .|++..++|+.|+|.+.
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadim--e~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM--ENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhh--ccCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            3456889999999999999999999999999998884  3466676  89999999999999 69999999999999863

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

Probab=98.99  E-value=9.3e-09  Score=76.48  Aligned_cols=83  Identities=18%  Similarity=0.278  Sum_probs=69.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-C-CCceeEEEEEecCHHHHHHHH-HhCCCeeC---Ceee
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-F-GQPKGYAYVEFLQSEAVQEAL-HLNESELH---GRQL  117 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~-g~~~g~afv~f~~~~~a~~a~-~l~~~~~~---g~~i  117 (176)
                      ...-++|||.+||.++..-+|..+|..|-..+.+.|.... . .-.+-+||++|.+..+|.+|+ .||+..|+   +..|
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            3447999999999999999999999998777766664433 2 235689999999999999999 79999995   7899


Q ss_pred             EEEeccCCC
Q 030488          118 KVTVKRTNV  126 (176)
Q Consensus       118 ~v~~a~~~~  126 (176)
                      ++++++++.
T Consensus       111 hiElAKSNt  119 (284)
T KOG1457|consen  111 HIELAKSNT  119 (284)
T ss_pred             EeeehhcCc
Confidence            999998765

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

Probab=98.95  E-value=7.9e-09  Score=87.60  Aligned_cols=82  Identities=17%  Similarity=0.310  Sum_probs=74.7

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCC----CCceeEEEEEecCHHHHHHHH-HhCCCeeCCeee
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF----GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQL  117 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~----g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i  117 (176)
                      .+...++|||+||++.++++.|...|..||+|..++|++.++    ...+.|+||.|.+..++++|+ .|++..+.+..+
T Consensus       170 gDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~  249 (877)
T KOG0151|consen  170 GDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEM  249 (877)
T ss_pred             CCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeee
Confidence            356688999999999999999999999999999999999873    456789999999999999999 799999999999


Q ss_pred             EEEeccC
Q 030488          118 KVTVKRT  124 (176)
Q Consensus       118 ~v~~a~~  124 (176)
                      ++-+.+.
T Consensus       250 K~gWgk~  256 (877)
T KOG0151|consen  250 KLGWGKA  256 (877)
T ss_pred             eeccccc
Confidence            9999864

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

Probab=98.95  E-value=3.9e-08  Score=80.41  Aligned_cols=78  Identities=24%  Similarity=0.423  Sum_probs=68.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeE-EEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNR-VTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~-~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      .....|-+.+||+.||++||.+||+..-.|.. +.++.+..+++.|-|||+|++.+.|++||.-|...|.-+-|.|-.+
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRS  179 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHHHHHhhccceEEeehh
Confidence            45678999999999999999999998754544 6677777888999999999999999999987888999999999765

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

Probab=98.82  E-value=1.5e-09  Score=80.35  Aligned_cols=76  Identities=26%  Similarity=0.323  Sum_probs=69.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ..++|||+|+-..++++.|.++|-+.|+|..|.|+.++.++.+ ||||.|.++-++.-|+ -+|+..+.+..|.|.+.
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            3589999999999999999999999999999999988888877 9999999999999999 48999999988888754

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

Probab=98.82  E-value=5.6e-09  Score=78.90  Aligned_cols=81  Identities=20%  Similarity=0.404  Sum_probs=73.9

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      .+.+..+||.|.|..+++++.|-..|.+|-.....++++++ ||+++||+||.|.+..++..|+ +|++..++.+.|++.
T Consensus       186 w~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklR  265 (290)
T KOG0226|consen  186 WDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLR  265 (290)
T ss_pred             CccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhh
Confidence            44567899999999999999999999999888888888887 9999999999999999999999 899999999999887


Q ss_pred             ecc
Q 030488          121 VKR  123 (176)
Q Consensus       121 ~a~  123 (176)
                      .+.
T Consensus       266 kS~  268 (290)
T KOG0226|consen  266 KSE  268 (290)
T ss_pred             hhh
Confidence            653

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

Probab=98.79  E-value=7e-09  Score=85.79  Aligned_cols=72  Identities=24%  Similarity=0.487  Sum_probs=65.2

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLK  118 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~  118 (176)
                      ......+|+|-|||..|++++|...|+.||+|..|+.-..+    .+.+||+|-|..+|++|+ +|+..+|.|+.|+
T Consensus        71 ~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~----~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   71 KDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNK----RGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             ccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccccc----CceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            35678999999999999999999999999999987665444    789999999999999999 7999999999888

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

Probab=98.77  E-value=5e-08  Score=77.05  Aligned_cols=83  Identities=27%  Similarity=0.502  Sum_probs=74.0

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCee--------EEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCee
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVN--------RVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESEL  112 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~--------~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~  112 (176)
                      ......+|||-+||..+++++|.++|.++|.|.        .|.|.+++ |++.|+-|.|.|.+...|++|| -+++..+
T Consensus        62 ~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf  141 (351)
T KOG1995|consen   62 DKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDF  141 (351)
T ss_pred             cccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccc
Confidence            356678999999999999999999999999885        46677777 8999999999999999999999 5999999


Q ss_pred             CCeeeEEEeccCC
Q 030488          113 HGRQLKVTVKRTN  125 (176)
Q Consensus       113 ~g~~i~v~~a~~~  125 (176)
                      ++..|+|.++...
T Consensus       142 ~gn~ikvs~a~~r  154 (351)
T KOG1995|consen  142 CGNTIKVSLAERR  154 (351)
T ss_pred             cCCCchhhhhhhc
Confidence            9999999998643

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

Probab=98.75  E-value=3.7e-08  Score=80.52  Aligned_cols=76  Identities=28%  Similarity=0.487  Sum_probs=66.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      .....|-+.+|||++|++||.+||+.+ .|+++.+.+ .+|+..|-|||+|.+.+++++|++.+...+..+.|.|-.+
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r-~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPR-RNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTA   83 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcC-ceeEEEEec-cCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEcc
Confidence            445678899999999999999999998 677755542 2699999999999999999999999999999999999876

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

Probab=98.72  E-value=2.2e-07  Score=61.33  Aligned_cols=76  Identities=20%  Similarity=0.254  Sum_probs=63.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhh--CCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeC----CeeeEE
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQS--CGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELH----GRQLKV  119 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~--~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~----g~~i~v  119 (176)
                      ++|.|.|||...|.++|.+++..  .|....+.|+.|. ++-+.|||||.|.+.+.|.... .+++..+.    .+...|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            68999999999999999988875  3566778888887 7889999999999999999988 69988774    456666


Q ss_pred             Eecc
Q 030488          120 TVKR  123 (176)
Q Consensus       120 ~~a~  123 (176)
                      .+|+
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            7665

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

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

Probab=98.50  E-value=6e-08  Score=80.24  Aligned_cols=83  Identities=31%  Similarity=0.480  Sum_probs=76.5

Q ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEE
Q 030488           41 NREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV  119 (176)
Q Consensus        41 ~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v  119 (176)
                      ..++.+.+++|+-.|+..++.-+|.+||+.+|.|..|.++.|+ ++.++|.|||+|.+.+++..||.|.|..+-|.+|.|
T Consensus       173 ~~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~v  252 (549)
T KOG0147|consen  173 SPEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIV  252 (549)
T ss_pred             CchHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEe
Confidence            3455667899999999999999999999999999999999999 799999999999999999999999999999999999


Q ss_pred             Eecc
Q 030488          120 TVKR  123 (176)
Q Consensus       120 ~~a~  123 (176)
                      ....
T Consensus       253 q~sE  256 (549)
T KOG0147|consen  253 QLSE  256 (549)
T ss_pred             cccH
Confidence            8764

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

Probab=98.47  E-value=1.3e-07  Score=78.70  Aligned_cols=80  Identities=24%  Similarity=0.436  Sum_probs=74.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      .....|||++||..+++.++++++..||++....++.+. +|.++||||.+|.+......|+ .||+..+.++.|.|..|
T Consensus       287 ~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A  366 (500)
T KOG0120|consen  287 DSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRA  366 (500)
T ss_pred             cccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehh
Confidence            346789999999999999999999999999999999988 6999999999999999999999 69999999999999987


Q ss_pred             cC
Q 030488          123 RT  124 (176)
Q Consensus       123 ~~  124 (176)
                      -.
T Consensus       367 ~~  368 (500)
T KOG0120|consen  367 IV  368 (500)
T ss_pred             hc
Confidence            43

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

Probab=98.47  E-value=8.4e-07  Score=71.34  Aligned_cols=74  Identities=30%  Similarity=0.473  Sum_probs=67.6

Q ss_pred             CCEEEEcCCCCC-CCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           47 SRSVFVGNVDYS-CTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        47 ~~~i~v~~lp~~-~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      +..|.|.||.+. +|.+.|..+|..||.|.+|+|..++    +.-|.|++.+...|+-|+ .|+++.+.|+.|+|.+++-
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH  372 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKH  372 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC----CcceeeeecchhHHHHHHHHhhcceecCceEEEeeccC
Confidence            578899999765 9999999999999999999999876    567999999999999999 7999999999999999864

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

Probab=98.42  E-value=1.2e-06  Score=69.35  Aligned_cols=75  Identities=25%  Similarity=0.424  Sum_probs=64.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCC--CeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCG--TVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G--~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      ....+|||||-|++|++||.+.+...|  .+.++++.-++ +|+++|||+|...+..+.++.+ -|...+|+|+.-.|.
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            356799999999999999999998877  46677777778 6999999999999999999999 588889999866664

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

Probab=98.41  E-value=1.6e-07  Score=70.40  Aligned_cols=72  Identities=28%  Similarity=0.528  Sum_probs=63.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ....+.+.|.+++..+.+.+|.++|+.+|.+....+.       .+++||+|.+.++|..|+ .|++..+.++.|.+...
T Consensus        96 ~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~-------~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen   96 SRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDAR-------RNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             ccccceeeeccchhhhhHHHHhhhhcccCCCchhhhh-------ccccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence            4557889999999999999999999999998555442       679999999999999999 79999999999999544

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.36  E-value=4.7e-07  Score=71.23  Aligned_cols=81  Identities=32%  Similarity=0.605  Sum_probs=71.0

Q ss_pred             CCCCEEE-EcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVF-VGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~-v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      ....++| |++|+..++.++|+.+|..+|.|..++++.+. ++..++|++|.|.+......++......+.++.+.+...
T Consensus       182 ~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  261 (285)
T KOG4210|consen  182 GPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALNDQTRSIGGRPLRLEED  261 (285)
T ss_pred             CccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhcccCcccCcccccccC
Confidence            3455666 99999999999999999999999999999887 799999999999999999888833778889999999988


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      ...
T Consensus       262 ~~~  264 (285)
T KOG4210|consen  262 EPR  264 (285)
T ss_pred             CCC
Confidence            654

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

Probab=98.27  E-value=2.1e-06  Score=57.73  Aligned_cols=69  Identities=23%  Similarity=0.402  Sum_probs=42.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhC-----CCeeCCeeeEEEe
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN-----ESELHGRQLKVTV  121 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~-----~~~~~g~~i~v~~  121 (176)
                      ..|+|.+++..++.++|++.|++||.|..|.+...     ...|+|-|.+.++|+.|+ .+.     ...|.+..+.++.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G-----~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG-----DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC-----CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            46889999999999999999999999999988754     347999999999999999 433     3456666666654

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

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

Probab=98.24  E-value=1.4e-06  Score=64.98  Aligned_cols=63  Identities=25%  Similarity=0.461  Sum_probs=51.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCee
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESEL  112 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~  112 (176)
                      ..+|||.||..++||++|+.+|+.|-....++|. .+.|  ...||++|++.+.|..|+ .|++..|
T Consensus       210 cstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~-~~~g--~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  210 CSTLFIANLGPNCTEDELKQLLSRYPGFHILKIR-ARGG--MPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEe-cCCC--cceEeecHHHHHHHHHHHHHhhccee
Confidence            4679999999999999999999999766555553 2223  458999999999999999 6888776

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

Probab=98.23  E-value=7e-06  Score=61.31  Aligned_cols=76  Identities=17%  Similarity=0.330  Sum_probs=67.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeC-CeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELH-GRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~-g~~i~v~~  121 (176)
                      ..+...+|+.|||.+++.+.|..+|.+|.....++++...    .+.|||+|.+...+..|. .+.+..|. ...|.|.+
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~  218 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITF  218 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC----CceeEEecchhhhhHHHhhhhccceeccCceEEecc
Confidence            4567889999999999999999999999999999998765    789999999999999999 79998885 77888877


Q ss_pred             cc
Q 030488          122 KR  123 (176)
Q Consensus       122 a~  123 (176)
                      ++
T Consensus       219 a~  220 (221)
T KOG4206|consen  219 AK  220 (221)
T ss_pred             cC
Confidence            64

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

Probab=98.23  E-value=3e-05  Score=62.01  Aligned_cols=76  Identities=24%  Similarity=0.272  Sum_probs=61.3

Q ss_pred             CCCEEEEcCC--CCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeC-C-eeeEEE
Q 030488           46 DSRSVFVGNV--DYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELH-G-RQLKVT  120 (176)
Q Consensus        46 ~~~~i~v~~l--p~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~-g-~~i~v~  120 (176)
                      .++.|.+.=|  -+.+|.+-|..+....|+|.+|.|.+. +   ---|.|+|++.+.|++|. +||+..|. | ++|+|+
T Consensus       119 pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk-n---gVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIe  194 (494)
T KOG1456|consen  119 PNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK-N---GVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIE  194 (494)
T ss_pred             CCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec-c---ceeeEEeechhHHHHHHHhhcccccccccceeEEEE
Confidence            3455555544  456999999999999999999988754 3   345999999999999999 79999883 4 699999


Q ss_pred             eccCC
Q 030488          121 VKRTN  125 (176)
Q Consensus       121 ~a~~~  125 (176)
                      +|++.
T Consensus       195 yAkP~  199 (494)
T KOG1456|consen  195 YAKPT  199 (494)
T ss_pred             ecCcc
Confidence            99874

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.18  E-value=1.1e-05  Score=63.65  Aligned_cols=79  Identities=20%  Similarity=0.357  Sum_probs=62.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHH----H--HHHhhhCCCeeEEEEeeCC-C-C--CceeEEEEEecCHHHHHHHH-HhCCCee
Q 030488           44 EVDSRSVFVGNVDYSCTPEE----V--QQHFQSCGTVNRVTIRTDK-F-G--QPKGYAYVEFLQSEAVQEAL-HLNESEL  112 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~----l--~~~f~~~G~i~~~~~~~~~-~-g--~~~g~afv~f~~~~~a~~a~-~l~~~~~  112 (176)
                      .....-+||-+||+.+..++    |  .++|.+||.|..|.+.+.. + .  .+---.||+|.+.++|..|| +.++..+
T Consensus       111 VvQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~  190 (480)
T COG5175         111 VVQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLL  190 (480)
T ss_pred             eeecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccc
Confidence            34467799999999877665    2  6899999999998886543 1 1  11122499999999999999 7999999


Q ss_pred             CCeeeEEEec
Q 030488          113 HGRQLKVTVK  122 (176)
Q Consensus       113 ~g~~i~v~~a  122 (176)
                      +|+.|+..+-
T Consensus       191 DGr~lkatYG  200 (480)
T COG5175         191 DGRVLKATYG  200 (480)
T ss_pred             cCceEeeecC
Confidence            9999999865

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

Probab=98.14  E-value=9.2e-06  Score=69.40  Aligned_cols=74  Identities=23%  Similarity=0.409  Sum_probs=66.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCe-eEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i-~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      +.|-+.|+|++++.+||.+||..|-.+ .+|.+..+..|...|-|.|.|++.++|.+|. .|++..|..+.|.+.+
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            478899999999999999999999766 5677777778999999999999999999999 7999999999988864

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

Probab=98.12  E-value=1.5e-05  Score=50.76  Aligned_cols=67  Identities=22%  Similarity=0.422  Sum_probs=45.9

Q ss_pred             CEEEEcCCCCCCCHHHH----HHHhhhCC-CeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           48 RSVFVGNVDYSCTPEEV----QQHFQSCG-TVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l----~~~f~~~G-~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ..|+|.|||.+.+...|    ++++.-+| .|.+|  .       .+.|+|.|.+.+.|+.|. .|++..+-|..|.|.+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~-------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~   73 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--S-------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSF   73 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-----------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEES
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e-------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEE
Confidence            46899999999887765    55555676 55554  1       467999999999999999 7999999999999998


Q ss_pred             cc
Q 030488          122 KR  123 (176)
Q Consensus       122 a~  123 (176)
                      ..
T Consensus        74 ~~   75 (90)
T PF11608_consen   74 SP   75 (90)
T ss_dssp             S-
T ss_pred             cC
Confidence            74

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

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.08  E-value=2.1e-05  Score=63.13  Aligned_cols=79  Identities=18%  Similarity=0.299  Sum_probs=68.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCC-ee--EEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGT-VN--RVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~-i~--~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      .....|-+.+||++.+.++|..||..|-. |.  .|+++.+..|+..|-|||+|.+.++|.+|. +.+.+....+.|.|-
T Consensus       278 ~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvf  357 (508)
T KOG1365|consen  278 RSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVF  357 (508)
T ss_pred             CCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEe
Confidence            34678999999999999999999998863 33  488999889999999999999999999999 788888888999997


Q ss_pred             ecc
Q 030488          121 VKR  123 (176)
Q Consensus       121 ~a~  123 (176)
                      .+.
T Consensus       358 p~S  360 (508)
T KOG1365|consen  358 PCS  360 (508)
T ss_pred             ecc
Confidence            764

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

Probab=98.04  E-value=4.1e-05  Score=61.27  Aligned_cols=77  Identities=30%  Similarity=0.367  Sum_probs=69.2

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYS-CTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~-~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ..+...+.|-+|... ++-+.|..+|..||.|++|++++.+    .|.|.|+..+..+.++|+ .||+..+-|.+|.|..
T Consensus       284 ~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~  359 (494)
T KOG1456|consen  284 GAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCV  359 (494)
T ss_pred             CCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc----cceeEEEcCcHHHHHHHHHHhccCccccceEEEee
Confidence            456788999999886 6778899999999999999999887    677999999999999999 6999999999999998


Q ss_pred             ccC
Q 030488          122 KRT  124 (176)
Q Consensus       122 a~~  124 (176)
                      ++.
T Consensus       360 SkQ  362 (494)
T KOG1456|consen  360 SKQ  362 (494)
T ss_pred             ccc
Confidence            864

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

Probab=97.91  E-value=3.7e-05  Score=62.10  Aligned_cols=77  Identities=21%  Similarity=0.282  Sum_probs=63.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCe-eeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGR-QLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~-~i~v~~a  122 (176)
                      .+..+|++.|+|.++++++|+..|..-|...+....   .++.+.+|++.+.+.++|..|+ .++++.+... .|+|+++
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkf---f~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFS  488 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKF---FQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFS  488 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeee---cCCCcceeecccCChhHhhhhccccccccCCCCceEEEEee
Confidence            345689999999999999999999998876443221   2334779999999999999999 8999999764 8999998


Q ss_pred             cC
Q 030488          123 RT  124 (176)
Q Consensus       123 ~~  124 (176)
                      ++
T Consensus       489 ks  490 (492)
T KOG1190|consen  489 KS  490 (492)
T ss_pred             cc
Confidence            75

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

Probab=97.91  E-value=0.0002  Score=52.32  Aligned_cols=62  Identities=23%  Similarity=0.419  Sum_probs=54.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeC
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELH  113 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~  113 (176)
                      ...+|.|++||.+.++++|+++..+.|.|-...+.+|      +++.|+|...++++-|+ +|+...+.
T Consensus       114 Se~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  114 SEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             cceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc------cceeeeeeehhhHHHHHHhhcccccc
Confidence            4578999999999999999999999999977777664      57999999999999999 78877664

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

Probab=97.88  E-value=4.1e-05  Score=44.90  Aligned_cols=52  Identities=19%  Similarity=0.364  Sum_probs=41.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL  105 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~  105 (176)
                      +.|-|.+.+.+..+ ++..+|..||.|..+.+...     ..+.+|.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~-----~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPES-----TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCCC-----CcEEEEEECCHHHHHhhC
Confidence            45778888877664 45568899999999888622     568999999999999985

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

Probab=97.84  E-value=4.2e-05  Score=62.09  Aligned_cols=68  Identities=26%  Similarity=0.391  Sum_probs=57.7

Q ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeC---C-C--C-C-------ceeEEEEEecCHHHHHHHHH
Q 030488           41 NREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD---K-F--G-Q-------PKGYAYVEFLQSEAVQEALH  106 (176)
Q Consensus        41 ~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~---~-~--g-~-------~~g~afv~f~~~~~a~~a~~  106 (176)
                      ..++.+.++|.+-|||.+-.-+.|.++|..+|.|+.|+|+..   . +  + .       .+-+|+|+|...+.|.+|.+
T Consensus       225 ~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e  304 (484)
T KOG1855|consen  225 DEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARE  304 (484)
T ss_pred             cccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHH
Confidence            345578999999999999888999999999999999999887   2 1  1 1       26789999999999999996


Q ss_pred             hC
Q 030488          107 LN  108 (176)
Q Consensus       107 l~  108 (176)
                      +.
T Consensus       305 ~~  306 (484)
T KOG1855|consen  305 LL  306 (484)
T ss_pred             hh
Confidence            44

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

Probab=97.82  E-value=7.2e-05  Score=62.73  Aligned_cols=77  Identities=21%  Similarity=0.295  Sum_probs=63.2

Q ss_pred             CCCCEEEEcCCCCCC--CH----HHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeC-Cee
Q 030488           45 VDSRSVFVGNVDYSC--TP----EEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELH-GRQ  116 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~--t~----~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~-g~~  116 (176)
                      .-...|+|-|+|.--  ..    .-|..+|+++|+|..+.++.+..|..+||.|++|.+..+|+.|+ .|||+.|+ .++
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            345789999999642  22    23578899999999999998887779999999999999999999 79999985 567


Q ss_pred             eEEEe
Q 030488          117 LKVTV  121 (176)
Q Consensus       117 i~v~~  121 (176)
                      +.|..
T Consensus       136 f~v~~  140 (698)
T KOG2314|consen  136 FFVRL  140 (698)
T ss_pred             EEeeh
Confidence            77754

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

Probab=97.78  E-value=8.9e-05  Score=61.51  Aligned_cols=63  Identities=30%  Similarity=0.501  Sum_probs=49.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC--C--CCcee---EEEEEecCHHHHHHHH-Hh
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK--F--GQPKG---YAYVEFLQSEAVQEAL-HL  107 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~--~--g~~~g---~afv~f~~~~~a~~a~-~l  107 (176)
                      ..-.++||||+||++++|+.|...|..||.+ .|.++...  .  -..+|   |+|+.|+++.+++..| +.
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            3447889999999999999999999999987 33444211  1  23466   9999999999998888 53

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.70  E-value=0.0002  Score=47.54  Aligned_cols=75  Identities=20%  Similarity=0.187  Sum_probs=50.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEE-EeeC-------CCCCceeEEEEEecCHHHHHHHHHhCCCeeCCe-ee
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVT-IRTD-------KFGQPKGYAYVEFLQSEAVQEALHLNESELHGR-QL  117 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~-~~~~-------~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~-~i  117 (176)
                      ..-|-|=+.|+. ....|.++|++||.|.+.. +..+       ..........|.|.++.+|++||..|+..|.|. .+
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~mv   84 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSLMV   84 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCEEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcEEE
Confidence            455777799987 5577888999999997654 1111       111235688999999999999999999999886 44


Q ss_pred             EEEec
Q 030488          118 KVTVK  122 (176)
Q Consensus       118 ~v~~a  122 (176)
                      -|.+.
T Consensus        85 GV~~~   89 (100)
T PF05172_consen   85 GVKPC   89 (100)
T ss_dssp             EEEE-
T ss_pred             EEEEc
Confidence            46655

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=97.60  E-value=6.4e-05  Score=60.36  Aligned_cols=76  Identities=24%  Similarity=0.305  Sum_probs=62.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhh---C-CCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEe
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQS---C-GTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTV  121 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~---~-G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~  121 (176)
                      +.-.|-+.+||+++++.++.+||..   . |..+.|-+++..+|+..|-|||.|..+++|+.||.-|...|+-+.|.+-.
T Consensus       160 ~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElFR  239 (508)
T KOG1365|consen  160 NQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELFR  239 (508)
T ss_pred             cceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            3456778899999999999999963   2 34567777776789999999999999999999997777777777766643

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

Probab=97.55  E-value=0.0001  Score=56.16  Aligned_cols=71  Identities=20%  Similarity=0.403  Sum_probs=58.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-C--------CCce----eEEEEEecCHHHHHHHH-HhCCCe
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-F--------GQPK----GYAYVEFLQSEAVQEAL-HLNESE  111 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~--------g~~~----g~afv~f~~~~~a~~a~-~l~~~~  111 (176)
                      ....||+++||+..+...|+++|..||.|-.|.|-... +        |.+.    --+.|+|.+...|..+. .||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            45789999999999999999999999999999886543 2        2222    23569999999999888 699999


Q ss_pred             eCCee
Q 030488          112 LHGRQ  116 (176)
Q Consensus       112 ~~g~~  116 (176)
                      |.|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99863

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.53  E-value=0.00042  Score=48.88  Aligned_cols=57  Identities=28%  Similarity=0.427  Sum_probs=45.6

Q ss_pred             HHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccCCC
Q 030488           63 EVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRTNV  126 (176)
Q Consensus        63 ~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~~~  126 (176)
                      +|.+.|..||.+.=++++-       +.-+|+|.+-++|.+|+.+++..++|+.|+|.+..+..
T Consensus        52 ~ll~~~~~~GevvLvRfv~-------~~mwVTF~dg~sALaals~dg~~v~g~~l~i~LKtpdW  108 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVG-------DTMWVTFRDGQSALAALSLDGIQVNGRTLKIRLKTPDW  108 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEET-------TCEEEEESSCHHHHHHHHGCCSEETTEEEEEEE-----
T ss_pred             HHHHHHHhCCceEEEEEeC-------CeEEEEECccHHHHHHHccCCcEECCEEEEEEeCCccH
Confidence            6778888999988888874       35799999999999999999999999999999886543

; PDB: 1UFW_A 2DNR_A.

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

Probab=97.53  E-value=0.00033  Score=58.77  Aligned_cols=61  Identities=23%  Similarity=0.316  Sum_probs=50.9

Q ss_pred             HHHHHhhhCCCeeEEEEeeC-CC---CCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           63 EVQQHFQSCGTVNRVTIRTD-KF---GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        63 ~l~~~f~~~G~i~~~~~~~~-~~---g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      +++.-+.+||.|..|.++++ .+   .-..|-.||+|.+.++++.|. +|+|.+|.++.|...+-.
T Consensus       425 dvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  425 DVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             HHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            34555578999999999887 32   345778999999999999999 799999999999888754

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

Probab=97.44  E-value=0.00074  Score=56.19  Aligned_cols=65  Identities=32%  Similarity=0.384  Sum_probs=58.6

Q ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHhh-hCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHH
Q 030488           42 REEVDSRSVFVGNVDYSCTPEEVQQHFQ-SCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALH  106 (176)
Q Consensus        42 ~~~~~~~~i~v~~lp~~~t~~~l~~~f~-~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~  106 (176)
                      ..-...++||||+||.-++.++|..+|. -||.|..+-|-+|. -+..+|-|=|+|.+..+..+||.
T Consensus       365 q~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIs  431 (520)
T KOG0129|consen  365 QPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAIS  431 (520)
T ss_pred             cccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHh
Confidence            3445689999999999999999999999 69999999999995 68899999999999999999993

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=97.42  E-value=6.8e-05  Score=57.12  Aligned_cols=62  Identities=23%  Similarity=0.393  Sum_probs=49.7

Q ss_pred             HHHHHHhh-hCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           62 EEVQQHFQ-SCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        62 ~~l~~~f~-~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      ++|...|+ +||.|+++.+..+..-.-.|=++|.|...++|++|+ .||+..+.|++|..++.-
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            34444445 899999987776553344677999999999999999 799999999999998763

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

Probab=97.34  E-value=0.00036  Score=56.28  Aligned_cols=76  Identities=25%  Similarity=0.318  Sum_probs=65.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC---C-CCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEecc
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK---F-GQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKR  123 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~---~-g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~  123 (176)
                      ..|.|.||.+++|.++++.+|.-.|.|..+.|..+.   + ....-.|||-|.+...+..|-.|.++.+-++.|.|...-
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~   87 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYG   87 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecC
Confidence            479999999999999999999999999999887633   1 345678999999999998888899999989888887653

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

Probab=97.31  E-value=0.00017  Score=63.02  Aligned_cols=78  Identities=21%  Similarity=0.285  Sum_probs=70.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      ...++|.|+|+..|.++|+.++.++|.+.++.+++.+.|+.+|-|+|.|.++.++..++ ..+...+....+.|..+.+
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            57799999999999999999999999999999999999999999999999999999999 6888788777777777544

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

Probab=97.30  E-value=0.0012  Score=52.44  Aligned_cols=77  Identities=21%  Similarity=0.408  Sum_probs=60.6

Q ss_pred             CCCCCEEEEcCCC----CCCC-------HHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCe
Q 030488           44 EVDSRSVFVGNVD----YSCT-------PEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESE  111 (176)
Q Consensus        44 ~~~~~~i~v~~lp----~~~t-------~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~  111 (176)
                      ....++|.|.||=    ...+       .++|.+-..+||.|.+|.|.-.   .+.|.+-|.|.+.++|+.|| .|+|..
T Consensus       262 ~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~---hPdGvvtV~f~n~eeA~~ciq~m~GR~  338 (382)
T KOG1548|consen  262 ARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDR---HPDGVVTVSFRNNEEADQCIQTMDGRW  338 (382)
T ss_pred             ccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEecc---CCCceeEEEeCChHHHHHHHHHhcCee
Confidence            3456788888882    1233       3456677789999999977532   23789999999999999999 699999


Q ss_pred             eCCeeeEEEecc
Q 030488          112 LHGRQLKVTVKR  123 (176)
Q Consensus       112 ~~g~~i~v~~a~  123 (176)
                      |+|+.|..++..
T Consensus       339 fdgRql~A~i~D  350 (382)
T KOG1548|consen  339 FDGRQLTASIWD  350 (382)
T ss_pred             ecceEEEEEEeC
Confidence            999999988764

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=97.28  E-value=0.0024  Score=38.53  Aligned_cols=52  Identities=21%  Similarity=0.307  Sum_probs=42.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhC---CCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSC---GTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL  105 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~---G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~  105 (176)
                      ...|+|.++. +.+.++|+.+|..|   .....|.++-|.      -|-|.|.+.+.|.+||
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt------ScNvvf~d~~~A~~AL   59 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT------SCNVVFKDEETAARAL   59 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC------cEEEEECCHHHHHHHH
Confidence            4679999996 57888999999998   124578888765      3889999999999998

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

Probab=97.22  E-value=0.00043  Score=60.98  Aligned_cols=77  Identities=19%  Similarity=0.386  Sum_probs=67.4

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCC--eeeEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHG--RQLKV  119 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g--~~i~v  119 (176)
                      .....+.+||++|+.|+....|...|..||.|..|.+-..     ..||+|.|++...+++|+ .|.+..|.+  +.|.|
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg-----q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rv  525 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG-----QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRV  525 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC-----CcceeeecccCccchhhHHHHhcCcCCCCCccccc
Confidence            4456788999999999999999999999999998877433     569999999999999999 799999976  77999


Q ss_pred             EeccC
Q 030488          120 TVKRT  124 (176)
Q Consensus       120 ~~a~~  124 (176)
                      .++..
T Consensus       526 dla~~  530 (975)
T KOG0112|consen  526 DLASP  530 (975)
T ss_pred             ccccC
Confidence            98864

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

Probab=96.81  E-value=0.0014  Score=55.49  Aligned_cols=75  Identities=19%  Similarity=0.251  Sum_probs=60.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhh-CCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCee---CCeeeE
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQS-CGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESEL---HGRQLK  118 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~-~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~---~g~~i~  118 (176)
                      ...++.|||.||-.-.|.-.|+.++.. .|.|+..+|  |+   .+..|||.|.+.++|.+.+ +||+...   +.+.|.
T Consensus       441 ~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--Dk---IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~  515 (718)
T KOG2416|consen  441 KEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--DK---IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLI  515 (718)
T ss_pred             CCccceEeeecccccchHHHHHHHHhhccCchHHHHH--HH---hhcceeEecccHHHHHHHHHHHhccccCCCCCceeE
Confidence            445788999999999999999999995 556666522  22   2668999999999999999 8999766   567888


Q ss_pred             EEecc
Q 030488          119 VTVKR  123 (176)
Q Consensus       119 v~~a~  123 (176)
                      +.+..
T Consensus       516 adf~~  520 (718)
T KOG2416|consen  516 ADFVR  520 (718)
T ss_pred             eeecc
Confidence            88764

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.69  E-value=0.0023  Score=48.94  Aligned_cols=75  Identities=23%  Similarity=0.371  Sum_probs=62.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCC----CeeCCeeeEEEec
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNE----SELHGRQLKVTVK  122 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~----~~~~g~~i~v~~a  122 (176)
                      ..|+|.||+.-++-+.|.+.|+.||+|+...++.|..++..+-++|.|...-.+.+|+ .++.    .+..+...-|+..
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP~  111 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEPM  111 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCChh
Confidence            7899999999999999999999999999888888878888889999999999999998 4532    2335566666554

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.68  E-value=0.0077  Score=47.11  Aligned_cols=61  Identities=23%  Similarity=0.272  Sum_probs=48.7

Q ss_pred             HHHHHHhhhCCCeeEEEEeeCCC-C-CceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           62 EEVQQHFQSCGTVNRVTIRTDKF-G-QPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        62 ~~l~~~f~~~G~i~~~~~~~~~~-g-~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      +++++-.++||.|..|.|.-..+ - .-.---||+|...++|.+|+ .||+..|+|+.+...+-
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFY  364 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheec
Confidence            46778889999999988776652 1 12234699999999999999 89999999998877654

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

Probab=96.68  E-value=0.0011  Score=57.13  Aligned_cols=77  Identities=13%  Similarity=0.083  Sum_probs=64.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeE-EEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNR-VTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~-~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      .....|||-.||..+++.++.++|...-.|++ |.|....+++..+.|||.|..++++..|+ .-+.+.+..+.|+|..
T Consensus       432 ~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~s  510 (944)
T KOG4307|consen  432 GAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDS  510 (944)
T ss_pred             CccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEeec
Confidence            34678999999999999999999998777766 77776678888999999999988888877 4566677778888864

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=96.67  E-value=0.00082  Score=53.24  Aligned_cols=79  Identities=19%  Similarity=0.321  Sum_probs=60.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHH---HHHhhhCCCeeEEEEeeCCC----CCceeEEEEEecCHHHHHHHH-HhCCCeeCCee
Q 030488           45 VDSRSVFVGNVDYSCTPEEV---QQHFQSCGTVNRVTIRTDKF----GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQ  116 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l---~~~f~~~G~i~~~~~~~~~~----g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  116 (176)
                      .....+||-+|+.....+.+   .++|.+||.|..|.+..+.+    -....-++|+|...++|..|| ..++..++|+.
T Consensus        75 Vqknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~  154 (327)
T KOG2068|consen   75 VQKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRA  154 (327)
T ss_pred             hhhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhh
Confidence            34567888899887655544   46889999999998877651    122334899999999999999 79999999998


Q ss_pred             eEEEecc
Q 030488          117 LKVTVKR  123 (176)
Q Consensus       117 i~v~~a~  123 (176)
                      |+..+..
T Consensus       155 lka~~gt  161 (327)
T KOG2068|consen  155 LKASLGT  161 (327)
T ss_pred             hHHhhCC
Confidence            7776553

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

Probab=96.59  E-value=0.00045  Score=60.85  Aligned_cols=81  Identities=22%  Similarity=0.407  Sum_probs=66.5

Q ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           42 REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        42 ~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      ++...+.+||+|||+..+++.+|+..|..+|.|.+|.|-+.+-+....|+||.|.+.+.+-.|+ ++.+..|..-.+++.
T Consensus       367 DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~g  446 (975)
T KOG0112|consen  367 DDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIG  446 (975)
T ss_pred             cchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccc
Confidence            3445689999999999999999999999999999999987765666779999999999988888 788877754444444


Q ss_pred             ec
Q 030488          121 VK  122 (176)
Q Consensus       121 ~a  122 (176)
                      +.
T Consensus       447 lG  448 (975)
T KOG0112|consen  447 LG  448 (975)
T ss_pred             cc
Confidence            43

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.42  E-value=0.014  Score=37.25  Aligned_cols=54  Identities=15%  Similarity=0.264  Sum_probs=40.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN  108 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~  108 (176)
                      ....||+ .|..+...||.++|+.||.| .|.++.|.      -|||...+.+.+..++ .+.
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~dT------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWINDT------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCE-EEEEECTT------EEEEEECCCHHHHHHHHHHT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcCC------cEEEEeecHHHHHHHHHHhc
Confidence            3455665 99999999999999999998 55566543      5999999999999988 454

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

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

Probab=96.36  E-value=0.0041  Score=50.87  Aligned_cols=71  Identities=21%  Similarity=0.417  Sum_probs=54.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCC-eeCCeeeEEEecc
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNES-ELHGRQLKVTVKR  123 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~-~~~g~~i~v~~a~  123 (176)
                      ..+|++||.+.++.++|..+|...-.-.+-.++..     .||+||.+.+...|.+|+ .+++. ++.|.++.|+.+-
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k-----~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv   74 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK-----SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee-----cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence            46899999999999999999975411111112222     789999999999999999 67764 6899999998763

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

Probab=96.34  E-value=0.00017  Score=63.07  Aligned_cols=67  Identities=31%  Similarity=0.501  Sum_probs=56.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCC
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHG  114 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g  114 (176)
                      .++||+||+..+.+.+|...|..+|.|..+.+.-.. +++.+|.|+++|.+.+.+.+||+++...+-|
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            569999999999999999999999988877766333 6888999999999999999999765555544

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=96.18  E-value=0.078  Score=46.53  Aligned_cols=67  Identities=10%  Similarity=0.210  Sum_probs=49.0

Q ss_pred             EEEEcCC--CCCCCHHHHHHHhhhCCCe-----eEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           49 SVFVGNV--DYSCTPEEVQQHFQSCGTV-----NRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        49 ~i~v~~l--p~~~t~~~l~~~f~~~G~i-----~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      ++|| |+  -..++..+|..++..-+.|     -.|.|.       ..|.||+.... .+...+ .|++..+.|+.|.|+
T Consensus       488 ~~~~-~~g~~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~-------~~~s~v~~~~~-~~~~~~~~~~~~~~~~~~~~~~  558 (629)
T PRK11634        488 LYRI-EVGRDDGVEVRHIVGAIANEGDISSRYIGNIKLF-------ASHSTIELPKG-MPGEVLQHFTRTRILNKPMNMQ  558 (629)
T ss_pred             EEEE-ecccccCCCHHHHHHHHHhhcCCChhhCCcEEEe-------CCceEEEcChh-hHHHHHHHhccccccCCceEEE
Confidence            3555 34  3468889999998876654     356665       45889998654 466777 799999999999999


Q ss_pred             eccC
Q 030488          121 VKRT  124 (176)
Q Consensus       121 ~a~~  124 (176)
                      .+..
T Consensus       559 ~~~~  562 (629)
T PRK11634        559 LLGD  562 (629)
T ss_pred             ECCC
Confidence            8753

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=96.15  E-value=0.0097  Score=43.69  Aligned_cols=78  Identities=15%  Similarity=0.138  Sum_probs=47.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhh-CCCe---eEEEEeeCC--C-CCceeEEEEEecCHHHHHHHH-HhCCCeeCC--
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQS-CGTV---NRVTIRTDK--F-GQPKGYAYVEFLQSEAVQEAL-HLNESELHG--  114 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~-~G~i---~~~~~~~~~--~-g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g--  114 (176)
                      ....+|.|++||+++|++++.+.+.. ++.-   ..+.-....  . -....-|||.|.+.+++...+ .++++.|.+  
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            44578999999999999998887766 5544   233322222  1 223556999999999988888 799988743  


Q ss_pred             ---eeeEEEec
Q 030488          115 ---RQLKVTVK  122 (176)
Q Consensus       115 ---~~i~v~~a  122 (176)
                         ....|++|
T Consensus        85 g~~~~~~VE~A   95 (176)
T PF03467_consen   85 GNEYPAVVEFA   95 (176)
T ss_dssp             S-EEEEEEEE-
T ss_pred             CCCcceeEEEc
Confidence               23455555

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.60  E-value=0.084  Score=37.21  Aligned_cols=73  Identities=19%  Similarity=0.263  Sum_probs=53.9

Q ss_pred             CCCCCEEEEcCCCCCCCH-H---HHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeE
Q 030488           44 EVDSRSVFVGNVDYSCTP-E---EVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLK  118 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~-~---~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~  118 (176)
                      +.+..+|.|.=|..++.. +   .+...++.||+|.+|.+.-      +.-|.|.|.+..+|=.|+ +++. ..-|..+.
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG------rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~q  155 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG------RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQ  155 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC------CceEEEEehhhHHHHHHHHhhcC-CCCCceEE
Confidence            455678888876665432 3   4556678899999998863      456999999999999999 6665 55667777


Q ss_pred             EEecc
Q 030488          119 VTVKR  123 (176)
Q Consensus       119 v~~a~  123 (176)
                      +.+-.
T Consensus       156 CsWqq  160 (166)
T PF15023_consen  156 CSWQQ  160 (166)
T ss_pred             eeccc
Confidence            77653

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=95.41  E-value=0.35  Score=32.67  Aligned_cols=67  Identities=12%  Similarity=0.125  Sum_probs=50.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCC-CeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCG-TVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHG  114 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G-~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  114 (176)
                      ...+.+...|..++.++|..+.+.+- .|..++|+++.+. ++-.+.+.|.+.++|+.-. .+||+.++.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~p-nrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTP-NRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCC-ceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            44555656666677777776666654 4678889877543 5678999999999999988 799988864

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

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=95.31  E-value=0.01  Score=49.25  Aligned_cols=73  Identities=16%  Similarity=0.239  Sum_probs=58.6

Q ss_pred             CCEEEEcCCCCC-CCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccC
Q 030488           47 SRSVFVGNVDYS-CTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        47 ~~~i~v~~lp~~-~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~  124 (176)
                      .+.|-+.-+|+. -|.++|..+|.+||.|..|.+-..     .-.|.|+|.+..+|-.|-..++..|+++.|+|.+-.+
T Consensus       372 hs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~-----~~~a~vTF~t~aeag~a~~s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS-----SLHAVVTFKTRAEAGEAYASHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhcCccccccccCc-----hhhheeeeeccccccchhccccceecCceeEEEEecC
Confidence            444555555655 356899999999999999988554     3469999999999988888899999999999998654

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=95.25  E-value=0.12  Score=31.56  Aligned_cols=54  Identities=17%  Similarity=0.340  Sum_probs=42.1

Q ss_pred             CCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEE
Q 030488           58 SCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV  119 (176)
Q Consensus        58 ~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v  119 (176)
                      .++-++++..|..|.- .  +|..+++    | =||.|.+..+|++|. ..++..+-+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~--~I~~d~t----G-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-D--RIRDDRT----G-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-c--eEEecCC----E-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            5788999999999954 2  3444543    2 489999999999999 78888888777654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=95.07  E-value=0.058  Score=45.80  Aligned_cols=72  Identities=18%  Similarity=0.290  Sum_probs=56.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhh--CCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhC--CCeeCCeeeEE
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQS--CGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN--ESELHGRQLKV  119 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~--~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~--~~~~~g~~i~v  119 (176)
                      .+.+.|.|.-||..+-+|+++.+|..  +-++.+|.+-.+.      --||+|++..+|+.|. .|.  -++|-|+.|..
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~------nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            34677889999999999999999985  5677888876543      3699999999999988 343  45777887766


Q ss_pred             Eec
Q 030488          120 TVK  122 (176)
Q Consensus       120 ~~a  122 (176)
                      .++
T Consensus       247 RIK  249 (684)
T KOG2591|consen  247 RIK  249 (684)
T ss_pred             hhh
Confidence            554

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=95.02  E-value=0.077  Score=39.23  Aligned_cols=60  Identities=18%  Similarity=0.230  Sum_probs=43.7

Q ss_pred             CHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhC--CCeeCCeeeEEEeccC
Q 030488           60 TPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN--ESELHGRQLKVTVKRT  124 (176)
Q Consensus        60 t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~--~~~~~g~~i~v~~a~~  124 (176)
                      ..+.|+++|..++.+..+.....     .+-..|.|.+.++|..|. .|+  +..+.|..|+|-++..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s-----FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS-----FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT-----TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC-----CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            45789999999998877766543     455899999999999999 688  8999999999998853

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=94.91  E-value=0.03  Score=48.27  Aligned_cols=72  Identities=24%  Similarity=0.314  Sum_probs=61.5

Q ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           42 REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        42 ~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      ....+..++||+|+...+..+-++..+..+|.|.++....        |+|.+|........|+ .++...++|..+.+.
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~--------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~  106 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK--------FGFCEFLKHIGDLRASRLLTELNIDDQKLIEN  106 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh--------hcccchhhHHHHHHHHHHhcccCCCcchhhcc
Confidence            3445678999999999999999999999999998776542        9999999999999999 688889999887776


Q ss_pred             e
Q 030488          121 V  121 (176)
Q Consensus       121 ~  121 (176)
                      .
T Consensus       107 ~  107 (668)
T KOG2253|consen  107 V  107 (668)
T ss_pred             c
Confidence            5

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=94.67  E-value=0.19  Score=31.32  Aligned_cols=58  Identities=19%  Similarity=0.405  Sum_probs=35.5

Q ss_pred             CCCCHHHHHHHhhhCCC-----eeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           57 YSCTPEEVQQHFQSCGT-----VNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        57 ~~~t~~~l~~~f~~~G~-----i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ..++..+|..++...+.     |-.|.|.       ..|+||+-... .++.++ .|++..+.|+.|+|+.|
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~-------~~~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIF-------DNFSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE--------SS-EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEe-------eeEEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            35888999999987754     4577776       45899998764 577788 79999999999999875

; PDB: 2G0C_A 3MOJ_B.

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=94.17  E-value=0.12  Score=40.83  Aligned_cols=66  Identities=20%  Similarity=0.218  Sum_probs=49.1

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCe-eeEEEe
Q 030488           50 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGR-QLKVTV  121 (176)
Q Consensus        50 i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~-~i~v~~  121 (176)
                      |=|-++|+.- ..-|..+|++||.|.+....  .   +-.+-+|.|.+.-+|++||..|++.|+|. .|-|..
T Consensus       200 VTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~--~---ngNwMhirYssr~~A~KALskng~ii~g~vmiGVkp  266 (350)
T KOG4285|consen  200 VTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTP--S---NGNWMHIRYSSRTHAQKALSKNGTIIDGDVMIGVKP  266 (350)
T ss_pred             EEEeccCccc-hhHHHHHHHhhCeeeeeecC--C---CCceEEEEecchhHHHHhhhhcCeeeccceEEeeee
Confidence            4444677653 35677899999999775443  2   25588999999999999998899999885 344554

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=93.29  E-value=0.06  Score=47.80  Aligned_cols=71  Identities=23%  Similarity=0.209  Sum_probs=59.3

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCee--CCeeeEEEeccCC
Q 030488           50 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESEL--HGRQLKVTVKRTN  125 (176)
Q Consensus        50 i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~--~g~~i~v~~a~~~  125 (176)
                      .++.|.+-+.+...|..+|.+||.|.+++..++     ...|.|+|.+.+.|-.|+ +++|+++  -|-+.+|.+|+..
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~-----~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRD-----LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheeccc-----ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccc
Confidence            344455556788889999999999999988777     668999999999999999 7999876  5778999998754

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

Probab=93.15  E-value=0.0075  Score=48.89  Aligned_cols=71  Identities=14%  Similarity=0.102  Sum_probs=56.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEE
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVT  120 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~  120 (176)
                      .++|+|++|+..+...++.++|..+|.|...++.   .+...-+|.|+|....+...|+.+++.++.-+...+.
T Consensus       151 rRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~a---sk~~s~~c~~sf~~qts~~halr~~gre~k~qhsr~a  221 (479)
T KOG4676|consen  151 RRTREVQSLISAAILPESGESFERKGEVSYAHTA---SKSRSSSCSHSFRKQTSSKHALRSHGRERKRQHSRRA  221 (479)
T ss_pred             Hhhhhhhcchhhhcchhhhhhhhhcchhhhhhhh---ccCCCcchhhhHhhhhhHHHHHHhcchhhhhhhhhhh
Confidence            4789999999999999999999999998766553   3334567889999998888999888888765444443

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=91.85  E-value=0.08  Score=41.88  Aligned_cols=77  Identities=19%  Similarity=0.157  Sum_probs=61.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCC-eeCCeeeEEEec
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNES-ELHGRQLKVTVK  122 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~-~~~g~~i~v~~a  122 (176)
                      ...++|++++.+.+.+.++..++..+|.+....+.... ...+++++.+.|...+.+..|+.+... .+.+..+...+.
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            36789999999999999899999999987766665544 578899999999999999999976664 555555554443

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=91.59  E-value=0.95  Score=35.63  Aligned_cols=47  Identities=6%  Similarity=0.169  Sum_probs=35.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCe-eEEEEeeCCCCCceeEEEEEecCH
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRTDKFGQPKGYAYVEFLQS   98 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i-~~~~~~~~~~g~~~g~afv~f~~~   98 (176)
                      ..-|+++|||.++...||+..+.+-+-+ .++.+.-     +.+-||+.|.+.
T Consensus       330 ~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~iswkg-----~~~k~flh~~~~  377 (396)
T KOG4410|consen  330 KTDIKLTNLSRDIRVKDLKSELRKRECTPMSISWKG-----HFGKCFLHFGNR  377 (396)
T ss_pred             ccceeeccCccccchHHHHHHHHhcCCCceeEeeec-----CCcceeEecCCc
Confidence            4559999999999999999999987654 3444422     266799999664

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=90.55  E-value=1.5  Score=37.82  Aligned_cols=79  Identities=22%  Similarity=0.331  Sum_probs=60.5

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHhhhC----CCeeEEEEeeCCCCCc-------------------------------
Q 030488           44 EVDSRSVFVGNVDYS-CTPEEVQQHFQSC----GTVNRVTIRTDKFGQP-------------------------------   87 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~-~t~~~l~~~f~~~----G~i~~~~~~~~~~g~~-------------------------------   87 (176)
                      ...+++|-|.|+.|. +...+|.-+|..|    |.|.+|.|.....|+.                               
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            345788999999997 7888999888865    5888888765432221                               


Q ss_pred             -----------------eeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           88 -----------------KGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        88 -----------------~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                                       .=||.|+|.+.+.|.+.- .++|.++...-..+.+.
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLR  303 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLR  303 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeee
Confidence                             247899999999999888 79999997766666554

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=90.27  E-value=1.7  Score=36.36  Aligned_cols=67  Identities=12%  Similarity=0.160  Sum_probs=56.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCC-CeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCG-TVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHG  114 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G-~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  114 (176)
                      ...|+|=.+|..+|.-||-.|...+- .|.+++|++|.... +=.++|.|.+.++|...- .+||..|+.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pn-rymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPN-RYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCc-eEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            78899999999999999999998765 57899999865332 446899999999999999 799998864

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

Probab=89.96  E-value=0.53  Score=40.07  Aligned_cols=76  Identities=17%  Similarity=0.243  Sum_probs=46.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhh-hCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCee---CC-eeeEEE
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQ-SCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESEL---HG-RQLKVT  120 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~-~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~---~g-~~i~v~  120 (176)
                      +++.|.|+|...|...|...-. ..|.-..+.++.|- +..+.|||||.|.+.+++..+. +.|++..   .. +...+.
T Consensus       389 tt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~it  468 (549)
T KOG4660|consen  389 TTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASIT  468 (549)
T ss_pred             hhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeee
Confidence            3344444444433333322222 24445566777775 5667999999999999999988 6888654   32 344555


Q ss_pred             ecc
Q 030488          121 VKR  123 (176)
Q Consensus       121 ~a~  123 (176)
                      +|+
T Consensus       469 YAr  471 (549)
T KOG4660|consen  469 YAR  471 (549)
T ss_pred             hhh
Confidence            554

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.09  E-value=6.5  Score=32.58  Aligned_cols=62  Identities=15%  Similarity=0.093  Sum_probs=48.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCe-eEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESE  111 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i-~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~  111 (176)
                      ..-.+.|-|-++|.....+||...|+.|+.- =+|.|+-+      -.||..|.+...|..||.+...+
T Consensus       388 ~dlpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDd------thalaVFss~~~AaeaLt~kh~~  450 (528)
T KOG4483|consen  388 SDLPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDD------THALAVFSSVNRAAEALTLKHDW  450 (528)
T ss_pred             ccccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeec------ceeEEeecchHHHHHHhhccCce
Confidence            3356788899999999999999999999753 34555543      37999999999999999764333

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

Probab=83.81  E-value=0.14  Score=38.74  Aligned_cols=60  Identities=30%  Similarity=0.468  Sum_probs=49.6

Q ss_pred             CCCEEEEcC----CCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH
Q 030488           46 DSRSVFVGN----VDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL  105 (176)
Q Consensus        46 ~~~~i~v~~----lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~  105 (176)
                      ...+++.|+    |...++++.+.+.|++-+++..+++.++.+|+++.+.|+++.-..+.-.++
T Consensus        79 ~q~~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~  142 (267)
T KOG4454|consen   79 EQRTLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFAL  142 (267)
T ss_pred             hhcccccCCCcchhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHh
Confidence            356777787    777899999999999999999999998888999999999986655554555

>KOG4019 consensus Calcineurin-mediated signaling pathway inhibitor DSCR1 [Signal transduction mechanisms; General function prediction only]

Probab=83.77  E-value=1.1  Score=32.98  Aligned_cols=74  Identities=12%  Similarity=0.210  Sum_probs=52.1

Q ss_pred             CEEEEcCCCCCCCHH-----HHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCe-eeEEE
Q 030488           48 RSVFVGNVDYSCTPE-----EVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGR-QLKVT  120 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~-----~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~-~i~v~  120 (176)
                      .++.+.+|+..+..+     ....+|.+|-+..-..+.+.     .++.-|.|.+.+.|..|. .++...|.|. .++.-
T Consensus        11 ~~~~~c~i~~~VF~~~~~k~~~~~lFrq~n~~~~fq~lrs-----frrvRi~f~~p~~a~~a~i~~~~~~f~~~~~~k~y   85 (193)
T KOG4019|consen   11 TAIIACDIHEEVFVNREDKALFENLFRQINEDATFQLLRS-----FRRVRINFSNPEAAADARIKLHSTSFNGKNELKLY   85 (193)
T ss_pred             ceeeeecccHHhhccHHHHHHHHhHHhhhCcchHHHHHHh-----hceeEEeccChhHHHHHHHHhhhcccCCCceEEEE
Confidence            457777887764332     33455666655544444432     566789999999999999 8999999998 88888


Q ss_pred             eccCCC
Q 030488          121 VKRTNV  126 (176)
Q Consensus       121 ~a~~~~  126 (176)
                      ++....
T Consensus        86 faQ~~~   91 (193)
T KOG4019|consen   86 FAQPGH   91 (193)
T ss_pred             EccCCC
Confidence            887544

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

Probab=83.59  E-value=0.084  Score=43.49  Aligned_cols=74  Identities=22%  Similarity=0.260  Sum_probs=61.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEee-CCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRT-DKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~-~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ..+.+-|.|+|+...++-|..++.+||.++.|..+. +..   ....-|+|...+.+..|| .+++..+....++|.+-
T Consensus        79 rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~e---tavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~Yi  154 (584)
T KOG2193|consen   79 RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSE---TAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYI  154 (584)
T ss_pred             HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchH---HHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccC
Confidence            356689999999999999999999999998886533 221   223457899999999999 89999999999999875

>PF07530 PRE_C2HC: Associated with zinc fingers; InterPro: IPR006579 This domain is present in proteins found exclusively in the arthropods, including a number of Drosophila species, the silk moth and the gypsy moth

Probab=81.45  E-value=3.4  Score=25.32  Aligned_cols=61  Identities=21%  Similarity=0.342  Sum_probs=43.3

Q ss_pred             HHHHHHhhhCC-CeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccC
Q 030488           62 EEVQQHFQSCG-TVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        62 ~~l~~~f~~~G-~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~  124 (176)
                      ++|.+.|...| .|..+.-+..+ +......-||+.....+...+  ++=..++++.|+|+..+.
T Consensus         2 ~~I~~~L~~~G~~v~~i~~~~~~~~k~pl~mf~veL~p~~~~k~i--~~Ik~l~~~~V~vE~~~k   64 (68)
T PF07530_consen    2 EEIKEELKDQGHPVRNIHNMHSRNTKKPLNMFFVELEPKPNNKEI--YKIKTLCGQRVKVERPRK   64 (68)
T ss_pred             HHHHHHHHHcCCceEEEEccccCCCCCCceEEEEeeccCccccce--eehHhhCCeEEEEecCCC
Confidence            56778888877 57777777766 567778888888765553332  444578899999997753

These proteins are possibly involved in RNA binding or single strand DNA binding.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	176
3ucg_A	89	Crystal Structure Of A Rna Binding Domain Of Hypoth		3e-25
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		3e-25
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		1e-24
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		4e-08
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		2e-07
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		4e-07
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		4e-07
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		4e-07
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		4e-07
2do0_A	114	Solution Structure Of The Rna Binding Domain Of Het		1e-06
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		2e-06
2do4_A	100	Solution Structure Of The Rna Binding Domain Of Squ		2e-06
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		3e-06
2fc9_A	101	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		7e-06
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		7e-06
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		2e-05
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		2e-05
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		3e-05
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		5e-05
2cq4_A	114	Solution Structure Of Rna Binding Domain In Rna Bin		7e-05
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-04
2cpe_A	113	Solution Structure Of The Rna Recognition Motif Of		3e-04
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		3e-04
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		3e-04
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		4e-04
2dng_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		8e-04

>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 =  110 bits (276), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 51/87 (58%), Positives = 65/87 (74%), Gaps = 1/87 (1%)
Query: 44  EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQ 102
           E D+RS++VGNVDY  T EE++ HF  CG+VNRVTI  DKF G PKG+AY+EF   E+V+
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 103 EALHLNESELHGRQLKVTVKRTNVPGM 129
            +L L+ES   GRQ+KV  KRTN PG+
Sbjct: 63  TSLALDESLFRGRQIKVIPKRTNRPGI 89

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

Iteration: 1
 Score =  110 bits (276), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 51/87 (58%), Positives = 65/87 (74%), Gaps = 1/87 (1%)
Query: 44  EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQ 102
           E D+RS++VGNVDY  T EE++ HF  CG+VNRVTI  DKF G PKG+AY+EF   E+V+
Sbjct: 2   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 61
Query: 103 EALHLNESELHGRQLKVTVKRTNVPGM 129
            +L L+ES   GRQ+KV  KRTN PG+
Sbjct: 62  TSLALDESLFRGRQIKVIPKRTNRPGI 88

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

Iteration: 1
 Score =  108 bits (270), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 47/93 (50%), Positives = 68/93 (73%), Gaps = 1/93 (1%)
Query: 38  SLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFL 96
           S   ++E+D RSV+VGNVDY  T ++++ HF SCG++NR+TI  DKF G PKGYAY+EF 
Sbjct: 27  SAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFA 86
Query: 97  QSEAVQEALHLNESELHGRQLKVTVKRTNVPGM 129
           +  +V  A+ ++E+   GR +KV  KRTN+PG+
Sbjct: 87  ERNSVDAAVAMDETVFRGRTIKVLPKRTNMPGI 119

>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 = 54.3 bits (129), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 49/75 (65%), Gaps = 3/75 (4%)
Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL- 105
           R+++VGN+ YS T E+V++ F   G V  V +  D+   +PKG+ +VE +Q E+V EA+ 
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIA 60
Query: 106 HLNESELHGRQLKVT 120
            L+ ++  GR ++VT
Sbjct: 61  KLDNTDFMGRTIRVT 75

>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 = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL- 105
           RSVFVGN+ Y  T E+++  F   G V    +  D+  G+PKGY + E+   E    A+ 
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 106 HLNESELHGRQLKV 119
           +LN  E  GR L+V
Sbjct: 69  NLNGREFSGRALRV 82

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLN 108
           +VFVG +D      E++  F   G+V  V I TD+ G  KGY +V F     VQ+ +  +
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-S 69
Query: 109 ESELHGRQLKV 119
           +   HG++LK+
Sbjct: 70  QINFHGKKLKL 80

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLN 108
           +VFVG +D      E++  F   G+V  V I TD+ G  KGY +V F     VQ+ +  +
Sbjct: 12  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-S 70
Query: 109 ESELHGRQLKV 119
           +   HG++LK+
Sbjct: 71  QINFHGKKLKL 81

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLN 108
           +VFVG +D      E++  F   G+V  V I TD+ G  KGY +V F     VQ+ +  +
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-S 69
Query: 109 ESELHGRQLKV 119
           +   HG++LK+
Sbjct: 70  QINFHGKKLKL 80

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 30/80 (37%), Positives = 47/80 (58%), Gaps = 2/80 (2%)
Query: 42  REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAV 101
           +EE D R+VFVGN++     E + + F   G + +VTI  D+ G+PK + +V F   E+V
Sbjct: 12  QEEAD-RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESV 70
Query: 102 QEALH-LNESELHGRQLKVT 120
             A+  LN   L+GR + V+
Sbjct: 71  SYAIALLNGIRLYGRPINVS 90

>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein M Length = 114

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 35/103 (33%), Positives = 48/103 (46%), Gaps = 1/103 (0%)
Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF 95
           GSS A +      +VFV N+DY    +++++ F   G V R  I  DK G+ +G   V F
Sbjct: 4   GSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTF 63
Query: 96  LQS-EAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRRP 137
            QS EAVQ     N   L  R + V +    +P      P RP
Sbjct: 64  EQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERP 106

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 44/78 (56%), Gaps = 4/78 (5%)
Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHL 107
           R ++VGN+D + T + ++Q+FQ  G +  + I  DK  +   YA+VE+ QS     AL  
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQ- 59
Query: 108 NESELHGRQLKVTVKRTN 125
               L+G+Q++  + + N
Sbjct: 60  ---TLNGKQIENNIVKIN 74

>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous Cell Carcinoma Antigen Recognized By T Cells 3 Length = 100

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 45  VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFL-QSEAVQE 103
           ++   +F+  + +SCT EE+++  ++ GTV  + + T++ G+PKG AYVE+  +S+A Q 
Sbjct: 15  LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQA 74
Query: 104 ALHLNESELHGRQLKVTVKRT 124
            + ++   +    +KV +  +
Sbjct: 75  VMKMDGMTIKENIIKVAISNS 95

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/96 (26%), Positives = 52/96 (54%), Gaps = 10/96 (10%)
Query: 30  QDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRV-TIRTDKFGQPK 88
            DP A G +         +++FV  V+Y  T  ++++ F+  G + R+  + + + G+P+
Sbjct: 93  NDPNAQGDAF--------KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPR 144
Query: 89  GYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR 123
           GYA++E+     +  A  H +  ++ GR++ V V+R
Sbjct: 145 GYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180

>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 101

Iteration: 1
 Score = 46.6 bits (109), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 48/78 (61%), Gaps = 4/78 (5%)
Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
           +S+++ + N+ YS T E +Q+ F+       + +  ++ G+ KGYA++EF   E  +EAL
Sbjct: 14  ESKTLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAFIEFASFEDAKEAL 70
Query: 106 H-LNESELHGRQLKVTVK 122
           +  N+ E+ GR +++ ++
Sbjct: 71  NSCNKREIEGRAIRLELQ 88

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 46.6 bits (109), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/96 (26%), Positives = 52/96 (54%), Gaps = 10/96 (10%)
Query: 30  QDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRV-TIRTDKFGQPK 88
            DP A G +         +++FV  V+Y  T  ++++ F+  G + R+  + + + G+P+
Sbjct: 93  NDPNAQGDAF--------KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPR 144
Query: 89  GYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR 123
           GYA++E+     +  A  H +  ++ GR++ V V+R
Sbjct: 145 GYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/76 (28%), Positives = 46/76 (60%), Gaps = 3/76 (3%)
Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ-PKGYAYVEFLQSEAVQEALHLN 108
           +FVG + ++C   E++++F+  G V  V +  D   Q P+G+ ++ F   ++V +A++++
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 109 ESELHGRQLKVTVKRT 124
             ++ G+  KV VKR 
Sbjct: 73  FHDIMGK--KVEVKRA 86

>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 = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 40  ANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQS 98
           A++ E D+   FVG + +  + ++++ +F   G V   TI+ D   G+ +G+ ++ F  +
Sbjct: 4   ASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDA 63
Query: 99  EAVQEALHLNESELHGRQL 117
            +V++ L   E  L GR +
Sbjct: 64  ASVEKVLDQKEHRLDGRVI 82

>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 = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG-QPKGYAYVEFLQSEAVQEALH- 106
           +V+V N+ +S T  ++ + F   G V +VTI  DK   + KG A++ FL  ++ Q     
Sbjct: 18  TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 107 LNESELHGRQLKVTV 121
           +N  +L GR +K ++
Sbjct: 78  INNKQLFGRVIKASI 92

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 18/69 (26%), Positives = 41/69 (59%), Gaps = 1/69 (1%)
Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLN 108
           +F+G + +  T ++++ +F   G V   T++ D   G+ +G+ +V F +SE+V + +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 109 ESELHGRQL 117
           E +L+G+ +
Sbjct: 62  EHKLNGKVI 70

>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 23 Length = 114

Iteration: 1
 Score = 43.1 bits (100), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 43  EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG-QPKGYAYVEFLQSEAV 101
           EE D+R+VF   +     P +++  F + G V  V I +D+   + KG AYVEF + ++V
Sbjct: 21  EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 80
Query: 102 QEALHLNESELHG 114
             A+ L    L G
Sbjct: 81  PLAIGLTGQRLLG 93

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/105 (28%), Positives = 48/105 (45%), Gaps = 7/105 (6%)
Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVE 94
           GSS   ++  +   VFVG++    T E+++  F   G ++   +  D   G+ KGY +V 
Sbjct: 4   GSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVS 63
Query: 95  FLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPN 138
           F      + A+ H+    L GRQ+     RTN    K   P  P+
Sbjct: 64  FYNKLDAENAIVHMGGQWLGGRQI-----RTNWATRKPPAPSGPS 103

>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing Sarcoma(Ews) Protein Length = 113

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 30/105 (28%), Positives = 52/105 (49%), Gaps = 10/105 (9%)
Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTV--NRVT------IRTDK- 83
            + GSS    E+ D+ +++V  ++ S T +++   F+ CG V  N+ T      I  DK 
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60
Query: 84  FGQPKGYAYVEFLQSEAVQEALH-LNESELHGRQLKVTVKRTNVP 127
            G+PKG A V +      + A+   +  +  G +LKV++ R   P
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 105

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG-QPKGYAYVEFLQSEAVQEAL-HL 107
           V+VG++ Y    + ++Q F   G +  + +  D    + KG+A+VE+   EA Q AL  +
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 108 NESELHGRQLKV 119
           N   L GR +KV
Sbjct: 91  NSVMLGGRNIKV 102

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVE 94
           GSS  NR   D+ ++ V N+       ++Q+ F+  G+++R+ +  DK  GQ KG+A++ 
Sbjct: 4   GSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFIS 63
Query: 95  FLQSEAVQEAL 105
           F + E    A+
Sbjct: 64  FHRREDAARAI 74

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG-QPKGYAYVEFLQSEAVQEAL-HL 107
           V+VG++ Y    + ++Q F   G +  + +  D    + KG+A+VE+   EA Q AL  +
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 108 NESELHGRQLKV 119
           N   L GR +KV
Sbjct: 76  NSVMLGGRNIKV 87

>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 4h Length = 103

Iteration: 1
 Score = 39.7 bits (91), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 25/88 (28%), Positives = 46/88 (52%), Gaps = 10/88 (11%)
Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIR---TDKFGQPKGYAYVEFLQSEAVQEAL 105
           + +VGN+ ++    ++   F+     +   +R   TDKF   KG+ YVEF + ++++EAL
Sbjct: 17  TAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKF---KGFCYVEFDEVDSLKEAL 73
Query: 106 HLNESELHGRQLKVTVKRTNVPGMKQHR 133
             + + L  R L+V +      G KQ +
Sbjct: 74  TYDGALLGDRSLRVDIAE----GRKQDK 97

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	176
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	9e-48
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-44
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-39
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	7e-29
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	5e-26
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-25
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-23
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-23
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-17
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-23
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	7e-22
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	9e-22
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-21
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-21
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	3e-21
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	3e-21
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-21
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	4e-21
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-21
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	9e-21
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-20
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-20
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-20
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-20
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	4e-20
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	4e-20
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	4e-20
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	4e-20
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	6e-20
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	8e-20
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	8e-20
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-19
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-19
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-19
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-19
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-19
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-19
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	5e-19
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	6e-19
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	8e-19
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-15
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	9e-19
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	9e-19
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-18
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-18
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-16
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-18
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-15
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	4e-18
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	4e-18
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	4e-18
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	5e-18
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	5e-18
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	5e-18
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	5e-18
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	6e-18
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-18
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-12
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	7e-18
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	8e-18
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	8e-18
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	9e-18
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	9e-18
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	9e-18
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	9e-18
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-17
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-17
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-17
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-17
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-17
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	3e-17
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	3e-17
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	5e-17
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	6e-17
1x4e_A	85	RNA binding motif, single-stranded interacting pro	6e-17
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	7e-17
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	7e-17
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	8e-17
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	8e-17
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-16
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-16
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-16
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	9e-16
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-16
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-16
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-12
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-16
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-16
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	4e-16
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-16
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-16
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-14
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-14
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	6e-16
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-12
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	6e-16
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-16
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-15
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	1e-15
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-15
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-14
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-15
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-15
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	4e-15
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-15
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	3e-15
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	5e-15
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	6e-15
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	6e-15
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	8e-15
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	9e-15
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-14
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-14
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-14
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-14
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-14
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-14
2div_A	99	TRNA selenocysteine associated protein; structural	4e-14
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	5e-14
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	5e-14
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	5e-14
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	7e-14
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	7e-14
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	7e-14
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	6e-12
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	7e-14
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-13
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-13
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-13
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-12
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-13
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-13
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-13
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-13
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-13
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	5e-13
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	6e-13
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-13
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	6e-13
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	8e-13
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	9e-13
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-12
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-12
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-12
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-12
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-12
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-12
2dis_A	109	Unnamed protein product; structural genomics, RRM	5e-12
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	6e-12
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	6e-12
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	8e-12
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-11
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-11
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-11
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-09
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-11
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-11
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	8e-11
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-10
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-10
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-09
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-09
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	5e-10
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	9e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-09
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-09
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-09
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	6e-09
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	8e-09
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	3e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-07
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	1e-07
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	3e-07
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	8e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-06
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-06
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	7e-06
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-05
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	1e-05
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	2e-05
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	7e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	3e-04

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score =  150 bits (381), Expect = 9e-48
 Identities = 51/121 (42%), Positives = 78/121 (64%), Gaps = 3/121 (2%)

Query: 11  EATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQS 70
            A  ++  H+K+     ++  P     S   ++E+D RSV+VGNVDY  T ++++ HF S
Sbjct: 2   IAPCMQTTHSKMTAGAYTEGPPQP--LSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSS 59

Query: 71  CGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGM 129
           CG++NR+TI  DKF G PKGYAY+EF +  +V  A+ ++E+   GR +KV  KRTN+PG+
Sbjct: 60  CGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRTNMPGI 119

Query: 130 K 130
            
Sbjct: 120 S 120

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score =  141 bits (358), Expect = 1e-44
 Identities = 51/87 (58%), Positives = 65/87 (74%), Gaps = 1/87 (1%)

Query: 44  EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQ 102
           E D+RS++VGNVDY  T EE++ HF  CG+VNRVTI  DKF G PKG+AY+EF   E+V+
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 103 EALHLNESELHGRQLKVTVKRTNVPGM 129
            +L L+ES   GRQ+KV  KRTN PG+
Sbjct: 63  TSLALDESLFRGRQIKVIPKRTNRPGI 89

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score =  129 bits (326), Expect = 2e-39
 Identities = 31/118 (26%), Positives = 52/118 (44%), Gaps = 8/118 (6%)

Query: 23  GNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD 82
           G+  +S + P        + EE D+R+VF   +     P +++  F + G V  V I +D
Sbjct: 1   GSSGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISD 60

Query: 83  KF-GQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNP 139
           +   + KG AYVEF + ++V  A+ L    L G  + V   +         + R   P
Sbjct: 61  RNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAE-------KNRLSGP 111

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score =  101 bits (254), Expect = 7e-29
 Identities = 30/88 (34%), Positives = 49/88 (55%), Gaps = 1/88 (1%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAY 92
           ++G S +   +E   R+VFVGN++     E + + F   G + +VTI  D+ G+PK + +
Sbjct: 2   SSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGF 61

Query: 93  VEFLQSEAVQEALH-LNESELHGRQLKV 119
           V F   E+V  A+  LN   L+GR + V
Sbjct: 62  VCFKHPESVSYAIALLNGIRLYGRPINV 89

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 94.8 bits (236), Expect = 5e-26
 Identities = 26/116 (22%), Positives = 45/116 (38%), Gaps = 3/116 (2%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRTDKFGQPKGYA 91
            + GSS             + N+ +S T  +V Q  +      N V +  D  GQ  G A
Sbjct: 1   GSSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQA 60

Query: 92  YVEFLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNPFMVYQSRG 147
            V+F   +  +++  L+  +L+GR+    V    +  M++     P       S G
Sbjct: 61  LVQFKNEDDARKSERLHRKKLNGRE--AFVHVVTLEDMREIEKNPPAQGKSGPSSG 114

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 93.1 bits (232), Expect = 2e-25
 Identities = 16/77 (20%), Positives = 40/77 (51%)

Query: 43  EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQ 102
           E     ++F+GN++ + +  E++         N + +   + G  + + YV+F  +E ++
Sbjct: 13  ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLE 72

Query: 103 EALHLNESELHGRQLKV 119
           +AL L   ++ G ++K+
Sbjct: 73  KALELTGLKVFGNEIKL 89

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 88.6 bits (220), Expect = 2e-23
 Identities = 28/106 (26%), Positives = 50/106 (47%), Gaps = 10/106 (9%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNR--------VTIRTDKF 84
            + GSS    E+ D+ +++V  ++ S T +++   F+ CG V          + I  DK 
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60

Query: 85  -GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPG 128
            G+PKG A V +      + A+   +  +  G +LKV++ R   P 
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 106

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 90.0 bits (224), Expect = 2e-23
 Identities = 17/93 (18%), Positives = 42/93 (45%), Gaps = 8/93 (8%)

Query: 27  ASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ 86
            S     +        E     ++F+GN++ + +  E++         N + +   + G 
Sbjct: 1   GSHMVEGS--------ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGT 52

Query: 87  PKGYAYVEFLQSEAVQEALHLNESELHGRQLKV 119
            + + YV+F  +E +++AL L   ++ G ++K+
Sbjct: 53  NRKFGYVDFESAEDLEKALELTGLKVFGNEIKL 85

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 74.6 bits (184), Expect = 2e-17
 Identities = 17/80 (21%), Positives = 41/80 (51%), Gaps = 5/80 (6%)

Query: 41  NREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEA 100
           +++   +R++   N+ ++ T +E+++ F+    +  V     + G+ KG AY+EF     
Sbjct: 93  SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEAD 148

Query: 101 VQEAL-HLNESELHGRQLKV 119
            ++ L     +E+ GR + +
Sbjct: 149 AEKNLEEKQGAEIDGRSVSL 168

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 86.9 bits (216), Expect = 4e-23
 Identities = 21/89 (23%), Positives = 45/89 (50%), Gaps = 1/89 (1%)

Query: 32  PAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYA 91
            +           ++   +F+  + +SCT EE+++  ++ GTV  + + T++ G+PKG A
Sbjct: 2   SSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLA 61

Query: 92  YVEFLQSEAVQEAL-HLNESELHGRQLKV 119
           YVE+       +A+  ++   +    +KV
Sbjct: 62  YVEYENESQASQAVMKMDGMTIKENIIKV 90

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 83.8 bits (208), Expect = 7e-22
 Identities = 26/89 (29%), Positives = 46/89 (51%), Gaps = 2/89 (2%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYA 91
           ++G S ++        +V+V N+ +S T  ++ + F   G V +VTI  DK   + KG A
Sbjct: 2   SSGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVA 61

Query: 92  YVEFLQSEAVQEALH-LNESELHGRQLKV 119
           ++ FL  ++ Q     +N  +L GR +K 
Sbjct: 62  FILFLDKDSAQNCTRAINNKQLFGRVIKA 90

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 83.9 bits (208), Expect = 9e-22
 Identities = 32/106 (30%), Positives = 48/106 (45%), Gaps = 1/106 (0%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAY 92
            + GSS A +      +VFV N+DY    +++++ F   G V R  I  DK G+ +G   
Sbjct: 1   GSSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGT 60

Query: 93  VEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRP 137
           V F QS    +A+   N   L  R + V +    +P      P RP
Sbjct: 61  VTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERP 106

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 84.2 bits (208), Expect = 1e-21
 Identities = 26/98 (26%), Positives = 46/98 (46%), Gaps = 1/98 (1%)

Query: 23  GNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRT 81
           G+ MAS       G    + +  +   V +  + + CT EE+ Q F     V N +T+  
Sbjct: 18  GSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPV 77

Query: 82  DKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV 119
           D  G+  G A+V+F   E  ++AL  ++  +  R ++V
Sbjct: 78  DPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEV 115

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 82.7 bits (205), Expect = 2e-21
 Identities = 22/94 (23%), Positives = 40/94 (42%), Gaps = 10/94 (10%)

Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVN--------RVTIRTDKF-GQ 86
           G    +    D+ ++FV  +  + T E V  +F+  G +          + + TD+  G+
Sbjct: 2   GHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK 61

Query: 87  PKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV 119
            KG A V F    + + A+   +  E  G  +KV
Sbjct: 62  LKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKV 95

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 82.4 bits (204), Expect = 3e-21
 Identities = 25/109 (22%), Positives = 39/109 (35%), Gaps = 17/109 (15%)

Query: 40  ANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSE 99
            +      RSVFV          ++ ++F + G V  V +  DK      +A VE     
Sbjct: 1   GSSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK----GVFAIVEMGDVG 56

Query: 100 AVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNPFMVYQSRGA 148
           A +  L  ++  L G +L+V             RPR    F    S+  
Sbjct: 57  AREAVLSQSQHSLGGHRLRV-------------RPREQKEFQSPASKSP 92

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 82.3 bits (204), Expect = 3e-21
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 3/77 (3%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK--FGQPKGYAYVEFLQSEAVQEA 104
             + F+GN+ Y  T E +++ F+    ++ V +  +     + KG+ Y EF   +++  A
Sbjct: 19  PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 77

Query: 105 LHLNESELHGRQLKVTV 121
           L LNE  L  R+++V V
Sbjct: 78  LSLNEESLGNRRIRVDV 94

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 82.3 bits (204), Expect = 4e-21
 Identities = 24/91 (26%), Positives = 47/91 (51%), Gaps = 3/91 (3%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF--GQPKGY 90
            + GSS +   +    + F+GN+ Y  T E +++ F+    ++ V +  +     + KG+
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGF 59

Query: 91  AYVEFLQSEAVQEALHLNESELHGRQLKVTV 121
            Y EF   +++  AL LNE  L  ++++V V
Sbjct: 60  GYAEFEDLDSLLSALSLNEESLGNKRIRVDV 90

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 82.3 bits (204), Expect = 4e-21
 Identities = 27/107 (25%), Positives = 46/107 (42%), Gaps = 7/107 (6%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYA 91
            + GSS    E     +V+VG +D   +   + + F   G V    +  D+  GQ +GY 
Sbjct: 1   GSSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYG 60

Query: 92  YVEFLQSEAVQEALH-LNESELHGRQLKVTVKRTNVPGMKQHRPRRP 137
           +VEFL  E    A+  ++  +L+G+ ++V     N           P
Sbjct: 61  FVEFLSEEDADYAIKIMDMIKLYGKPIRV-----NKASAHNKNLSGP 102

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 82.0 bits (203), Expect = 4e-21
 Identities = 26/100 (26%), Positives = 50/100 (50%), Gaps = 2/100 (2%)

Query: 22  VGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRT 81
           +G+        AA  ++   +       ++VG++ ++ T + ++  F+  G +  + +  
Sbjct: 1   MGHHHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMM 60

Query: 82  DKF-GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV 119
           D   G+ KGY ++ F  SE  ++AL  LN  EL GR +KV
Sbjct: 61  DSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV 100

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 80.7 bits (200), Expect = 9e-21
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEA 104
            S  +FV N+ Y+ + E++++ F + G ++ +    D    +PKG+A+V F+  E   +A
Sbjct: 7   GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66

Query: 105 LH-LNESELHGRQLKV 119
              ++     GR L V
Sbjct: 67  YAEVDGQVFQGRMLHV 82

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 80.9 bits (200), Expect = 1e-20
 Identities = 25/92 (27%), Positives = 41/92 (44%), Gaps = 8/92 (8%)

Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVE 94
           GSS    +  + ++VF+ N+ +    E + +  Q  G +  V +         KG A+ +
Sbjct: 4   GSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQ 63

Query: 95  FLQSEAVQEAL-------HLNESELHGRQLKV 119
           F+  EA Q+ L            +L GRQLKV
Sbjct: 64  FMTQEAAQKCLAAASLEAEGGGLKLDGRQLKV 95

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 79.8 bits (197), Expect = 3e-20
 Identities = 15/82 (18%), Positives = 35/82 (42%)

Query: 42  REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAV 101
           + +V +RSV++       T +++++  +  G V  + +R       KG  +V F   E+ 
Sbjct: 6   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 65

Query: 102 QEALHLNESELHGRQLKVTVKR 123
           ++ +     +     L +  K 
Sbjct: 66  KKFVETPGQKYKETDLLILFKD 87

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 81.0 bits (200), Expect = 3e-20
 Identities = 27/98 (27%), Positives = 46/98 (46%), Gaps = 2/98 (2%)

Query: 24  NEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK 83
           N      D  +GGS  +       R ++VG +      + +   F   G +  + I  D 
Sbjct: 40  NCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY 99

Query: 84  F-GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV 119
              + +G+A+VEF  +E    A+ ++NESEL GR ++V
Sbjct: 100 ETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 137

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 79.6 bits (197), Expect = 3e-20
 Identities = 25/109 (22%), Positives = 49/109 (44%), Gaps = 9/109 (8%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYA 91
            + GSS  NR   D+ ++ V N+       ++Q+ F+  G+++R+ +  DK  GQ KG+A
Sbjct: 1   GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60

Query: 92  YVEFLQSEAVQEALH-LNESELHGRQLKVTVKRTNVPGMKQHRPRRPNP 139
           ++ F + E    A+  ++        L V   + +           P+ 
Sbjct: 61  FISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS-------TNSGPSS 102

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 79.6 bits (197), Expect = 4e-20
 Identities = 23/90 (25%), Positives = 45/90 (50%), Gaps = 2/90 (2%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYA 91
            + GSS          + +VGN+ ++    ++   F+    +  V +  DK   + KG+ 
Sbjct: 1   GSSGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFC 59

Query: 92  YVEFLQSEAVQEALHLNESELHGRQLKVTV 121
           YVEF + ++++EAL  + + L  R L+V +
Sbjct: 60  YVEFDEVDSLKEALTYDGALLGDRSLRVDI 89

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 79.4 bits (196), Expect = 4e-20
 Identities = 23/101 (22%), Positives = 48/101 (47%), Gaps = 3/101 (2%)

Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRTDKFGQPKGYAYVE 94
           GSS  + +  +   V +  + + C+ EE+ Q F     V N +T+  D  G+  G A+V+
Sbjct: 4   GSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQ 63

Query: 95  FLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPR 135
           F   E  ++AL  ++  +  R   + + +++   ++   P 
Sbjct: 64  FASQEIAEKALKKHKERIGHRY--IEIFKSSRAEVRTSGPS 102

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 79.6 bits (197), Expect = 4e-20
 Identities = 27/106 (25%), Positives = 50/106 (47%), Gaps = 7/106 (6%)

Query: 35  GGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYV 93
           G S  +  +     ++ V N+ Y  +P+ +++ F+  G V  V I  +     P+G+A+V
Sbjct: 1   GSSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFV 60

Query: 94  EFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPN 138
            F      Q+A   ++ +EL GR+L+V V R       +     P+
Sbjct: 61  RFHDRRDAQDAEAAMDGAELDGRELRVQVARY-----GRRDLSGPS 101

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 79.6 bits (197), Expect = 4e-20
 Identities = 29/100 (29%), Positives = 48/100 (48%), Gaps = 7/100 (7%)

Query: 42  REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEA 100
             +   RSVFVGN+ Y  T E+++  F   G V    +  D+  G+PKGY + E+   E 
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 101 VQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNP 139
              A+ +LN  E  GR L+V     +    ++++    + 
Sbjct: 63  ALSAMRNLNGREFSGRALRV-----DNAASEKNKEELKSL 97

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 78.8 bits (195), Expect = 6e-20
 Identities = 27/106 (25%), Positives = 46/106 (43%), Gaps = 12/106 (11%)

Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVE 94
           GSS ++      R ++VG +      + +   F   G +  + I  D    + +G+A+VE
Sbjct: 1   GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60

Query: 95  FLQSEAVQEALH-LNESELHGRQLKVTVKRTNVPGMKQHRPRRPNP 139
           F  +E    A+  +NESEL GR ++V             +P R   
Sbjct: 61  FELAEDAAAAIDNMNESELFGRTIRV----------NLAKPMRIKE 96

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 79.0 bits (195), Expect = 8e-20
 Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 1/89 (1%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAY 92
           ++G S        D   V V  + +S    +V+  F     V+ V +  D  G+  G   
Sbjct: 2   SSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGL 60

Query: 93  VEFLQSEAVQEALHLNESELHGRQLKVTV 121
           V+FL  +   EAL  N   +  R ++V+ 
Sbjct: 61  VKFLSPQDTFEALKRNRMLMIQRYVEVSP 89

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 78.4 bits (194), Expect = 8e-20
 Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 3/95 (3%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL 105
           SR V++G++ Y  T E++     + G V  + +  D   G+ KGYA++EF   E+   A+
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61

Query: 106 -HLNESELHGRQLKV-TVKRTNVPGMKQHRPRRPN 138
            +LN  +L  R LK      +++ G+        +
Sbjct: 62  RNLNGYQLGSRFLKCGYSSNSDISGVSLEHHHHHH 96

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 77.6 bits (192), Expect = 2e-19
 Identities = 24/95 (25%), Positives = 46/95 (48%), Gaps = 7/95 (7%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEA 104
            S  ++VG++ ++ T + ++  F+  G ++ + +  D   G+ KGY ++ F  SE  + A
Sbjct: 4   GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63

Query: 105 LH-LNESELHGRQLKVTVKRTNVPGMKQHRPRRPN 138
           L  LN  EL GR ++V          +      P+
Sbjct: 64  LEQLNGFELAGRPMRV-----GHVTERLDGGSGPS 93

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 77.3 bits (191), Expect = 2e-19
 Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 3/89 (3%)

Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF 95
           GSS ++       +V +    ++ T + V +          + I  +  G   GY +V+F
Sbjct: 1   GSSGSSGT--TCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDF 57

Query: 96  LQSEAVQEALHLNESELHGRQLKVTVKRT 124
              E V++AL  N   + GR ++V  +++
Sbjct: 58  SNEEEVKQALKCNREYMGGRYIEVFREKS 86

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 77.7 bits (192), Expect = 2e-19
 Identities = 28/105 (26%), Positives = 54/105 (51%), Gaps = 6/105 (5%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAY 92
            + GSS  +    +S+++ + N+ YS T E +Q+ F+    +    +  ++ G+ KGYA+
Sbjct: 1   GSSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIK---VPQNQNGKSKGYAF 57

Query: 93  VEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRR 136
           +EF   E  +EAL   N+ E+ GR +++ ++     G     P  
Sbjct: 58  IEFASFEDAKEALNSCNKREIEGRAIRLELQGP--RGSPNSGPSS 100

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 77.3 bits (191), Expect = 3e-19
 Identities = 18/91 (19%), Positives = 45/91 (49%), Gaps = 4/91 (4%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF--GQPKGY 90
            + GSS    ++  +  + V N+ +     E+++ F + G +  V +       G  +G+
Sbjct: 1   GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60

Query: 91  AYVEFLQSEAVQEALH--LNESELHGRQLKV 119
            +V+F+  +  ++A +   + + L+GR+L +
Sbjct: 61  GFVDFITKQDAKKAFNALCHSTHLYGRRLVL 91

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 76.5 bits (189), Expect = 3e-19
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL- 105
           +  +FV N+ +  T + ++  F  CG V    I+ +  G+ KG   V+F   E  + A  
Sbjct: 8   ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVKFESPEVAERACR 66

Query: 106 HLNESELHGRQLKVTVKR 123
            +N  +L GR++ V + R
Sbjct: 67  MMNGMKLSGREIDVRIDR 84

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 76.4 bits (189), Expect = 4e-19
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEA 104
             R ++VG +      + +   F   G +  + I  D    + +G+A+VEF  +E    A
Sbjct: 6   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65

Query: 105 L-HLNESELHGRQLKV 119
           + ++NESEL GR ++V
Sbjct: 66  IDNMNESELFGRTIRV 81

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 76.5 bits (189), Expect = 5e-19
 Identities = 22/105 (20%), Positives = 47/105 (44%), Gaps = 7/105 (6%)

Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVE 94
           GSS ++    D   +FVG + +    + ++Q F   G ++ V +  D+   + +G+ +V 
Sbjct: 1   GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 60

Query: 95  FLQSEAVQEALH-LNESELHGRQLKVTVKRTNVPGMKQHRPRRPN 138
           F   +  ++A+  +N   + GRQ++V                 P+
Sbjct: 61  FENIDDAKDAMMAMNGKSVDGRQIRVDQAGK-----SSDNRSGPS 100

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 76.1 bits (188), Expect = 6e-19
 Identities = 30/93 (32%), Positives = 51/93 (54%), Gaps = 8/93 (8%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALH 106
           R+++VGN+ YS T E+V++ F   G V  V +  D+   +PKG+ +VE  Q E+V EA+ 
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIA 60

Query: 107 -LNESELHGRQLKVTVKRTNVPGMKQHRPRRPN 138
            L+ ++  GR ++VT         K+      +
Sbjct: 61  KLDNTDFMGRTIRVTEANP-----KKSLEHHHH 88

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 78.9 bits (195), Expect = 8e-19
 Identities = 30/123 (24%), Positives = 50/123 (40%), Gaps = 5/123 (4%)

Query: 26  MASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF- 84
           M   Q    G ++           V+VG++ Y    + ++Q F   G +  + +  D   
Sbjct: 7   MTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVT 66

Query: 85  GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV---TVKRTNVPGMKQHRPRRPNPF 140
            + KG+A+VE+   EA Q AL  +N   L GR +KV   +      P + Q         
Sbjct: 67  MKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFN 126

Query: 141 MVY 143
            +Y
Sbjct: 127 RIY 129

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 69.3 bits (170), Expect = 3e-15
 Identities = 32/138 (23%), Positives = 63/138 (45%), Gaps = 11/138 (7%)

Query: 9   EEEA-TALRQMHAKV--GNEM----ASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTP 61
            E A  AL QM++ +  G  +     S    A         E      ++V +V    + 
Sbjct: 80  PEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSD 139

Query: 62  EEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV 119
           ++++  F++ G +   T+  D   G+ KGY ++E+ ++++ Q+A+  +N  +L G+ L+ 
Sbjct: 140 DDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLR- 198

Query: 120 TVKRTNVPGMKQHRPRRP 137
            V +   P M    P  P
Sbjct: 199 -VGKAVTPPMPLLTPATP 215

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 76.1 bits (188), Expect = 9e-19
 Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 2/87 (2%)

Query: 34  AGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYV 93
           + GSS    ++   R+++VGN+    T   + Q F   G      + T+       Y +V
Sbjct: 2   SSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFV 60

Query: 94  EFLQSEAVQEAL-HLNESELHGRQLKV 119
           EF +      AL  +N  ++ G+++KV
Sbjct: 61  EFYEHRDAAAALAAMNGRKILGKEVKV 87

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 76.8 bits (189), Expect = 9e-19
 Identities = 20/111 (18%), Positives = 41/111 (36%), Gaps = 3/111 (2%)

Query: 23  GNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRT 81
           G+  +S + P+    S +         V++  + +    + V   F+    V + + I  
Sbjct: 1   GSSGSSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAY 60

Query: 82  DKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQH 132
              G+  G  +VEF      + AL  ++  +  R   + V      GM + 
Sbjct: 61  GPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRF--IQVHPITKKGMLEK 109

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 76.3 bits (188), Expect = 1e-18
 Identities = 21/88 (23%), Positives = 40/88 (45%), Gaps = 10/88 (11%)

Query: 42  REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVN--------RVTIRTDKF-GQPKGYAY 92
           ++  D+ ++FV  +  + T E V  +F+  G +          + + TD+  G+ KG A 
Sbjct: 2   QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61

Query: 93  VEFLQSEAVQEAL-HLNESELHGRQLKV 119
           V F    + + A+   +  E  G  +KV
Sbjct: 62  VSFDDPPSAKAAIDWFDGKEFSGNPIKV 89

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 78.1 bits (193), Expect = 1e-18
 Identities = 19/100 (19%), Positives = 43/100 (43%), Gaps = 8/100 (8%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVT------IRTDKFGQPKGYAYVEFLQSEA 100
           +R ++VGN+ +  T E +   F +   +  +T      +   +  Q K +A++EF   + 
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 101 VQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNPF 140
             +A+  +     G+ LK  ++R +           P+ +
Sbjct: 64  TTQAMAFDGIIFQGQSLK--IRRPHDYQPLPGMSENPSVY 101

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 72.4 bits (178), Expect = 2e-16
 Identities = 20/103 (19%), Positives = 41/103 (39%), Gaps = 2/103 (1%)

Query: 19  HAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVT 78
           H        S+         ++      +  +F+G +      ++V++   S G +    
Sbjct: 86  HDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFN 145

Query: 79  IRTD-KFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV 119
           +  D   G  KGYA+ E++      +A+  LN  +L  ++L V
Sbjct: 146 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 188

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 76.5 bits (189), Expect = 2e-18
 Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 6/79 (7%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVT------IRTDKFGQPKGYAYVEFLQSEA 100
           +R ++VGN+ +  T E +   F +   +  +T      +   +  Q K +A++EF   + 
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 101 VQEALHLNESELHGRQLKV 119
             +A+  +     G+ LK+
Sbjct: 64  TTQAMAFDGIIFQGQSLKI 82

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 68.8 bits (169), Expect = 2e-15
 Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 2/72 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL-HL 107
           +F+G +      ++V++   S G +    +  D   G  KGYA+ E++      +A+  L
Sbjct: 97  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156

Query: 108 NESELHGRQLKV 119
           N  +L  ++L V
Sbjct: 157 NGMQLGDKKLLV 168

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 74.3 bits (183), Expect = 4e-18
 Identities = 19/90 (21%), Positives = 43/90 (47%), Gaps = 2/90 (2%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRTDKFGQPKGYA 91
            + GSS ++  +     + V N+ ++ + +E+   F     +   V ++ ++ G P G A
Sbjct: 1   GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 92  YVEFLQSEAVQEALH-LNESELHGRQLKVT 120
            V F   +    A+  LN+  +  R++K++
Sbjct: 61  MVAFESRDEATAAVIDLNDRPIGSRKVKLS 90

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 77.5 bits (190), Expect = 4e-18
 Identities = 26/149 (17%), Positives = 54/149 (36%), Gaps = 4/149 (2%)

Query: 32  PAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGT--VNRVTIRTDKF-GQPK 88
                 ++         ++++GN+ +  T E++ +   S G   +  +    ++  GQ K
Sbjct: 53  GKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSK 112

Query: 89  GYAYVEFLQSEAVQEALH-LNESELHGRQLKVTVKRTNVPGMKQHRPRRPNPFMVYQSRG 147
           G+A V      + ++ +  L + ELHG+   VT          + + R+          G
Sbjct: 113 GFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEG 172

Query: 148 AIIPPFLYSPYGYGKIPRFRMPMRYSPYY 176
              PP   S   + +  R R     +   
Sbjct: 173 KAGPPGGSSRAAFPQGGRGRGRFPGAVPG 201

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 74.4 bits (183), Expect = 4e-18
 Identities = 22/102 (21%), Positives = 38/102 (37%), Gaps = 3/102 (2%)

Query: 34  AGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYV 93
           + GSS ++ +      V +  + Y  T  ++   F       RV I     G+  G A V
Sbjct: 2   SSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADV 60

Query: 94  EFLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPR 135
           EF   E    A+  +++ +  R   V +   +  G     P 
Sbjct: 61  EFATHEDAVAAMAKDKANMQHR--YVELFLNSTAGTSGSGPS 100

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 74.2 bits (183), Expect = 5e-18
 Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 45  VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQE 103
           V+   +FV  V    T E++   F   G +  + +  D+  G  KGY  VE+   +  Q 
Sbjct: 21  VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 80

Query: 104 AL-HLNESELHGRQLKV 119
           A+  LN  +L G+ + V
Sbjct: 81  AMEGLNGQDLMGQPISV 97

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 75.6 bits (186), Expect = 5e-18
 Identities = 30/151 (19%), Positives = 63/151 (41%), Gaps = 8/151 (5%)

Query: 15  LRQMHAKVGNEMASKQDPAAGGSSLANREEVD-SRSVFVGNVDYSCTPEEVQQHFQSCGT 73
           L+ + +    E++  +D    G +    + +  S +++VGN+ +  T E++ + F   G 
Sbjct: 6   LKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGD 65

Query: 74  VNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQ 131
           + ++ +  DK      G+ +VE+      + A+ ++N + L  R ++         G + 
Sbjct: 66  IKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQY 125

Query: 132 HRPRRPNPFMVYQSRGAIIPPFLYSPYGYGK 162
            R R        Q R      +     GYGK
Sbjct: 126 GRGRSGG-----QVRDEYRQDYDAGRGGYGK 151

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 75.3 bits (185), Expect = 5e-18
 Identities = 24/119 (20%), Positives = 44/119 (36%), Gaps = 6/119 (5%)

Query: 27  ASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGT--VNRVTIRTDKF 84
               +         +       +V+VG+  +  T +++ Q  +S G   V  +    ++ 
Sbjct: 35  PKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRA 94

Query: 85  -GQPKGYAYVEFLQSEAVQEALH-LNESELHGRQLKVTV--KRTNVPGMKQHRPRRPNP 139
            GQ KGYA V      +V + L  L    L+G ++ V    ++       Q R R    
Sbjct: 95  NGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKRECVR 153

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 73.6 bits (181), Expect = 5e-18
 Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 6/79 (7%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVT------IRTDKFGQPKGYAYVEFLQSEA 100
           +R ++VGN+ +  T E +   F +   +  +T      +   +  Q K +A++EF   + 
Sbjct: 6   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 65

Query: 101 VQEALHLNESELHGRQLKV 119
             +A+  +     G+ LK+
Sbjct: 66  TTQAMAFDGIIFQGQSLKI 84

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 73.4 bits (181), Expect = 6e-18
 Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 2/86 (2%)

Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVE 94
           GSS        +  + V  +    T  ++++ F   G +  V+I  D+   + +G+A+V 
Sbjct: 4   GSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 63

Query: 95  FLQSEAVQEAL-HLNESELHGRQLKV 119
           F   +  +EA    N  EL GR+++V
Sbjct: 64  FENVDDAKEAKERANGMELDGRRIRV 89

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 75.6 bits (187), Expect = 6e-18
 Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH- 106
           R ++VGN+D + T + ++Q+FQ  G +  + I  DK  +   YA+VE+ QS     AL  
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60

Query: 107 LNESELHGRQLKV 119
           LN  ++    +K+
Sbjct: 61  LNGKQIENNIVKI 73

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 59.5 bits (145), Expect = 7e-12
 Identities = 24/119 (20%), Positives = 50/119 (42%), Gaps = 16/119 (13%)

Query: 9   EEEA-TALRQMHAKV--GNE---MASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPE 62
             +A  AL+ ++ K    N      + Q   +      N        +FVG+++ +   E
Sbjct: 51  SHDANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTFN--------LFVGDLNVNVDDE 102

Query: 63  EVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV 119
            ++  F+   +     +  D + G  +GY +V F   +  Q A+  +   +L+GR L++
Sbjct: 103 TLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 73.4 bits (181), Expect = 7e-18
 Identities = 24/88 (27%), Positives = 39/88 (44%), Gaps = 6/88 (6%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAY 92
            + GSS   +       +FVGN+    T EE+++ F+  G    V I  D     KG+ +
Sbjct: 1   GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGF 55

Query: 93  VEFLQSEAVQEALH-LNESELHGRQLKV 119
           +        + A   L+   L G+QL+V
Sbjct: 56  IRLETRTLAEIAKVELDNMPLRGKQLRV 83

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 73.0 bits (180), Expect = 8e-18
 Identities = 18/80 (22%), Positives = 40/80 (50%), Gaps = 3/80 (3%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF--GQPKGYAYVEFLQSEAVQEA 104
              V +G +  + T + + + F + G +  + +  ++      KGYAYVEF   +  ++A
Sbjct: 4   PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA 63

Query: 105 L-HLNESELHGRQLKVTVKR 123
           L H++  ++ G+++  T   
Sbjct: 64  LKHMDGGQIDGQEITATAVL 83

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 73.4 bits (181), Expect = 8e-18
 Identities = 30/96 (31%), Positives = 48/96 (50%), Gaps = 5/96 (5%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH 106
             +VFVG +D      E++  F   G+V  V I TD+ G  KGY +V F     VQ+ + 
Sbjct: 9   PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68

Query: 107 LNESELHGRQLKV--TVKRTNVPGMKQHRPRRPNPF 140
            ++   HG++LK+   +++ N+     H   RP  F
Sbjct: 69  -SQINFHGKKLKLGPAIRKQNLS--TYHVQPRPLIF 101

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 73.1 bits (180), Expect = 9e-18
 Identities = 20/88 (22%), Positives = 42/88 (47%), Gaps = 2/88 (2%)

Query: 34  AGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRTDKFGQPKGYAY 92
           + GSS A+  +     + V N+ ++ + +E+   F     +   V ++ ++ G P G A 
Sbjct: 2   SSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61

Query: 93  VEFLQSEAVQEAL-HLNESELHGRQLKV 119
           V F   +    A+  LN+  +  R++K+
Sbjct: 62  VAFESRDEATAAVIDLNDRPIGSRKVKL 89

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 73.5 bits (181), Expect = 9e-18
 Identities = 21/106 (19%), Positives = 43/106 (40%), Gaps = 7/106 (6%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAY 92
            + GSS  +  +   + + V N+ +     +++Q F   G +  V I  ++    KG+ +
Sbjct: 1   GSSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-RGSKGFGF 59

Query: 93  VEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRP 137
           V F  S     A   L+ + + GR+++V          +      P
Sbjct: 60  VTFENSADADRAREKLHGTVVEGRKIEVNNATA-----RVMTNSGP 100

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 73.0 bits (180), Expect = 9e-18
 Identities = 19/92 (20%), Positives = 40/92 (43%), Gaps = 9/92 (9%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGT--VNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL 105
           ++++GN+ +  T E++ +   S G   +  +    ++  GQ KG+A V      + ++ +
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 106 H-LNESELHGRQLKVTVKRTNVPGMKQHRPRR 136
             L + ELHG+   V           +H    
Sbjct: 63  DLLPKRELHGQNPVV-----TPSNKLEHHHHH 89

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 73.5 bits (181), Expect = 9e-18
 Identities = 21/98 (21%), Positives = 43/98 (43%), Gaps = 2/98 (2%)

Query: 24  NEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK 83
           +     ++          +  V+   +FV ++      +E+Q+ F   G +  + +  D+
Sbjct: 3   HSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDR 62

Query: 84  F-GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV 119
             G  KGYA VE+   +    A   LN +E+ G+ ++V
Sbjct: 63  RTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 100

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 73.8 bits (181), Expect = 1e-17
 Identities = 25/115 (21%), Positives = 42/115 (36%), Gaps = 8/115 (6%)

Query: 28  SKQDPAAGGSSLANREEVDSRS--VFVGNVDYSCTPEEVQQHFQSCGTV----NRVTIRT 81
           S      G S+   +         V +  + ++ T EEV   F     +      +   T
Sbjct: 2   SSGSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVT 61

Query: 82  DKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRR 136
              G+P G A+V F   E  Q AL  ++  L  R   + + R+    ++Q   R 
Sbjct: 62  YPDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRY--IELFRSTAAEVQQVLNRF 114

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 73.1 bits (180), Expect = 1e-17
 Identities = 17/80 (21%), Positives = 41/80 (51%), Gaps = 5/80 (6%)

Query: 41  NREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEA 100
           +++   +R++   N+ ++ T +E+++ F+    +    +  D  G+ KG AY+EF     
Sbjct: 10  SKKVRAARTLLAKNLSFNITEDELKEVFEDALEI--RLVSQD--GKSKGIAYIEFKSEAD 65

Query: 101 VQEAL-HLNESELHGRQLKV 119
            ++ L     +E+ GR + +
Sbjct: 66  AEKNLEEKQGAEIDGRSVSL 85

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 74.0 bits (182), Expect = 1e-17
 Identities = 25/114 (21%), Positives = 49/114 (42%), Gaps = 10/114 (8%)

Query: 27  ASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-G 85
             +Q       +  N E    R++ V  +  +    +++Q F+  G +  V I  D+   
Sbjct: 22  LQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETR 81

Query: 86  QPKGYAYVEFLQSEAVQEALH-LNESELHGRQLKVTVKRTNVPGMKQHRPRRPN 138
           Q +GY +V+F    + Q+A+  LN   +  ++LKV +  +          +RP 
Sbjct: 82  QSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAAS--------GHQRPG 127

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 73.2 bits (180), Expect = 2e-17
 Identities = 26/100 (26%), Positives = 43/100 (43%), Gaps = 5/100 (5%)

Query: 45  VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQE 103
           V+   +FV  V    T E++   F   G +  + +  D+  G  KGY  VE+   +  Q 
Sbjct: 20  VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 79

Query: 104 AL-HLNESELHGRQLKV---TVKRTNVPGMKQHRPRRPNP 139
           A+  LN  +L G+ + V    V+       +  R R  +P
Sbjct: 80  AMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRSP 119

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 73.2 bits (180), Expect = 2e-17
 Identities = 24/114 (21%), Positives = 51/114 (44%), Gaps = 9/114 (7%)

Query: 27  ASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-G 85
             +    +        +     S+ V N+ Y  +P+ +++ F+  G V  V I  D++  
Sbjct: 27  GQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTK 86

Query: 86  QPKGYAYVEFLQSEAVQEALH-LNESELHGRQLKVTVKRTNVPGMKQHRPRRPN 138
           + +G+A+V F      ++A+  ++ + L GR+L+V + R         RP   +
Sbjct: 87  ESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG-------RPPDSH 133

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 72.6 bits (178), Expect = 3e-17
 Identities = 23/105 (21%), Positives = 41/105 (39%), Gaps = 4/105 (3%)

Query: 41  NREEVDSRSVFVGNVDYSCTPEEVQQHFQSC---GTVNRVTIRTDKFGQPKGYAYVEFLQ 97
             E  +   V +  + +SC+ E+VQ     C     V  V     + G+  G A+VE   
Sbjct: 11  GPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELES 70

Query: 98  SEAVQEALHLNESELHGRQLKVT-VKRTNVPGMKQHRPRRPNPFM 141
            + V+ AL  +   +  R ++V    RT +  + +H         
Sbjct: 71  EDDVKLALKKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGP 115

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 71.9 bits (177), Expect = 3e-17
 Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 108
           + V N+D+  +  ++Q+ F   GT+ +  +  D+ G+  G A V F +     +A+   N
Sbjct: 32  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 91

Query: 109 ESELHGRQLKVTV 121
              L GR + + +
Sbjct: 92  GVPLDGRPMNIQL 104

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 71.5 bits (176), Expect = 5e-17
 Identities = 25/107 (23%), Positives = 45/107 (42%), Gaps = 10/107 (9%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYA 91
            + GSS  N     S+++FV  +    T E +++ F       R  I TD+  G  KG+ 
Sbjct: 1   GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFG 57

Query: 92  YVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRP 137
           +V+F   E  + A   + + E+ G ++ +   +      K      P
Sbjct: 58  FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKP-----KGEGGSGP 99

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 73.0 bits (179), Expect = 6e-17
 Identities = 28/136 (20%), Positives = 59/136 (43%), Gaps = 10/136 (7%)

Query: 6   KEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVD-SRSVFVGNVDYSCTPEEV 64
           K  ++ A           ++         G     +  +V+   S+ V N+ Y  +P+ +
Sbjct: 28  KVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTL 87

Query: 65  QQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK 122
           ++ F+  G V  V I  D++  + +G+A+V F      ++A+  ++ + L GR+L+V + 
Sbjct: 88  RRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 147

Query: 123 RTNVPGMKQHRPRRPN 138
           R         RP   +
Sbjct: 148 RYG-------RPPDSH 156

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 70.6 bits (174), Expect = 6e-17
 Identities = 17/81 (20%), Positives = 35/81 (43%), Gaps = 2/81 (2%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEA 104
            S  +++  +    T +++ +  Q  G +       DK   + KGY +V+F    A Q+A
Sbjct: 4   GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63

Query: 105 L-HLNESELHGRQLKVTVKRT 124
           +  L  S +  +  K +   +
Sbjct: 64  VTALKASGVQAQMAKQSGPSS 84

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 71.6 bits (176), Expect = 7e-17
 Identities = 23/118 (19%), Positives = 53/118 (44%), Gaps = 7/118 (5%)

Query: 23  GNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD 82
           G+  +S     + G++ + +E  +  ++F+ ++      +++ Q F   G V    +  D
Sbjct: 1   GSSGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID 60

Query: 83  KF-GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPN 138
           K     K + +V +    + Q A+  +N  ++  ++LKV +KR+     K      P+
Sbjct: 61  KQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRS-----KNDSKSGPS 113

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 72.6 bits (178), Expect = 7e-17
 Identities = 31/140 (22%), Positives = 56/140 (40%), Gaps = 11/140 (7%)

Query: 1   MKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCT 60
            K R    +         + +V NE   + +P    S       V+   +FV ++     
Sbjct: 33  RKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRS-------VEGWILFVTSIHEEAQ 85

Query: 61  PEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLK 118
            +E+Q+ F   G +  + +  D+  G  KGYA VE+   +    A   LN +E+ G+ ++
Sbjct: 86  EDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ 145

Query: 119 V--TVKRTNVPGMKQHRPRR 136
           V     +      K  + RR
Sbjct: 146 VDWCFVKGPKRVKKSEKRRR 165

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 71.3 bits (175), Expect = 8e-17
 Identities = 15/107 (14%), Positives = 35/107 (32%), Gaps = 7/107 (6%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL 105
            + V    ++ +     ++   +  G V  V I       +  G A V F  +   +E +
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65

Query: 106 -HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNPFMVYQSRGAIIP 151
            +L+ + + G  +        +    Q R +     +        +P
Sbjct: 66  KNLHLTSVMGNIIHA-----QLDIKGQQRMKYYELIVNGSYTPQTVP 107

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 71.8 bits (176), Expect = 8e-17
 Identities = 19/101 (18%), Positives = 36/101 (35%), Gaps = 1/101 (0%)

Query: 19  HAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVT 78
            + + +    +Q     G S    +      V +  + Y  T  ++   F       RV 
Sbjct: 18  GSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVH 76

Query: 79  IRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV 119
           I     G+  G A VEF   E    A+  + + +  R +++
Sbjct: 77  IEIGPDGRVTGEADVEFATHEEAVAAMSKDRANMQHRYIEL 117

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 70.8 bits (174), Expect = 1e-16
 Identities = 25/109 (22%), Positives = 45/109 (41%), Gaps = 10/109 (9%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYA 91
            + GSS   ++  +   VFVG++    T E+++  F   G ++   +  D   G+ KGY 
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60

Query: 92  YVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNP 139
           +V F      + A+  +    L GRQ++              +P  P  
Sbjct: 61  FVSFFNKWDAENAIQQMGGQWLGGRQIRT--------NWATRKPPAPKS 101

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 70.0 bits (172), Expect = 2e-16
 Identities = 23/104 (22%), Positives = 50/104 (48%), Gaps = 3/104 (2%)

Query: 35  GGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYV 93
           G S  +  ++ D+  +F+G +  +   ++++  F+  G +  +T+  D+F G  KG A++
Sbjct: 1   GSSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60

Query: 94  EFLQSEAVQEAL-HLNESE-LHGRQLKVTVKRTNVPGMKQHRPR 135
            + + E+  +A   L+E + L G    + VK  +        P 
Sbjct: 61  TYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRGGSGPS 104

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 70.0 bits (172), Expect = 2e-16
 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 5/79 (6%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ----PKGYAYVEFLQSEAV 101
            S  +F+ N+++S T E ++  F   G +   TI   K         G+ +VE+ + E  
Sbjct: 4   GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63

Query: 102 QEALH-LNESELHGRQLKV 119
           Q+AL  L    + G +L+V
Sbjct: 64  QKALKQLQGHTVDGHKLEV 82

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 70.5 bits (173), Expect = 2e-16
 Identities = 20/113 (17%), Positives = 44/113 (38%), Gaps = 7/113 (6%)

Query: 27  ASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ 86
             + D    G       E  ++ + V N+D+  +  ++Q+ F   GT+ +  +  D+ G+
Sbjct: 16  KWQHDLFDSGCGGGEGVETGAK-LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR 74

Query: 87  PKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPN 138
             G A V F +     +A+       L GR + + +  + +           +
Sbjct: 75  SLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQID-----LEHHHH 122

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 73.5 bits (181), Expect = 2e-16
 Identities = 20/121 (16%), Positives = 43/121 (35%), Gaps = 18/121 (14%)

Query: 7   EMEEEA-TALRQMHAKV-GNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEV 64
              + A  A+ + H  V  NE+                  +   ++++ N   S T   +
Sbjct: 89  ARYDGALAAITKTHKVVGQNEI--------------IVSHLTECTLWMTNFPPSYTQRNI 134

Query: 65  QQHFQSCGTVNR-VTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK 122
           +   Q    V   + + + +F   + +AY++    E  +  +  LN  ++ G  L   V 
Sbjct: 135 RDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS 194

Query: 123 R 123
            
Sbjct: 195 N 195

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 73.1 bits (180), Expect = 4e-16
 Identities = 17/102 (16%), Positives = 40/102 (39%), Gaps = 7/102 (6%)

Query: 26  MASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG 85
             + +      +   NRE     +V V N+  S    +V ++F+ CG +  V +      
Sbjct: 25  GLTSKKANE--ALTRNREL---TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL-K 78

Query: 86  QPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVT-VKRTNV 126
           +   +A +EF + +    A+      +   ++ V+ +    +
Sbjct: 79  KNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHLTECTL 120

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 71.9 bits (177), Expect = 9e-16
 Identities = 20/118 (16%), Positives = 52/118 (44%), Gaps = 6/118 (5%)

Query: 9   EEEA-TALRQMHAKV--GNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEE-V 64
           +E+A   + +++     G  + +K       S   +   ++ R + + N+      E  +
Sbjct: 169 KEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLL 228

Query: 65  QQHFQSCGTVNRVTIRTDKF--GQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVT 120
           ++ F+  G++ ++ I   +         A++ F   ++ + AL +N S L  R++ V+
Sbjct: 229 RESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVS 286

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 69.7 bits (171), Expect = 3e-16
 Identities = 21/101 (20%), Positives = 45/101 (44%), Gaps = 3/101 (2%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
               +F+G ++     + ++  F   G ++ V +  D+  + +G+A++ F      + A 
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAA 65

Query: 106 -HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNPFMVYQS 145
             +N   LHG+ +K  V++   P  +    RRP      +S
Sbjct: 66  KDMNGKSLHGKAIK--VEQAKKPSFQSGGRRRPPASSRNRS 104

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 71.1 bits (175), Expect = 3e-16
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL 105
           + ++ V  +    T  E+   F++ G +N   I  D   G   GYA+V+F      Q A+
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62

Query: 106 -HLNESELHGRQLKV 119
             LN   +  ++LKV
Sbjct: 63  KVLNGITVRNKRLKV 77

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 61.4 bits (150), Expect = 1e-12
 Identities = 28/121 (23%), Positives = 56/121 (46%), Gaps = 14/121 (11%)

Query: 9   EEEA-TALRQMHAK-VGNEMA--SKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEV 64
           E ++  A++ ++   V N+    S   P          E +   +++V N+  + T +++
Sbjct: 55  EMDSQRAIKVLNGITVRNKRLKVSYARPG--------GESIKDTNLYVTNLPRTITDDQL 106

Query: 65  QQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK 122
              F   G++ +  I  DK  G+P+G A+V + + E  QEA+  LN     G    ++V+
Sbjct: 107 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 166

Query: 123 R 123
            
Sbjct: 167 L 167

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 68.8 bits (169), Expect = 3e-16
 Identities = 20/86 (23%), Positives = 44/86 (51%), Gaps = 7/86 (8%)

Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF 95
           GSS ++ E+    +++VG +  + T  +++ HF   G +  +T+        +  A+++F
Sbjct: 1   GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQF 55

Query: 96  LQSEAVQEALH--LNESELHGRQLKV 119
              +A + A     N+  ++GR+L V
Sbjct: 56  ATRQAAEVAAEKSFNKLIVNGRRLNV 81

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 70.1 bits (172), Expect = 3e-16
 Identities = 26/112 (23%), Positives = 48/112 (42%), Gaps = 13/112 (11%)

Query: 30  QDPAAGGSSLANREEVD-SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQP 87
           Q    G   + NR   D +  + V  +    T  ++++ F   G +  V+I  D+   + 
Sbjct: 28  QQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRS 87

Query: 88  KGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPN 138
           +G+A+V F   +  +EA    N  EL GR+++V               +RP+
Sbjct: 88  RGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS----------ITKRPH 129

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 69.6 bits (171), Expect = 4e-16
 Identities = 22/111 (19%), Positives = 43/111 (38%), Gaps = 4/111 (3%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYA 91
           +       ++++     +FVG + Y  T   ++++F+  G +    + TD+  G+ +GY 
Sbjct: 3   SGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYG 62

Query: 92  YVEFLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNPFMV 142
           +V      A + A       + GR  K  V      G K    +      V
Sbjct: 63  FVTMADRAAAERACKDPNPIIDGR--KANVNLA-YLGAKPRSLQTGFAIGV 110

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 68.3 bits (168), Expect = 4e-16
 Identities = 17/75 (22%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL 105
           + ++FVG+++ +   E ++  F+   +     +  D   G  +GY +V F   +  Q A+
Sbjct: 1   TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60

Query: 106 H-LNESELHGRQLKV 119
             +   +L+GR L++
Sbjct: 61  DSMQGQDLNGRPLRI 75

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 72.7 bits (179), Expect = 5e-16
 Identities = 22/129 (17%), Positives = 45/129 (34%), Gaps = 11/129 (8%)

Query: 9   EEEA-TALRQMHAKVGNEMASKQ---DPAAGGSSLANREEVDSRSVFVGNVDYSCT-PEE 63
           ++ A  A   +    G  +  +         G        + SR + V  +       + 
Sbjct: 147 KDSAARAKSDLL---GKPLGPRTLYVHWTDAGQ--LTPALLHSRCLCVDRLPPGFNDVDA 201

Query: 64  VQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK 122
           + +   +  +     +   + GQ KG+A +E+  +E  +EA    +   L G  L+V+  
Sbjct: 202 LCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 261

Query: 123 RTNVPGMKQ 131
               PG   
Sbjct: 262 APGPPGRSM 270

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 68.1 bits (167), Expect = 2e-14
 Identities = 20/96 (20%), Positives = 42/96 (43%), Gaps = 7/96 (7%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTI-RTDKFGQPKGYAYVEFLQSEAVQEAL-HL 107
           + V N+  S T ++ ++  +  G++ R  +  +++ GQ KGY + E+++ ++   A   L
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157

Query: 108 NESELHGRQLKVTVKRTNVPGMKQHRPRRPNPFMVY 143
               L  R L V     +     Q  P   +   + 
Sbjct: 158 LGKPLGPRTLYV-----HWTDAGQLTPALLHSRCLC 188

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 68.1 bits (167), Expect = 2e-14
 Identities = 18/85 (21%), Positives = 36/85 (42%), Gaps = 7/85 (8%)

Query: 42  REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAV 101
           R+  + R + +  +    T +EV              ++     + KG A+V  L  E  
Sbjct: 17  RQFRNRRKILIRGLPGDVTNQEVHDLLSDYE------LKYCFVDKYKGTAFVTLLNGEQA 70

Query: 102 QEAL-HLNESELHGRQLKVTVKRTN 125
           + A+   ++S L  R+L V ++ T+
Sbjct: 71  EAAINAFHQSRLRERELSVQLQPTD 95

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 70.3 bits (173), Expect = 6e-16
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 2/75 (2%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL 105
             ++ V  +  + T EE +  F S G +    +  DK  GQ  GY +V ++  +  ++A+
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 106 H-LNESELHGRQLKV 119
           + LN   L  + +KV
Sbjct: 62  NTLNGLRLQTKTIKV 76

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 60.3 bits (147), Expect = 4e-12
 Identities = 23/120 (19%), Positives = 51/120 (42%), Gaps = 14/120 (11%)

Query: 9   EEEA-TALRQMH-AKVGNEMA--SKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEV 64
            ++A  A+  ++  ++  +    S   P+           +   +++V  +  + T +E+
Sbjct: 54  PKDAEKAINTLNGLRLQTKTIKVSYARPS--------SASIRDANLYVSGLPKTMTQKEL 105

Query: 65  QQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK 122
           +Q F   G +    I  D+  G  +G  ++ F +    +EA+  LN  +  G    +TVK
Sbjct: 106 EQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK 165

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 68.9 bits (169), Expect = 6e-16
 Identities = 17/106 (16%), Positives = 45/106 (42%), Gaps = 8/106 (7%)

Query: 34  AGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYV 93
           +GG  +      +   ++VGN+      ++++  F   G +  + ++  +      +A+V
Sbjct: 9   SGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR--GGPPFAFV 66

Query: 94  EFLQSEAVQEALH-LNESELHGRQLKVTVKRTNVPGMKQHRPRRPN 138
           EF      ++A++  +  +  G +L+V   R+      +     P+
Sbjct: 67  EFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS-----GRGTGSGPS 107

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 68.1 bits (167), Expect = 8e-16
 Identities = 13/75 (17%), Positives = 29/75 (38%), Gaps = 6/75 (8%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
              + ++GN+ +  T  ++   FQ+ G +       +     KG  ++++   E     +
Sbjct: 26  RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-----KGCCFIKYDTHEQAAVCI 80

Query: 106 -HLNESELHGRQLKV 119
             L      GR L+ 
Sbjct: 81  VALANFPFQGRNLRT 95

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 68.4 bits (168), Expect = 1e-15
 Identities = 15/88 (17%), Positives = 34/88 (38%), Gaps = 1/88 (1%)

Query: 37  SSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFL 96
           + +A ++E D  ++++ N+  S   +E++   +  G V    I  D  G  +G  +    
Sbjct: 15  AQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARME 74

Query: 97  QSEAVQEAL-HLNESELHGRQLKVTVKR 123
            +E  +  + H N   +           
Sbjct: 75  STEKCEAVIGHFNGKFIKTPPGVSAPTE 102

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 68.3 bits (167), Expect = 1e-15
 Identities = 25/108 (23%), Positives = 47/108 (43%), Gaps = 5/108 (4%)

Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSC---GTVNRVTIRTDKFGQPKGYAY 92
           GS L   E  D   +    + +SCT E+V   F  C      N +    ++ G+ +G A 
Sbjct: 1   GSKLEE-EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDAL 59

Query: 93  VEFLQSEAVQEALHLNESELHGRQLKVT-VKRTNVPGMKQHRPRRPNP 139
           +E    + VQ+AL  +   +  R ++V  +   +V  + +    + +P
Sbjct: 60  IEMESEQDVQKALEKHRMYMGQRYVEVYEINNEDVDALMKSLQVKSSP 107

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 69.6 bits (171), Expect = 2e-15
 Identities = 24/99 (24%), Positives = 43/99 (43%), Gaps = 4/99 (4%)

Query: 42  REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEA 100
           +E    R +F+G + +  T E ++ HF+  GT+    +  D    + +G+ +V +   E 
Sbjct: 8   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 67

Query: 101 VQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNP 139
           V  A++    ++ GR   V  KR  V      RP     
Sbjct: 68  VDAAMNARPHKVDGR--VVEPKRA-VSREDSQRPGAHLT 103

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 67.3 bits (165), Expect = 2e-14
 Identities = 25/137 (18%), Positives = 54/137 (39%), Gaps = 4/137 (2%)

Query: 3   IRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPE 62
           +    +EE   A+     KV   +   +   +   S      +  + +FVG +       
Sbjct: 60  VTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEH 119

Query: 63  EVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTV 121
            ++ +F+  G +  + I TD+  G+ +G+A+V F   ++V + +      ++G   +V  
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 179

Query: 122 ---KRTNVPGMKQHRPR 135
              K+         R R
Sbjct: 180 ALSKQEMASASSSQRGR 196

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 67.3 bits (165), Expect = 2e-15
 Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 2/85 (2%)

Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF 95
           GS +    +   + + V N+ +     +++Q F   G +  V I  ++    KG+ +V F
Sbjct: 18  GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-RGSKGFGFVTF 76

Query: 96  LQSEAVQEAL-HLNESELHGRQLKV 119
             S     A   L+ + + GR+++V
Sbjct: 77  ENSADADRAREKLHGTVVEGRKIEV 101

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 68.3 bits (168), Expect = 3e-15
 Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 3/83 (3%)

Query: 42  REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEA 100
            E+  +  +FVG +     P+E ++ F   GT+    +  DK  GQ +G+ +V +  ++A
Sbjct: 82  DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141

Query: 101 VQEALHLNESELHGRQLKVTVKR 123
           V         +   R+  + +KR
Sbjct: 142 VDRVCQNKFIDFKDRK--IEIKR 162

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 67.9 bits (167), Expect = 4e-15
 Identities = 21/92 (22%), Positives = 48/92 (52%), Gaps = 5/92 (5%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEA 104
           +S  +F+G +++  T + ++++F   GTV  + I  D   G+ +G+ ++ F +  +V E 
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61

Query: 105 LHLNESELHGRQLKVTVKRTNVPGMKQHRPRR 136
           +   +  L G+   +  KR  +P  +Q +  +
Sbjct: 62  VK-TQHILDGK--VIDPKRA-IPRDEQDKTGK 89

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 67.0 bits (164), Expect = 3e-15
 Identities = 20/91 (21%), Positives = 39/91 (42%), Gaps = 3/91 (3%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL- 105
           +R +++ N+ Y  T EE+   F   G + ++ +      + +G AYV +      + A+ 
Sbjct: 8   NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVD 65

Query: 106 HLNESELHGRQLKVTVKRTNVPGMKQHRPRR 136
           HL+   +  R L V     N    K    ++
Sbjct: 66  HLSGFNVSNRYLVVLYYNANRAFQKMDTKKK 96

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 66.9 bits (164), Expect = 3e-15
 Identities = 29/105 (27%), Positives = 45/105 (42%), Gaps = 3/105 (2%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYA 91
           ++G S + N    +   +FVG +D+S T E ++ +F   G V    I  DK   Q +G+ 
Sbjct: 2   SSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFG 61

Query: 92  YVEFLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRR 136
           +V+F     V   L      L GR   +  K     GM+   P  
Sbjct: 62  FVKFKDPNCVGTVLASRPHTLDGR--NIDPKPCTPRGMQPSGPSS 104

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 66.6 bits (163), Expect = 5e-15
 Identities = 19/98 (19%), Positives = 42/98 (42%), Gaps = 6/98 (6%)

Query: 23  GNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD 82
           G+  +S          + N+    + +V+ G +    T + ++Q F   G +  + +  +
Sbjct: 1   GSSGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE 60

Query: 83  KFGQPKGYAYVEFLQSEAVQEALH-LNESELHGRQLKV 119
                KGY++V F   E+   A+  +N + + G  +K 
Sbjct: 61  -----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKC 93

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 66.6 bits (163), Expect = 6e-15
 Identities = 20/94 (21%), Positives = 43/94 (45%), Gaps = 2/94 (2%)

Query: 32  PAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGY 90
            AA  ++    E  +  ++F+ ++    T  ++   F   G V    +  DK     K +
Sbjct: 25  AAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCF 84

Query: 91  AYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR 123
            +V F   ++ Q A+  +N  ++  ++LKV +K+
Sbjct: 85  GFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 68.3 bits (166), Expect = 6e-15
 Identities = 14/75 (18%), Positives = 31/75 (41%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHL 107
           RSV++       T +++++  +  G V  + +R       KG  +V F   E+ ++ +  
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET 169

Query: 108 NESELHGRQLKVTVK 122
              +     L +  K
Sbjct: 170 PGQKYKETDLLILFK 184

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 66.6 bits (162), Expect = 8e-15
 Identities = 23/102 (22%), Positives = 39/102 (38%), Gaps = 5/102 (4%)

Query: 23  GNEMASKQDPAAGGSSLANREE--VDSRSVFVGNVDYSCTPEEVQQHFQSC---GTVNRV 77
           G+ MAS       G           +   V +  + +SC+ E+VQ     C        V
Sbjct: 18  GSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGV 77

Query: 78  TIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV 119
                + G+  G A+VE    + V+ AL  +   +  R ++V
Sbjct: 78  HFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEV 119

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 65.7 bits (161), Expect = 9e-15
 Identities = 22/95 (23%), Positives = 41/95 (43%), Gaps = 2/95 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 108
           +F+ N+D S   + +   F + G +    +  D+    KGY +V F   EA + A+  +N
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMN 66

Query: 109 ESELHGRQLKVTVKRTNVPGMKQHRPRRPNPFMVY 143
              L+ R++ V   ++      +   R      VY
Sbjct: 67  GMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVY 101

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 65.3 bits (160), Expect = 1e-14
 Identities = 26/103 (25%), Positives = 54/103 (52%), Gaps = 8/103 (7%)

Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVE 94
           GSS        S  +FVG + ++C   E++++F+  G V  V +  D    +P+G+ ++ 
Sbjct: 1   GSS--GSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFIT 58

Query: 95  FLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRRP 137
           F   ++V +A++++  ++ G++  V VKR   P  +  +   P
Sbjct: 59  FEDEQSVDQAVNMHFHDIMGKK--VEVKRA-EP--RDSKSSGP 96

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 65.0 bits (159), Expect = 2e-14
 Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 8/92 (8%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH-L 107
            V+VGN+       E+++ F   G +  V I  +    P G+A+VEF      ++A+  L
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGL 57

Query: 108 NESELHGRQLKVTVKRTNVPGMKQHRPRRPNP 139
           +   + G +++V +        ++ R  RP  
Sbjct: 58  DGKVICGSRVRVELST---GMPRRSRFDRPPA 86

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 66.4 bits (162), Expect = 2e-14
 Identities = 21/108 (19%), Positives = 44/108 (40%), Gaps = 2/108 (1%)

Query: 27  ASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ 86
             + D    G       E  ++ + V N+D+  +  ++Q+ F   GT+ +  +  D+ G+
Sbjct: 69  KWQHDLFDSGCGGGEGVETGAK-LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR 127

Query: 87  PKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHR 133
             G A V F +     +A+       L GR + + +  + +     H 
Sbjct: 128 SLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHH 175

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 64.6 bits (158), Expect = 2e-14
 Identities = 19/96 (19%), Positives = 37/96 (38%), Gaps = 8/96 (8%)

Query: 25  EMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF 84
             +S   P           E+ +  +FV          E+ + F   G +  V I     
Sbjct: 9   HHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI----- 63

Query: 85  GQPKGYAYVEFLQSEAVQEALH-LNESELHGRQLKV 119
               G+A+VEF ++E+  +A+  ++      + L+V
Sbjct: 64  --LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEV 97

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 63.7 bits (156), Expect = 3e-14
 Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 2/73 (2%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALH- 106
            VFVG++    T   +   F   G ++   +  D   G+ KGY +V F      + A+  
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 107 LNESELHGRQLKV 119
           +    L GRQ++ 
Sbjct: 68  MGGQWLGGRQIRT 80

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 63.8 bits (156), Expect = 3e-14
 Identities = 16/74 (21%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH- 106
             +++GN+  + T ++++Q F              +     GYA+V++        A+  
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLP-----LAGQVLLKSGYAFVDYPDQNWAIRAIET 63

Query: 107 LN-ESELHGRQLKV 119
           L+ + ELHG+ ++V
Sbjct: 64  LSGKVELHGKIMEV 77

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 63.9 bits (156), Expect = 4e-14
 Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 3/80 (3%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCG-TVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQE 103
            + S+++G+++       + + F + G TV  V I  ++  G P GY +VEF      ++
Sbjct: 8   MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEK 67

Query: 104 ALH-LNESELHGRQLKVTVK 122
            LH +N   L G       K
Sbjct: 68  CLHKINGKPLPGATPAKRFK 87

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 63.8 bits (156), Expect = 5e-14
 Identities = 22/107 (20%), Positives = 46/107 (42%), Gaps = 13/107 (12%)

Query: 36  GSSLANREEVDSRS---VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAY 92
           GSS ++ + +       ++V N+D     E +++ F   GT+    +  +  G+ KG+ +
Sbjct: 1   GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGF 59

Query: 93  VEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPN 138
           V F   E   +A+  +N   +  + L V         + Q +  R +
Sbjct: 60  VCFSSPEEATKAVTEMNGRIVATKPLYV--------ALAQRKEERQS 98

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 63.5 bits (155), Expect = 5e-14
 Identities = 13/89 (14%), Positives = 33/89 (37%), Gaps = 8/89 (8%)

Query: 39  LANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGT--VNRVTIRTDKF-GQPKGYAYVEF 95
           + +       ++ + N+      + +        +  VN + +  DK   Q +G+A+V+ 
Sbjct: 1   MGHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQL 60

Query: 96  LQSEAVQEAL-HLNESE----LHGRQLKV 119
             +    + L  L        + G+ + V
Sbjct: 61  SSAMDASQLLQILQSLHPPLKIDGKTIGV 89

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 63.4 bits (155), Expect = 5e-14
 Identities = 24/106 (22%), Positives = 46/106 (43%), Gaps = 12/106 (11%)

Query: 36  GSSLANREE---VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAY 92
           GSS ++ +E      + ++V N+  S + E +++ F +        ++     + + YA+
Sbjct: 1   GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK-----KIRDYAF 55

Query: 93  VEFLQSEAVQEALH-LNESELHGRQLKVTVKRTNVPGMKQHRPRRP 137
           V F   E   EA+  LN   L G  ++VT+ +   P  K       
Sbjct: 56  VHFSNREDAVEAMKALNGKVLDGSPIEVTLAK---PVDKDSSGPSS 98

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 63.0 bits (154), Expect = 7e-14
 Identities = 26/103 (25%), Positives = 48/103 (46%), Gaps = 15/103 (14%)

Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF 95
           GSS ++ +   S  + VGN+  +CT +E++  F+  G V    I        K YA+V  
Sbjct: 1   GSSGSSGKA--STKLHVGNISPTCTNQELRAKFEEYGPVIECDI-------VKDYAFVHM 51

Query: 96  LQSEAVQEALH-LNESELHGRQLKVTVKRTNVPGMKQHRPRRP 137
            ++E   EA+  L+ +E  G+++ V +  +     +      P
Sbjct: 52  ERAEDAVEAIRGLDNTEFQGKRMHVQLSTS-----RLRTASGP 89

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 63.0 bits (154), Expect = 7e-14
 Identities = 22/95 (23%), Positives = 42/95 (44%), Gaps = 16/95 (16%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
           ++  +FVGNV  +CT +E++  F+  G V    +        K YA+V   +    + A+
Sbjct: 8   NTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAI 60

Query: 106 H-LNESELHGRQLKVTVKRTNVPGMKQHRPRRPNP 139
             LN  E+ G+++ V +             ++  P
Sbjct: 61  AQLNGKEVKGKRINVELSTK--------GQKKSGP 87

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 65.8 bits (161), Expect = 7e-14
 Identities = 20/95 (21%), Positives = 39/95 (41%), Gaps = 10/95 (10%)

Query: 27  ASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-G 85
               +P+A              S++VG++    T   + + F   G +  + +  D    
Sbjct: 3   LGSMNPSA--------PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITR 54

Query: 86  QPKGYAYVEFLQSEAVQEALH-LNESELHGRQLKV 119
           +  GYAYV F Q    + AL  +N   + G+ +++
Sbjct: 55  RSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRI 89

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 60.4 bits (147), Expect = 6e-12
 Identities = 32/158 (20%), Positives = 60/158 (37%), Gaps = 23/158 (14%)

Query: 9   EEEA-TALRQMH-AKVGNE----MASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPE 62
             +A  AL  M+   +  +    M S++DP+   S + N        +F+ N+D S   +
Sbjct: 67  PADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN--------IFIKNLDKSIDNK 118

Query: 63  EVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV 121
            +   F + G +    +  D+    KGY +V F   EA + A+  +N   L+ R++ V  
Sbjct: 119 ALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177

Query: 122 KRTNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYG 159
            ++      +   R    +           P      G
Sbjct: 178 FKSRKEREAELGARAKEFYPYDV-------PDYAGSSG 208

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 63.0 bits (154), Expect = 7e-14
 Identities = 21/94 (22%), Positives = 36/94 (38%), Gaps = 13/94 (13%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
               +F+GN+    T +E++  F+  G V    I        K Y +V      A ++A+
Sbjct: 7   GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDI-------IKNYGFVHIEDKTAAEDAI 59

Query: 106 H-LNESELHGRQLKVTVKRTNVPGMKQHRPRRPN 138
             L+  +LHG  + V          K      P+
Sbjct: 60  RNLHHYKLHGVNINV-----EASKNKSKASSGPS 88

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 62.3 bits (152), Expect = 2e-13
 Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 4/84 (4%)

Query: 34  AGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYV 93
           + GSS +       R +FVG ++   + E+V + FQ  G ++  T+     G  KG A+V
Sbjct: 2   SSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFV 61

Query: 94  EFLQSEAVQEALHLNESELHGRQL 117
           +F      Q A+      LHG Q 
Sbjct: 62  KFSSHTEAQAAI----HALHGSQT 81

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 62.6 bits (152), Expect = 2e-13
 Identities = 27/100 (27%), Positives = 43/100 (43%), Gaps = 8/100 (8%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEV---QQHFQSCGTVNRVTIRTDKFG---- 85
            + GSS A+   V    VFV  +       EV    ++F   G +++V I          
Sbjct: 1   GSSGSSGASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQ 60

Query: 86  QPKGYAYVEFLQSEAVQEALH-LNESELHGRQLKVTVKRT 124
            P   AYV +++SE    A+  +N   + GR LK ++  T
Sbjct: 61  GPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTT 100

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 63.8 bits (156), Expect = 2e-13
 Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 4/78 (5%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQP---KGYAYVEFLQSEAVQ 102
           D+  +FVG V  + + +++++ F+  G V  + +  D+   P   KG  +V F   +A  
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 103 EAL-HLNESELHGRQLKV 119
           EA   L+  ++       
Sbjct: 62  EAQNALHNMKVLPGMHHP 79

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 61.9 bits (151), Expect = 1e-12
 Identities = 25/119 (21%), Positives = 44/119 (36%), Gaps = 12/119 (10%)

Query: 9   EEEA-TALRQMHAK---VGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEV 64
            + A  A   +H      G     +  PA           V+ R +F+G +   CT  ++
Sbjct: 57  RKAALEAQNALHNMKVLPGMHHPIQMKPADS----EKNNAVEDRKLFIGMISKKCTENDI 112

Query: 65  QQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNES---ELHGRQLKV 119
           +  F S G +    I     G  +G A+V F      Q A+  ++++   E     + V
Sbjct: 113 RVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV 171

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 61.9 bits (151), Expect = 2e-13
 Identities = 22/104 (21%), Positives = 47/104 (45%), Gaps = 9/104 (8%)

Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF 95
           GSS ++      + +FV N+  + T E +++ F   G + RV          K YA++ F
Sbjct: 1   GSSGSSGMA-KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK-------LKDYAFIHF 52

Query: 96  LQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPN 138
            + +   +A+  +N  +L G  +++   +      K+ + +R  
Sbjct: 53  DERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQA 96

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 61.6 bits (150), Expect = 2e-13
 Identities = 19/102 (18%), Positives = 46/102 (45%), Gaps = 9/102 (8%)

Query: 26  MASKQDPAAGGSSLANREEVDSRSVFVGNVDY-SCTPEEVQQHFQSCGTVNRVTIRTDKF 84
           M S        S L  R       +F+GN+   + + E++ + F   G + ++ I+    
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---- 56

Query: 85  GQPKGYAYVEFLQSEAVQEALH-LNESELHGRQLKVTVKRTN 125
                + +++F   ++V++A+   ++    G++L + V  +N
Sbjct: 57  ---NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN 95

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 61.6 bits (150), Expect = 3e-13
 Identities = 26/119 (21%), Positives = 52/119 (43%), Gaps = 17/119 (14%)

Query: 23  GNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYS-CTPEEVQQHFQSCGTVNRVTIRT 81
           G+   S +  A+  ++  + + ++SR VF+GN++ +     +V+  F   G V   ++  
Sbjct: 4   GSSGMSLKLQASNVTNKNDPKSINSR-VFIGNLNTALVKKSDVETIFSKYGRVAGCSV-- 60

Query: 82  DKFGQPKGYAYVEFLQSEAVQEALH-LNESELHGRQLKVTVKRTNVPGMKQHRPRRPNP 139
                 KGYA+V++      + A+   N   L G+ L + +           +P R  P
Sbjct: 61  -----HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP-------KPDRSGP 107

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 64.3 bits (157), Expect = 4e-13
 Identities = 17/79 (21%), Positives = 34/79 (43%), Gaps = 6/79 (7%)

Query: 42  REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAV 101
           +       +FVGN+    T E+ ++ F+  G  + V I  D     +G+ ++        
Sbjct: 17  KTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLA 71

Query: 102 QEALH-LNESELHGRQLKV 119
           + A   L+ + L  R L++
Sbjct: 72  EIAKAELDGTILKSRPLRI 90

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 63.9 bits (156), Expect = 5e-13
 Identities = 23/126 (18%), Positives = 42/126 (33%), Gaps = 7/126 (5%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 108
           + V N+    + E ++Q F   G V +  +  D  G+  G  +VEF      ++AL    
Sbjct: 99  LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCG 158

Query: 109 ESE-LHGRQLKV-TVKRTNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRF 166
           +   L     +   V+       +   P +         +    PP    P  +     F
Sbjct: 159 DGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTFE----F 214

Query: 167 RMPMRY 172
               R+
Sbjct: 215 EYASRW 220

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 60.9 bits (148), Expect = 5e-13
 Identities = 16/81 (19%), Positives = 31/81 (38%), Gaps = 7/81 (8%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
            S  + V N+      +EV    +         ++     + K  A+V  L  E  Q A+
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYD------LKYCYVDRNKRTAFVTLLNGEQAQNAI 57

Query: 106 H-LNESELHGRQLKVTVKRTN 125
              ++    G+ L V ++ T+
Sbjct: 58  QMFHQYSFRGKDLIVQLQPTD 78

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 60.3 bits (147), Expect = 6e-13
 Identities = 22/85 (25%), Positives = 46/85 (54%), Gaps = 3/85 (3%)

Query: 40  ANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQS 98
           A++ E D+  +FVG + +  + ++++ +F   G V   TI+ D   G+ +G+ ++ F  +
Sbjct: 4   ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDA 63

Query: 99  EAVQEALHLNESELHGRQLKVTVKR 123
            +V++ L   E  L GR   +  K+
Sbjct: 64  ASVEKVLDQKEHRLDGR--VIDPKK 86

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 60.7 bits (148), Expect = 6e-13
 Identities = 12/76 (15%), Positives = 31/76 (40%), Gaps = 6/76 (7%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH 106
           +  ++VG +  + +   + + F   G++  +            +AY+++   +A Q A  
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACA 71

Query: 107 -LNESELHGRQLKVTV 121
            +    L G   ++ V
Sbjct: 72  KMRGFPLGGPDRRLRV 87

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 60.7 bits (148), Expect = 6e-13
 Identities = 21/105 (20%), Positives = 41/105 (39%), Gaps = 5/105 (4%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYA 91
            + GSS   R    +  + V  + +  T ++++++F + G V  V ++ D   G  KG+ 
Sbjct: 1   GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60

Query: 92  YVEFLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRR 136
           +V F + E   + +      + GR      K        Q     
Sbjct: 61  FVRFTEYETQVKVMS-QRHMIDGR--WCDCKLP-NSKQSQDSGPS 101

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 60.8 bits (147), Expect = 8e-13
 Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

Query: 40  ANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF---GQPKGYAYVEFL 96
            +     SR VFVG +      +E+   F+  G +        +      PKGYA++ F 
Sbjct: 1   GSSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60

Query: 97  QSEAVQEALHLNESELHGRQLKVTVKR 123
           +  +VQ  +     E     L V+   
Sbjct: 61  EESSVQALIDACLEEDGKLYLCVSSPT 87

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 60.6 bits (147), Expect = 9e-13
 Identities = 22/111 (19%), Positives = 40/111 (36%), Gaps = 10/111 (9%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAY 92
            + GSS           V V  +  S + ++++ H +  G V    +  D      G   
Sbjct: 1   GSSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGV 54

Query: 93  VEFLQSEAVQEAL-HLNESELHGRQLKVT---VKRTNVPGMKQHRPRRPNP 139
           VEF++ E +  A+  L+ ++    + +     VK          R R   P
Sbjct: 55  VEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSGP 105

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 60.4 bits (147), Expect = 1e-12
 Identities = 19/116 (16%), Positives = 45/116 (38%), Gaps = 8/116 (6%)

Query: 27  ASKQDPAAGGSSLANREEVD-SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF- 84
            S  +        ++    + ++ +++ N+    T  ++   F          I+     
Sbjct: 4   GSSGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMT 63

Query: 85  GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNP 139
           G+ +G A++ F   E   +AL  +N  +L+G+ L +   +      K+ R   P+ 
Sbjct: 64  GRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN-----KKQRSSGPSS 114

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 59.8 bits (145), Expect = 1e-12
 Identities = 21/95 (22%), Positives = 42/95 (44%), Gaps = 7/95 (7%)

Query: 32  PAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVN-RVTIRTDKFGQPKGY 90
            ++G  S        +  V+VGN+       ++++  +  G+V  R+T +      P+  
Sbjct: 4   GSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQG-----PRRR 58

Query: 91  AYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT 124
           A++ +  S A Q+A+  L    L    L+V + R 
Sbjct: 59  AFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQ 93

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 61.0 bits (148), Expect = 1e-12
 Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 5/75 (6%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
               V+VGN+  +    E+++ F   G +  V +  +    P G+A+VEF       +A+
Sbjct: 72  LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAV 127

Query: 106 H-LNESELHGRQLKV 119
             L+   L G +++V
Sbjct: 128 RELDGRTLCGCRVRV 142

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 59.6 bits (145), Expect = 1e-12
 Identities = 21/92 (22%), Positives = 42/92 (45%), Gaps = 8/92 (8%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAY 92
            + GSS   R      +++V   D   TP  ++  F   G +  +++   +       A+
Sbjct: 1   GSSGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR-----NCAF 53

Query: 93  VEFLQSEAVQEAL-HLNESELHGRQLKVTVKR 123
           V + + E+  +A+  LN +++   QLKV + R
Sbjct: 54  VTYEKMESADQAVAELNGTQVESVQLKVNIAR 85

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 59.0 bits (144), Expect = 2e-12
 Identities = 18/75 (24%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLN 108
           +FVG +  + T E+V+ +F+  G V+   +  DK   + +G+ +V F   + V++   ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 109 ESELHGRQLKVTVKR 123
             E++ +   V  K+
Sbjct: 62  FHEINNKM--VECKK 74

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 59.4 bits (144), Expect = 2e-12
 Identities = 17/88 (19%), Positives = 29/88 (32%), Gaps = 3/88 (3%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAY 92
            + GSS +  +    R + + N+      E +       G V                  
Sbjct: 1   GSSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTD--SETAVVN 58

Query: 93  VEFLQSEAVQEAL-HLNESELHGRQLKV 119
           V +   +  ++AL  LN  +L    LKV
Sbjct: 59  VTYSSKDQARQALDKLNGFQLENFTLKV 86

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 58.7 bits (142), Expect = 5e-12
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 6/81 (7%)

Query: 45  VDSRSVFVGNVDYSCTPEEVQQHFQSCGT-VNRVTIRTDKF--GQPKGYAYVEFLQSEAV 101
             +  +F+G +      EE+ +        V  V +        + +G+A+VE+    A 
Sbjct: 6   SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 65

Query: 102 QEA---LHLNESELHGRQLKV 119
             A   L     +L G Q+ V
Sbjct: 66  AMARRKLMPGRIQLWGHQIAV 86

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 57.1 bits (139), Expect = 6e-12
 Identities = 14/75 (18%), Positives = 34/75 (45%), Gaps = 3/75 (4%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLN 108
           +FVG +      E+++++F   G V  + +  D    + +G+ ++ F + E V++ +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 109 ESELHGRQLKVTVKR 123
              +     K  +K 
Sbjct: 62  YHNVGLS--KCEIKV 74

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 58.0 bits (141), Expect = 6e-12
 Identities = 13/92 (14%), Positives = 42/92 (45%), Gaps = 13/92 (14%)

Query: 50  VFVGNVDY-SCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH-L 107
           +F+GN+   + + E++ + F   G + ++ I+         + +++F   ++V++A+   
Sbjct: 13  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECE 65

Query: 108 NESELHGRQLKVTVKRTNVPGMKQHRPRRPNP 139
           ++    G++L + V         + +    + 
Sbjct: 66  SQEMNFGKKLILEVSS----SNARPQFDHGDH 93

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 57.2 bits (139), Expect = 1e-11
 Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 3/74 (4%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVT-IRTDKF-GQPKGYAYVEFLQSEAVQEAL- 105
            +F+GN+D     + +   F + G + +   I  D   G  KGYA++ F   +A   A+ 
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 106 HLNESELHGRQLKV 119
            +N   L  R + V
Sbjct: 67  AMNGQYLCNRPITV 80

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 56.7 bits (138), Expect = 1e-11
 Identities = 16/75 (21%), Positives = 34/75 (45%), Gaps = 3/75 (4%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLN 108
           +F+G + +  T E ++++F   G V    +  D    + +G+ +V F+    V + L  +
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 109 ESELHGRQLKVTVKR 123
             EL  +   +  K 
Sbjct: 63  RHELDSK--TIDPKV 75

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 57.7 bits (140), Expect = 1e-11
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 3/85 (3%)

Query: 40  ANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQS 98
             RE+   R +F+G + +  T E ++ +++  G +    +  D    + +G+ +V F   
Sbjct: 20  KKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSM 79

Query: 99  EAVQEALHLNESELHGRQLKVTVKR 123
             V  A+      + GR   V  KR
Sbjct: 80  AEVDAAMAARPHSIDGR--VVEPKR 102

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 57.3 bits (139), Expect = 1e-11
 Identities = 22/116 (18%), Positives = 43/116 (37%), Gaps = 13/116 (11%)

Query: 27  ASKQDPAAGGSSLANREEVDSRS--VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF 84
           +S          +     + S    +F+G + +  T E ++++F   G V    +  D  
Sbjct: 3   SSHHHHHHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL 62

Query: 85  -GQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNP 139
             + +G+ +V F+    V + L  +  EL  +   +  K           PRR  P
Sbjct: 63  TKRSRGFGFVTFMDQAGVDKVLAQSRHELDSK--TIDPKVAF--------PRRAQP 108

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 59.3 bits (143), Expect = 2e-11
 Identities = 12/86 (13%), Positives = 24/86 (27%), Gaps = 2/86 (2%)

Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVE 94
             +  NR +  S  +   N     T E   +     G     +++      +      +E
Sbjct: 112 EQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLE 171

Query: 95  FLQSEAVQEAL-HLNESELHGRQLKV 119
           +       E L  LN  ++       
Sbjct: 172 WDSKSDALETLGFLNHYQMKNPNGPY 197

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 54.3 bits (130), Expect = 1e-09
 Identities = 26/129 (20%), Positives = 41/129 (31%), Gaps = 6/129 (4%)

Query: 46  DSRSVFVGNVDYS-CTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEA 104
           DS  + V  +D S    + V   F   G V +V     K     G A VE     AV  A
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK----PGAAMVEMADGYAVDRA 58

Query: 105 L-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKI 163
           + HLN + + G+++ V V +       Q                +    F          
Sbjct: 59  ITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNR 118

Query: 164 PRFRMPMRY 172
            +    + +
Sbjct: 119 IQHPSNVLH 127

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 56.7 bits (137), Expect = 3e-11
 Identities = 18/75 (24%), Positives = 30/75 (40%), Gaps = 6/75 (8%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
               +   N+       E+Q+ F   G++ RV +           A VEFL+    ++A 
Sbjct: 9   SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-----GITAIVEFLEPLEARKAF 63

Query: 106 -HLNESELHGRQLKV 119
            HL  S+ H   L +
Sbjct: 64  RHLAYSKFHHVPLYL 78

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 56.0 bits (135), Expect = 4e-11
 Identities = 18/90 (20%), Positives = 35/90 (38%), Gaps = 8/90 (8%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAY 92
            + GSS ++ +   S  V V  +  S    ++ +  +  GT+  V +        K  A 
Sbjct: 1   GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQAL 55

Query: 93  VEFLQSEAVQEALH---LNESELHGRQLKV 119
           VEF   ++ +E +         + G+Q   
Sbjct: 56  VEFENIDSAKECVTFAADVPVYIAGQQAFF 85

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 55.6 bits (134), Expect = 8e-11
 Identities = 23/109 (21%), Positives = 43/109 (39%), Gaps = 15/109 (13%)

Query: 35  GGSSLANREEVDSRS---VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYA 91
           GG+          RS   V V  +  S + ++++ H +  G V    +  D      G  
Sbjct: 1   GGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTG 54

Query: 92  YVEFLQSEAVQEALH-LNESELHGRQLKVTVKRTNVPGMKQHRPRRPNP 139
            VEF++ E +  A+  L+ ++    + +    R     +K   PR P+ 
Sbjct: 55  VVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR-----VKVDGPRSPSY 98

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 54.9 bits (132), Expect = 1e-10
 Identities = 14/76 (18%), Positives = 25/76 (32%), Gaps = 8/76 (10%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL- 105
           SR + +  +    T  EV       G V  + +        K  A++E    EA    + 
Sbjct: 16  SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVN 70

Query: 106 --HLNESELHGRQLKV 119
                   L G+ + +
Sbjct: 71  YYTSVTPVLRGQPIYI 86

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 54.8 bits (132), Expect = 1e-10
 Identities = 16/90 (17%), Positives = 29/90 (32%), Gaps = 8/90 (8%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAY 92
            + GSS    +   SR + +  +    T  EV       G V  + +        K  A+
Sbjct: 1   GSSGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAF 55

Query: 93  VEFLQSEAVQEAL---HLNESELHGRQLKV 119
           +E    EA    +         L  + + +
Sbjct: 56  LELATEEAAITMVNYYSAVTPHLRNQPIYI 85

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 54.2 bits (130), Expect = 3e-10
 Identities = 17/96 (17%), Positives = 30/96 (31%), Gaps = 8/96 (8%)

Query: 27  ASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ 86
           +S   P       +    V SR + +  +    T  EV       G V  + +       
Sbjct: 11  SSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG---- 66

Query: 87  PKGYAYVEFLQSEAVQEAL---HLNESELHGRQLKV 119
            K  A++E    EA    +         L G+ + +
Sbjct: 67  -KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI 101

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 55.7 bits (134), Expect = 3e-10
 Identities = 24/103 (23%), Positives = 44/103 (42%), Gaps = 6/103 (5%)

Query: 45  VDSRSVFVGNVD-YSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQE 103
           + +  + V N++    TP+ +   F   G V RV I  +K    K  A V+       Q 
Sbjct: 1   MGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQL 56

Query: 104 AL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNPFMVYQS 145
           A+ HLN  +LHG+ +++T+ +     + +           Y +
Sbjct: 57  AMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGN 99

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 53.7 bits (129), Expect = 2e-09
 Identities = 17/86 (19%), Positives = 36/86 (41%), Gaps = 5/86 (5%)

Query: 41  NREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEA 100
                 S ++ + N+  S + E+++  F S G V +      K    +  A ++    E 
Sbjct: 114 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK---DRKMALIQMGSVEE 170

Query: 101 VQEAL-HLNESEL-HGRQLKVTVKRT 124
             +AL  L+  +L     L+V+  ++
Sbjct: 171 AVQALIDLHNHDLGENHHLRVSFSKS 196

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 55.4 bits (133), Expect = 5e-10
 Identities = 25/116 (21%), Positives = 46/116 (39%), Gaps = 6/116 (5%)

Query: 32  PAAGGSSLANREEVDSRSVFVGNVD-YSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGY 90
              G  ++       +  + V N++    TP+ +   F   G V RV I  +K    K  
Sbjct: 19  SHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KEN 74

Query: 91  AYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNPFMVYQS 145
           A V+       Q A+ HLN  +LHG+ +++T+ +     + +           Y +
Sbjct: 75  ALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGN 130

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 53.1 bits (127), Expect = 3e-09
 Identities = 19/93 (20%), Positives = 39/93 (41%), Gaps = 5/93 (5%)

Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF 95
           GS         S ++ + N+  S + E+++  F S G V +      K    +  A ++ 
Sbjct: 140 GSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK---DRKMALIQM 196

Query: 96  LQSEAVQEAL-HLNESEL-HGRQLKVTVKRTNV 126
              E   +AL  L+  +L     L+V+  ++ +
Sbjct: 197 GSVEEAVQALIDLHNHDLGENHHLRVSFSKSTI 229

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 52.6 bits (127), Expect = 5e-10
 Identities = 18/78 (23%), Positives = 29/78 (37%), Gaps = 7/78 (8%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
            S  VFVG      T +E+++ F   G V  V I        + +A+V F   +  Q   
Sbjct: 4   GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF----RAFAFVTFADDQIAQSLC 59

Query: 106 HLNESELHGRQLKVTVKR 123
              +  + G    V +  
Sbjct: 60  G-EDLIIKGIS--VHISN 74

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 52.2 bits (126), Expect = 9e-10
 Identities = 12/84 (14%), Positives = 39/84 (46%), Gaps = 7/84 (8%)

Query: 47  SRSVFVGNVDYSCTPEEVQQH----FQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQ 102
           + ++++ N++     +E+++     F   G +  + I   +  + +G A+V F +  +  
Sbjct: 8   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSAT 65

Query: 103 EAL-HLNESELHGRQLKVTVKRTN 125
            AL  +     + + +++   +T+
Sbjct: 66  NALRSMQGFPFYDKPMRIQYAKTD 89

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 52.1 bits (125), Expect = 1e-09
 Identities = 15/97 (15%), Positives = 28/97 (28%), Gaps = 9/97 (9%)

Query: 26  MASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG 85
           M              ++    S  V +  +       ++ +  Q  G ++ V +      
Sbjct: 1   MGHHHHHHMENYDDPHKTPA-SPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK--- 56

Query: 86  QPKGYAYVEFLQSEAVQEAL---HLNESELHGRQLKV 119
             K  A VEF        A+     N+  + G    V
Sbjct: 57  --KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV 91

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 51.5 bits (124), Expect = 1e-09
 Identities = 20/84 (23%), Positives = 30/84 (35%), Gaps = 7/84 (8%)

Query: 40  ANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSE 99
           ++        VFVG      T EE+QQ F   G V  V I        + +A+V F   +
Sbjct: 4   SHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF----RAFAFVTFADDK 59

Query: 100 AVQEALHLNESELHGRQLKVTVKR 123
             Q      +  + G    V +  
Sbjct: 60  VAQSLCG-EDLIIKGIS--VHISN 80

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 52.1 bits (125), Expect = 2e-09
 Identities = 21/101 (20%), Positives = 35/101 (34%), Gaps = 9/101 (8%)

Query: 26  MASKQDPAAGGSSLANREEVDSRS------VFVGNVDYSCTPEEVQQHFQSCGTVNRVTI 79
           M S        S L  R    S+       + + N+   C+ ++++   +        T 
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLE--TTF 58

Query: 80  RTDKFGQPKGYAYVEFLQSEAVQEALH-LNESELHGRQLKV 119
            +       G   +EF   E + EAL  LN  E  G  + V
Sbjct: 59  SSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV 99

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 51.1 bits (122), Expect = 6e-09
 Identities = 20/107 (18%), Positives = 35/107 (32%), Gaps = 8/107 (7%)

Query: 18  MHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQH----FQSCGT 73
           M      +   +   +    S     E  S+ V + N++     E++Q        S G 
Sbjct: 1   MKETAAAKFERQHMDSPDLGSTPPHTEP-SQVVLITNINPEVPKEKLQALLYALASSQGD 59

Query: 74  VNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV 119
           +  + I  D      G AY+ F   E+ Q  +         G  L +
Sbjct: 60  I--LDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI 104

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 51.0 bits (122), Expect = 8e-09
 Identities = 21/97 (21%), Positives = 39/97 (40%), Gaps = 7/97 (7%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVT------IRTDKFGQPKGYAYVEFLQSEA 100
           +  ++V N+      ++++  F      +  T      IR  K G+ KG A++     +A
Sbjct: 45  NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA 104

Query: 101 VQEALH-LNESELHGRQLKVTVKRTNVPGMKQHRPRR 136
             +AL   N   L G+ + V   R+  P       +R
Sbjct: 105 AAKALKEANGYVLFGKPMVVQFARSARPKQDPKEGKR 141

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 48.6 bits (116), Expect = 3e-08
 Identities = 11/72 (15%), Positives = 27/72 (37%), Gaps = 3/72 (4%)

Query: 51  FVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL-HLN 108
            + +       + +   F   G V  +    D+  G+ KG+ +VE       ++ +   +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 109 ESELHGR-QLKV 119
              L  + +L +
Sbjct: 76  GKRLDLKHRLFL 87

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 49.1 bits (116), Expect = 1e-07
 Identities = 20/136 (14%), Positives = 51/136 (37%), Gaps = 10/136 (7%)

Query: 47  SRSVFVGNVDYSCTPEEVQQH----FQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQ 102
           + ++++ N++     +E+++     F   G +  + I   +  + +G A+V F +  +  
Sbjct: 9   NHTIYINNLNEKIKKDELKKSLYAIFSQFGQI--LDILVSRSLKMRGQAFVIFKEVSSAT 66

Query: 103 EALH-LNESELHGRQLKVTVKRTN---VPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPY 158
            AL  +     + + +++   +T+   +  MK     R       + +    P    +  
Sbjct: 67  NALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQ 126

Query: 159 GYGKIPRFRMPMRYSP 174
           G G  P         P
Sbjct: 127 GGGATPVVGAVQGPVP 142

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 46.5 bits (110), Expect = 1e-07
 Identities = 24/94 (25%), Positives = 42/94 (44%), Gaps = 8/94 (8%)

Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQH----FQSCGTVNRVTIRTDKFGQPKGYA 91
           GSS ++    D   V V N+DY  + +E+QQ     F   G V  V +      Q K   
Sbjct: 1   GSSGSSGNGAD---VQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVV 57

Query: 92  YVEFLQSEAVQEALHLNESELHGRQLKVTVKRTN 125
            +E LQ +A+     L+  ++  +++ V++    
Sbjct: 58  QMENLQ-DAIGAVNSLHRYKIGSKKILVSLATGA 90

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 45.7 bits (109), Expect = 3e-07
 Identities = 19/102 (18%), Positives = 36/102 (35%), Gaps = 11/102 (10%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSC-GTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH- 106
           S+FVG++        + + F     +     +  D+ G  KGY +V+F      + AL  
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70

Query: 107 LN-ESELHGRQLKVTVKRTNVPGMKQHRPRRPNPFMVYQSRG 147
                 L  + +++         +   +  R  P     S G
Sbjct: 71  CQGAVGLGSKPVRL--------SVAIPKASRVKPVESGPSSG 104

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 44.6 bits (105), Expect = 8e-07
 Identities = 14/85 (16%), Positives = 28/85 (32%), Gaps = 12/85 (14%)

Query: 40  ANREEVDSRSVFVGNVDYSCTPEEVQQHFQSC-----GTVNRVTIRTDKFGQPKGYAYVE 94
            +       +V V  +  +   E +  +F++      G V           +      + 
Sbjct: 1   GSSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ-------RLGCGGVLT 53

Query: 95  FLQSEAVQEALHLNESELHGRQLKV 119
           F +    +  L   + ELHG QL +
Sbjct: 54  FREPADAERVLAQADHELHGAQLSL 78

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 46.8 bits (110), Expect = 1e-06
 Identities = 32/176 (18%), Positives = 66/176 (37%), Gaps = 7/176 (3%)

Query: 4   RLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEE 63
           R + ME +     +   +         DP    ++  +      +++FV  V+Y  T  +
Sbjct: 63  REERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAF----KTLFVARVNYDTTESK 118

Query: 64  VQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV 121
           +++ F+  G + R+ +   K  G+P+GYA++E+     +  A  H +  ++ GR++ V V
Sbjct: 119 LRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV 178

Query: 122 KRTN-VPGMKQHRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSPYY 176
           +R   V G +  R                I                  P+ +    
Sbjct: 179 ERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRD 234

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 43.0 bits (101), Expect = 3e-06
 Identities = 11/68 (16%), Positives = 29/68 (42%), Gaps = 9/68 (13%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNE 109
           V  G +    +  ++    + CG V+ + +  +K      Y++  +  +E  + A     
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK-----PYSFARYRTTEESKRAY---- 80

Query: 110 SELHGRQL 117
             L+G+++
Sbjct: 81  VTLNGKEV 88

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 42.0 bits (99), Expect = 7e-06
 Identities = 13/85 (15%), Positives = 30/85 (35%), Gaps = 9/85 (10%)

Query: 43  EEVDSRSVFVGNV------DYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFL 96
            +     + V NV              + + F   G +       +  G+ KGY ++E+ 
Sbjct: 11  ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEED-GKTKGYIFLEYA 69

Query: 97  QSEAVQEAL-HLNESELHGR-QLKV 119
                 +A+ + +  +L  +   +V
Sbjct: 70  SPAHAVDAVKNADGYKLDKQHTFRV 94

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 41.8 bits (98), Expect = 1e-05
 Identities = 16/101 (15%), Positives = 36/101 (35%), Gaps = 9/101 (8%)

Query: 23  GNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYS-CTPEEVQQHFQSCGTVNRVTIRT 81
           G+  +S + P        ++++   R + + N+ +S  +   V +  +  G +    +  
Sbjct: 1   GSSGSSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR 60

Query: 82  DKFGQPKGYAYVEFLQSEAVQEAL---HLNESELHGRQLKV 119
                 K  A++E    E     +           GR +KV
Sbjct: 61  M-----KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV 96

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 3/81 (3%)

Query: 26  MASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG 85
           +A     AA  + +A   +     + V N+ Y  T + + Q F   GTV ++   T    
Sbjct: 7   LALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ 66

Query: 86  QPKGYAYVEFLQSEAVQEALH 106
                A +++    + Q A  
Sbjct: 67  ---FQALLQYADPVSAQHAKL 84

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 42.0 bits (98), Expect = 2e-05
 Identities = 19/94 (20%), Positives = 37/94 (39%), Gaps = 3/94 (3%)

Query: 13  TALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCG 72
            AL+ +++     +A     AA  + +A   +     + V N+ Y  T + + Q F   G
Sbjct: 12  AALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFG 71

Query: 73  TVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH 106
           TV ++   T         A +++    + Q A  
Sbjct: 72  TVLKIITFTKNNQ---FQALLQYADPVSAQHAKL 102

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 38.5 bits (90), Expect = 7e-05
 Identities = 13/78 (16%), Positives = 29/78 (37%), Gaps = 9/78 (11%)

Query: 50  VFVGNV------DYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQE 103
           + V NV              + + F   G +       +  G+ KGY ++E+       +
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEED-GKTKGYIFLEYASPAHAVD 62

Query: 104 AL-HLNESELHGR-QLKV 119
           A+ + +  +L  +   +V
Sbjct: 63  AVKNADGYKLDKQHTFRV 80

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 39.8 bits (92), Expect = 1e-04
 Identities = 17/149 (11%), Positives = 46/149 (30%), Gaps = 28/149 (18%)

Query: 6   KEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTP---- 61
           +++ + A     +      + A  ++   G  S        +++++VG +D +       
Sbjct: 97  EDIGKLALRTEVLDCFGREKFADYREDMGGIGS----FRKKNKTLYVGGIDGALNSKHLK 152

Query: 62  -----EEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQ 116
                  ++  F   G ++R+          K   +V+F      + A       +  + 
Sbjct: 153 PAQIESRIRFVFSRLGDIDRIRYVES-----KNCGFVKFKYQANAEFAK----EAMSNQT 203

Query: 117 LKVTVKRTNVPGMKQHRPR------RPNP 139
           L +   +      +            P+P
Sbjct: 204 LLLPSDKEWDDRREGTGLLVKWANEDPDP 232

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

 Score = 40.2 bits (93), Expect = 2e-04
 Identities = 24/152 (15%), Positives = 51/152 (33%), Gaps = 31/152 (20%)

Query: 41  NREEVDS-RSVFVGNVDYSCTPEEVQQHFQSCG----TVNRVTIRT-DKFGQPKGYAYVE 94
           N +++ +     +  ++    P E ++ F        + + +              + V 
Sbjct: 351 NCDKLTTIIESSLNVLE----PAEYRKMFDRLSVFPPSAH-IPTILLSLIWFDVIKSDVM 405

Query: 95  FLQSEAVQEAL---HLNES--ELHGRQLKVTVKRTNVPGMKQHRP--RRPNPFMVYQSRG 147
            + ++  + +L      ES   +    L++ VK  N   +  HR      N    + S  
Sbjct: 406 VVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYAL--HRSIVDHYNIPKTFDSDD 463

Query: 148 AIIPP---FLYSPYGY--------GKIPRFRM 168
            I P    + YS  G+         ++  FRM
Sbjct: 464 LIPPYLDQYFYSHIGHHLKNIEHPERMTLFRM 495

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 37.7 bits (87), Expect = 3e-04
 Identities = 15/73 (20%), Positives = 28/73 (38%), Gaps = 5/73 (6%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 108
           + + N  Y  T + +       G V R+      F +    A VEF      Q+A   LN
Sbjct: 28  LSIQNPLYPITVDVLYTVCNPVGKVQRIV----IFKRNGIQAMVEFESVLCAQKAKAALN 83

Query: 109 ESELHGRQLKVTV 121
            ++++     + +
Sbjct: 84  GADIYAGCCTLKI 96

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	176
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.92
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.91
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.89
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.89
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.88
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.88
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.88
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.88
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.88
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.88
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.88
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.88
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.88
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.88
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.88
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.88
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.88
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.88
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.88
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.87
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.87
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.87
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.87
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.87
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.87
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.87
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.87
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.87
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.87
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.87
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.87
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.87
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.87
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.87
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.87
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.87
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.87
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.87
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.87
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.87
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.86
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.86
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.86
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.86
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.86
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.86
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.86
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.86
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.86
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.86
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.86
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.86
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.86
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.86
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.86
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.86
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.86
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.86
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.86
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.86
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.86
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.86
2div_A	99	TRNA selenocysteine associated protein; structural	99.85
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.85
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.85
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.85
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.85
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.85
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.85
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.85
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.85
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.85
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.85
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.84
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.84
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.84
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.84
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.84
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.84
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.84
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.84
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.84
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.84
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.84
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.84
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.84
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.84
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.83
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.83
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.83
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.83
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.83
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.83
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.83
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.83
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.83
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.83
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.83
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.83
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.83
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.83
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.83
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.82
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.82
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.82
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.82
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.82
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.82
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.82
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.82
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.82
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.82
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.82
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.82
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.82
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.81
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.81
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.81
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.81
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.81
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.81
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.81
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.81
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.81
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.81
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.81
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.81
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.81
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.81
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.69
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.8
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.8
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.8
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.8
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.8
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.8
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.8
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.8
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.8
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.8
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.8
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.79
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.79
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.79
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.79
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.79
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.79
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.79
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.79
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.78
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.78
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.78
1x5p_A	97	Negative elongation factor E; structure genomics,	99.78
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.78
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.78
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.78
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.77
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.77
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.77
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.76
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.76
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.76
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.76
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.76
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.75
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.75
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.75
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.75
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.75
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.75
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.75
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.74
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.74
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.73
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.73
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.72
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.72
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.71
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.7
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.7
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.7
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.7
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.7
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.69
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.69
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.68
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.68
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.68
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.67
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.67
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.67
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.65
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.64
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.64
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.64
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.63
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.63
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.62
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.6
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.58
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.54
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.53
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.5
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.4
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.33
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.33
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.13
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.03
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.77
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.4
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.07
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.81
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.66
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.5
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.35
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	97.21
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.87
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.43
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.03
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	95.08
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.06
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	91.63
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	83.96

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

Probab=99.92  E-value=4.5e-24  Score=152.73  Aligned_cols=86  Identities=21%  Similarity=0.412  Sum_probs=79.4

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      .....++|||+|||+++|+++|+++|++||.|..|.|+.++ ++.+++||||+|.+.++|++|| .||+..|+|+.|+|+
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  114 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD  114 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567999999999999999999999999999999999998 6899999999999999999999 699999999999999


Q ss_pred             eccCCCCC
Q 030488          121 VKRTNVPG  128 (176)
Q Consensus       121 ~a~~~~~~  128 (176)
                      ++++..+.
T Consensus       115 ~a~~~~~~  122 (156)
T 1h2v_Z          115 WDAGFKEG  122 (156)
T ss_dssp             EESCCCTT
T ss_pred             ECCCCCCc
Confidence            99875543

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.91  E-value=1.1e-23  Score=139.87  Aligned_cols=80  Identities=25%  Similarity=0.484  Sum_probs=76.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      .++++|||+|||+++|+++|+++|++||.|.+|.|++++ +|.++|||||+|.+.++|++|+ .||+..|+|+.|+|++|
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~A   96 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA   96 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            456899999999999999999999999999999999998 7999999999999999999999 79999999999999999


Q ss_pred             cC
Q 030488          123 RT  124 (176)
Q Consensus       123 ~~  124 (176)
                      ++
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            75

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.89  E-value=1.1e-21  Score=161.24  Aligned_cols=83  Identities=27%  Similarity=0.597  Sum_probs=77.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ....++|||+|||++||+++|+++|++||.|+.|.|+.++ ++.++|||||+|.+.++|++|| .||++.|+|+.|.|.+
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~  178 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  178 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3456899999999999999999999999999999999997 7999999999999999999999 7999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      +....
T Consensus       179 a~~~~  183 (437)
T 3pgw_S          179 ERGRT  183 (437)
T ss_pred             eCCCC
Confidence            98643

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

Probab=99.89  E-value=3.2e-22  Score=135.33  Aligned_cols=80  Identities=15%  Similarity=0.226  Sum_probs=76.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      .+.++|||+|||+++|+++|+++|++||.|.+|.|+.|+ +++++|||||+|.+.++|++|| .||+..|+|+.|+|+++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            456899999999999999999999999999999999998 6999999999999999999999 79999999999999998


Q ss_pred             cC
Q 030488          123 RT  124 (176)
Q Consensus       123 ~~  124 (176)
                      ..
T Consensus        84 ~~   85 (110)
T 3s8s_A           84 IK   85 (110)
T ss_dssp             ST
T ss_pred             CC
Confidence            64

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

Probab=99.88  E-value=5.8e-22  Score=135.20  Aligned_cols=83  Identities=19%  Similarity=0.449  Sum_probs=77.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ..+.++|||+|||.++|+++|+++|++||.|..|.|+.++++.++|||||+|.+.++|++|+ .||+..|+|+.|+|+++
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            34578999999999999999999999999999999999989999999999999999999999 69999999999999999


Q ss_pred             cCCC
Q 030488          123 RTNV  126 (176)
Q Consensus       123 ~~~~  126 (176)
                      +...
T Consensus        84 ~~~~   87 (116)
T 2fy1_A           84 KKPS   87 (116)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            7643

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

Probab=99.88  E-value=1.5e-21  Score=132.94  Aligned_cols=84  Identities=23%  Similarity=0.487  Sum_probs=77.0

Q ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeE
Q 030488           41 NREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLK  118 (176)
Q Consensus        41 ~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~  118 (176)
                      ...+...++|||+|||+++|+++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|++|| .+++ .|.|+.|+
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~   89 (116)
T 2cqd_A           11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKAN   89 (116)
T ss_dssp             CCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECE
T ss_pred             CcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEE
Confidence            3345678999999999999999999999999999999999987 7999999999999999999999 5887 89999999


Q ss_pred             EEeccCC
Q 030488          119 VTVKRTN  125 (176)
Q Consensus       119 v~~a~~~  125 (176)
                      |+++...
T Consensus        90 V~~a~~~   96 (116)
T 2cqd_A           90 VNLAYLG   96 (116)
T ss_dssp             EEESTTT
T ss_pred             EEEcccC
Confidence            9999753

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

Probab=99.88  E-value=2.4e-21  Score=131.59  Aligned_cols=86  Identities=23%  Similarity=0.473  Sum_probs=79.7

Q ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeE
Q 030488           41 NREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLK  118 (176)
Q Consensus        41 ~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~  118 (176)
                      ..+..+.++|||+|||+++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|| .||+..|+|+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (115)
T 2dgo_A            9 KKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIR   88 (115)
T ss_dssp             CCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3345678999999999999999999999999999999999997 7999999999999999999999 6999999999999


Q ss_pred             EEeccCCC
Q 030488          119 VTVKRTNV  126 (176)
Q Consensus       119 v~~a~~~~  126 (176)
                      |.+++...
T Consensus        89 V~~a~~~~   96 (115)
T 2dgo_A           89 TNWATRKP   96 (115)
T ss_dssp             EEESSCCC
T ss_pred             EEEccCCC
Confidence            99997654

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

Probab=99.88  E-value=2.7e-21  Score=131.09  Aligned_cols=84  Identities=29%  Similarity=0.406  Sum_probs=78.2

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      .....++|||+|||+++++++|+++|++||.|..|.|+.++++.+++||||+|.+.++|++|| .||+..|+|+.|.|++
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEE
Confidence            345578999999999999999999999999999999999999999999999999999999999 6999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      ++...
T Consensus        91 a~~~~   95 (114)
T 2do0_A           91 DERAL   95 (114)
T ss_dssp             CSCCC
T ss_pred             cccCC
Confidence            97543

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.88  E-value=5.7e-23  Score=155.81  Aligned_cols=78  Identities=24%  Similarity=0.418  Sum_probs=73.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCC--CeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCG--TVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G--~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ..++|||+|||+++|+++|+++|++||  .|.+|.|++++ +++++|||||+|.+.++|++|| .||++.|+|+.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            567899999999999999999999999  99999999998 8999999999999999999999 6999999999999998


Q ss_pred             cc
Q 030488          122 KR  123 (176)
Q Consensus       122 a~  123 (176)
                      ++
T Consensus       147 a~  148 (229)
T 3q2s_C          147 VN  148 (229)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

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

Probab=99.88  E-value=1.9e-22  Score=139.22  Aligned_cols=84  Identities=26%  Similarity=0.435  Sum_probs=78.3

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      ...+.++|||+|||+++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|| .||+..|+|+.|.|+
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            44567899999999999999999999999999999999997 7999999999999999999999 699999999999999


Q ss_pred             eccCCC
Q 030488          121 VKRTNV  126 (176)
Q Consensus       121 ~a~~~~  126 (176)
                      ++.+..
T Consensus        98 ~a~~~~  103 (126)
T 3ex7_B           98 WCFVRG  103 (126)
T ss_dssp             ESEESS
T ss_pred             EecCCC
Confidence            997643

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

Probab=99.88  E-value=1.4e-21  Score=130.28  Aligned_cols=85  Identities=24%  Similarity=0.416  Sum_probs=79.0

Q ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEE
Q 030488           42 REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV  119 (176)
Q Consensus        42 ~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v  119 (176)
                      .+..+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|| .||+..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (103)
T 2cq0_A           10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNV   89 (103)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            345668999999999999999999999999999999999997 7999999999999999999999 69999999999999


Q ss_pred             EeccCCC
Q 030488          120 TVKRTNV  126 (176)
Q Consensus       120 ~~a~~~~  126 (176)
                      +++++..
T Consensus        90 ~~a~~~~   96 (103)
T 2cq0_A           90 EWAKPST   96 (103)
T ss_dssp             EESSCCC
T ss_pred             EECCCCC
Confidence            9997643

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

Probab=99.88  E-value=1.2e-21  Score=129.75  Aligned_cols=83  Identities=22%  Similarity=0.514  Sum_probs=77.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      ....++|||+|||.++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++||.+++..|+|+.|+|.++
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            4567899999999999999999999999999999999987 799999999999999999999999999999999999999


Q ss_pred             cCCC
Q 030488          123 RTNV  126 (176)
Q Consensus       123 ~~~~  126 (176)
                      .+..
T Consensus        87 ~~~~   90 (99)
T 2dgs_A           87 EPRD   90 (99)
T ss_dssp             CCCC
T ss_pred             CCCc
Confidence            8643

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

Probab=99.88  E-value=1.6e-21  Score=130.01  Aligned_cols=83  Identities=20%  Similarity=0.388  Sum_probs=77.9

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ...+.++|||+|||+++|+++|+++|++||.|..|.|+.+ ++.+++||||+|.+.++|++|| .||+..|.|+.|.|++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            4557899999999999999999999999999999999998 8999999999999999999999 6999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      +++..
T Consensus        90 a~~~~   94 (103)
T 2d9p_A           90 AQRKE   94 (103)
T ss_dssp             CSSCC
T ss_pred             ecccc
Confidence            98644

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

Probab=99.88  E-value=8.6e-23  Score=133.56  Aligned_cols=80  Identities=20%  Similarity=0.371  Sum_probs=73.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCC-CeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-Hh-CCCeeCCeeeEEEec
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCG-TVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HL-NESELHGRQLKVTVK  122 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G-~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l-~~~~~~g~~i~v~~a  122 (176)
                      +++|||+|||+++|+++|+++|++|| .|.+|+|++++ ++.++|||||+|.+.++|++|| .+ ++..++|+.|.|+++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            46899999999999999999999999 89999999998 7999999999999999999999 55 456799999999999


Q ss_pred             cCCC
Q 030488          123 RTNV  126 (176)
Q Consensus       123 ~~~~  126 (176)
                      .+..
T Consensus        81 ~~~~   84 (91)
T 2lxi_A           81 DPKP   84 (91)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            7654

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

Probab=99.88  E-value=1.9e-21  Score=129.03  Aligned_cols=84  Identities=25%  Similarity=0.561  Sum_probs=78.8

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ...+.++|||+|||+++|+++|+++|++||.|..|.|+.++++.++|||||+|.+.++|++|+ .||+..|+|+.|+|++
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            445678999999999999999999999999999999999999999999999999999999999 7999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      +++..
T Consensus        93 a~~~~   97 (100)
T 2do4_A           93 SNSGP   97 (100)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            98643

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

Probab=99.88  E-value=1.2e-21  Score=128.60  Aligned_cols=82  Identities=28%  Similarity=0.574  Sum_probs=76.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ...++|||+|||.++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|+ .||+..|+|+.|+|+++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            356899999999999999999999999999999999987 6999999999999999999999 69999999999999999


Q ss_pred             cCCC
Q 030488          123 RTNV  126 (176)
Q Consensus       123 ~~~~  126 (176)
                      +...
T Consensus        83 ~~~~   86 (95)
T 2dnz_A           83 TERL   86 (95)
T ss_dssp             SCCC
T ss_pred             cccc
Confidence            7643

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

Probab=99.88  E-value=1.8e-21  Score=132.27  Aligned_cols=84  Identities=21%  Similarity=0.345  Sum_probs=78.5

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      .....++|||+|||+++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|| .||+..|+|+.|+|+
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999999998 7999999999999999999999 799999999999999


Q ss_pred             eccCCC
Q 030488          121 VKRTNV  126 (176)
Q Consensus       121 ~a~~~~  126 (176)
                      ++++..
T Consensus       101 ~a~~~~  106 (115)
T 2cpz_A          101 LKRSKN  106 (115)
T ss_dssp             CCCCSC
T ss_pred             EcCCCC
Confidence            997643

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

Probab=99.88  E-value=2.1e-21  Score=136.18  Aligned_cols=83  Identities=25%  Similarity=0.444  Sum_probs=77.9

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      .....++|||+|||.++|+++|+++|+.||.|..|.|+.++ +++++|||||+|.+.++|++|| .||+..|.|+.|+|+
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            45567999999999999999999999999999999999987 6899999999999999999999 699999999999999


Q ss_pred             eccCC
Q 030488          121 VKRTN  125 (176)
Q Consensus       121 ~a~~~  125 (176)
                      ++++.
T Consensus       118 ~a~~~  122 (139)
T 1u6f_A          118 LAASG  122 (139)
T ss_dssp             ESSCC
T ss_pred             ECCCC
Confidence            99864

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

Probab=99.88  E-value=6.3e-22  Score=131.99  Aligned_cols=84  Identities=29%  Similarity=0.519  Sum_probs=78.2

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      .....++|||+|||+++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|| .||+..|+|+.|.|+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34567999999999999999999999999999999999988 6999999999999999999999 699999999999999


Q ss_pred             eccCCC
Q 030488          121 VKRTNV  126 (176)
Q Consensus       121 ~a~~~~  126 (176)
                      +++...
T Consensus        89 ~a~~~~   94 (103)
T 2dnm_A           89 VARYGR   94 (103)
T ss_dssp             ECSSCC
T ss_pred             ECCcCC
Confidence            998654

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

Probab=99.87  E-value=2.6e-21  Score=129.33  Aligned_cols=83  Identities=28%  Similarity=0.397  Sum_probs=78.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCC---eeeEE
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHG---RQLKV  119 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g---~~i~v  119 (176)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.++++.++|||||+|.+.++|++|| .||+..+.+   +.|.|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            45689999999999999999999999999999999999999999999999999999999999 699999988   99999


Q ss_pred             EeccCCC
Q 030488          120 TVKRTNV  126 (176)
Q Consensus       120 ~~a~~~~  126 (176)
                      .+++...
T Consensus        92 ~~a~~~~   98 (105)
T 2dnh_A           92 KFADTDK   98 (105)
T ss_dssp             EESCSSC
T ss_pred             EECccCc
Confidence            9998654

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

Probab=99.87  E-value=1.5e-21  Score=130.49  Aligned_cols=84  Identities=26%  Similarity=0.466  Sum_probs=78.5

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      .....++|||+|||+++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|| .||+..|+|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            44567999999999999999999999999999999999998 7999999999999999999999 699999999999999


Q ss_pred             eccCCC
Q 030488          121 VKRTNV  126 (176)
Q Consensus       121 ~a~~~~  126 (176)
                      ++++..
T Consensus        91 ~a~~~~   96 (105)
T 1x5u_A           91 KASAHN   96 (105)
T ss_dssp             ETTTTS
T ss_pred             ECCCCC
Confidence            997643

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

Probab=99.87  E-value=1.5e-21  Score=129.15  Aligned_cols=83  Identities=25%  Similarity=0.490  Sum_probs=78.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ..+.++|||+|||+++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|| .||+..|.|+.|+|++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            3457899999999999999999999999999999999998 8999999999999999999999 7999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      +++..
T Consensus        85 a~~~~   89 (99)
T 1whw_A           85 STIKK   89 (99)
T ss_dssp             CCCCS
T ss_pred             cCCCc
Confidence            98654

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

Probab=99.87  E-value=4.3e-21  Score=127.98  Aligned_cols=82  Identities=24%  Similarity=0.462  Sum_probs=76.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      ....++|||+|||+++|+++|+++|++|| |..|.|+.++ ++.++|||||+|.+.++|++||.||+..|.|+.|+|+++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   90 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIA   90 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEEEe
Confidence            45578999999999999999999999997 9999999998 799999999999999999999999999999999999999


Q ss_pred             cCCC
Q 030488          123 RTNV  126 (176)
Q Consensus       123 ~~~~  126 (176)
                      ++..
T Consensus        91 ~~~~   94 (103)
T 2dng_A           91 EGRK   94 (103)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            7643

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

Probab=99.87  E-value=1.2e-21  Score=130.34  Aligned_cols=83  Identities=27%  Similarity=0.495  Sum_probs=77.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ..+.++|||+|||+++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|| .||+..|+|+.|+|.+
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            4567899999999999999999999999999999999986 7899999999999999999999 7999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      +++..
T Consensus        89 a~~~~   93 (102)
T 2cqb_A           89 AKPMR   93 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98654

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.87  E-value=1.6e-21  Score=126.45  Aligned_cols=83  Identities=59%  Similarity=1.000  Sum_probs=78.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccC
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~  124 (176)
                      +.++|||+|||+++|+++|+++|++||.|..+.++.++ ++.++|||||+|.+.++|++|+.+|+..|.|+.|+|+++++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEETTT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEccC
Confidence            45899999999999999999999999999999999997 79999999999999999999999999999999999999987


Q ss_pred             CCCC
Q 030488          125 NVPG  128 (176)
Q Consensus       125 ~~~~  128 (176)
                      ..|+
T Consensus        85 ~~pg   88 (89)
T 3ucg_A           85 NRPG   88 (89)
T ss_dssp             TSCC
T ss_pred             CCCC
Confidence            6553

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

Probab=99.87  E-value=3.2e-21  Score=129.30  Aligned_cols=85  Identities=20%  Similarity=0.501  Sum_probs=78.7

Q ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeC-C-CCCceeEEEEEecCHHHHHHHH-Hh-CCCeeCCeee
Q 030488           42 REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-K-FGQPKGYAYVEFLQSEAVQEAL-HL-NESELHGRQL  117 (176)
Q Consensus        42 ~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~-~-~g~~~g~afv~f~~~~~a~~a~-~l-~~~~~~g~~i  117 (176)
                      ......++|||+|||+++|+++|+++|++||.|..|.|+.+ + ++.++|||||+|.+.++|++|| .| |+..|.|+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l   89 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   89 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEE
Confidence            34567899999999999999999999999999999999998 4 7999999999999999999999 68 9999999999


Q ss_pred             EEEeccCCC
Q 030488          118 KVTVKRTNV  126 (176)
Q Consensus       118 ~v~~a~~~~  126 (176)
                      +|+++++..
T Consensus        90 ~v~~a~~~~   98 (107)
T 2cph_A           90 VLEWADSEV   98 (107)
T ss_dssp             EEEECCCCC
T ss_pred             EEEeCCCCC
Confidence            999998653

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

Probab=99.87  E-value=1.7e-21  Score=129.59  Aligned_cols=83  Identities=22%  Similarity=0.523  Sum_probs=77.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ..+.++|||+|||+++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|| .||+..|+|+.|+|++
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            4567899999999999999999999999999999999987 7889999999999999999999 7999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      +++..
T Consensus        89 a~~~~   93 (102)
T 1x5s_A           89 AGKSS   93 (102)
T ss_dssp             EECCC
T ss_pred             CCCCC
Confidence            97643

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

Probab=99.87  E-value=8.1e-21  Score=126.58  Aligned_cols=84  Identities=23%  Similarity=0.432  Sum_probs=77.0

Q ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           42 REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        42 ~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      ......++|||+|||+++|+++|+++|++||.|..|.|+.++.+ +++||||+|.+.++|++|| .||+..|+|+.|+|+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   88 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   88 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34566799999999999999999999999999999999988754 8999999999999999999 699999999999999


Q ss_pred             eccCCC
Q 030488          121 VKRTNV  126 (176)
Q Consensus       121 ~a~~~~  126 (176)
                      ++++..
T Consensus        89 ~a~~~~   94 (103)
T 2cq3_A           89 NATARV   94 (103)
T ss_dssp             ECCSSC
T ss_pred             EcccCC
Confidence            998654

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

Probab=99.87  E-value=2.1e-21  Score=125.38  Aligned_cols=80  Identities=24%  Similarity=0.438  Sum_probs=74.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      .+.++|||+|||.++++++|+++|++||.|.+|.++.++ ++.++|||||+|.+.++|++|+ .||+..++|+.|+|+++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            356899999999999999999999999999999999997 7999999999999999999999 69999999999999999


Q ss_pred             cC
Q 030488          123 RT  124 (176)
Q Consensus       123 ~~  124 (176)
                      ++
T Consensus        84 ~~   85 (87)
T 3bs9_A           84 TR   85 (87)
T ss_dssp             C-
T ss_pred             CC
Confidence            75

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

Probab=99.87  E-value=3.5e-21  Score=129.87  Aligned_cols=84  Identities=27%  Similarity=0.467  Sum_probs=78.0

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhC------CCeeCC
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLN------ESELHG  114 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~------~~~~~g  114 (176)
                      .....++|||+|||+++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|| .+|      +..|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            44567899999999999999999999999999999999997 6899999999999999999999 699      999999


Q ss_pred             eeeEEEeccCCC
Q 030488          115 RQLKVTVKRTNV  126 (176)
Q Consensus       115 ~~i~v~~a~~~~  126 (176)
                      +.|+|.++.+..
T Consensus        91 ~~l~v~~a~~~~  102 (111)
T 1x4h_A           91 RQLKVDLAVTRD  102 (111)
T ss_dssp             CEEEEECCCCCC
T ss_pred             EEEEEEECCCCc
Confidence            999999997643

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

Probab=99.87  E-value=2.9e-21  Score=128.99  Aligned_cols=82  Identities=26%  Similarity=0.500  Sum_probs=76.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-C-CCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-F-GQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~-g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~  121 (176)
                      ....++|||+|||+++|+++|+++|++|| |..|.|+.++ + +.++|||||+|.+.++|++||.||+..|.|+.|.|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEEEEE
Confidence            45578999999999999999999999999 9999999988 5 8999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      +++..
T Consensus        91 a~~~~   95 (104)
T 1wi8_A           91 ADQAQ   95 (104)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            98643

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

Probab=99.87  E-value=2.3e-21  Score=129.38  Aligned_cols=83  Identities=19%  Similarity=0.311  Sum_probs=77.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhh-CCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCe-eCCeeeEEE
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQS-CGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESE-LHGRQLKVT  120 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~-~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~-~~g~~i~v~  120 (176)
                      ....++|||+|||+++|+++|+++|++ ||.|..|.|+.++++.++|||||+|.+.++|++|| .|++.. |+|+.|.|+
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            345789999999999999999999999 99999999999999999999999999999999999 699999 999999999


Q ss_pred             eccCCC
Q 030488          121 VKRTNV  126 (176)
Q Consensus       121 ~a~~~~  126 (176)
                      ++.+..
T Consensus        86 ~a~~~~   91 (104)
T 2dhg_A           86 VAIPKA   91 (104)
T ss_dssp             BCCCCC
T ss_pred             EccCCC
Confidence            997543

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

Probab=99.87  E-value=1.6e-21  Score=128.30  Aligned_cols=82  Identities=26%  Similarity=0.438  Sum_probs=76.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEE-EEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRV-TIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~-~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ...++|||+|||+++|+++|+++|++||.|..+ .|+.++ ++.++|||||+|.+.++|++|+ .||+..|+|+.|+|++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            457899999999999999999999999999999 999985 7999999999999999999999 5999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      +.+..
T Consensus        83 a~~~~   87 (96)
T 1x5t_A           83 AFKKD   87 (96)
T ss_dssp             SCCCC
T ss_pred             ecccC
Confidence            97643

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.87  E-value=2.2e-21  Score=125.39  Aligned_cols=80  Identities=25%  Similarity=0.535  Sum_probs=75.1

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~  121 (176)
                      ...+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|+++++..|+|+.|.|++
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34567999999999999999999999999999999999997 79999999999999999999998889999999999987


Q ss_pred             c
Q 030488          122 K  122 (176)
Q Consensus       122 a  122 (176)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

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

Probab=99.87  E-value=4.3e-22  Score=131.22  Aligned_cols=81  Identities=16%  Similarity=0.348  Sum_probs=74.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCC--eeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCC----eeCCe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGT--VNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNES----ELHGR  115 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~--i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~----~~~g~  115 (176)
                      ...-.+|||+|||+++|+++|+++|++||.  |.+|+|++|+ +++++|||||+|.+.++|++|| .||+.    .|+|+
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr   85 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK   85 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTE
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCE
Confidence            345689999999999999999999999995  5799999998 7999999999999999999999 69886    58999


Q ss_pred             eeEEEeccC
Q 030488          116 QLKVTVKRT  124 (176)
Q Consensus       116 ~i~v~~a~~  124 (176)
                      .|.|++|++
T Consensus        86 ~i~V~~Aks   94 (95)
T 2lkz_A           86 TIGVDFAKS   94 (95)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEccC
Confidence            999999975

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

Probab=99.87  E-value=3.4e-21  Score=123.35  Aligned_cols=79  Identities=22%  Similarity=0.447  Sum_probs=74.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      +.+|||+|||+++++++|+++|++||.|.++.++.++ ++.++|||||+|.+.++|++|+ .||+..++|+.|+|+++++
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            3589999999999999999999999999999999996 7999999999999999999999 6999999999999999975


Q ss_pred             C
Q 030488          125 N  125 (176)
Q Consensus       125 ~  125 (176)
                      .
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.87  E-value=6.6e-21  Score=126.99  Aligned_cols=83  Identities=24%  Similarity=0.428  Sum_probs=76.0

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      .....++|||+|||+++++++|+++|++||.|..|.|+.++.+ +++||||+|.+.++|++|| .||+..|.|+.|+|++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            4566899999999999999999999999999999999988644 6899999999999999999 6999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      +++..
T Consensus        90 a~~~~   94 (103)
T 2cqi_A           90 ATTPS   94 (103)
T ss_dssp             CCCTT
T ss_pred             CCCCc
Confidence            98643

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

Probab=99.87  E-value=2e-21  Score=130.16  Aligned_cols=85  Identities=20%  Similarity=0.419  Sum_probs=78.1

Q ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCee---CCee
Q 030488           42 REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESEL---HGRQ  116 (176)
Q Consensus        42 ~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~---~g~~  116 (176)
                      ......++|||+|||.++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|| .||+..+   .|+.
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~   87 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRP   87 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCce
Confidence            345667999999999999999999999999999999999988 6999999999999999999999 6999988   8999


Q ss_pred             eEEEeccCCC
Q 030488          117 LKVTVKRTNV  126 (176)
Q Consensus       117 i~v~~a~~~~  126 (176)
                      |.|.+++...
T Consensus        88 l~v~~a~~~~   97 (106)
T 2dgp_A           88 IQVKPADSES   97 (106)
T ss_dssp             CEEEECCCCS
T ss_pred             EEEEECCccc
Confidence            9999997643

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

Probab=99.87  E-value=3.1e-21  Score=126.62  Aligned_cols=82  Identities=23%  Similarity=0.359  Sum_probs=76.6

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      .....++|||+|||+++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|+ .||+..|+|+.|+|+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS   90 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34557899999999999999999999999999999999988 6899999999999999999999 699999999999999


Q ss_pred             eccC
Q 030488          121 VKRT  124 (176)
Q Consensus       121 ~a~~  124 (176)
                      ++++
T Consensus        91 ~a~~   94 (95)
T 2cqc_A           91 GPSS   94 (95)
T ss_dssp             CCSC
T ss_pred             ecCC
Confidence            9864

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

Probab=99.87  E-value=1.8e-21  Score=127.83  Aligned_cols=82  Identities=34%  Similarity=0.551  Sum_probs=76.9

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      .....++|||+|||+++++++|+++|++||.|..|.|+.++++.++|||||+|.+.++|++|+ .||+..|+|+.|+|++
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            345578999999999999999999999999999999999988999999999999999999999 6999999999999999


Q ss_pred             ccC
Q 030488          122 KRT  124 (176)
Q Consensus       122 a~~  124 (176)
                      ++.
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            864

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

Probab=99.86  E-value=1.3e-21  Score=139.97  Aligned_cols=83  Identities=27%  Similarity=0.519  Sum_probs=77.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      .....+|||+|||+++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|| .||+..|.|+.|.|.+
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  146 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  146 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            4557899999999999999999999999999999999997 7999999999999999999999 6999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      +++..
T Consensus       147 a~~~~  151 (158)
T 2kn4_A          147 ARYGR  151 (158)
T ss_dssp             ECCSS
T ss_pred             CCCCC
Confidence            98654

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

Probab=99.86  E-value=2.2e-21  Score=129.93  Aligned_cols=83  Identities=27%  Similarity=0.453  Sum_probs=77.5

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      ...+.++|||+|||.++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|+ .||+..|.|+.|.|+
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   98 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999998 6999999999999999999999 699999999999999


Q ss_pred             eccCC
Q 030488          121 VKRTN  125 (176)
Q Consensus       121 ~a~~~  125 (176)
                      ++++.
T Consensus        99 ~a~~~  103 (106)
T 1p27_B           99 WCFVR  103 (106)
T ss_dssp             ESEES
T ss_pred             eecCC
Confidence            99764

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

Probab=99.86  E-value=5.1e-22  Score=138.97  Aligned_cols=120  Identities=21%  Similarity=0.377  Sum_probs=80.4

Q ss_pred             HHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCcccccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-
Q 030488            5 LKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-   83 (176)
Q Consensus         5 ~~e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-   83 (176)
                      |.+.+++..+..+|..............   ............++|||+|||+++|+++|+++|++||.|..|.|+.++ 
T Consensus         8 ~~~~~~~~~~~~a~~~~~g~~~~g~~~~---~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~   84 (135)
T 2lea_A            8 HHHSSGLVPRGSHMASMTGGQQMGRGSM---SYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY   84 (135)
T ss_dssp             ---------------------------C---CSCCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSS
T ss_pred             cccccCCCchhhhhhhccCCCCCCCCCC---CcCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC
Confidence            5566677667776666544332222111   112223344567899999999999999999999999999999999987 


Q ss_pred             CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccCCCC
Q 030488           84 FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVP  127 (176)
Q Consensus        84 ~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~~~~  127 (176)
                      ++.++|||||+|.+.++|++|| .||+..|.|+.|+|+++++..+
T Consensus        85 ~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~  129 (135)
T 2lea_A           85 TKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  129 (135)
T ss_dssp             SSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCC
T ss_pred             CCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            7999999999999999999999 6999999999999999986543

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

Probab=99.86  E-value=3.6e-21  Score=130.37  Aligned_cols=85  Identities=28%  Similarity=0.560  Sum_probs=78.4

Q ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCee--------EEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCe
Q 030488           42 REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVN--------RVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESE  111 (176)
Q Consensus        42 ~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~--------~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~  111 (176)
                      .+....++|||+|||+++|+++|+++|++||.|.        .|.|+.++ ++.++|||||+|.+.++|++|| .||+..
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   89 (113)
T 2cpe_A           10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   89 (113)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCc
Confidence            3456789999999999999999999999999998        69999996 7999999999999999999999 699999


Q ss_pred             eCCeeeEEEeccCCC
Q 030488          112 LHGRQLKVTVKRTNV  126 (176)
Q Consensus       112 ~~g~~i~v~~a~~~~  126 (176)
                      |.|+.|+|++++...
T Consensus        90 ~~g~~l~V~~a~~~~  104 (113)
T 2cpe_A           90 FQGSKLKVSLARKKP  104 (113)
T ss_dssp             ETTEECEEECSSCCC
T ss_pred             cCCCEEEEEECCCCC
Confidence            999999999998643

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

Probab=99.86  E-value=2.4e-21  Score=131.92  Aligned_cols=78  Identities=26%  Similarity=0.445  Sum_probs=72.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccCC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTN  125 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~~  125 (176)
                      ..+|||+|||+++|+++|+++|++||.|.+|+|+.++ +.++|||||+|.+.++|++|| .|++..|+|+.|+|.++++.
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~-~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC-CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            5689999999999999999999999999999999886 347999999999999999999 79999999999999998754

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

Probab=99.86  E-value=1.8e-21  Score=125.17  Aligned_cols=80  Identities=28%  Similarity=0.530  Sum_probs=75.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ..+.++|||+|||+++++++|+++|++||.|..+.++.++ ++.++|||||+|.+.++|++|+ .||+..++|+.|+|++
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            3467899999999999999999999999999999999886 7899999999999999999999 7999999999999998


Q ss_pred             cc
Q 030488          122 KR  123 (176)
Q Consensus       122 a~  123 (176)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=1.1e-21  Score=131.16  Aligned_cols=81  Identities=19%  Similarity=0.308  Sum_probs=76.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEecc
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKR  123 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~  123 (176)
                      +...++|||+|||+++|+++|+++|++||.|.+|.|+.++.+.++|||||+|.+.++|++||.+++..|+|+.|.|.++.
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   87 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEHH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEch
Confidence            44568999999999999999999999999999999999988999999999999999999999999999999999999874


Q ss_pred             C
Q 030488          124 T  124 (176)
Q Consensus       124 ~  124 (176)
                      .
T Consensus        88 ~   88 (103)
T 1s79_A           88 D   88 (103)
T ss_dssp             H
T ss_pred             H
Confidence            3

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=1.3e-20  Score=125.58  Aligned_cols=85  Identities=19%  Similarity=0.388  Sum_probs=77.1

Q ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEE
Q 030488           41 NREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV  119 (176)
Q Consensus        41 ~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v  119 (176)
                      .....+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++||. +++.|+|+.|.|
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~l~v   87 (103)
T 2cqg_A            9 KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDC   87 (103)
T ss_dssp             SCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEE
T ss_pred             CCccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH-cCCeeCCeEEEE
Confidence            3345667899999999999999999999999999999999997 79999999999999999999997 467999999999


Q ss_pred             EeccCCC
Q 030488          120 TVKRTNV  126 (176)
Q Consensus       120 ~~a~~~~  126 (176)
                      .++.+..
T Consensus        88 ~~a~~~~   94 (103)
T 2cqg_A           88 KLPNSKQ   94 (103)
T ss_dssp             ECCCTTC
T ss_pred             EecCCCC
Confidence            9997643

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

Probab=99.86  E-value=3.6e-21  Score=126.09  Aligned_cols=81  Identities=30%  Similarity=0.505  Sum_probs=75.9

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      .....++|||+|||+++++++|+++|++||.|..|.|+.++ ++.+++||||+|.+.++|++|+ .||+..|.|+.|+|+
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   91 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS   91 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            34567899999999999999999999999999999999987 6899999999999999999999 799999999999999


Q ss_pred             ecc
Q 030488          121 VKR  123 (176)
Q Consensus       121 ~a~  123 (176)
                      +++
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            975

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.86  E-value=5.3e-22  Score=129.36  Aligned_cols=79  Identities=24%  Similarity=0.399  Sum_probs=70.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCC--CeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCG--TVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G--~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      .+|||+|||+++|+++|+++|++||  .|.++.|+.++ +|+++|||||+|.+.++|++|| .||+..|+|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5799999999999999999999999  99999999998 8999999999999999999999 799999999999999997


Q ss_pred             CCC
Q 030488          124 TNV  126 (176)
Q Consensus       124 ~~~  126 (176)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            654

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=2.6e-21  Score=129.08  Aligned_cols=81  Identities=21%  Similarity=0.339  Sum_probs=74.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEecc
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKR  123 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~  123 (176)
                      ....++|||+|||+++|+++|+++|++||.+ .|.|+.+++++++|||||+|.+.++|++||++|+..|+++.|+|..+.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~~   90 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNS   90 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECC
Confidence            3556899999999999999999999999954 999999999999999999999999999999889999999999999886


Q ss_pred             CC
Q 030488          124 TN  125 (176)
Q Consensus       124 ~~  125 (176)
                      ..
T Consensus        91 ~~   92 (102)
T 1wez_A           91 TA   92 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

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

Probab=99.86  E-value=6e-21  Score=126.36  Aligned_cols=81  Identities=26%  Similarity=0.450  Sum_probs=75.8

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeE--------EEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCee
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNR--------VTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESEL  112 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~--------~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~  112 (176)
                      .....++|||+|||+++|+++|+++|++||.|..        +.|+.++ ++.++|||||+|.+.++|++|+ .||+..|
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            3456799999999999999999999999999999        9999997 7999999999999999999999 6999999


Q ss_pred             CCeeeEEEecc
Q 030488          113 HGRQLKVTVKR  123 (176)
Q Consensus       113 ~g~~i~v~~a~  123 (176)
                      .|+.|+|++|+
T Consensus        89 ~g~~l~V~~A~   99 (99)
T 2la6_A           89 SGNPIKVSFAT   99 (99)
T ss_dssp             SSSBCEEEECC
T ss_pred             CCcEEEEEecC
Confidence            99999999874

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

Probab=99.86  E-value=4.4e-21  Score=128.28  Aligned_cols=83  Identities=27%  Similarity=0.441  Sum_probs=77.1

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~  121 (176)
                      .....++|||+|||+++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++||..++..|+|+.|.|++
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKP   91 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEEE
Confidence            45667999999999999999999999999999999999997 79999999999999999999995599999999999999


Q ss_pred             ccCC
Q 030488          122 KRTN  125 (176)
Q Consensus       122 a~~~  125 (176)
                      +.+.
T Consensus        92 a~~~   95 (105)
T 2dh8_A           92 CTPR   95 (105)
T ss_dssp             SCCS
T ss_pred             ccCC
Confidence            8754

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

Probab=99.86  E-value=3.5e-21  Score=129.81  Aligned_cols=84  Identities=25%  Similarity=0.424  Sum_probs=78.1

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      ...+.++|||+|||+++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|+ .||+..|+|+.|+|+
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999987 7999999999999999999999 699999999999999


Q ss_pred             eccCCC
Q 030488          121 VKRTNV  126 (176)
Q Consensus       121 ~a~~~~  126 (176)
                      ++++..
T Consensus       102 ~a~~~~  107 (110)
T 1oo0_B          102 WCFVKG  107 (110)
T ss_dssp             ESEESS
T ss_pred             EcccCC
Confidence            997643

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.86  E-value=1e-20  Score=126.18  Aligned_cols=77  Identities=22%  Similarity=0.453  Sum_probs=70.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ..+.++|||+|||+++|+++|+++|++||.|..|.|+       ++||||+|.+.++|++|| .||+..|+|+.|.|+++
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            3457899999999999999999999999999999987       569999999999999999 69999999999999999


Q ss_pred             cCCCC
Q 030488          123 RTNVP  127 (176)
Q Consensus       123 ~~~~~  127 (176)
                      ++...
T Consensus        81 ~~~~~   85 (103)
T 2dgu_A           81 KPPDQ   85 (103)
T ss_dssp             CCCCC
T ss_pred             CCCcc
Confidence            86543

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

Probab=99.86  E-value=5.4e-21  Score=125.92  Aligned_cols=79  Identities=32%  Similarity=0.513  Sum_probs=75.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      +++|||+|||.++++++|+++|++||.|.+|.|+.++ ++.++|||||+|.+.++|++|+ .|++..|+|+.|+|+++++
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            5799999999999999999999999999999999997 7999999999999999999999 7999999999999999976


Q ss_pred             C
Q 030488          125 N  125 (176)
Q Consensus       125 ~  125 (176)
                      .
T Consensus        82 ~   82 (96)
T 2x1f_A           82 S   82 (96)
T ss_dssp             S
T ss_pred             C
Confidence            4

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

Probab=99.86  E-value=9.8e-21  Score=127.39  Aligned_cols=77  Identities=22%  Similarity=0.390  Sum_probs=71.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCC-----eeeE
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHG-----RQLK  118 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g-----~~i~  118 (176)
                      ...++|||+|||+++|+++|+++|++||.|..|.|+.+      |||||+|.+.++|++|| .||+..|.|     +.|+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~   86 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   86 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEE
Confidence            45789999999999999999999999999999999875      89999999999999999 699999999     9999


Q ss_pred             EEeccCCCC
Q 030488          119 VTVKRTNVP  127 (176)
Q Consensus       119 v~~a~~~~~  127 (176)
                      |+++++..+
T Consensus        87 V~~a~~~~~   95 (108)
T 1x4c_A           87 VKVDGPRSP   95 (108)
T ss_dssp             EEESSCCSC
T ss_pred             EEeCCCCCC
Confidence            999987543

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

Probab=99.86  E-value=8e-21  Score=127.39  Aligned_cols=80  Identities=23%  Similarity=0.441  Sum_probs=76.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ....++|||+|||+++|+++|+++|++||.|..|.|+.+++++++|||||+|.+.++|++|| .||+..|.|+.|+|+++
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  105 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV  105 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            45678999999999999999999999999999999999999999999999999999999999 69999999999999998


Q ss_pred             c
Q 030488          123 R  123 (176)
Q Consensus       123 ~  123 (176)
                      .
T Consensus       106 ~  106 (107)
T 3ulh_A          106 T  106 (107)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.86  E-value=2.6e-21  Score=133.12  Aligned_cols=85  Identities=53%  Similarity=0.985  Sum_probs=78.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      ..+.++|||+|||+++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++||.||+..|+|+.|+|+++
T Consensus        33 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a  112 (124)
T 2jwn_A           33 EIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPK  112 (124)
T ss_dssp             HHHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEEC
Confidence            3457899999999999999999999999999999999986 799999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 030488          123 RTNVPG  128 (176)
Q Consensus       123 ~~~~~~  128 (176)
                      ++..++
T Consensus       113 ~~~~~~  118 (124)
T 2jwn_A          113 RTNMPG  118 (124)
T ss_dssp             SCCCSS
T ss_pred             CCCCCC
Confidence            875543

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

Probab=99.86  E-value=4.1e-21  Score=131.03  Aligned_cols=81  Identities=22%  Similarity=0.366  Sum_probs=75.6

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      ...+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|+ .||+..|+|+.|+|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45567999999999999999999999999999999999987 7999999999999999999999 699999999999999


Q ss_pred             ecc
Q 030488          121 VKR  123 (176)
Q Consensus       121 ~a~  123 (176)
                      +++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            874

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

Probab=99.86  E-value=7.8e-21  Score=125.49  Aligned_cols=82  Identities=28%  Similarity=0.538  Sum_probs=75.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCC--C--CceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEE
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF--G--QPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV  119 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~--g--~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v  119 (176)
                      .+.++|||+|||+++|+++|+++|++||.|..|.|+.++.  |  .++|||||+|.+.++|++|+ .||+..|+|+.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            3568999999999999999999999999999999998763  3  88999999999999999999 69999999999999


Q ss_pred             EeccCCC
Q 030488          120 TVKRTNV  126 (176)
Q Consensus       120 ~~a~~~~  126 (176)
                      ++++...
T Consensus        83 ~~a~~~~   89 (98)
T 2cpf_A           83 RISERAT   89 (98)
T ss_dssp             ECSSCSS
T ss_pred             EEccCCC
Confidence            9997643

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

Probab=99.86  E-value=4.7e-21  Score=130.40  Aligned_cols=82  Identities=17%  Similarity=0.403  Sum_probs=76.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      ....++|||+|||+++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++||..++..|+|+.|+|.++
T Consensus        24 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a  103 (116)
T 1x4b_A           24 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEEC
Confidence            3456899999999999999999999999999999999997 699999999999999999999955999999999999999


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      .+.
T Consensus       104 ~~~  106 (116)
T 1x4b_A          104 VAR  106 (116)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            764

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

Probab=99.85  E-value=6.4e-21  Score=126.14  Aligned_cols=81  Identities=22%  Similarity=0.420  Sum_probs=76.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCee-EEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCee----e
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVN-RVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQ----L  117 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~-~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~----i  117 (176)
                      ...++|||+|||+++++++|+++|++||.|. .|.|+.++ ++.++|||||+|.+.++|++|+ .||+..|.|+.    |
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l   86 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF   86 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeE
Confidence            4578999999999999999999999999999 99999998 7999999999999999999999 59999999999    9


Q ss_pred             EEEeccCC
Q 030488          118 KVTVKRTN  125 (176)
Q Consensus       118 ~v~~a~~~  125 (176)
                      +|.+++..
T Consensus        87 ~v~~a~~~   94 (99)
T 2div_A           87 KLNYATYS   94 (99)
T ss_dssp             CEEETTCC
T ss_pred             EEeecCCC
Confidence            99999754

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

Probab=99.85  E-value=2.6e-20  Score=125.40  Aligned_cols=81  Identities=17%  Similarity=0.391  Sum_probs=74.0

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      .....++|||+|||+++|+++|+++|++||.|..|.|..  ++.+++||||+|.+.++|++|| .||+..|+|+.|+|++
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN--RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC--SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE--CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            455679999999999999999999999999999999954  4567999999999999999999 7999999999999999


Q ss_pred             ccCC
Q 030488          122 KRTN  125 (176)
Q Consensus       122 a~~~  125 (176)
                      +++.
T Consensus        96 a~~~   99 (109)
T 1x4a_A           96 PRSG   99 (109)
T ss_dssp             CCCC
T ss_pred             cccC
Confidence            9764

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.85  E-value=2.9e-21  Score=134.36  Aligned_cols=84  Identities=14%  Similarity=0.302  Sum_probs=77.5

Q ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeE--EEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCC----eeC
Q 030488           42 REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNR--VTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNES----ELH  113 (176)
Q Consensus        42 ~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~--~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~----~~~  113 (176)
                      ......++|||+|||+++|+++|+++|++||.|..  |+|++++ +++++|||||+|.+. +|++|| .||+.    .|+
T Consensus        18 ~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~   96 (131)
T 2m2b_A           18 SSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTID   96 (131)
T ss_dssp             CCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGG
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCC
Confidence            34566889999999999999999999999999976  9999999 899999999999999 999999 79999    999


Q ss_pred             CeeeEEEeccCCC
Q 030488          114 GRQLKVTVKRTNV  126 (176)
Q Consensus       114 g~~i~v~~a~~~~  126 (176)
                      |+.|+|+++++..
T Consensus        97 gr~l~V~~a~~~~  109 (131)
T 2m2b_A           97 GKTINVEFAKGSK  109 (131)
T ss_dssp             GCCCCCEECCCSC
T ss_pred             CEEEEEEECCCCC
Confidence            9999999997643

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

Probab=99.85  E-value=1.2e-20  Score=123.09  Aligned_cols=82  Identities=27%  Similarity=0.492  Sum_probs=75.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+ ++.+++||||+|.+.++|++|+ .||+..|+|+.|+|+++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            345789999999999999999999999999999999874 7889999999999999999999 69999999999999999


Q ss_pred             cCCC
Q 030488          123 RTNV  126 (176)
Q Consensus       123 ~~~~  126 (176)
                      ++..
T Consensus        84 ~~~~   87 (92)
T 2dgv_A           84 RNAS   87 (92)
T ss_dssp             SCCS
T ss_pred             CCCC
Confidence            8643

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=7.6e-22  Score=134.13  Aligned_cols=82  Identities=24%  Similarity=0.315  Sum_probs=76.6

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCe-eEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i-~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~  121 (176)
                      ...+.++|||+|||+++|+++|+++|++||.| ..|.|+.+++++++|||||+|.+.++|++||.+|+..|+|+.|.|.+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHV   90 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEEE
Confidence            34567899999999999999999999999999 89999999999999999999999999999996699999999999999


Q ss_pred             ccC
Q 030488          122 KRT  124 (176)
Q Consensus       122 a~~  124 (176)
                      +..
T Consensus        91 a~~   93 (114)
T 2cpy_A           91 VTL   93 (114)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            864

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.85  E-value=5.4e-21  Score=123.63  Aligned_cols=81  Identities=22%  Similarity=0.515  Sum_probs=74.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCC-ceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQ-PKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~-~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ..++|||+|||.++|+++|+++|++||.|..+.|+.+. ++. ++|||||+|.+.++|++|+ .||+..++|+.|+|+++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            46899999999999999999999999999999999887 343 8999999999999999999 69999999999999999


Q ss_pred             cCCC
Q 030488          123 RTNV  126 (176)
Q Consensus       123 ~~~~  126 (176)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

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

Probab=99.85  E-value=1.1e-20  Score=127.28  Aligned_cols=83  Identities=28%  Similarity=0.540  Sum_probs=77.5

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      .....++|||+|||.++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|+ .|++..|.|+.|+|+
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999987 7899999999999999999999 699999999999999


Q ss_pred             eccCC
Q 030488          121 VKRTN  125 (176)
Q Consensus       121 ~a~~~  125 (176)
                      ++++.
T Consensus       102 ~a~~k  106 (108)
T 2jrs_A          102 HVTER  106 (108)
T ss_dssp             CSCSS
T ss_pred             EcccC
Confidence            99754

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=6.3e-21  Score=125.94  Aligned_cols=82  Identities=18%  Similarity=0.295  Sum_probs=75.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ....++|||+|||+++++++|+++|++||.|..+.++.++ +++++|||||+|.+.++|++|| .||+..|+|+.|+|++
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            3456899999999999999999999999999888777766 7999999999999999999999 7999999999999999


Q ss_pred             ccCC
Q 030488          122 KRTN  125 (176)
Q Consensus       122 a~~~  125 (176)
                      ++.+
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8754

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

Probab=99.85  E-value=2.2e-20  Score=121.74  Aligned_cols=81  Identities=21%  Similarity=0.386  Sum_probs=76.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEecc
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKR  123 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~  123 (176)
                      ....++|||+|||+++|+++|+++|++| .|..|.|+.+.+++++|||||+|.+.++|++||.+|+..|+|+.|.|.++.
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~a~   85 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFREK   85 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEEES
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEECC
Confidence            4567899999999999999999999999 999999999988999999999999999999999999999999999999997


Q ss_pred             CC
Q 030488          124 TN  125 (176)
Q Consensus       124 ~~  125 (176)
                      ..
T Consensus        86 ~~   87 (91)
T 2dgw_A           86 SG   87 (91)
T ss_dssp             SC
T ss_pred             cC
Confidence            64

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.85  E-value=1.1e-20  Score=136.26  Aligned_cols=85  Identities=26%  Similarity=0.449  Sum_probs=77.5

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      .....++|||+|||+++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|| .||+..|.|+.|.|.
T Consensus        68 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  147 (165)
T 1rk8_A           68 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  147 (165)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34557889999999999999999999999999999999997 8999999999999999999999 699999999999999


Q ss_pred             eccCCCC
Q 030488          121 VKRTNVP  127 (176)
Q Consensus       121 ~a~~~~~  127 (176)
                      ++.+..+
T Consensus       148 ~a~~~~~  154 (165)
T 1rk8_A          148 WCFVKGP  154 (165)
T ss_dssp             ESEECC-
T ss_pred             EecCCCC
Confidence            9976543

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

Probab=99.85  E-value=6.1e-21  Score=132.49  Aligned_cols=84  Identities=24%  Similarity=0.352  Sum_probs=78.2

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      ...+.++|||+|||+++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|| .|++..|+|+.|+|+
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~  121 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD  121 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEES
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999987 7899999999999999999999 699999999999999


Q ss_pred             eccCCC
Q 030488          121 VKRTNV  126 (176)
Q Consensus       121 ~a~~~~  126 (176)
                      ++++..
T Consensus       122 ~a~~~~  127 (129)
T 2kxn_B          122 FSITKR  127 (129)
T ss_dssp             CCSSSS
T ss_pred             EecCCC
Confidence            998654

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=2.6e-20  Score=124.54  Aligned_cols=81  Identities=22%  Similarity=0.388  Sum_probs=75.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeE-EEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNR-VTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~-~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      ....++|||+|||+++|+++|+++|++||.|.. |.|+.+.+++++|||||+|.+.++|++||..++..|+|+.|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~~   91 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEEC
Confidence            456789999999999999999999999999987 8898888899999999999999999999965999999999999988


Q ss_pred             cC
Q 030488          123 RT  124 (176)
Q Consensus       123 ~~  124 (176)
                      ..
T Consensus        92 ~~   93 (104)
T 1wg5_A           92 SR   93 (104)
T ss_dssp             CT
T ss_pred             CH
Confidence            64

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=3.6e-21  Score=130.61  Aligned_cols=82  Identities=32%  Similarity=0.504  Sum_probs=76.7

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~  121 (176)
                      .+...++|||+|||+++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++||.||+..|+|+.|.|.+
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~  100 (114)
T 2cq4_A           21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQA  100 (114)
T ss_dssp             THHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEE
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEe
Confidence            34457899999999999999999999999999999999988 68999999999999999999999999999999999999


Q ss_pred             ccC
Q 030488          122 KRT  124 (176)
Q Consensus       122 a~~  124 (176)
                      ++.
T Consensus       101 a~~  103 (114)
T 2cq4_A          101 SQA  103 (114)
T ss_dssp             HHH
T ss_pred             cCC
Confidence            864

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.84  E-value=1.3e-21  Score=130.02  Aligned_cols=79  Identities=15%  Similarity=0.282  Sum_probs=74.8

Q ss_pred             CCCEEEEcCCCC------CCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCC-ee
Q 030488           46 DSRSVFVGNVDY------SCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHG-RQ  116 (176)
Q Consensus        46 ~~~~i~v~~lp~------~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g-~~  116 (176)
                      ..++|||+|||+      ++++++|+++|++||.|.+|.|++++ |++++|||||+|.+.++|++|| .||+..|.| +.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            467999999999      99999999999999999999999998 6999999999999999999999 799999999 99


Q ss_pred             eEEEeccC
Q 030488          117 LKVTVKRT  124 (176)
Q Consensus       117 i~v~~a~~  124 (176)
                      |+|.++.+
T Consensus        85 l~V~~a~~   92 (100)
T 3ns6_A           85 LFLYTMKD   92 (100)
T ss_dssp             CEEEESHH
T ss_pred             EEEEECch
Confidence            99999864

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.84  E-value=1.6e-20  Score=134.38  Aligned_cols=79  Identities=27%  Similarity=0.404  Sum_probs=74.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCC--CeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCG--TVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G--~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ..++|||+|||+++|+++|+++|++||  .|..|.|+.|+ +|+++|||||+|.+.++|++|| .||+..|+|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            468999999999999999999999999  99999999997 7999999999999999999999 6999999999999999


Q ss_pred             ccC
Q 030488          122 KRT  124 (176)
Q Consensus       122 a~~  124 (176)
                      +..
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            853

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.84  E-value=1.4e-20  Score=128.64  Aligned_cols=81  Identities=23%  Similarity=0.359  Sum_probs=76.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCC---eeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEE
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGT---VNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVT  120 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~---i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~  120 (176)
                      ....++|||+|||+++|+++|+++|+.||.   |..|.|+.++.++++|||||+|.+.++|++||.+|+..|+|+.|+|.
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~   93 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVF   93 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEE
Confidence            456789999999999999999999999999   89999999989999999999999999999999999999999999999


Q ss_pred             eccC
Q 030488          121 VKRT  124 (176)
Q Consensus       121 ~a~~  124 (176)
                      ++..
T Consensus        94 ~a~~   97 (118)
T 2db1_A           94 KSHR   97 (118)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8853

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

Probab=99.84  E-value=2.9e-20  Score=123.41  Aligned_cols=80  Identities=29%  Similarity=0.557  Sum_probs=73.2

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      .....++|||+|||+++|+++|+++|++||.|   .++.+.+++++|||||+|.+.++|++|| .||+..|.|+.|+|++
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            34568999999999999999999999999987   5677778999999999999999999999 6999999999999999


Q ss_pred             ccCC
Q 030488          122 KRTN  125 (176)
Q Consensus       122 a~~~  125 (176)
                      +++.
T Consensus        88 a~~~   91 (101)
T 2fc9_A           88 QGPR   91 (101)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            9764

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

Probab=99.84  E-value=3.6e-21  Score=121.02  Aligned_cols=74  Identities=22%  Similarity=0.468  Sum_probs=70.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           49 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        49 ~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      +|||+|||+++++++|+++|++||.|..|.++.++ ++.++|||||+|.+.++|++|+++++..|+|+.|.|.+|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            58999999999999999999999999999999988 799999999999999999999999999999999999875

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=2e-20  Score=123.32  Aligned_cols=79  Identities=20%  Similarity=0.273  Sum_probs=73.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHH----HHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEE
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQ----QHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV  119 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~----~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v  119 (176)
                      .+.++|||+|||+++++++|+    ++|++||.|.+|.|+.++.+  ++||||+|.+.++|++|| .||+..|+|+.|+|
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            356899999999999999999    99999999999999988755  889999999999999999 69999999999999


Q ss_pred             EeccCC
Q 030488          120 TVKRTN  125 (176)
Q Consensus       120 ~~a~~~  125 (176)
                      +++++.
T Consensus        85 ~~a~~~   90 (96)
T 2dgx_A           85 SLATGA   90 (96)
T ss_dssp             EECCCS
T ss_pred             EEcCCC
Confidence            999754

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.84  E-value=1.6e-20  Score=126.60  Aligned_cols=84  Identities=19%  Similarity=0.401  Sum_probs=73.9

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~  121 (176)
                      ...+.++|||+|||+++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++||...+..|+|+.|.|.+
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~~  100 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKV  100 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEEE
Confidence            44567899999999999999999999999999999999987 69999999999999999999996556999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      +.+..
T Consensus       101 a~~~~  105 (109)
T 2rs2_A          101 AFPRR  105 (109)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            97543

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=2.5e-20  Score=125.30  Aligned_cols=82  Identities=21%  Similarity=0.312  Sum_probs=74.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCC-eeEEEEe-eCC-CCCceeEEEEEecCHHHHHHHH-HhC--CCeeCCeeeE
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGT-VNRVTIR-TDK-FGQPKGYAYVEFLQSEAVQEAL-HLN--ESELHGRQLK  118 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~-i~~~~~~-~~~-~g~~~g~afv~f~~~~~a~~a~-~l~--~~~~~g~~i~  118 (176)
                      .+.++|||+|||+++|+++|+++|.+||. |..|.|+ .++ ++.++|||||+|.+.++|++|+ .|+  +..++|+.|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            45689999999999999999999999998 9999998 666 6899999999999999999999 686  5899999999


Q ss_pred             EEeccCCC
Q 030488          119 VTVKRTNV  126 (176)
Q Consensus       119 v~~a~~~~  126 (176)
                      |+++++..
T Consensus        86 V~~a~~~~   93 (109)
T 2dis_A           86 VDWAEPEI   93 (109)
T ss_dssp             EEESCSSC
T ss_pred             EEEcCCCC
Confidence            99997643

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.84  E-value=3.1e-20  Score=125.55  Aligned_cols=84  Identities=27%  Similarity=0.446  Sum_probs=75.6

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHH---HHhhhCCCeeEEEEeeCC-C---CCceeEEEEEecCHHHHHHHH-HhCCCeeCC
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQ---QHFQSCGTVNRVTIRTDK-F---GQPKGYAYVEFLQSEAVQEAL-HLNESELHG  114 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~---~~f~~~G~i~~~~~~~~~-~---g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  114 (176)
                      .....++|||+|||+++++++|+   ++|++||.|..|.|+.++ +   +.++|||||+|.+.++|++|| .||+..|+|
T Consensus        11 r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   90 (111)
T 2cpi_A           11 RVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG   90 (111)
T ss_dssp             CCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             cccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECC
Confidence            34567899999999999999999   999999999999999887 3   356799999999999999999 699999999


Q ss_pred             eeeEEEeccCCC
Q 030488          115 RQLKVTVKRTNV  126 (176)
Q Consensus       115 ~~i~v~~a~~~~  126 (176)
                      +.|+|+++.+..
T Consensus        91 r~l~V~~a~~k~  102 (111)
T 2cpi_A           91 RTLKASLGTTKY  102 (111)
T ss_dssp             EEEEEESCCCCS
T ss_pred             EEEEEEeccccc
Confidence            999999997643

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

Probab=99.84  E-value=5.6e-20  Score=126.52  Aligned_cols=83  Identities=20%  Similarity=0.413  Sum_probs=77.7

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      .....++|||+|||+++++++|+++|++||.|..|.|+.++++.++|||||+|.+.++|++|+ .||+..|+|+.|+|++
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            345678999999999999999999999999999999999989999999999999999999999 6999999999999999


Q ss_pred             ccCC
Q 030488          122 KRTN  125 (176)
Q Consensus       122 a~~~  125 (176)
                      +...
T Consensus       111 a~~~  114 (124)
T 2kt5_A          111 VASQ  114 (124)
T ss_dssp             ECCT
T ss_pred             eCCC
Confidence            9754

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=1.3e-20  Score=127.06  Aligned_cols=78  Identities=26%  Similarity=0.374  Sum_probs=73.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccC
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~  124 (176)
                      +..+|||+|||+++|+++|+++|+.| .|..|.|+.+++|+++|||||+|.+.++|++||.+|+..|+|+.|.|..+..
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCc
Confidence            35799999999999999999999999 8999999999899999999999999999999999999999999999988753

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.84  E-value=1.4e-21  Score=137.19  Aligned_cols=82  Identities=21%  Similarity=0.328  Sum_probs=74.5

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      .....++|||+|||+++|+++|+++|++|| |..|.|+++++++++|||||+|.+.++|++||.+|+..|+++.|+|..+
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLN  120 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEEC
Confidence            345678999999999999999999999999 6799999998999999999999999999999999999999999999988


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      ...
T Consensus       121 ~~~  123 (139)
T 2hgn_A          121 STT  123 (139)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            653

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

Probab=99.83  E-value=1.6e-20  Score=126.65  Aligned_cols=85  Identities=20%  Similarity=0.391  Sum_probs=76.8

Q ss_pred             ccccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeE
Q 030488           40 ANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLK  118 (176)
Q Consensus        40 ~~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~  118 (176)
                      ........++|||+|||.++|+++|+++|++||.|..|.|+.++. .++|||||+|.+.++|++|+ .|++..|+|+.|+
T Consensus        22 ~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  100 (109)
T 2err_A           22 NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKLHGTVVEGRKIE  100 (109)
T ss_dssp             CCSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT-BCTTEEEEECCCSHHHHHHHHHHTTCEETTEECE
T ss_pred             CccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC-CCceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            334456789999999999999999999999999999999998764 48999999999999999999 6999999999999


Q ss_pred             EEeccCC
Q 030488          119 VTVKRTN  125 (176)
Q Consensus       119 v~~a~~~  125 (176)
                      |+++++.
T Consensus       101 V~~a~~~  107 (109)
T 2err_A          101 VNNATAR  107 (109)
T ss_dssp             EEECCCS
T ss_pred             EEECCCC
Confidence            9999753

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=1.9e-20  Score=125.12  Aligned_cols=77  Identities=19%  Similarity=0.264  Sum_probs=70.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhC--CCeeCCeeeEEE
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN--ESELHGRQLKVT  120 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~--~~~~~g~~i~v~  120 (176)
                      ....++|||+|||+++|+++|+++|++||.|.+|.|+++     +|||||+|.+.++|++|+ .++  +..|.|+.|.|.
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            345789999999999999999999999999999999876     799999999999999999 576  478999999999


Q ss_pred             eccCC
Q 030488          121 VKRTN  125 (176)
Q Consensus       121 ~a~~~  125 (176)
                      +++..
T Consensus        88 ~A~~~   92 (105)
T 1sjq_A           88 FSNHK   92 (105)
T ss_dssp             CCSSS
T ss_pred             EcCCC
Confidence            99764

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

Probab=99.83  E-value=9.3e-20  Score=121.12  Aligned_cols=81  Identities=23%  Similarity=0.459  Sum_probs=73.0

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      .....++|||+|||+++|+++|+++|+.|+   .|.++.++ ++.++|||||+|.+.++|++|| .||+..|.|+.|+|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            456689999999999999999999999873   67788886 7999999999999999999999 699999999999999


Q ss_pred             eccCCC
Q 030488          121 VKRTNV  126 (176)
Q Consensus       121 ~a~~~~  126 (176)
                      ++++..
T Consensus        88 ~a~~~~   93 (102)
T 2fc8_A           88 WAKPKG   93 (102)
T ss_dssp             ECCCCC
T ss_pred             EecCCC
Confidence            998643

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=7.5e-21  Score=126.83  Aligned_cols=82  Identities=35%  Similarity=0.627  Sum_probs=76.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|+ .||+..|.|+.|+|+++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            346899999999999999999999999999999999987 7999999999999999999999 69999999999999999


Q ss_pred             cCCC
Q 030488          123 RTNV  126 (176)
Q Consensus       123 ~~~~  126 (176)
                      .+..
T Consensus        86 ~~~~   89 (104)
T 1p1t_A           86 ASEK   89 (104)
T ss_dssp             TCTT
T ss_pred             CCcc
Confidence            7643

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.83  E-value=1.1e-20  Score=124.00  Aligned_cols=80  Identities=19%  Similarity=0.303  Sum_probs=72.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ...++|||+|||+++|+++|+++|++||.|..+.++.++ ++.++|||||+|.+.++|++|| .||+..|+|+.|+|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            346899999999999999999999999999888888776 7899999999999999999999 69999999999999987


Q ss_pred             cC
Q 030488          123 RT  124 (176)
Q Consensus       123 ~~  124 (176)
                      .+
T Consensus        93 ~s   94 (95)
T 2ek1_A           93 SS   94 (95)
T ss_dssp             C-
T ss_pred             cC
Confidence            53

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

Probab=99.83  E-value=1.1e-19  Score=123.25  Aligned_cols=83  Identities=18%  Similarity=0.354  Sum_probs=76.6

Q ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCee--------
Q 030488           42 REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESEL--------  112 (176)
Q Consensus        42 ~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~--------  112 (176)
                      ....+.++|||+|||+++|+++|+++|++||.|..|.|+.++++.++|||||+|.+.++|++|| .||+..|        
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~   99 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   99 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccC
Confidence            3455679999999999999999999999999999999999999999999999999999999999 6999999        


Q ss_pred             CCeeeEEEeccC
Q 030488          113 HGRQLKVTVKRT  124 (176)
Q Consensus       113 ~g~~i~v~~a~~  124 (176)
                      .++.|.|.++.+
T Consensus       100 ~~~~l~v~~a~p  111 (114)
T 1x5o_A          100 PTEPLLCKFSGP  111 (114)
T ss_dssp             CSSCBEEEECCC
T ss_pred             CCCceeEEccCC
Confidence            577899999874

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.83  E-value=6.9e-21  Score=126.45  Aligned_cols=82  Identities=27%  Similarity=0.510  Sum_probs=73.8

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC--CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK--FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~--~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~  120 (176)
                      .....++|||+|||+++++++|+++|++|| |.+|.|+.++  +++++|||||+|.+.++|++||.|++..|+|+.|+|+
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVD   93 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCCE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEEE
Confidence            445679999999999999999999999999 9999999987  7999999999999999999999999999999999999


Q ss_pred             eccCC
Q 030488          121 VKRTN  125 (176)
Q Consensus       121 ~a~~~  125 (176)
                      ++++.
T Consensus        94 ~a~~~   98 (100)
T 2j76_E           94 VADQA   98 (100)
T ss_dssp             ECCCS
T ss_pred             eccCC
Confidence            99753

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=1.5e-19  Score=120.21  Aligned_cols=79  Identities=16%  Similarity=0.193  Sum_probs=71.0

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-Hh--CCCeeCCeeeEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HL--NESELHGRQLKV  119 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l--~~~~~~g~~i~v  119 (176)
                      ...+.++|||+|||+++|+++|+++|++||.|.+|.|+.+     +|||||+|.+.++|++|+ .|  ++..|.|+.|.|
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            3456789999999999999999999999999999998865     899999999999999999 55  578899999999


Q ss_pred             EeccCCC
Q 030488          120 TVKRTNV  126 (176)
Q Consensus       120 ~~a~~~~  126 (176)
                      .+++...
T Consensus        86 ~~a~~~~   92 (101)
T 2cq1_A           86 QYSNHKE   92 (101)
T ss_dssp             EECSCSS
T ss_pred             EEcCccc
Confidence            9997643

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.83  E-value=2e-20  Score=130.95  Aligned_cols=81  Identities=23%  Similarity=0.355  Sum_probs=76.3

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCC---eeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGT---VNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV  119 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~---i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v  119 (176)
                      .....++|||+|||+++|+++|+++|++||.   |..|.|++++.|+++|||||+|.+.++|++||.+|+..|+|+.|.|
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~V  119 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEV  119 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEEE
Confidence            3456789999999999999999999999999   8999999998999999999999999999999999999999999999


Q ss_pred             Eecc
Q 030488          120 TVKR  123 (176)
Q Consensus       120 ~~a~  123 (176)
                      ..+.
T Consensus       120 ~~a~  123 (136)
T 2hgl_A          120 FKSH  123 (136)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            9875

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

Probab=99.83  E-value=2e-19  Score=118.99  Aligned_cols=77  Identities=29%  Similarity=0.455  Sum_probs=70.5

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhC--CCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSC--GTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV  119 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~--G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v  119 (176)
                      .....++|||+|||+++|+++|+++|++|  |.|..|.+.       ++||||+|.+.++|++|| .||+..|+|+.|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            34567999999999999999999999999  999999875       679999999999999999 69999999999999


Q ss_pred             EeccCCC
Q 030488          120 TVKRTNV  126 (176)
Q Consensus       120 ~~a~~~~  126 (176)
                      +++++..
T Consensus        84 ~~a~~~~   90 (99)
T 2cpd_A           84 TLAKPVD   90 (99)
T ss_dssp             ECCCCCC
T ss_pred             EECCCCC
Confidence            9998643

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.83  E-value=3.5e-20  Score=123.44  Aligned_cols=77  Identities=16%  Similarity=0.222  Sum_probs=69.7

Q ss_pred             CCCCCEEEEcCCCC-CCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCC--CeeCCeeeEE
Q 030488           44 EVDSRSVFVGNVDY-SCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNE--SELHGRQLKV  119 (176)
Q Consensus        44 ~~~~~~i~v~~lp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~--~~~~g~~i~v  119 (176)
                      ..+.++|||+|||+ ++|+++|+++|++||.|.+|.|+++     ++||||+|.+.++|++|| .|++  ..|.|+.|.|
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   86 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   86 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEE
Confidence            34678999999999 9999999999999999999999876     689999999999999999 6775  5699999999


Q ss_pred             EeccCC
Q 030488          120 TVKRTN  125 (176)
Q Consensus       120 ~~a~~~  125 (176)
                      .+++..
T Consensus        87 ~~a~~~   92 (102)
T 1x4d_A           87 HLSQKY   92 (102)
T ss_dssp             EEECCC
T ss_pred             EECCCC
Confidence            999854

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

Probab=99.83  E-value=1.1e-19  Score=118.73  Aligned_cols=76  Identities=29%  Similarity=0.564  Sum_probs=70.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ....++|||+|||+++|+++|+++|++||.|..|.++       ++||||+|.+.++|++|+ .||+..|.|+.|+|+++
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   79 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS   79 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC-------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE-------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            4567899999999999999999999999999999997       459999999999999999 79999999999999999


Q ss_pred             cCCC
Q 030488          123 RTNV  126 (176)
Q Consensus       123 ~~~~  126 (176)
                      ++..
T Consensus        80 ~~~~   83 (92)
T 2dgt_A           80 TSRL   83 (92)
T ss_dssp             SCCC
T ss_pred             cCCC
Confidence            7643

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

Probab=99.83  E-value=8.2e-20  Score=118.82  Aligned_cols=75  Identities=28%  Similarity=0.558  Sum_probs=69.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ....++|||+|||+++|+++|+++|++||.|..|.++       ++||||+|.+.++|++|+ .||+..|+|+.|+|+++
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   78 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS   78 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            4567899999999999999999999999999999997       459999999999999999 69999999999999999


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      ++.
T Consensus        79 ~~~   81 (90)
T 2dnp_A           79 TKG   81 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

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

Probab=99.83  E-value=1.1e-19  Score=118.28  Aligned_cols=76  Identities=25%  Similarity=0.481  Sum_probs=70.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ....++|||+|||+++|+++|+++|++||.|..|.|+       ++||||+|.+.++|++|+ .||+..|+|+.|+|+++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   77 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS   77 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECS
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEEC
Confidence            3457899999999999999999999999999999997       679999999999999999 79999999999999999


Q ss_pred             cCCC
Q 030488          123 RTNV  126 (176)
Q Consensus       123 ~~~~  126 (176)
                      ++..
T Consensus        78 ~~~~   81 (90)
T 2dnq_A           78 KNKS   81 (90)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8643

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

Probab=99.83  E-value=5.7e-21  Score=122.94  Aligned_cols=79  Identities=22%  Similarity=0.325  Sum_probs=73.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|+ .||+..|.|+.|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            457899999999999999999999999999999999987 7999999999999999999999 69999999998887765


Q ss_pred             c
Q 030488          123 R  123 (176)
Q Consensus       123 ~  123 (176)
                      +
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.82  E-value=3.2e-20  Score=136.34  Aligned_cols=83  Identities=19%  Similarity=0.435  Sum_probs=74.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      ....++|||+|||+++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++||..++..|+|+.|.|.++
T Consensus       101 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~~~~~~~G~~i~v~~a  180 (196)
T 1l3k_A          101 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA  180 (196)
T ss_dssp             --CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHhCCcEECCEEEEEEec
Confidence            3456899999999999999999999999999999999998 799999999999999999999976899999999999999


Q ss_pred             cCCC
Q 030488          123 RTNV  126 (176)
Q Consensus       123 ~~~~  126 (176)
                      .+..
T Consensus       181 ~~k~  184 (196)
T 1l3k_A          181 LSKQ  184 (196)
T ss_dssp             C---
T ss_pred             CChh
Confidence            7643

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.82  E-value=5.8e-20  Score=121.59  Aligned_cols=76  Identities=17%  Similarity=0.204  Sum_probs=69.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCe--eCCeeeEEE
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESE--LHGRQLKVT  120 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~--~~g~~i~v~  120 (176)
                      ..++++|||+|||+++|+++|+++|++||.|.+|.++++     +|||||+|.+.++|++|+ .|++..  |.|+.|.|.
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~-----kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~   92 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK-----KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            346789999999999999999999999999999999864     789999999999999999 688765  789999999


Q ss_pred             eccC
Q 030488          121 VKRT  124 (176)
Q Consensus       121 ~a~~  124 (176)
                      +++.
T Consensus        93 ~S~~   96 (100)
T 3r27_A           93 YSTS   96 (100)
T ss_dssp             ECSC
T ss_pred             eccc
Confidence            9975

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

Probab=99.82  E-value=1.2e-19  Score=119.97  Aligned_cols=79  Identities=27%  Similarity=0.449  Sum_probs=72.7

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ...+.++|||+|||+++|+++|+++|++||.|..|.+..+     ++||||+|.+.++|++|+ .||+..|.|+.|+|++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~-----kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   85 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEE
Confidence            3456789999999999999999999999999999999865     789999999999999999 7999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      +++..
T Consensus        86 a~~~~   90 (99)
T 2cpj_A           86 ACHSA   90 (99)
T ss_dssp             SSCCS
T ss_pred             cCCCC
Confidence            97643

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

Probab=99.82  E-value=1e-19  Score=127.36  Aligned_cols=81  Identities=27%  Similarity=0.509  Sum_probs=75.2

Q ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEE
Q 030488           42 REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV  119 (176)
Q Consensus        42 ~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v  119 (176)
                      ......++|||+|||.++|+++|+++|++||.|..+.|+.++ ++.++|||||+|.+.++|++|+ .||+..|.|+.|+|
T Consensus        58 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  137 (140)
T 2ku7_A           58 GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV  137 (140)
T ss_dssp             SSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEE
T ss_pred             CCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            345568999999999999999999999999999999999986 7999999999999999999999 79999999999999


Q ss_pred             Eec
Q 030488          120 TVK  122 (176)
Q Consensus       120 ~~a  122 (176)
                      ++|
T Consensus       138 ~~A  140 (140)
T 2ku7_A          138 NLA  140 (140)
T ss_dssp             EC-
T ss_pred             EeC
Confidence            875

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

Probab=99.82  E-value=3.6e-20  Score=126.08  Aligned_cols=75  Identities=21%  Similarity=0.391  Sum_probs=65.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCee-----eE
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQ-----LK  118 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~-----i~  118 (176)
                      ...++|||+|||+++|+++|+++|++||.|..|.|+.+      |||||+|.+.++|++|| .||+..|+|+.     |+
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            34689999999999999999999999999999999865      89999999999999999 69999999998     77


Q ss_pred             EEeccCC
Q 030488          119 VTVKRTN  125 (176)
Q Consensus       119 v~~a~~~  125 (176)
                      |..+...
T Consensus        88 v~~~~~~   94 (115)
T 3beg_B           88 VKVDGPR   94 (115)
T ss_dssp             EEECC--
T ss_pred             eccCCCC
Confidence            7776543

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

Probab=99.82  E-value=4.7e-20  Score=131.71  Aligned_cols=116  Identities=19%  Similarity=0.334  Sum_probs=90.2

Q ss_pred             HHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCcccccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-
Q 030488            5 LKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-   83 (176)
Q Consensus         5 ~~e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-   83 (176)
                      |...+++..|+..++...-.........   .............+|||+|||.++|+++|+++|++||.|..+.++.+. 
T Consensus        48 f~~~~~a~~A~~~l~~~~~~g~~i~v~~---~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~  124 (166)
T 3md3_A           48 YHQSHDANIALQTLNGKQIENNIVKINW---AFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQ  124 (166)
T ss_dssp             ESSHHHHHHHHHHHTTCEETTEECEEEE---CCCCCCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTT
T ss_pred             eCCHHHHHHHHHHcCCCccCCCeeEEEE---cCCCCCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCC
Confidence            4456677777777665432111111000   111112234567899999999999999999999999999999999996 


Q ss_pred             CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           84 FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        84 ~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      ++.++|||||+|.+.++|.+|+ .||+..++|+.|+|.+|+
T Consensus       125 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          125 TGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             TCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             CCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecC
Confidence            7999999999999999999999 699999999999999986

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

Probab=99.82  E-value=1.6e-19  Score=119.08  Aligned_cols=78  Identities=17%  Similarity=0.362  Sum_probs=71.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeC--CeeeEEE
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELH--GRQLKVT  120 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~--g~~i~v~  120 (176)
                      ....++|||+|||+++|+++|+++|++||.|..|.+..+     ++||||+|.+.++|++|+ .||+..|.  |+.|+|+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-----CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            445689999999999999999999999999999999765     789999999999999999 69999999  9999999


Q ss_pred             eccCCC
Q 030488          121 VKRTNV  126 (176)
Q Consensus       121 ~a~~~~  126 (176)
                      ++++..
T Consensus        89 ~a~~~~   94 (97)
T 1why_A           89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             ECCCCC
Confidence            998643

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.82  E-value=4.9e-20  Score=118.39  Aligned_cols=72  Identities=14%  Similarity=0.153  Sum_probs=68.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      +..|||+||++.+|+++|+++|.+||+|.++++..+     +|||||+|.+.++|++|+ .||+..+.|+.|+|+.|.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~~-----kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLN-----QGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCC-----CcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            578999999999999999999999999999999763     999999999999999999 799999999999999884

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.82  E-value=1.8e-19  Score=120.50  Aligned_cols=78  Identities=19%  Similarity=0.184  Sum_probs=69.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCC--CeeCCeeeEEE
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNE--SELHGRQLKVT  120 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~--~~~~g~~i~v~  120 (176)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+.+     +|||||+|.+.++|++|+ .|++  ..|.|+.|.|+
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~   86 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            355789999999999999999999999999999998865     799999999999999999 5754  56999999999


Q ss_pred             eccCCC
Q 030488          121 VKRTNV  126 (176)
Q Consensus       121 ~a~~~~  126 (176)
                      +++...
T Consensus        87 ~a~~~~   92 (104)
T 1wex_A           87 YSTSKR   92 (104)
T ss_dssp             ECSSSS
T ss_pred             EccCcc
Confidence            997643

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=1.7e-19  Score=121.40  Aligned_cols=79  Identities=20%  Similarity=0.421  Sum_probs=73.2

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      .....++|||+|||.++++++|+++|++||.|..|.|+.+     ++||||+|.+.++|++|+ .|++..|+|+.|+|.+
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   95 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   95 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEe
Confidence            3456789999999999999999999999999999999876     789999999999999999 7999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      +++..
T Consensus        96 a~~~~  100 (109)
T 1x4g_A           96 GKESP  100 (109)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98643

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.82  E-value=4e-20  Score=123.79  Aligned_cols=80  Identities=16%  Similarity=0.297  Sum_probs=73.5

Q ss_pred             CCCCCEEEEcCCCCCC------CHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCe-
Q 030488           44 EVDSRSVFVGNVDYSC------TPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGR-  115 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~------t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~-  115 (176)
                      ....++|||+|||+.+      |+++|+++|++||.|..|.|+ ..+|+++|||||+|.+.++|++|| .||+..|+|+ 
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            4457899999999999      789999999999999999988 458899999999999999999999 6999999998 


Q ss_pred             eeEEEeccC
Q 030488          116 QLKVTVKRT  124 (176)
Q Consensus       116 ~i~v~~a~~  124 (176)
                      .|+|.++..
T Consensus        91 ~l~V~~a~~   99 (105)
T 2nlw_A           91 TFRVNLFTD   99 (105)
T ss_dssp             EEEEECSCC
T ss_pred             eEEEEEcch
Confidence            999999864

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.82  E-value=1.1e-20  Score=118.80  Aligned_cols=74  Identities=18%  Similarity=0.430  Sum_probs=70.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           49 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        49 ~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      +|||+|||+++|+++|+++|++||.|..+.++.++ ++.++|||||+|.+.++|++|+.+++..++|+.|.|.+|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            58999999999999999999999999999999887 699999999999999999999977999999999999875

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=1.1e-19  Score=116.72  Aligned_cols=75  Identities=23%  Similarity=0.444  Sum_probs=69.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-Hh-CCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HL-NESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l-~~~~~~g~~i~v~~  121 (176)
                      ....++|||+|||.++++++|+++|++||.|..|.++.+     +|||||+|.+.++|++|+ .| ++..++|+.|+|++
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~-----kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~   83 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKW   83 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC-----CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEe
Confidence            456789999999999999999999999999999999875     799999999999999999 58 99999999999998


Q ss_pred             cc
Q 030488          122 KR  123 (176)
Q Consensus       122 a~  123 (176)
                      ++
T Consensus        84 ak   85 (85)
T 2ytc_A           84 GR   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.81  E-value=1.7e-20  Score=118.42  Aligned_cols=74  Identities=22%  Similarity=0.491  Sum_probs=69.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ++|||+|||+++++++|+++|++||.|..+.++.++ ++.++|||||+|.+.++|++|+ .++ ..++|+.|.|++|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            479999999999999999999999999999999987 6999999999999999999999 577 9999999999986

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

Probab=99.81  E-value=8.6e-20  Score=121.13  Aligned_cols=75  Identities=25%  Similarity=0.486  Sum_probs=70.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccCCC
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNV  126 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~~~  126 (176)
                      ++|||+|||+++|+++|+++|++||.|..|.++.+    ++|||||+|.+.++|++|+ .|++..++|+.|+|+++++..
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            47999999999999999999999999999999877    6899999999999999999 699999999999999998654

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=7.9e-20  Score=125.87  Aligned_cols=81  Identities=17%  Similarity=0.254  Sum_probs=73.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEE-EEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRV-TIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~-~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      ....++|||+|||+++|+++|+++|+.||.|..+ .+..+.+++++|||||+|.+.++|++||.+|+..|+|+.|.|.++
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEEC
Confidence            4567899999999999999999999999999874 444455899999999999999999999999999999999999998


Q ss_pred             cC
Q 030488          123 RT  124 (176)
Q Consensus       123 ~~  124 (176)
                      ..
T Consensus       102 ~~  103 (124)
T 1wel_A          102 TK  103 (124)
T ss_dssp             CH
T ss_pred             CH
Confidence            54

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.81  E-value=2e-20  Score=125.73  Aligned_cols=81  Identities=23%  Similarity=0.320  Sum_probs=75.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCC---eeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEE
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGT---VNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVT  120 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~---i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~  120 (176)
                      ....++|||+|||+++|+++|+++|+.||.   |..|.|+.++.|+++|||||+|.+.++|++||.+|+..|+|+.|.|.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~   87 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVY   87 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCCCE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEEEE
Confidence            456789999999999999999999999998   89999999988999999999999999999999999999999999999


Q ss_pred             eccC
Q 030488          121 VKRT  124 (176)
Q Consensus       121 ~a~~  124 (176)
                      ++..
T Consensus        88 ~a~~   91 (107)
T 2lmi_A           88 EINN   91 (107)
T ss_dssp             ECCH
T ss_pred             ECCH
Confidence            8854

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=4.3e-20  Score=127.11  Aligned_cols=79  Identities=24%  Similarity=0.282  Sum_probs=73.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCe----eEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEE
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTV----NRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVT  120 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i----~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~  120 (176)
                      .+..+|||+|||+++|+++|+++|++||.|    ..|.|+.+.+|+++|||||+|.+.++|++||..|+..|.++.|.|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V~  100 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELF  100 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEEE
Confidence            457899999999999999999999999975    6899999989999999999999999999999669999999999998


Q ss_pred             ecc
Q 030488          121 VKR  123 (176)
Q Consensus       121 ~a~  123 (176)
                      .+.
T Consensus       101 ~a~  103 (123)
T 2dha_A          101 RST  103 (123)
T ss_dssp             EEC
T ss_pred             ECC
Confidence            874

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.81  E-value=5e-20  Score=130.77  Aligned_cols=80  Identities=24%  Similarity=0.438  Sum_probs=73.7

Q ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           42 REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        42 ~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      ......++|||+|||+++|+++|+++|++||.|.+|.|+.+    ++|||||+|.+.++|+.|+ .||+..|+|+.|+|+
T Consensus        68 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  143 (150)
T 2i2y_A           68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVE  143 (150)
T ss_dssp             SSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34556799999999999999999999999999999999876    4899999999999999999 699999999999999


Q ss_pred             eccCC
Q 030488          121 VKRTN  125 (176)
Q Consensus       121 ~a~~~  125 (176)
                      ++++.
T Consensus       144 ~a~~~  148 (150)
T 2i2y_A          144 LSNGE  148 (150)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            99764

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

Probab=99.81  E-value=6.1e-20  Score=124.13  Aligned_cols=79  Identities=19%  Similarity=0.269  Sum_probs=70.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCC-CeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCG-TVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G-~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ....+|||+|||+++|+++|+++|++|| .|..+.|..+   +++|||||+|.+.++|++|| .||+..|+|+.|+|+++
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~---~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR---DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC---SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC---CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            3468999999999999999999999999 8999988543   46899999999999999999 79999999999999999


Q ss_pred             cCCC
Q 030488          123 RTNV  126 (176)
Q Consensus       123 ~~~~  126 (176)
                      +...
T Consensus       103 ~~~p  106 (111)
T 2jvr_A          103 DNPP  106 (111)
T ss_dssp             CC--
T ss_pred             CCCC
Confidence            7543

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.81  E-value=1.2e-20  Score=122.63  Aligned_cols=77  Identities=35%  Similarity=0.672  Sum_probs=71.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccCC
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTN  125 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~~  125 (176)
                      ++|||+|||.++++++|+++|++||.|.+|.++.++ ++.++|||||+|.+.+ |++|+ .||+..++|+.|+|++|...
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            589999999999999999999999999999999988 6999999999999999 99999 69999999999999999754

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=2.1e-19  Score=122.67  Aligned_cols=78  Identities=19%  Similarity=0.253  Sum_probs=70.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhC--CCeeCCeeeEEE
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN--ESELHGRQLKVT  120 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~--~~~~~g~~i~v~  120 (176)
                      ..+.++|||+|||+++|+++|+++|++||.|.+|.|+.+     +|||||+|.+.++|++|+ .++  +..|.|+.|+|.
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~  102 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ  102 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEE
Confidence            445789999999999999999999999999999999876     799999999999999999 576  468999999999


Q ss_pred             eccCCC
Q 030488          121 VKRTNV  126 (176)
Q Consensus       121 ~a~~~~  126 (176)
                      +++...
T Consensus       103 ~a~~k~  108 (119)
T 2ad9_A          103 FSNHKE  108 (119)
T ss_dssp             ECSSSS
T ss_pred             EccCCC
Confidence            997643

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=2.6e-19  Score=121.47  Aligned_cols=80  Identities=18%  Similarity=0.304  Sum_probs=71.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCee----EEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeE
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVN----RVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLK  118 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~----~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~  118 (176)
                      ....++|||+|||+++|+++|+++|++||.|.    .+.+.   ++.++|||||+|.+.++|++|| .||+..|.|+.|+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~---~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   98 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILV   98 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE---CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC---CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            34678999999999999999999999999984    44443   7888999999999999999999 6999999999999


Q ss_pred             EEeccCCC
Q 030488          119 VTVKRTNV  126 (176)
Q Consensus       119 v~~a~~~~  126 (176)
                      |+++++..
T Consensus        99 v~~a~~~~  106 (115)
T 2cpx_A           99 IEFGKNKK  106 (115)
T ss_dssp             EEECCCCS
T ss_pred             EEEccCCC
Confidence            99998644

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

Probab=99.81  E-value=2.4e-19  Score=118.20  Aligned_cols=80  Identities=21%  Similarity=0.364  Sum_probs=71.2

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      .....++|||+|||+++|+++|+++|++||.|. +.++.+   .++|||||+|.+.++|++|+ .||+..|+|+.|+|++
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~---~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   90 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ---GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVAL   90 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC---CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            345578999999999999999999999999996 666653   56899999999999999999 7999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      +++..
T Consensus        91 a~~~~   95 (97)
T 2e5j_A           91 ARQQR   95 (97)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98643

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.81  E-value=4.2e-20  Score=117.94  Aligned_cols=72  Identities=18%  Similarity=0.356  Sum_probs=66.6

Q ss_pred             CCEEEEcCCCCCC------CHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCe-eeE
Q 030488           47 SRSVFVGNVDYSC------TPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGR-QLK  118 (176)
Q Consensus        47 ~~~i~v~~lp~~~------t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~-~i~  118 (176)
                      +++|||+|||..+      |+++|+++|++||.|.+|.|+ ..+|+++|||||+|.+.++|++|+ .||+..|+|+ .|+
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            3689999999999      779999999999999999987 458899999999999999999999 6999999999 887


Q ss_pred             E
Q 030488          119 V  119 (176)
Q Consensus       119 v  119 (176)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

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

Probab=99.81  E-value=3.7e-19  Score=117.45  Aligned_cols=76  Identities=18%  Similarity=0.456  Sum_probs=70.0

Q ss_pred             cCCCCCEEEEcCCCC-CCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           43 EEVDSRSVFVGNVDY-SCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      .....++|||+|||+ ++++++|+++|++||.|..|.+.       +|||||+|.+.++|++|+ .||+..++|+.|+|+
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   90 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            445689999999998 99999999999999999999984       789999999999999999 699999999999999


Q ss_pred             eccCC
Q 030488          121 VKRTN  125 (176)
Q Consensus       121 ~a~~~  125 (176)
                      +++..
T Consensus        91 ~a~~~   95 (97)
T 2xnq_A           91 VSSSN   95 (97)
T ss_dssp             ECCCC
T ss_pred             ecCCC
Confidence            99753

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

Probab=99.81  E-value=9.7e-20  Score=119.93  Aligned_cols=76  Identities=18%  Similarity=0.456  Sum_probs=69.3

Q ss_pred             CCCCCEEEEcCCCC-CCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDY-SCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ..+.++|||+|||+ ++|+++|+++|++||.|..|.|.       +|||||+|.+.++|+.|+ .||+..+.|+.|+|++
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   79 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            35578999999999 99999999999999999999995       789999999999999999 6999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      +++..
T Consensus        80 a~~~~   84 (96)
T 2kvi_A           80 SSSNA   84 (96)
T ss_dssp             EECCC
T ss_pred             cCcCC
Confidence            97643

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.69  E-value=2e-21  Score=132.36  Aligned_cols=82  Identities=26%  Similarity=0.446  Sum_probs=76.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeE--------EEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeC
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNR--------VTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELH  113 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~--------~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~  113 (176)
                      ..+.++|||+|||+++++++|+++|++||.|..        |.|+.++ ++.++|||||+|.+.++|++|| .||+..|.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            456789999999999999999999999999998        8899886 7899999999999999999999 69999999


Q ss_pred             CeeeEEEeccCC
Q 030488          114 GRQLKVTVKRTN  125 (176)
Q Consensus       114 g~~i~v~~a~~~  125 (176)
                      |+.|+|+++++.
T Consensus        84 g~~l~V~~a~~~   95 (116)
T 2lcw_A           84 GNPIKVSFATRR   95 (116)
Confidence            999999999764

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.80  E-value=4.8e-19  Score=119.36  Aligned_cols=76  Identities=24%  Similarity=0.445  Sum_probs=70.0

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYS-CTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~-~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ....++|||+|||++ +|+++|+++|++||.|..|.|       +++||||+|.+.++|++|+ .|++..|+|+.|+|++
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   96 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM   96 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            344689999999999 999999999999999999998       3889999999999999999 7999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      ++...
T Consensus        97 a~~~~  101 (110)
T 1wf1_A           97 AGEPK  101 (110)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            97543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.80  E-value=2.2e-19  Score=124.25  Aligned_cols=80  Identities=21%  Similarity=0.306  Sum_probs=72.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHH----HHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeE
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQ----QHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLK  118 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~----~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~  118 (176)
                      ..+.++|||+|||+.+++++|+    ++|++||.|.+|.+.  ++++++|||||+|.+.++|+.|+ .||+..|.|+.|+
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~--~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD--LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC--CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec--cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            3457899999999999999876    699999999988774  46888999999999999999999 7999999999999


Q ss_pred             EEeccCC
Q 030488          119 VTVKRTN  125 (176)
Q Consensus       119 v~~a~~~  125 (176)
                      |.+++..
T Consensus       104 V~~a~~~  110 (127)
T 2a3j_A          104 ITFSETP  110 (127)
T ss_dssp             EEECCCC
T ss_pred             EEEccCc
Confidence            9999764

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

Probab=99.80  E-value=2.4e-19  Score=120.67  Aligned_cols=78  Identities=22%  Similarity=0.432  Sum_probs=71.3

Q ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           42 REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        42 ~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      ......++|||+|||+++|+++|+++|++||.|..|.++       +|||||+|.+.++|++|+ .||+..|+|+.|.|+
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            345678999999999999999999999999999999998       789999999999999999 699999999999999


Q ss_pred             eccCCC
Q 030488          121 VKRTNV  126 (176)
Q Consensus       121 ~a~~~~  126 (176)
                      +++...
T Consensus        99 ~a~~~~  104 (108)
T 2jvo_A           99 YSKLPA  104 (108)
T ss_dssp             SCSCCC
T ss_pred             EecCCC
Confidence            998643

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.80  E-value=9.2e-20  Score=125.83  Aligned_cols=79  Identities=24%  Similarity=0.388  Sum_probs=72.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCee--EEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVN--RVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~--~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~  121 (176)
                      .....+|||+|||+++|+++|+++|++| .|.  .|.|+.++.|+++|||||+|.+.++|++||.+++..|+|+.|.|..
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFK  117 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEEE
Confidence            3557899999999999999999999999 676  9999999889999999999999999999997788999999999988


Q ss_pred             cc
Q 030488          122 KR  123 (176)
Q Consensus       122 a~  123 (176)
                      +.
T Consensus       118 a~  119 (126)
T 2hgm_A          118 SS  119 (126)
T ss_dssp             EC
T ss_pred             CC
Confidence            74

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.80  E-value=8.7e-20  Score=121.32  Aligned_cols=79  Identities=32%  Similarity=0.585  Sum_probs=74.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccC
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~  124 (176)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.++++.++|||||+|.+.++|++|+. ++..|+|+.|.|..+..
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~-~~~~~~g~~l~v~~a~~   85 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKLGPAIR   85 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT-CCCEETTEECEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh-CCCeECCEEEEEEECCc
Confidence            44689999999999999999999999999999999999999999999999999999999999 99999999999998864

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.80  E-value=2.4e-20  Score=123.86  Aligned_cols=81  Identities=20%  Similarity=0.352  Sum_probs=73.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      ....++|||+|||+++|+++|+++|++||.|.. .++.+. ++.++|||||+|.+.++|++||+||+..|.|+.|+|.++
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEc
Confidence            345789999999999999999999999999877 555554 688999999999999999999999999999999999999


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      ++.
T Consensus        93 ~~~   95 (101)
T 1fj7_A           93 KGR   95 (101)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            764

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.80  E-value=5.4e-20  Score=137.69  Aligned_cols=117  Identities=20%  Similarity=0.281  Sum_probs=88.7

Q ss_pred             HHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCcccccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCC
Q 030488            5 LKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF   84 (176)
Q Consensus         5 ~~e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~   84 (176)
                      |...+++..|++.++.............   .............+|||+|||+++|+++|+++|++||.|..|.|+.+..
T Consensus        64 F~~~~~A~~Ai~~~~~~~~~g~~i~~~~---~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~  140 (213)
T 4f02_A           64 FQQPADAERALDTMNFDVIKGKPVRIMW---SQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN  140 (213)
T ss_dssp             ESSHHHHHHHHHHHTTCEETTEECEEEE---CCCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT
T ss_pred             eCCHHHHHHHHHHhhhhhcCCccccccc---ccccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCC
Confidence            4456677777777765433211111000   1111222234567999999999999999999999999999999998763


Q ss_pred             CCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccCC
Q 030488           85 GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTN  125 (176)
Q Consensus        85 g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~~  125 (176)
                       .++|||||+|.+.++|++|| .||+..|+|+.|.|.++++.
T Consensus       141 -~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          141 -GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             -EEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCH
T ss_pred             -CCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence             47999999999999999999 79999999999999998753

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=4.1e-19  Score=116.08  Aligned_cols=75  Identities=21%  Similarity=0.426  Sum_probs=67.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCC-eeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCC-CeeCCeeeEEEe
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGT-VNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNE-SELHGRQLKVTV  121 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~-i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~-~~~~g~~i~v~~  121 (176)
                      ...++|||+|||+++|+++|+++|++||. |..+.+.      +++||||+|.+.++|++|+ .||+ ..|+|+.|+|++
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~   79 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDY   79 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEE
Confidence            45689999999999999999999999999 6666653      3789999999999999999 6999 999999999999


Q ss_pred             ccCC
Q 030488          122 KRTN  125 (176)
Q Consensus       122 a~~~  125 (176)
                      +++.
T Consensus        80 a~~~   83 (93)
T 2cqh_A           80 SVSK   83 (93)
T ss_dssp             CCCC
T ss_pred             ccCc
Confidence            9764

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=1.2e-18  Score=114.22  Aligned_cols=76  Identities=28%  Similarity=0.380  Sum_probs=67.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEecc
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKR  123 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~  123 (176)
                      ...++|||+|||+++|+++|+++|++||.|.+|  +.++ ++.   ||||+|.+.++|++||.|++..|+|+.|.|.++.
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~l~g~~~~g~~l~V~~a~   80 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPRE   80 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHTCSCCEETTEECCCBCSC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHhcCCeEECCEEEEEEECC
Confidence            346799999999999999999999999999987  4454 454   9999999999999999999999999999999876


Q ss_pred             CC
Q 030488          124 TN  125 (176)
Q Consensus       124 ~~  125 (176)
                      ..
T Consensus        81 ~~   82 (94)
T 2e5g_A           81 QK   82 (94)
T ss_dssp             CS
T ss_pred             cC
Confidence            43

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

Probab=99.80  E-value=3.8e-19  Score=132.45  Aligned_cols=82  Identities=23%  Similarity=0.466  Sum_probs=77.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ...++|||+|||.++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|.+|+ .||+..|+|+.|.|.++
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            456899999999999999999999999999999999997 7999999999999999999999 69999999999999999


Q ss_pred             cCCC
Q 030488          123 RTNV  126 (176)
Q Consensus       123 ~~~~  126 (176)
                      .+..
T Consensus       203 ~~~~  206 (216)
T 2qfj_A          203 VTPP  206 (216)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8653

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

Probab=99.80  E-value=2.5e-19  Score=118.88  Aligned_cols=75  Identities=17%  Similarity=0.322  Sum_probs=69.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      ...++|||+|||.++++++|+++|++||.|.+|.+..     ++|||||+|.+.++|++|+ .||+..|+|+.|+|++++
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP-----EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            4468999999999999999999999999999999984     3899999999999999999 799999999999999987


Q ss_pred             C
Q 030488          124 T  124 (176)
Q Consensus       124 ~  124 (176)
                      +
T Consensus       100 ~  100 (101)
T 2la4_A          100 E  100 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5

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

Probab=99.79  E-value=1.9e-19  Score=118.31  Aligned_cols=78  Identities=22%  Similarity=0.428  Sum_probs=70.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ....++|||+|||+++|+++|+++|++||.|..+    ..++.++|||||+|.+.++|++|+ .|++..|+|+.|.|+++
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   88 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            4457899999999999999999999999988665    347888999999999999999999 69999999999999999


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      ++.
T Consensus        89 ~~~   91 (96)
T 1fjc_A           89 GEK   91 (96)
T ss_dssp             SSS
T ss_pred             CCC
Confidence            764

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

Probab=99.79  E-value=5.5e-19  Score=128.88  Aligned_cols=80  Identities=21%  Similarity=0.437  Sum_probs=75.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.++++.++|||||+|.+.++|++|| .||+..|+|+.|+|+++.
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~  165 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  165 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            3468999999999999999999999999999999999989999999999999999999999 699999999999999986


Q ss_pred             C
Q 030488          124 T  124 (176)
Q Consensus       124 ~  124 (176)
                      .
T Consensus       166 ~  166 (177)
T 2f3j_A          166 S  166 (177)
T ss_dssp             S
T ss_pred             C
Confidence            5

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.79  E-value=1.6e-19  Score=118.84  Aligned_cols=80  Identities=14%  Similarity=0.338  Sum_probs=72.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHH----HHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeE
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQ----QHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLK  118 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~----~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~  118 (176)
                      ..+.++|||+|||+++++++|+    ++|++||.|..|.+.  +++.++|||||+|.+.++|+.|+ .||+..++|+.|+
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~--~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS--RSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECC--HHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEE--cCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            3457899999999999999999    999999999999886  35677899999999999999999 6999999999999


Q ss_pred             EEeccCC
Q 030488          119 VTVKRTN  125 (176)
Q Consensus       119 v~~a~~~  125 (176)
                      |+++++.
T Consensus        83 v~~a~~~   89 (97)
T 1nu4_A           83 IQYAKTD   89 (97)
T ss_dssp             EEECSSC
T ss_pred             EEEccCC
Confidence            9999864

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=7.4e-19  Score=118.76  Aligned_cols=77  Identities=18%  Similarity=0.232  Sum_probs=69.3

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhC--CCeeCCeeeEE
Q 030488           44 EVDSRSVFVGNVDYS-CTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN--ESELHGRQLKV  119 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~-~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~--~~~~~g~~i~v  119 (176)
                      ..+.++|||+|||++ +|+++|+++|++||.|.+|.|+++     +|||||+|.+.++|++|+ .|+  +..|.|+.|+|
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   96 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   96 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            456889999999998 999999999999999999999754     799999999999999999 575  56799999999


Q ss_pred             EeccCC
Q 030488          120 TVKRTN  125 (176)
Q Consensus       120 ~~a~~~  125 (176)
                      .+++..
T Consensus        97 ~~a~~~  102 (112)
T 1x4f_A           97 DLSEKY  102 (112)
T ss_dssp             EEECSC
T ss_pred             EECccc
Confidence            999754

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.79  E-value=4.1e-19  Score=127.86  Aligned_cols=78  Identities=23%  Similarity=0.450  Sum_probs=74.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ....+|||+|||.++|+++|+++|++||.|..+.++.++ ++.++|||||+|.+.++|++|+ .||+..++|+.|.|++|
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            447899999999999999999999999999999999997 8999999999999999999999 69999999999999987

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.79  E-value=1.1e-18  Score=130.46  Aligned_cols=80  Identities=23%  Similarity=0.429  Sum_probs=74.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      .+.++|||+|||+++|+++|+++|++||.|.+|.|++++ +++++|||||+|.+.++|++|| .+++..+.|+.|+|..+
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            456899999999999999999999999999999999998 7999999999999999999999 79999999999999988


Q ss_pred             cC
Q 030488          123 RT  124 (176)
Q Consensus       123 ~~  124 (176)
                      ..
T Consensus        93 ~~   94 (213)
T 4f02_A           93 QR   94 (213)
T ss_dssp             CC
T ss_pred             cc
Confidence            64

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.79  E-value=6.6e-19  Score=126.86  Aligned_cols=117  Identities=17%  Similarity=0.287  Sum_probs=87.5

Q ss_pred             HHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCcccccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCC
Q 030488            5 LKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF   84 (176)
Q Consensus         5 ~~e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~   84 (176)
                      |.+.+++.+|++.++........... ................++|||+|||+++|+++|+++|++||.|..+.++.+.+
T Consensus        54 f~~~~~A~~A~~~l~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~  132 (175)
T 3nmr_A           54 FYTRKAALEAQNALHNMKVLPGMHHP-IQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD  132 (175)
T ss_dssp             ESSHHHHHHHHHHHTTTCCCTTCSSC-CEEEECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT
T ss_pred             ECCHHHHHHHHHHhcCcEEccCCccc-eEEccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCC
Confidence            44556777777776653221100000 00001112222334678999999999999999999999999999999999989


Q ss_pred             CCceeEEEEEecCHHHHHHHH-HhCCCeeC---CeeeEEEec
Q 030488           85 GQPKGYAYVEFLQSEAVQEAL-HLNESELH---GRQLKVTVK  122 (176)
Q Consensus        85 g~~~g~afv~f~~~~~a~~a~-~l~~~~~~---g~~i~v~~a  122 (176)
                      +.++|||||+|.+.++|++|+ .||+..+.   ++.|.|.+|
T Consensus       133 g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~a  174 (175)
T 3nmr_A          133 GLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA  174 (175)
T ss_dssp             SCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEEC
T ss_pred             CCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEec
Confidence            999999999999999999999 79998775   499999987

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

Probab=99.79  E-value=2.8e-19  Score=120.90  Aligned_cols=75  Identities=24%  Similarity=0.331  Sum_probs=69.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      ..++|||+|||+++|+++|+++|++||.|..|.|+.+     ++||||+|.+.++|++|| .||+..|.|+.|.|++++.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-----GITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSS-----SSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            4679999999999999999999999999999998753     789999999999999999 7999999999999999975


Q ss_pred             C
Q 030488          125 N  125 (176)
Q Consensus       125 ~  125 (176)
                      .
T Consensus        84 ~   84 (111)
T 1whx_A           84 G   84 (111)
T ss_dssp             T
T ss_pred             C
Confidence            3

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.78  E-value=3.3e-19  Score=125.57  Aligned_cols=84  Identities=23%  Similarity=0.313  Sum_probs=72.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEE------EEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCee
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRV------TIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQ  116 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~------~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  116 (176)
                      ....++|||+|||+++|+++|+++|++||.|..+      .+....++.++|||||+|.+.++|++|| .||+..|.|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            3457899999999999999999999999998764      2222247889999999999999999999 69999999999


Q ss_pred             eEEEeccCCCC
Q 030488          117 LKVTVKRTNVP  127 (176)
Q Consensus       117 i~v~~a~~~~~  127 (176)
                      |.|.++++..+
T Consensus       122 l~V~~a~~~~~  132 (143)
T 3egn_A          122 MVVQFARSARP  132 (143)
T ss_dssp             CEEEECCCSCC
T ss_pred             EEEEECCCCCC
Confidence            99999976543

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

Probab=99.78  E-value=1.3e-18  Score=118.01  Aligned_cols=78  Identities=23%  Similarity=0.384  Sum_probs=71.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      ...++|||+|||+++|+++|+++|++||.|..|.|+.+  +.++|||||+|.+.++|++|+ .||+..++|+.|.|.++.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            35689999999999999999999999999999999865  455899999999999999999 699999999999999987


Q ss_pred             C
Q 030488          124 T  124 (176)
Q Consensus       124 ~  124 (176)
                      +
T Consensus        84 ~   84 (115)
T 3lqv_A           84 A   84 (115)
T ss_dssp             H
T ss_pred             C
Confidence            4

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.78  E-value=1.4e-18  Score=124.51  Aligned_cols=113  Identities=22%  Similarity=0.371  Sum_probs=87.6

Q ss_pred             HHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCcccccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-
Q 030488            5 LKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-   83 (176)
Q Consensus         5 ~~e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-   83 (176)
                      |...+++..|++.++...-........     ............+|||+|||.++++++|+++|++||.|..+.++.++ 
T Consensus        52 f~~~~~A~~a~~~l~~~~~~g~~l~v~-----~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~  126 (168)
T 1b7f_A           52 FTSEMDSQRAIKVLNGITVRNKRLKVS-----YARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKL  126 (168)
T ss_dssp             ESSHHHHHHHHHHHTTCEETTEECEEE-----ECCCCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTT
T ss_pred             ECCHHHHHHHHHhcCCCEeCCcEEEEE-----ecCCCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCC
Confidence            445566777777666542211111100     01112233557899999999999999999999999999999999998 


Q ss_pred             CCCceeEEEEEecCHHHHHHHH-HhCCCeeCC--eeeEEEec
Q 030488           84 FGQPKGYAYVEFLQSEAVQEAL-HLNESELHG--RQLKVTVK  122 (176)
Q Consensus        84 ~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g--~~i~v~~a  122 (176)
                      ++.++|||||+|.+.++|.+|+ .||+..+.|  +.|+|.+|
T Consensus       127 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          127 TGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             TCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            8999999999999999999999 699999988  99999875

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=5.1e-18  Score=111.79  Aligned_cols=77  Identities=22%  Similarity=0.429  Sum_probs=69.3

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      .....++|||+||  ++|+++|+++|++||.|..|.|.     .++|||||+|.+.++|++|| .||+..|.|+.|+|.+
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-----TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-----CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            3456789999996  89999999999999999999985     34899999999999999999 7999999999999999


Q ss_pred             ccCCC
Q 030488          122 KRTNV  126 (176)
Q Consensus       122 a~~~~  126 (176)
                      +++..
T Consensus        84 a~~~~   88 (97)
T 1x5p_A           84 ARKQP   88 (97)
T ss_dssp             CSSCC
T ss_pred             CCCCC
Confidence            97643

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.78  E-value=2e-18  Score=126.73  Aligned_cols=83  Identities=22%  Similarity=0.481  Sum_probs=76.6

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~  121 (176)
                      +....++|||+|||+++|+++|+++|++||.|.+|.|+.++ ++.++|||||+|.+.++|++||.+++..+.|+.|.|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~   88 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR   88 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeec
Confidence            34567899999999999999999999999999999999997 79999999999999999999997799999999999999


Q ss_pred             ccCC
Q 030488          122 KRTN  125 (176)
Q Consensus       122 a~~~  125 (176)
                      +...
T Consensus        89 ~~~~   92 (196)
T 1l3k_A           89 AVSR   92 (196)
T ss_dssp             CCC-
T ss_pred             ccCc
Confidence            8653

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

Probab=99.78  E-value=1.1e-18  Score=128.23  Aligned_cols=82  Identities=22%  Similarity=0.426  Sum_probs=77.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ...++|||+|||+++++++|+++|++||.|..|.+..++ ++.++|||||+|.+.++|++|+ .||+..|+|+.|.|.++
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            567999999999999999999999999999999999997 8999999999999999999999 69999999999999999


Q ss_pred             cCCC
Q 030488          123 RTNV  126 (176)
Q Consensus       123 ~~~~  126 (176)
                      ++..
T Consensus       192 ~~~~  195 (198)
T 2yh0_A          192 SVGA  195 (198)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.78  E-value=2.9e-18  Score=122.85  Aligned_cols=77  Identities=19%  Similarity=0.270  Sum_probs=69.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCC--eeeEEEec
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHG--RQLKVTVK  122 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g--~~i~v~~a  122 (176)
                      ...+|||+||++.+|+++|+++|++||.|++|.|..+.   +++||||+|.+.++|++|+ .||+..|.|  +.|+|+++
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~---~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS---SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC---CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            34679999999999999999999999999999987543   4789999999999999999 799999965  99999999


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      +..
T Consensus       122 k~~  124 (164)
T 1sjr_A          122 KLT  124 (164)
T ss_dssp             SSS
T ss_pred             cCC
Confidence            864

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.77  E-value=8.2e-20  Score=130.93  Aligned_cols=80  Identities=21%  Similarity=0.459  Sum_probs=75.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEecc
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKR  123 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~  123 (176)
                      ....+|||+|||.++|+++|+++|++||.|..+.++.++ ++.++|||||+|.+.++|++|+.+++..++|+.|.|.++.
T Consensus        85 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           85 DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHHCSEECSSSSCEEEEECC
T ss_pred             cCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHhCCCEEeCCeEEEEeecC
Confidence            346799999999999999999999999999999999987 7999999999999999999999999999999999999997


Q ss_pred             C
Q 030488          124 T  124 (176)
Q Consensus       124 ~  124 (176)
                      +
T Consensus       165 p  165 (167)
T 2cjk_A          165 P  165 (167)
T ss_dssp             C
T ss_pred             C
Confidence            5

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.77  E-value=5.4e-18  Score=121.05  Aligned_cols=79  Identities=27%  Similarity=0.489  Sum_probs=75.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      .++|||+|||+++|+++|+++|++||.|.++.++.++ ++.++|||||+|.+.++|++|+ .|++..+.|+.|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            5799999999999999999999999999999999998 8999999999999999999999 6999999999999999875


Q ss_pred             C
Q 030488          125 N  125 (176)
Q Consensus       125 ~  125 (176)
                      .
T Consensus        82 ~   82 (167)
T 1fxl_A           82 S   82 (167)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.77  E-value=2.4e-18  Score=122.94  Aligned_cols=113  Identities=17%  Similarity=0.289  Sum_probs=86.4

Q ss_pred             HHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCcccccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-
Q 030488            5 LKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-   83 (176)
Q Consensus         5 ~~e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-   83 (176)
                      |.+.+++..|++.++...-........     ............+|||+|||.++++++|+++|++||.|..+.++.+. 
T Consensus        51 f~~~~~A~~a~~~l~~~~~~g~~l~v~-----~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~  125 (167)
T 1fxl_A           51 YIDPKDAEKAINTLNGLRLQTKTIKVS-----YARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV  125 (167)
T ss_dssp             ESSHHHHHHHHHHHTTCEETTEECEEE-----ECCCCCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT
T ss_pred             ECCHHHHHHHHHHcCCCccCCceEEEE-----ecCCCcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCC
Confidence            445667777777766532211111100     01111233457899999999999999999999999999999999988 


Q ss_pred             CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCee--eEEEec
Q 030488           84 FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQ--LKVTVK  122 (176)
Q Consensus        84 ~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~--i~v~~a  122 (176)
                      ++.++|||||+|.+.++|++|+ .||+..+.|+.  |.|.+|
T Consensus       126 ~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          126 TGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             TCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            7999999999999999999999 69999999965  777765

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

Probab=99.76  E-value=5.6e-18  Score=120.84  Aligned_cols=78  Identities=31%  Similarity=0.468  Sum_probs=73.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccCC
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTN  125 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~~  125 (176)
                      ++|||+|||.++|+++|+++|++||.|.+|.++.+++++++|||||+|.+.++|++|+ .+++..+.|+.|.|.++...
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            5899999999999999999999999999999999998899999999999999999999 79999999999999998654

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.76  E-value=5.6e-18  Score=121.29  Aligned_cols=80  Identities=28%  Similarity=0.428  Sum_probs=75.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      +.++|||+|||+++|+++|+++|++||.|.+|.++.++ ++.++|||||+|.+.++|++|+ .+++..+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            46899999999999999999999999999999999987 7999999999999999999999 699999999999999987


Q ss_pred             CC
Q 030488          124 TN  125 (176)
Q Consensus       124 ~~  125 (176)
                      +.
T Consensus        82 ~~   83 (168)
T 1b7f_A           82 PG   83 (168)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

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

Probab=99.76  E-value=3.8e-18  Score=112.04  Aligned_cols=78  Identities=21%  Similarity=0.226  Sum_probs=69.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEE-EEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRV-TIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~-~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ...++|||+|||+++|+++|+++|++||.|..| .|+.++.   .+.|||+|.+.++|++|+ .||+..|+|+.|+|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~---~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   89 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYI   89 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSS---SEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            456899999999999999999999999999999 4777653   233999999999999999 69999999999999999


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      .+.
T Consensus        90 ~~~   92 (96)
T 2e44_A           90 PDE   92 (96)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            764

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.76  E-value=7.9e-18  Score=124.35  Aligned_cols=80  Identities=19%  Similarity=0.301  Sum_probs=74.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccC
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~  124 (176)
                      ...++|||+|||+++|+++|+++|++||.|..|.|+++.++.++|||||+|.+.++|++|+.+.+..++|+.|.|.+++.
T Consensus       107 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          107 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD  186 (193)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTT
T ss_pred             cccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHH
Confidence            34689999999999999999999999999999999999899999999999999999999997666799999999998864

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

Probab=99.76  E-value=3.1e-18  Score=110.90  Aligned_cols=74  Identities=22%  Similarity=0.377  Sum_probs=68.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      ..++|||+|||+++++++|+++|++| .|..+.+.     +++|||||+|.+.++|++|+ .||+..++|+.|+|+++..
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   77 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCC
Confidence            46889999999999999999999999 99999885     45899999999999999999 6999999999999999865


Q ss_pred             C
Q 030488          125 N  125 (176)
Q Consensus       125 ~  125 (176)
                      .
T Consensus        78 ~   78 (88)
T 1wg1_A           78 D   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=4.8e-18  Score=114.93  Aligned_cols=76  Identities=18%  Similarity=0.380  Sum_probs=68.5

Q ss_pred             CCCCEEEE--cCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCee-----CCee
Q 030488           45 VDSRSVFV--GNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESEL-----HGRQ  116 (176)
Q Consensus        45 ~~~~~i~v--~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~-----~g~~  116 (176)
                      .+.++|||  +||++++|+++|+++|++||.|..|.|+.+     +|||||+|.+.++|++|+ .||+.+|     .++.
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~-----rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~   97 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   97 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcE
Confidence            34688999  779999999999999999999999988653     789999999999999999 7999998     6899


Q ss_pred             eEEEeccCC
Q 030488          117 LKVTVKRTN  125 (176)
Q Consensus       117 i~v~~a~~~  125 (176)
                      |.|.+++..
T Consensus        98 l~v~~a~~~  106 (114)
T 2cq2_A           98 LYLNFVEKV  106 (114)
T ss_dssp             CEEEEESCC
T ss_pred             EEEEecccC
Confidence            999998743

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2.6e-18  Score=111.18  Aligned_cols=76  Identities=22%  Similarity=0.352  Sum_probs=66.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccC
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~  124 (176)
                      ...++|||+|||+++|+++|+++|++||.|..|.|+.+    ++|||||+|.+.++|++|+.. ...+.++.|.|.++.+
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l~v~~a~~   77 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCGE-DLIIKGISVHISNAEP   77 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTTC-EEEETTEEEEEECCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHHhcC-CceeCCEEEEEEecCC
Confidence            35689999999999999999999999999999999865    589999999999999876432 4566999999999875


Q ss_pred             C
Q 030488          125 N  125 (176)
Q Consensus       125 ~  125 (176)
                      .
T Consensus        78 ~   78 (88)
T 1wf0_A           78 K   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.75  E-value=1.1e-17  Score=115.73  Aligned_cols=76  Identities=20%  Similarity=0.323  Sum_probs=68.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeE-EEEEecCHHHHHHHH-HhCCCeeCC--eeeEEEe
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGY-AYVEFLQSEAVQEAL-HLNESELHG--RQLKVTV  121 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~-afv~f~~~~~a~~a~-~l~~~~~~g--~~i~v~~  121 (176)
                      .-..|||+||++.+|+++|+++|++||.|.+|.|..+.    ++| |||+|.+.++|++|+ .||+..|.|  +.|+|++
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~  102 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  102 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEE
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEe
Confidence            34678899999999999999999999999999887643    677 999999999999999 799999988  8999999


Q ss_pred             ccCC
Q 030488          122 KRTN  125 (176)
Q Consensus       122 a~~~  125 (176)
                      ++..
T Consensus       103 ak~~  106 (130)
T 3zzy_A          103 SKLT  106 (130)
T ss_dssp             CSCS
T ss_pred             cCCC
Confidence            9864

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.75  E-value=4.4e-18  Score=110.58  Aligned_cols=77  Identities=25%  Similarity=0.366  Sum_probs=62.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEecc
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKR  123 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~  123 (176)
                      .....+|||+|||+++|+++|+++|++||.|.+|.|+++    ++|||||+|.+.++|+++.. ....+.|+.|.|..+.
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~~~~-~~~~~~g~~v~v~~a~   82 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQSLCG-EDLIIKGISVHISNAE   82 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHHHTT-CEEEETTEEEEEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHHHcC-CCcccCCEEEEEEEcC
Confidence            456789999999999999999999999999999999875    59999999999999884322 1334579999999987


Q ss_pred             CC
Q 030488          124 TN  125 (176)
Q Consensus       124 ~~  125 (176)
                      +.
T Consensus        83 ~k   84 (89)
T 3d2w_A           83 PK   84 (89)
T ss_dssp             --
T ss_pred             CC
Confidence            54

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.75  E-value=5.5e-18  Score=115.99  Aligned_cols=77  Identities=10%  Similarity=0.156  Sum_probs=68.5

Q ss_pred             CEEEEcCC----CCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecC----HHH----HHHHHH---hCCCe
Q 030488           48 RSVFVGNV----DYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQ----SEA----VQEALH---LNESE  111 (176)
Q Consensus        48 ~~i~v~~l----p~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~----~~~----a~~a~~---l~~~~  111 (176)
                      ..|||+||    |+.+++++|+++|++||+|.+|.++.|+ ||.++|||||+|.+    +++    |.+|+.   +++..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    9999999999999999999999999999 89999999999996    333    677763   69999


Q ss_pred             eCCeeeEEEeccC
Q 030488          112 LHGRQLKVTVKRT  124 (176)
Q Consensus       112 ~~g~~i~v~~a~~  124 (176)
                      |+|+.|+|.+.+.
T Consensus        83 I~Gr~irV~ln~~   95 (136)
T 2j8a_A           83 IMGFKFEVILNKH   95 (136)
T ss_dssp             ETTEEEEEEECCT
T ss_pred             ecCcEEEEEECcc
Confidence            9999999998753

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.75  E-value=5.7e-18  Score=109.10  Aligned_cols=72  Identities=28%  Similarity=0.535  Sum_probs=67.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhC----C-------CeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeC
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSC----G-------TVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELH  113 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~----G-------~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~  113 (176)
                      ...++|||+|||+++|+++|+++|++|    |       .|.++.+..+     +|||||+|.+.++|++|+.||+..|+
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~~A~~l~g~~~~   78 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAMAFDGIIFQ   78 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHHHHGGGTTCEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHHHHHhcCCCEEC
Confidence            346899999999999999999999999    8       8999999865     89999999999999999999999999


Q ss_pred             CeeeEEEe
Q 030488          114 GRQLKVTV  121 (176)
Q Consensus       114 g~~i~v~~  121 (176)
                      |+.|+|+.
T Consensus        79 g~~l~V~r   86 (87)
T 2hzc_A           79 GQSLKIRR   86 (87)
T ss_dssp             TEECEEEC
T ss_pred             CeEEEEeC
Confidence            99999974

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.75  E-value=1.6e-18  Score=125.24  Aligned_cols=78  Identities=22%  Similarity=0.428  Sum_probs=71.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ....++|||+|||.++|+++|+++|++||.|..+    ..++.++|||||+|.+.++|.+|+ .||+..|+|+.|.|+++
T Consensus        96 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  171 (175)
T 1fje_B           96 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT  171 (175)
T ss_dssp             TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEEC
T ss_pred             cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEec
Confidence            4457899999999999999999999999988665    557889999999999999999999 69999999999999999


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      ++.
T Consensus       172 ~~k  174 (175)
T 1fje_B          172 GEK  174 (175)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            753

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.74  E-value=7.1e-18  Score=131.36  Aligned_cols=121  Identities=13%  Similarity=0.264  Sum_probs=89.3

Q ss_pred             HHHHHHHHHHHHHHHHhhccccccCCCCC-CCCCCcc-cccCCCCCEEEEcCCCCC-CCHHHHHHHhhhCCCeeEEEEee
Q 030488            5 LKEMEEEATALRQMHAKVGNEMASKQDPA-AGGSSLA-NREEVDSRSVFVGNVDYS-CTPEEVQQHFQSCGTVNRVTIRT   81 (176)
Q Consensus         5 ~~e~e~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~-~~~~~~~~~i~v~~lp~~-~t~~~l~~~f~~~G~i~~~~~~~   81 (176)
                      |...+++..|++.++...-.......... +...... .......++|||+|||++ +|+++|+++|++||.|..|.|+.
T Consensus       166 f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~  245 (292)
T 2ghp_A          166 VTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPA  245 (292)
T ss_dssp             CSSHHHHHHHHHHHTTCEETTEECEEEECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCS
T ss_pred             ECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEe
Confidence            44566777777777654321111110000 0001111 123456799999999999 99999999999999999999999


Q ss_pred             CCC--CCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccCC
Q 030488           82 DKF--GQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRTN  125 (176)
Q Consensus        82 ~~~--g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~~  125 (176)
                      +..  +.++|||||+|.+.++|.+|+.||+..|+|+.|.|.++.+.
T Consensus       246 ~~~~tg~~~g~afV~F~~~~~A~~A~~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          246 GQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             CCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEECCCC
T ss_pred             cCCcCCCCceEEEEEeCCHHHHHHHHHhcCCEECCcEEEEEEecCC
Confidence            876  99999999999999999999999999999999999999753

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.74  E-value=4.5e-17  Score=111.92  Aligned_cols=74  Identities=26%  Similarity=0.291  Sum_probs=66.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeE-EEEEecCHHHHHHHH-HhCCCeeCC--eeeEEEec
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGY-AYVEFLQSEAVQEAL-HLNESELHG--RQLKVTVK  122 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~-afv~f~~~~~a~~a~-~l~~~~~~g--~~i~v~~a  122 (176)
                      ...|||+||++.+|+++|+++|++||.|.+|.|...     .|| |||+|.+.++|+.|+ .||+..|.|  +.|+|.+|
T Consensus        25 vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           25 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            345789999999999999999999999999999753     376 999999999999999 799999987  68999999


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      ++.
T Consensus       100 k~~  102 (124)
T 2e5i_A          100 RPT  102 (124)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            864

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.73  E-value=1.4e-17  Score=129.17  Aligned_cols=120  Identities=16%  Similarity=0.157  Sum_probs=91.5

Q ss_pred             HHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCcccccCCCCCEEEEcCCCCCC-CHHHHHHHhhhCCCeeEEEEeeCC
Q 030488            5 LKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSC-TPEEVQQHFQSCGTVNRVTIRTDK   83 (176)
Q Consensus         5 ~~e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~lp~~~-t~~~l~~~f~~~G~i~~~~~~~~~   83 (176)
                      |...+++.+|+..++...-..........  ............++|||+|||.++ |+++|+++|+.||.|..+.|+.+.
T Consensus       144 f~~~~~a~~A~~~l~~~~~~g~~i~v~~a--~~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~  221 (284)
T 3smz_A          144 YMKKDSAARAKSDLLGKPLGPRTLYVHWT--DAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ  221 (284)
T ss_dssp             ESSHHHHHHHHHHHTTCEETTEECEEEEC--CGGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS
T ss_pred             ECCHHHHHHHHHHhCCCEeCCcEEEEEEC--CCCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC
Confidence            44556677777777654221111110000  111112234567899999999995 999999999999999999999999


Q ss_pred             CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccCCC
Q 030488           84 FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNV  126 (176)
Q Consensus        84 ~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~~~  126 (176)
                      +|.++|||||+|.+.++|.+|+ .||+..|+|+.|.|.++.+..
T Consensus       222 ~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  265 (284)
T 3smz_A          222 DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGP  265 (284)
T ss_dssp             SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSS
T ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCC
Confidence            9999999999999999999999 699999999999999997643

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.73  E-value=2e-17  Score=123.26  Aligned_cols=75  Identities=31%  Similarity=0.426  Sum_probs=70.3

Q ss_pred             CCCEEEEcCCC-CCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           46 DSRSVFVGNVD-YSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        46 ~~~~i~v~~lp-~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      ++++|||+||| +.+|+++|+++|++||.|.+|+|+.++    +|||||+|.+.++|+.|| .||+..|.|+.|.|.+++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~   78 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSK   78 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcc
Confidence            46899999999 899999999999999999999998764    799999999999999999 699999999999999986


Q ss_pred             C
Q 030488          124 T  124 (176)
Q Consensus       124 ~  124 (176)
                      .
T Consensus        79 ~   79 (205)
T 3tyt_A           79 Q   79 (205)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=3.1e-17  Score=111.20  Aligned_cols=76  Identities=26%  Similarity=0.381  Sum_probs=66.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-C---CCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEE
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-F---GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV  119 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~---g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v  119 (176)
                      ...++|||+|||+++|+++|+++|++||.|. +.++.+. +   |+++|||||+|.+.++|++|| .|+  .++|+.|.|
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            4568999999999999999999999999999 8887776 4   799999999999999999999 673  478887777


Q ss_pred             Eecc
Q 030488          120 TVKR  123 (176)
Q Consensus       120 ~~a~  123 (176)
                      ..+.
T Consensus        83 ~~~~   86 (114)
T 2dnl_A           83 VSSP   86 (114)
T ss_dssp             ECCS
T ss_pred             ccCC
Confidence            6554

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

Probab=99.72  E-value=3e-17  Score=122.11  Aligned_cols=80  Identities=30%  Similarity=0.480  Sum_probs=72.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ...++|||+|||.++|+++|+++|++||.|.+|.|+.++ ++.++|||||+|.+.++|++|+ .|++..|.|+.|.|..+
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            446899999999999999999999999999999999988 7999999999999999999999 59999999999999876


Q ss_pred             cC
Q 030488          123 RT  124 (176)
Q Consensus       123 ~~  124 (176)
                      ..
T Consensus       106 ~~  107 (216)
T 2qfj_A          106 SN  107 (216)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=3.5e-17  Score=106.16  Aligned_cols=71  Identities=17%  Similarity=0.374  Sum_probs=63.3

Q ss_pred             CCE-EEEcCCCCCCCHHH----HHHHhhhC-CCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEE
Q 030488           47 SRS-VFVGNVDYSCTPEE----VQQHFQSC-GTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV  119 (176)
Q Consensus        47 ~~~-i~v~~lp~~~t~~~----l~~~f~~~-G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v  119 (176)
                      ..+ |||+|||+.+++++    |+++|++| |+|.+|      ++   |+|||+|.+.++|++|+ .|++..+.|+.|+|
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v   78 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI------TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIV   78 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEE
Confidence            445 99999999999988    55899999 499888      33   99999999999999999 79999999999999


Q ss_pred             EeccCCC
Q 030488          120 TVKRTNV  126 (176)
Q Consensus       120 ~~a~~~~  126 (176)
                      .+|+...
T Consensus        79 ~~A~~~s   85 (96)
T 2diu_A           79 SFTPKNR   85 (96)
T ss_dssp             ESSCCSC
T ss_pred             EecCCCc
Confidence            9998654

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.70  E-value=9.6e-17  Score=124.49  Aligned_cols=110  Identities=21%  Similarity=0.286  Sum_probs=88.3

Q ss_pred             HHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCcccccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-
Q 030488            5 LKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-   83 (176)
Q Consensus         5 ~~e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-   83 (176)
                      |...+++..|+..++...-.......           .......+|||+|||+++|+++|+++|++||.|..+.++.++ 
T Consensus        64 f~~~~~A~~A~~~l~~~~~~g~~i~v-----------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~  132 (284)
T 3smz_A           64 LLNGEQAEAAINAFHQSRLRERELSV-----------QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER  132 (284)
T ss_dssp             ESSHHHHHHHHHHHTTCEETTEECEE-----------EECCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT
T ss_pred             eCCHHHHHHHHHHcCCCeeCCeEEEE-----------EecCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCC
Confidence            44556677777766654321111100           012345799999999999999999999999999999999987 


Q ss_pred             CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccCC
Q 030488           84 FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTN  125 (176)
Q Consensus        84 ~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~~  125 (176)
                      ++.++|||||+|.+.++|.+|+ .|++..++|+.|.|.++...
T Consensus       133 ~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~  175 (284)
T 3smz_A          133 TGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAG  175 (284)
T ss_dssp             TCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGG
T ss_pred             CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            7999999999999999999999 79999999999999998653

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.70  E-value=3.4e-17  Score=117.18  Aligned_cols=78  Identities=22%  Similarity=0.510  Sum_probs=71.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccC
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~  124 (176)
                      +.++|||+|||+++|+++|+++|++||.|.+|.|+.++ ++.++|||||+|.+.++|++|+. +...++|+.|.|..+.+
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~~~~   80 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK-TQHILDGKVIDPKRAIP   80 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH-SCCEETTEECCCEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh-cccccCCeEcccccccc
Confidence            35799999999999999999999999999999999997 79999999999999999999996 35789999999988753

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.70  E-value=3e-16  Score=104.93  Aligned_cols=80  Identities=19%  Similarity=0.202  Sum_probs=71.0

Q ss_pred             CCCCEEEEcCCCC-----CCCHHHHHHHhhhCCCeeEEEEeeCC--CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCee
Q 030488           45 VDSRSVFVGNVDY-----SCTPEEVQQHFQSCGTVNRVTIRTDK--FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQ  116 (176)
Q Consensus        45 ~~~~~i~v~~lp~-----~~t~~~l~~~f~~~G~i~~~~~~~~~--~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  116 (176)
                      ..+++|+|.||..     +.++++|++.|++||.|.+|.|+.++  ++.++|||||+|.+.++|++|+ .||+..++|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4578999999962     23789999999999999999999986  3688999999999999999999 79999999999


Q ss_pred             eEEEeccC
Q 030488          117 LKVTVKRT  124 (176)
Q Consensus       117 i~v~~a~~  124 (176)
                      |.|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999853

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.70  E-value=1e-16  Score=124.25  Aligned_cols=75  Identities=15%  Similarity=0.218  Sum_probs=70.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeC-CeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELH-GRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~-g~~i~v~~a  122 (176)
                      ...++|||+|||.++|+++|+++|++||.|.+|.|+.++    +|||||+|.+.++|++|+ .||+..|. |+.|+|+++
T Consensus       205 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a  280 (282)
T 3pgw_A          205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFA  280 (282)
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEe
Confidence            356889999999999999999999999999999998765    589999999999999999 69999999 999999998


Q ss_pred             c
Q 030488          123 R  123 (176)
Q Consensus       123 ~  123 (176)
                      +
T Consensus       281 k  281 (282)
T 3pgw_A          281 K  281 (282)
T ss_pred             c
Confidence            6

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.69  E-value=1.5e-16  Score=123.27  Aligned_cols=80  Identities=14%  Similarity=0.328  Sum_probs=73.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHH----HHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeE
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQ----QHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLK  118 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~----~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~  118 (176)
                      ....++|||+|||+++|+++|+    ++|++||.|.+|.|+.  +++++|||||+|.+.++|++|| .||+..|.|+.|+
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~--~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   83 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   83 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC--CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEE
Confidence            4567999999999999999976    8999999999998875  7888999999999999999999 7999999999999


Q ss_pred             EEeccCC
Q 030488          119 VTVKRTN  125 (176)
Q Consensus       119 v~~a~~~  125 (176)
                      |.+++..
T Consensus        84 v~~a~~~   90 (282)
T 3pgw_A           84 IQYAKTD   90 (282)
T ss_pred             EEEeccC
Confidence            9998653

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.69  E-value=1.2e-16  Score=114.98  Aligned_cols=79  Identities=23%  Similarity=0.436  Sum_probs=71.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCC-C--CceeEEEEEecCHHHHHHHH-HhCCCeeC---CeeeE
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-G--QPKGYAYVEFLQSEAVQEAL-HLNESELH---GRQLK  118 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~-g--~~~g~afv~f~~~~~a~~a~-~l~~~~~~---g~~i~  118 (176)
                      +.++|||+|||+++|+++|+++|++||.|.+|.|+.++. +  .++|||||+|.+.++|++|+ .|++..+.   ++.|.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            468999999999999999999999999999999999884 4  89999999999999999999 69998775   57788


Q ss_pred             EEeccC
Q 030488          119 VTVKRT  124 (176)
Q Consensus       119 v~~a~~  124 (176)
                      |..+..
T Consensus        82 ~~~~~~   87 (175)
T 3nmr_A           82 MKPADS   87 (175)
T ss_dssp             EEECGG
T ss_pred             Eccccc
Confidence            887754

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.68  E-value=2.2e-16  Score=119.23  Aligned_cols=76  Identities=21%  Similarity=0.350  Sum_probs=69.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCC-CeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeC-CeeeEEEec
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCG-TVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELH-GRQLKVTVK  122 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G-~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~-g~~i~v~~a  122 (176)
                      ..++|||+|||.++++++|+++|++|| .|..|.++.+    .+|||||+|.+.++|++|+ .||+..+. |+.|+|.++
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a  225 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS  225 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEe
Confidence            468999999999999999999999999 9999999653    2789999999999999999 69999999 999999999


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      ++.
T Consensus       226 ~~~  228 (229)
T 2adc_A          226 KST  228 (229)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            763

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.68  E-value=1.1e-16  Score=119.18  Aligned_cols=76  Identities=16%  Similarity=0.179  Sum_probs=67.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCe--eEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCe----eeE
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTV--NRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGR----QLK  118 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i--~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~----~i~  118 (176)
                      +.++|||+|||+++|+++|+++|++||.|  .++++..++ +..+|||||+|.+.++|.+|| .||+..|.|.    ++.
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~-~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~  200 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK-SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYT  200 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC-SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEE
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC-CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceE
Confidence            46789999999999999999999999999  899998776 555799999999999999999 7999999886    466


Q ss_pred             EEec
Q 030488          119 VTVK  122 (176)
Q Consensus       119 v~~a  122 (176)
                      |.++
T Consensus       201 vk~~  204 (205)
T 3tyt_A          201 LKLC  204 (205)
T ss_dssp             CEEE
T ss_pred             EEec
Confidence            6654

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.68  E-value=1.3e-16  Score=117.56  Aligned_cols=76  Identities=21%  Similarity=0.356  Sum_probs=70.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCC-CeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeC-CeeeEEEec
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCG-TVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELH-GRQLKVTVK  122 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G-~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~-g~~i~v~~a  122 (176)
                      +.++|||+|||.++++++|+++|++|| .|..|.+..+.    +|+|||+|.+.++|.+|+ .||+..++ |+.|+|.++
T Consensus       119 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a  194 (198)
T 1qm9_A          119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS  194 (198)
T ss_dssp             CCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEee
Confidence            478999999999999999999999999 99999997543    789999999999999999 69999999 999999999


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      ++.
T Consensus       195 ~~~  197 (198)
T 1qm9_A          195 KST  197 (198)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            753

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.67  E-value=1e-16  Score=121.64  Aligned_cols=77  Identities=18%  Similarity=0.349  Sum_probs=70.2

Q ss_pred             CCCCCEEEEcCCCCCC---------CHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCee-
Q 030488           44 EVDSRSVFVGNVDYSC---------TPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESEL-  112 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~---------t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~-  112 (176)
                      ....++|||+||+..+         ++++|+++|++||.|++|.|+.+     +|||||+|.+.++|+.|+ +|++..| 
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~-----kG~AFV~F~~~~~Ae~A~~am~g~~l~  205 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES-----KNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC-----CCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            4567999999999998         79999999999999999999864     899999999999999999 7999999 


Q ss_pred             -----------CCeeeEEEeccCC
Q 030488          113 -----------HGRQLKVTVKRTN  125 (176)
Q Consensus       113 -----------~g~~i~v~~a~~~  125 (176)
                                 .|+.|.|.+|+..
T Consensus       206 ~~~~~e~~~~~~gr~L~V~wA~~~  229 (240)
T 3u1l_A          206 LPSDKEWDDRREGTGLLVKWANED  229 (240)
T ss_dssp             CTTSTTGGGGGGSCCCEEEECC--
T ss_pred             ccccccccccCCCCEEEEEEccCC
Confidence                       8999999999754

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.67  E-value=2.9e-16  Score=118.58  Aligned_cols=80  Identities=29%  Similarity=0.460  Sum_probs=73.6

Q ss_pred             ccCCCCCEEEEcCCCC-CCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEE
Q 030488           42 REEVDSRSVFVGNVDY-SCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV  119 (176)
Q Consensus        42 ~~~~~~~~i~v~~lp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v  119 (176)
                      ....+.++|||+|||+ ++++++|+++|++||.|.+|.|+.++    +|||||+|.+.++|++|+ .|++..|.|+.|.|
T Consensus        29 ~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v  104 (229)
T 2adc_A           29 LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI  104 (229)
T ss_dssp             GGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            3456689999999999 99999999999999999999999876    789999999999999999 69999999999999


Q ss_pred             EeccCC
Q 030488          120 TVKRTN  125 (176)
Q Consensus       120 ~~a~~~  125 (176)
                      .+++..
T Consensus       105 ~~a~~~  110 (229)
T 2adc_A          105 TLSKHQ  110 (229)
T ss_dssp             ECCSCC
T ss_pred             EEecCc
Confidence            998754

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.67  E-value=2.2e-16  Score=121.47  Aligned_cols=109  Identities=19%  Similarity=0.247  Sum_probs=84.6

Q ss_pred             HHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCcccccCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCC
Q 030488            5 LKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF   84 (176)
Q Consensus         5 ~~e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~   84 (176)
                      |...+++..|+..++...........           ....+..+|||+|||..+|+++|+++|++||.|..|.|+.+.+
T Consensus        65 f~~~~~A~~A~~~l~g~~i~g~~l~v-----------~~a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~  133 (261)
T 3sde_A           65 LESRTLAEIAKAELDGTILKSRPLRI-----------RFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDR  133 (261)
T ss_dssp             CSSHHHHHHHHHHHTTCEETTEECEE-----------EECCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT
T ss_pred             ECCHHHHHHHHHHcCCcEECCceeEe-----------eecccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCC
Confidence            44556667777766654321111110           0112467999999999999999999999999999999999989


Q ss_pred             CCceeEEEEEecCHHHHHHHH-HhC-CCeeC---CeeeEEEeccC
Q 030488           85 GQPKGYAYVEFLQSEAVQEAL-HLN-ESELH---GRQLKVTVKRT  124 (176)
Q Consensus        85 g~~~g~afv~f~~~~~a~~a~-~l~-~~~~~---g~~i~v~~a~~  124 (176)
                      |.++|||||+|.+.++|.+|+ .|| +..+.   ++.|.|.++..
T Consensus       134 g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~  178 (261)
T 3sde_A          134 GRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQ  178 (261)
T ss_dssp             SCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCC
T ss_pred             CCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccc
Confidence            999999999999999999999 684 44544   89999999864

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.65  E-value=4.3e-17  Score=117.70  Aligned_cols=83  Identities=19%  Similarity=0.376  Sum_probs=72.1

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      .....++|||+|||+++|+++|+++|..||.+..+.+....++.++|||||+|.+.++|++|++|++..|.|+.|.|.++
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~   88 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   88 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecC
Confidence            34567999999999999999999999999987663333334688899999999999999999999999999999999998


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      ...
T Consensus        89 ~~~   91 (175)
T 1fje_B           89 KGR   91 (175)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            753

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.64  E-value=7.6e-16  Score=119.84  Aligned_cols=81  Identities=17%  Similarity=0.260  Sum_probs=71.4

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      .....++|||+|||+++|+++|+++|+.||.|..|.|+.+..+ ++|||||+|.+.++|++|+++++..+.|+.|.|.++
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~  115 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK-NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL  115 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS-SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC-CcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEEEC
Confidence            4566899999999999999999999999999999999998755 479999999999999999999999999999999987


Q ss_pred             cC
Q 030488          123 RT  124 (176)
Q Consensus       123 ~~  124 (176)
                      ..
T Consensus       116 ~~  117 (292)
T 2ghp_A          116 TE  117 (292)
T ss_dssp             CS
T ss_pred             CC
Confidence            43

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.64  E-value=8.7e-16  Score=118.11  Aligned_cols=77  Identities=22%  Similarity=0.408  Sum_probs=70.9

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      .....++|||+|||+++|+++|+++|++||.|..|.|.++     +|||||+|.+.++|+.|+ .+++..|.|+.|.|.+
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            3456789999999999999999999999999999999755     799999999999999999 6999999999999998


Q ss_pred             ccC
Q 030488          122 KRT  124 (176)
Q Consensus       122 a~~  124 (176)
                      +.+
T Consensus        93 a~~   95 (261)
T 3sde_A           93 ATH   95 (261)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            864

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.64  E-value=3.5e-16  Score=115.16  Aligned_cols=76  Identities=30%  Similarity=0.496  Sum_probs=70.9

Q ss_pred             CCCEEEEcCCCC-CCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           46 DSRSVFVGNVDY-SCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        46 ~~~~i~v~~lp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      .+++|||+|||+ ++++++|+++|++||.|.+|.++.++    +|||||+|.+.++|++|+ .|++..+.|+.|.|.+++
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            468999999999 99999999999999999999998875    789999999999999999 699999999999999987


Q ss_pred             CC
Q 030488          124 TN  125 (176)
Q Consensus       124 ~~  125 (176)
                      ..
T Consensus        78 ~~   79 (198)
T 1qm9_A           78 HQ   79 (198)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.63  E-value=1.8e-16  Score=105.90  Aligned_cols=71  Identities=20%  Similarity=0.397  Sum_probs=64.3

Q ss_pred             EcCCCCCCCHHHHHHHh------------hhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeE
Q 030488           52 VGNVDYSCTPEEVQQHF------------QSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLK  118 (176)
Q Consensus        52 v~~lp~~~t~~~l~~~f------------~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~  118 (176)
                      +.+||+.+++++|++.|            ++||.|.+|.|+++.+++++|||||+|.+.++|++|+ .||+..++|+.|+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            56788888888877766            9999999999998888899999999999999999999 7999999999999


Q ss_pred             EEec
Q 030488          119 VTVK  122 (176)
Q Consensus       119 v~~a  122 (176)
                      |+++
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9876

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=7.3e-15  Score=99.14  Aligned_cols=79  Identities=20%  Similarity=0.324  Sum_probs=67.7

Q ss_pred             CCCCCEEEEcCCCCCCC-----------HHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCe
Q 030488           44 EVDSRSVFVGNVDYSCT-----------PEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESE  111 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t-----------~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~  111 (176)
                      ...+++|+|.||....+           +++|+++|++||.|.+|.| .++  .++|||||+|.+.++|++|+ .||+..
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            45678999999944332           5799999999999999966 444  36999999999999999999 799999


Q ss_pred             eCCeeeEEEeccCC
Q 030488          112 LHGRQLKVTVKRTN  125 (176)
Q Consensus       112 ~~g~~i~v~~a~~~  125 (176)
                      |+|+.|.|.++.+.
T Consensus        89 ~~gr~l~v~~a~~~  102 (112)
T 2dit_A           89 FGGRQITAQAWDGT  102 (112)
T ss_dssp             ETTEECEEEECCSC
T ss_pred             ECCcEEEEEEeCCC
Confidence            99999999998754

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.62  E-value=2.2e-15  Score=108.16  Aligned_cols=75  Identities=27%  Similarity=0.523  Sum_probs=67.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhC----C-------CeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCC
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSC----G-------TVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHG  114 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~----G-------~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g  114 (176)
                      +.++|||+|||+++|+++|+++|++|    |       .|.++.+..+     +|||||+|.+.++|++|+.+++..+.|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~-----~g~afV~f~~~~~A~~A~~~~~~~~~g   77 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAMAFDGIIFQG   77 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETT-----TTEEEEEESSHHHHHHHGGGTTCEETT
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCC-----CCEEEEEeCCHHHHHHHHHhCCcEecC
Confidence            35899999999999999999999999    6       7777777544     899999999999999999999999999


Q ss_pred             eeeEEEeccCC
Q 030488          115 RQLKVTVKRTN  125 (176)
Q Consensus       115 ~~i~v~~a~~~  125 (176)
                      +.|.|..+...
T Consensus        78 ~~i~v~~~~~~   88 (172)
T 2g4b_A           78 QSLKIRRPHDY   88 (172)
T ss_dssp             EECEEECCSSC
T ss_pred             ceeeecCCccc
Confidence            99999987643

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

Probab=99.60  E-value=3.8e-15  Score=109.24  Aligned_cols=75  Identities=27%  Similarity=0.495  Sum_probs=66.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhC----C-------CeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCC
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSC----G-------TVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHG  114 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~----G-------~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g  114 (176)
                      ..++|||+|||+++|+++|+++|++|    |       .|.++.+.     .++|||||+|.+.++|++||.||+..|.|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~-----~~~g~afV~F~~~~~A~~Al~l~g~~~~g   77 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-----QDKNFAFLEFRSVDETTQAMAFDGIIFQG   77 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE-----TTTTEEEEEESCSHHHHHHGGGTTEEETT
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec-----CCCCEEEEEeCCHHHHHHHHHhcCCEEcC
Confidence            46899999999999999999999999    5       56666654     34899999999999999999999999999


Q ss_pred             eeeEEEeccCC
Q 030488          115 RQLKVTVKRTN  125 (176)
Q Consensus       115 ~~i~v~~a~~~  125 (176)
                      +.|.|.++...
T Consensus        78 ~~i~v~~~~~~   88 (198)
T 2yh0_A           78 QSLKIRRPHDY   88 (198)
T ss_dssp             EEEEEECCCCC
T ss_pred             ceEEEeCCCCC
Confidence            99999988654

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.58  E-value=6.4e-15  Score=98.44  Aligned_cols=79  Identities=18%  Similarity=0.157  Sum_probs=68.7

Q ss_pred             CCCCEEEEcCC--CCCCC--------HHHHHHHhhhCCCeeEEEEeeCCC---CCceeEEEEEecCHHHHHHHH-HhCCC
Q 030488           45 VDSRSVFVGNV--DYSCT--------PEEVQQHFQSCGTVNRVTIRTDKF---GQPKGYAYVEFLQSEAVQEAL-HLNES  110 (176)
Q Consensus        45 ~~~~~i~v~~l--p~~~t--------~~~l~~~f~~~G~i~~~~~~~~~~---g~~~g~afv~f~~~~~a~~a~-~l~~~  110 (176)
                      .+++.|.|.|+  |.++.        +++|++.|++||.|.+|.|++++.   +.++|||||+|.+.++|++|+ .||+.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            35688999998  44443        368999999999999999998873   368999999999999999999 79999


Q ss_pred             eeCCeeeEEEecc
Q 030488          111 ELHGRQLKVTVKR  123 (176)
Q Consensus       111 ~~~g~~i~v~~a~  123 (176)
                      .++|+.|.|.+..
T Consensus        83 ~f~GR~i~v~~~~   95 (105)
T 3v4m_A           83 KFANRVVVTKYCD   95 (105)
T ss_dssp             EETTEECEEEEEC
T ss_pred             EeCCCEEEEEEeC
Confidence            9999999999874

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.54  E-value=4.3e-14  Score=96.30  Aligned_cols=78  Identities=26%  Similarity=0.299  Sum_probs=67.9

Q ss_pred             CCCEEEEcCCC--CCC---CHHHHHHHhhhCCCeeEEEEeeCCC-----CCceeEEEEEecCHHHHHHHH-HhCCCeeCC
Q 030488           46 DSRSVFVGNVD--YSC---TPEEVQQHFQSCGTVNRVTIRTDKF-----GQPKGYAYVEFLQSEAVQEAL-HLNESELHG  114 (176)
Q Consensus        46 ~~~~i~v~~lp--~~~---t~~~l~~~f~~~G~i~~~~~~~~~~-----g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  114 (176)
                      ++++|+|.|+-  .++   .+++|++.|++||.|.+|.|+.++.     +.++||+||+|.+.++|.+|+ .||+..++|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            46889999983  222   3689999999999999999998762     467899999999999999999 799999999


Q ss_pred             eeeEEEecc
Q 030488          115 RQLKVTVKR  123 (176)
Q Consensus       115 ~~i~v~~a~  123 (176)
                      +.|.|.+..
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999999874

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=2.9e-13  Score=89.54  Aligned_cols=65  Identities=22%  Similarity=0.238  Sum_probs=56.1

Q ss_pred             CCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccCCC
Q 030488           57 YSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRTNV  126 (176)
Q Consensus        57 ~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~~~  126 (176)
                      ..+++++|+++|++||.|..|.|+    ++++|||||+|.+.++|+.||.. ...+.++.|+|.+++...
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~----~~~rGfaFVeF~~~~~A~~Ai~~-~~~~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS----SKKPGTAVVEFATVKAAELAVQN-EVGLVDNPLKISWLEGQP   91 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE----SSSSSEEEEEESCHHHHHHHHHT-CCBCSSSBCEEECSSCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc----cCCCCEEEEEECCHHHHHHHHHh-cCCCCCCeEEEEEccCCC
Confidence            468999999999999999999998    35699999999999999999942 334679999999987643

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.50  E-value=5.3e-14  Score=111.95  Aligned_cols=75  Identities=20%  Similarity=0.407  Sum_probs=64.1

Q ss_pred             CCCCCEEEEcC--CCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeC---Ce--
Q 030488           44 EVDSRSVFVGN--VDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELH---GR--  115 (176)
Q Consensus        44 ~~~~~~i~v~~--lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~---g~--  115 (176)
                      ..++.+|||+|  |++.+|+++|+++|++||.|.+|.+..     ++|||||+|.+.++|++|+ +||+.++-   |+  
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~   89 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   89 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCccccccCCce
Confidence            45678999999  578999999999999999999987754     3799999999999999999 79999883   44  


Q ss_pred             eeEEEecc
Q 030488          116 QLKVTVKR  123 (176)
Q Consensus       116 ~i~v~~a~  123 (176)
                      .|.|.++.
T Consensus        90 ~ly~~~~~   97 (345)
T 3tht_A           90 TLYLNFVE   97 (345)
T ss_dssp             ECEEEECS
T ss_pred             EEEEEEee
Confidence            57777663

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.40  E-value=2e-12  Score=87.46  Aligned_cols=76  Identities=14%  Similarity=0.220  Sum_probs=63.5

Q ss_pred             CCCCEEEEcCCC--CCC--------CHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeC
Q 030488           45 VDSRSVFVGNVD--YSC--------TPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELH  113 (176)
Q Consensus        45 ~~~~~i~v~~lp--~~~--------t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~  113 (176)
                      .+++.|.|.|+=  .+.        .+++|++.|++||.|.+|.|.++.   .+||+||+|.+.++|++|+ .||+..++
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~---~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC---TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC---CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            456788888882  221        135789999999999999987653   4899999999999999999 79999999


Q ss_pred             CeeeEEEecc
Q 030488          114 GRQLKVTVKR  123 (176)
Q Consensus       114 g~~i~v~~a~  123 (176)
                      |+.|.|.++.
T Consensus        82 GR~i~v~~~~   91 (114)
T 3s6e_A           82 GKMITAAYVP   91 (114)
T ss_dssp             TEECEEEEEC
T ss_pred             CEEEEEEEEc
Confidence            9999999874

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.33  E-value=5e-12  Score=85.98  Aligned_cols=74  Identities=11%  Similarity=0.092  Sum_probs=65.6

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecC-HHHHHHHH-HhC--CCeeCCeeeE
Q 030488           44 EVDSRSVFVGNVDYS-CTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQ-SEAVQEAL-HLN--ESELHGRQLK  118 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~-~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~-~~~a~~a~-~l~--~~~~~g~~i~  118 (176)
                      -..+..|||+||+.+ ++.++|+++|++||.|..|.+..+.     ..|||.|.+ .++|+.|+ +++  +..|++..++
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~-----~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~   89 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-----KEGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   89 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC-----SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-----CEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEE
Confidence            456899999999999 9999999999999999999998874     369999999 88999999 674  7889999999


Q ss_pred             EEec
Q 030488          119 VTVK  122 (176)
Q Consensus       119 v~~a  122 (176)
                      +++.
T Consensus        90 ~evL   93 (121)
T 1owx_A           90 WEVL   93 (121)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            8765

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.33  E-value=1.1e-11  Score=79.62  Aligned_cols=75  Identities=27%  Similarity=0.381  Sum_probs=63.5

Q ss_pred             CCCCEEEEcCCCC----CCCH----HHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCee
Q 030488           45 VDSRSVFVGNVDY----SCTP----EEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQ  116 (176)
Q Consensus        45 ~~~~~i~v~~lp~----~~t~----~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~  116 (176)
                      .+..+|+|.-++.    ++..    .+|.+.|.+||.|..++++.++       +||+|.+.++|.+||.||+..++|+.
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~-------~fVtF~d~~sAlaAi~mnG~~v~Gr~   77 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK-------MWVTFLEGSSALNVLSLNGKELLNRT   77 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS-------EEEEESSHHHHHHGGGGTTCEETTEE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC-------EEEEECChHHHHHHHhcCCeEeCCeE
Confidence            3456788877662    3333    6789999999999999999764       89999999999999999999999999


Q ss_pred             eEEEeccCCC
Q 030488          117 LKVTVKRTNV  126 (176)
Q Consensus       117 i~v~~a~~~~  126 (176)
                      |+|.++.+..
T Consensus        78 LkV~lkt~dW   87 (91)
T 2dnr_A           78 ITIALKSPSG   87 (91)
T ss_dssp             EEEEECCCSS
T ss_pred             EEEEeCCCCc
Confidence            9999998654

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.13  E-value=1.4e-10  Score=74.85  Aligned_cols=73  Identities=23%  Similarity=0.291  Sum_probs=62.3

Q ss_pred             CCCCCEEEEcCCCCC-----CCH----HHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCC
Q 030488           44 EVDSRSVFVGNVDYS-----CTP----EEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHG  114 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~-----~t~----~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g  114 (176)
                      ..+..+|+|.-++.+     +..    .+|.+.|.+||.|..++++.++       +||+|.+.++|.+||.|++..++|
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~-------~fVtF~d~~sAl~AI~ldG~~v~G   84 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ-------MLVTFADSHSALSVLDVDGMKVKG   84 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE-------EEEECSCSHHHHHHHHGGGSEETT
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc-------EEEEEcChHHHHHHHhcCCeeeCC
Confidence            345678999888643     322    5689999999999999999773       999999999999999999999999


Q ss_pred             eeeEEEecc
Q 030488          115 RQLKVTVKR  123 (176)
Q Consensus       115 ~~i~v~~a~  123 (176)
                      +.|+|.+..
T Consensus        85 r~L~V~~k~   93 (95)
T 1ufw_A           85 RAVKISGPS   93 (95)
T ss_dssp             EEEEEECCC
T ss_pred             eEEEEeccC
Confidence            999999864

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=99.03  E-value=6.8e-10  Score=83.05  Aligned_cols=65  Identities=28%  Similarity=0.301  Sum_probs=58.5

Q ss_pred             CCHHHHHHHhhhCCCeeEEEEeeCC-----CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           59 CTPEEVQQHFQSCGTVNRVTIRTDK-----FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        59 ~t~~~l~~~f~~~G~i~~~~~~~~~-----~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      -.+++|.+.|++||.|.++.|+.+.     ++.++|++||+|.+.++|++|+ .||+..++|+.|.|.+..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            3567899999999999999998654     3589999999999999999999 799999999999999874

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.77  E-value=4.7e-08  Score=64.40  Aligned_cols=72  Identities=17%  Similarity=0.207  Sum_probs=65.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhC-----CCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEE
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSC-----GTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV  119 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~-----G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v  119 (176)
                      ..++|-+=|||..+++..|+.+++.+     |.|..+.+..|     -+-|+|+|.+...|.+|. +|++.+|.|+.|+|
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD-----H~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~   94 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD-----FNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRS   94 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT-----TTEEEEECSCHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC-----CCceEEEEccchhhHHHHhhcCCeeecCeEEEe
Confidence            35678888999999999999999999     99999999988     566999999999999988 99999999999999


Q ss_pred             Eec
Q 030488          120 TVK  122 (176)
Q Consensus       120 ~~a  122 (176)
                      .-.
T Consensus        95 gTv   97 (117)
T 2l9w_A           95 GTI   97 (117)
T ss_dssp             ECH
T ss_pred             cCH
Confidence            753

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.40  E-value=4.9e-06  Score=54.24  Aligned_cols=73  Identities=19%  Similarity=0.172  Sum_probs=62.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhh-----CCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEE
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQS-----CGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV  119 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~-----~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v  119 (176)
                      ....+|.|.|||..+.++.|+-+|+.     =|+|+.+....       +-|+|+|.+.+.|+..|+-..+.|.+..|.|
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-------~~AvItF~d~~va~rVL~k~~H~L~~~~LsV   78 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-------CGGVLTFREPADAERVLAQADHELHGAQLSL   78 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-------TEEEEEESSHHHHHHHHTCSCCBSSSSBCEE
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-------CcEEEEEcChHHHHHHhcCCcceecCeEEEE
Confidence            34688999999999999999999986     25888887753       4699999999999999987789999999999


Q ss_pred             EeccC
Q 030488          120 TVKRT  124 (176)
Q Consensus       120 ~~a~~  124 (176)
                      ...-+
T Consensus        79 ~P~~~   83 (104)
T 2dhx_A           79 RPAPP   83 (104)
T ss_dssp             EECCC
T ss_pred             EcCCC
Confidence            87544

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.07  E-value=8.4e-06  Score=53.33  Aligned_cols=73  Identities=12%  Similarity=0.198  Sum_probs=60.7

Q ss_pred             CCEEEEcCCCCCC-C----HHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           47 SRSVFVGNVDYSC-T----PEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        47 ~~~i~v~~lp~~~-t----~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      .++|+|.||+.++ +    .+.++.+|..|+++......+.     -.-..|.|.+.++|.+|- .||+..+.|+.|+|-
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS-----FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~Y   79 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTEFLGKEMKLY   79 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSEETTEECEEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc-----ceEEEEEeCChHHHHHHHHHhccceecCceeEEE
Confidence            4789999998865 2    2567899999999887766644     234789999999999999 799999999999999


Q ss_pred             eccC
Q 030488          121 VKRT  124 (176)
Q Consensus       121 ~a~~  124 (176)
                      ++.+
T Consensus        80 Fgq~   83 (104)
T 1wey_A           80 FAQT   83 (104)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            9874

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

Probab=97.81  E-value=0.00016  Score=46.34  Aligned_cols=67  Identities=15%  Similarity=0.174  Sum_probs=55.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-C--CCceeEEEEEecCHHHHHHHH-HhCCCeeCC
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-F--GQPKGYAYVEFLQSEAVQEAL-HLNESELHG  114 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~--g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  114 (176)
                      .+|.|.+||+++|++++.+.+.....+....++..+ +  ...-.-|+|.|.+.+++.... .++++.+.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEc
Confidence            478999999999999999999998887777666554 2  234567999999999999988 799998843

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.66  E-value=0.00031  Score=47.05  Aligned_cols=72  Identities=11%  Similarity=0.121  Sum_probs=59.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCC-eeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHG-RQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g-~~i~v~~a  122 (176)
                      ....-|-|-+.|+.. .+.|..+|++||.|.+.....     ...+-.|.|.+..+|++||..|+..|++ ..|-|...
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~-----~~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN-----TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS-----SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEEC
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC-----CCCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEEEC
Confidence            446778888999885 677888999999998877621     2568999999999999999999999985 67777764

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.50  E-value=0.00048  Score=44.36  Aligned_cols=52  Identities=23%  Similarity=0.354  Sum_probs=43.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHH
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH  106 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~  106 (176)
                      .+.++| ++|.++...||.++|+.||.| .|.++.|.      .|||.|.+++.|..|+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT------sAlvvf~~~~~a~~al~   67 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT------SAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT------EEEEECSCHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC------eEEEEecCHHHHHHHHH
Confidence            456667 999999999999999999954 56666653      69999999999999994

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.35  E-value=0.00042  Score=44.74  Aligned_cols=53  Identities=21%  Similarity=0.291  Sum_probs=43.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHH-hC
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH-LN  108 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~-l~  108 (176)
                      +.++| ++|.++...||.++|+.||. ..|.++.|.      .|||.|.+++.|..|+. +.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidDT------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEETT------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcCC------eEEEEecCHHHHHHHHHhcc
Confidence            34566 99999999999999999994 466777653      69999999999999994 53

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=97.21  E-value=0.00018  Score=59.14  Aligned_cols=59  Identities=20%  Similarity=0.224  Sum_probs=44.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHh
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHL  107 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l  107 (176)
                      +...++|+|. .|..+++.+|.++|++||+|.++.+-.++    .-||.|+|.+.++++.++..
T Consensus        50 ~qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~----g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           50 EQAQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF----GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HHHHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS----SEEEEEECC---CCHHHHSS
T ss_pred             HHhcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC----CeEEEEEeCCHHHHHHHHhc
Confidence            3446889997 79999999999999999999999887654    47999999999999988743

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

Probab=96.87  E-value=0.00097  Score=43.01  Aligned_cols=68  Identities=10%  Similarity=0.117  Sum_probs=48.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-C--CCceeEEEEEecCHHHHHHHH-HhCCCeeCC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-F--GQPKGYAYVEFLQSEAVQEAL-HLNESELHG  114 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~--g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  114 (176)
                      +-+|.|..||+.+|++++.+.+...-.+.....+..+ +  ...-.-|+|.|.+.+++.... ..++..+-+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            4679999999999999988777765444332222222 1  112356899999999999988 699988743

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.43  E-value=0.0047  Score=41.95  Aligned_cols=76  Identities=16%  Similarity=0.153  Sum_probs=54.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeE-EEEeeCC---------C----C-CceeEEEEEecCHHHHHHHHHhCCCe
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNR-VTIRTDK---------F----G-QPKGYAYVEFLQSEAVQEALHLNESE  111 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~-~~~~~~~---------~----g-~~~g~afv~f~~~~~a~~a~~l~~~~  111 (176)
                      ...|.|-+.|++.+ ..+-+.|++||.|.+ +.+..+.         .    . ...++..|.|.+..+|++||..|+..
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~i   85 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGAV   85 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTCE
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCeE
Confidence            34566778887655 556778999999854 2221100         0    0 13567899999999999999999999


Q ss_pred             eCCeeeEEEecc
Q 030488          112 LHGRQLKVTVKR  123 (176)
Q Consensus       112 ~~g~~i~v~~a~  123 (176)
                      |+|..|-|.+..
T Consensus        86 i~G~mIGV~Py~   97 (132)
T 3p3d_A           86 FNGVLLGVIPYT   97 (132)
T ss_dssp             ETTEECEEEECC
T ss_pred             eCcEEEEEEECC
Confidence            999999998764

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

Probab=96.03  E-value=0.0063  Score=42.23  Aligned_cols=33  Identities=9%  Similarity=0.138  Sum_probs=26.4

Q ss_pred             EEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCC
Q 030488           76 RVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNE  109 (176)
Q Consensus        76 ~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~  109 (176)
                      .+.|.++.. .++|||||+|.+.++|++|+ .+++
T Consensus         2 ~~kl~ln~~-~~~G~~fV~f~~~~~A~~al~~~~~   35 (158)
T 2kn4_A            2 QYKLILNGK-TLKGETTTEAVDAATAEKVFKQYAN   35 (158)
T ss_dssp             EEEEEEECS-SCEEEEEEECSSHHHHHHHHHHHHH
T ss_pred             cEEEEecCc-cccchhHHHHHHHHhHHHHHHhhcc
Confidence            355666554 58999999999999999999 6664

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

Probab=95.08  E-value=0.0043  Score=40.96  Aligned_cols=59  Identities=12%  Similarity=0.150  Sum_probs=14.1

Q ss_pred             HHHHHHHHHHHHHHHHhhcccccc---CCCCCCCCCCcccccCCCCCEEEEcCCCCCCCHHH
Q 030488            5 LKEMEEEATALRQMHAKVGNEMAS---KQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEE   63 (176)
Q Consensus         5 ~~e~e~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~i~v~~lp~~~t~~~   63 (176)
                      |...+++.+|+++++...-.....   ...+................+|||+|||+++|++.
T Consensus        52 f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           52 FETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             ESCHHHHHHHHHHHTTCEETTEECEEEESSCCCC----------------------------
T ss_pred             ECCHHHHHHHHHHcCCCEECCEEEEEEECCCccccccccccccCCCCceEeCCCCCCccccc
Confidence            455677778888877643211111   10111111111122233456799999999999864

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=95.06  E-value=0.0075  Score=41.60  Aligned_cols=39  Identities=13%  Similarity=0.227  Sum_probs=34.9

Q ss_pred             CCceeEEEEEecCHHHHHHHH-Hh-CCCeeCCeeeEEEeccC
Q 030488           85 GQPKGYAYVEFLQSEAVQEAL-HL-NESELHGRQLKVTVKRT  124 (176)
Q Consensus        85 g~~~g~afv~f~~~~~a~~a~-~l-~~~~~~g~~i~v~~a~~  124 (176)
                      ...+|+++|+|.+.++|++|+ ++ |+..++| .|.|..+..
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            356899999999999999999 78 9999999 999998754

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=91.63  E-value=0.65  Score=38.61  Aligned_cols=54  Identities=22%  Similarity=0.306  Sum_probs=43.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN  108 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~  108 (176)
                      ...++|+ +|..+...+|.++|+.||.| .|.++.+      ..|||.|.+.+.|..++ .++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS------SEEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC------CeEEEEECCHHHHHHHHHHHH
Confidence            4566676 88899999999999999954 6666543      36999999999999999 564

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

Probab=83.96  E-value=0.34  Score=30.51  Aligned_cols=53  Identities=11%  Similarity=0.075  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHHHHHhhcccccc---CCCCCC--CCCCcccccCCCCCEEEEcCCCC
Q 030488            5 LKEMEEEATALRQMHAKVGNEMAS---KQDPAA--GGSSLANREEVDSRSVFVGNVDY   57 (176)
Q Consensus         5 ~~e~e~~~~~~~~~~~~~~~~~~~---~~~~~~--~~~~~~~~~~~~~~~i~v~~lp~   57 (176)
                      |.+.+++.+|+++++...-.....   +..+..  ..............+||||||++
T Consensus        44 f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~ifvg~L~h  101 (101)
T 2hvz_A           44 FEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPPARRKLLEVLFNGPLEH  101 (101)
T ss_dssp             CSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCCSSCCCSCCCSCCCCSCCCSCCCCC
T ss_pred             ECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCCcccCCCCCccccCCCceecCCCCC
Confidence            455677778888777643211110   001111  01111111223367899999974

---

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	176
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-17
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-15
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-15
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	6e-15
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	7e-15
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	9e-15
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-14
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-14
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-13
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-13
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-13
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-13
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	6e-13
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	8e-13
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-12
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-12
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-12
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-12
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	3e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	3e-12
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-12
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	5e-12
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	5e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	5e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	5e-12
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-12
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	8e-12
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-11
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-11
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-11
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-11
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	5e-11
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	6e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-11
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	7e-11
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	8e-11
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-10
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-10
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-09
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-10
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-10
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-10
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-10
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-10
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-10
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-10
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-10
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-10
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-10
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-09
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-09
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	4e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	4e-09
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	5e-09
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-08
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-08
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	3e-08
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	6e-08
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	6e-08
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	6e-08
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	7e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	9e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-07
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-07
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 3e-07
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-07
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-07
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	4e-07
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	7e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-06
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-06
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	8e-06
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	5e-05
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	6e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	8e-05
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	8e-05
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	9e-05
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	0.001
d1ufwa_	95	d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens)	0.004

>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 = 70.4 bits (172), Expect = 5e-17
 Identities = 27/91 (29%), Positives = 44/91 (48%), Gaps = 1/91 (1%)

Query: 30  QDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG-QPK 88
           + P        + EE D+R+VF   +     P +++  F + G V  V I +D+   + K
Sbjct: 1   KSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 60

Query: 89  GYAYVEFLQSEAVQEALHLNESELHGRQLKV 119
           G AYVEF + ++V  A+ L    L G  + V
Sbjct: 61  GIAYVEFCEIQSVPLAIGLTGQRLLGVPIIV 91

>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 = 65.4 bits (159), Expect = 2e-15
 Identities = 16/73 (21%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLN 108
           +F+G + +  T E ++++F   G V    +  D    + +G+ +V F+    V + L  +
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 109 ESELHGRQLKVTV 121
             EL  + +   V
Sbjct: 63  RHELDSKTIDPKV 75

>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 = 65.0 bits (158), Expect = 5e-15
 Identities = 15/81 (18%), Positives = 41/81 (50%), Gaps = 4/81 (4%)

Query: 43  EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF--GQPKGYAYVEFLQSEA 100
           ++  +  + V N+ +     E+++ F + G +  V +       G  +G+ +V+F+  + 
Sbjct: 4   KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 63

Query: 101 VQEALH--LNESELHGRQLKV 119
            ++A +   + + L+GR+L +
Sbjct: 64  AKKAFNALCHSTHLYGRRLVL 84

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.2 bits (156), Expect = 6e-15
 Identities = 18/79 (22%), Positives = 37/79 (46%), Gaps = 2/79 (2%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTI-RTDKFGQPKGYAYVEFLQSEAVQEAL-H 106
           S++VG++    T   + + F   G +  + + R     +  GYAYV F Q    + AL  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 107 LNESELHGRQLKVTVKRTN 125
           +N   + G+ +++   + +
Sbjct: 62  MNFDVIKGKPVRIMWSQRD 80

>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 = 64.3 bits (156), Expect = 7e-15
 Identities = 18/79 (22%), Positives = 39/79 (49%), Gaps = 1/79 (1%)

Query: 42  REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEA 100
           +E    R +F+G + +  T E ++ HF+  GT+    +  D    + +G+ +V +   E 
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 101 VQEALHLNESELHGRQLKV 119
           V  A++    ++ GR ++ 
Sbjct: 61  VDAAMNARPHKVDGRVVEP 79

>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 = 64.0 bits (155), Expect = 9e-15
 Identities = 15/81 (18%), Positives = 35/81 (43%)

Query: 42  REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAV 101
           + +V +RSV++       T +++++  +  G V  + +R       KG  +V F   E+ 
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 60

Query: 102 QEALHLNESELHGRQLKVTVK 122
           ++ +     +     L +  K
Sbjct: 61  KKFVETPGQKYKETDLLILFK 81

>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 = 63.5 bits (154), Expect = 2e-14
 Identities = 16/80 (20%), Positives = 36/80 (45%), Gaps = 1/80 (1%)

Query: 41  NREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSE 99
            RE+   R +F+G + +  T E ++ +++  G +    +  D    + +G+ +V F    
Sbjct: 14  KREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMA 73

Query: 100 AVQEALHLNESELHGRQLKV 119
            V  A+      + GR ++ 
Sbjct: 74  EVDAAMAARPHSIDGRVVEP 93

>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 = 63.0 bits (153), Expect = 2e-14
 Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 2/83 (2%)

Query: 43  EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRTDKFGQPKGYAYVEFLQSEAV 101
           E +   +++V N+  + T +++   F   G++  +  +R    G+P+G A+V + + E  
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 102 QEAL-HLNESELHGRQLKVTVKR 123
           QEA+  LN     G    ++V+ 
Sbjct: 62  QEAISALNNVIPEGGSQPLSVRL 84

>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 = 61.3 bits (148), Expect = 1e-13
 Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 6/86 (6%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF------GQPKGYAYVEFLQSEAV 101
           R ++VGN+ +  T E +   F +   +  +T             Q K +A++EF   +  
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 102 QEALHLNESELHGRQLKVTVKRTNVP 127
            +A+  +     G+ LK+       P
Sbjct: 62  TQAMAFDGIIFQGQSLKIRRPHDYQP 87

>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 = 1e-13
 Identities = 22/91 (24%), Positives = 38/91 (41%), Gaps = 3/91 (3%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL- 105
           +R +++ N+ Y  T EE+   F   G + +  IR     + +G AYV +      + A  
Sbjct: 7   NRILYIRNLPYKITAEEMYDIFGKYGPIRQ--IRVGNTPETRGTAYVVYEDIFDAKNACD 64

Query: 106 HLNESELHGRQLKVTVKRTNVPGMKQHRPRR 136
           HL+   +  R L V     N    K    ++
Sbjct: 65  HLSGFNVCNRYLVVLYYNANRAFQKMDTKKK 95

>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 = 60.3 bits (146), Expect = 2e-13
 Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 108
           + V N+D+  +  ++Q+ F   GT+ +  +  D+ G+  G A V F +     +A+   N
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 109 ESELHGRQLKVTV 121
              L GR + + +
Sbjct: 63  GVPLDGRPMNIQL 75

>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 = 60.4 bits (146), Expect = 2e-13
 Identities = 17/71 (23%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ-PKGYAYVEFLQSEAVQEALHLN 108
           +F+G + +  T ++++ +F   G V   T++ D      +G+ +V F +SE+V + +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61

Query: 109 ESELHGRQLKV 119
           E +L+G+ +  
Sbjct: 62  EHKLNGKVIDP 72

>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 = 60.7 bits (147), Expect = 2e-13
 Identities = 19/108 (17%), Positives = 42/108 (38%), Gaps = 16/108 (14%)

Query: 34  AGGSSLANREEVDSRSVFVGNVD-YSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAY 92
           + GSS        +  VF+GN++       +V+  F   G +   ++        KG+A+
Sbjct: 2   SSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAF 54

Query: 93  VEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNP 139
           V+++     + A+   +   + G+ L + +           +  R  P
Sbjct: 55  VQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP-------KVNRSGP 95

>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 = 59.6 bits (144), Expect = 6e-13
 Identities = 18/85 (21%), Positives = 40/85 (47%), Gaps = 2/85 (2%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEA 104
            S +++VGN+ +  T E++ + F   G + ++ +  DK      G+ +VE+      + A
Sbjct: 6   KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 65

Query: 105 L-HLNESELHGRQLKVTVKRTNVPG 128
           + ++N + L  R ++         G
Sbjct: 66  MRYINGTRLDDRIIRTDWDAGFKEG 90

>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 = 58.9 bits (142), Expect = 8e-13
 Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRV-TIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
           + ++ V  +    T  E+   F++ G +N    +R  K G   GYA+V+F      Q A+
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 106 -HLNESELHGRQLKVTVKRTNVPG 128
             LN   +  ++LKV+  R   PG
Sbjct: 62  KVLNGITVRNKRLKVSYAR---PG 82

>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 = 1e-12
 Identities = 19/91 (20%), Positives = 45/91 (49%), Gaps = 7/91 (7%)

Query: 41  NREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEA 100
           +++   +R++   N+ ++ T +E+++ F+    +  V+      G+ KG AY+EF     
Sbjct: 10  SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEAD 65

Query: 101 VQEAL-HLNESELHGRQLKV--TVKRTNVPG 128
            ++ L     +E+ GR + +  T ++    G
Sbjct: 66  AEKNLEEKQGAEIDGRSVSLYYTGEKGGTRG 96

>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 = 58.1 bits (140), Expect = 1e-12
 Identities = 12/71 (16%), Positives = 34/71 (47%), Gaps = 1/71 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLN 108
           +FVG +      E+++++F   G V  + +  D    + +G+ ++ F + E V++ +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 109 ESELHGRQLKV 119
              +   + ++
Sbjct: 62  YHNVGLSKCEI 72

>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 = 58.6 bits (141), Expect = 1e-12
 Identities = 26/105 (24%), Positives = 46/105 (43%), Gaps = 6/105 (5%)

Query: 34  AGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAY 92
           + GSS +   +    + F+GN+ Y  T E +++ F+          R      + KG+ Y
Sbjct: 2   SSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGY 61

Query: 93  VEFLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRRP 137
            EF   +++  AL LNE  L  ++++V V         Q +   P
Sbjct: 62  AEFEDLDSLLSALSLNEESLGNKRIRVDVADQ-----AQDKDSGP 101

>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 = 58.6 bits (141), Expect = 1e-12
 Identities = 18/100 (18%), Positives = 36/100 (36%), Gaps = 3/100 (3%)

Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF 95
           GSS ++ +      V +  + Y  T  ++   F     +          G+  G A VEF
Sbjct: 4   GSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEI-GPDGRVTGEADVEF 62

Query: 96  LQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPR 135
              E    A+  +++ +  R ++  +   +  G     P 
Sbjct: 63  ATHEDAVAAMAKDKANMQHRYVE--LFLNSTAGTSGSGPS 100

>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 = 57.4 bits (138), Expect = 2e-12
 Identities = 13/71 (18%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCG-TVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLN 108
           +FVG +  + T E+V+ +F+  G   + + +      + +G+ +V F   + V++   ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 109 ESELHGRQLKV 119
             E++ + ++ 
Sbjct: 62  FHEINNKMVEC 72

>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 = 3e-12
 Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 3/82 (3%)

Query: 41  NREEVD-SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQS 98
           NR   D +  + V  +    T  ++++ F   G +  V+I  D +  + +G+A+V F   
Sbjct: 2   NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 61

Query: 99  EAVQEAL-HLNESELHGRQLKV 119
           +  +EA    N  EL GR+++V
Sbjct: 62  DDAKEAKERANGMELDGRRIRV 83

>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 = 57.8 bits (139), Expect = 3e-12
 Identities = 16/93 (17%), Positives = 41/93 (44%), Gaps = 3/93 (3%)

Query: 34  AGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYV 93
           +GG  +      +   ++VGN+      ++++  F   G +  + ++  +      +A+V
Sbjct: 1   SGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG--GPPFAFV 58

Query: 94  EFLQSEAVQEAL-HLNESELHGRQLKVTVKRTN 125
           EF      ++A+   +  +  G +L+V   R+ 
Sbjct: 59  EFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG 91

>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 = 57.9 bits (139), Expect = 3e-12
 Identities = 22/95 (23%), Positives = 43/95 (45%), Gaps = 10/95 (10%)

Query: 43  EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD---------KFGQPKGYAYV 93
           E+ D+ +++V  ++ S T +++   F+ CG V                 + G+PKG A V
Sbjct: 4   EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 63

Query: 94  EFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVP 127
            +      + A+   +  +  G +LKV++ R   P
Sbjct: 64  SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 98

>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 = 57.4 bits (138), Expect = 4e-12
 Identities = 16/77 (20%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQS-CGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
              + V N+ ++ + +E+   F         V ++ ++ G P G A V F   +    A+
Sbjct: 9   PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 68

Query: 106 -HLNESELHGRQLKVTV 121
             LN+  +  R++K+ +
Sbjct: 69  IDLNDRPIGSRKVKLVL 85

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.7 bits (136), Expect = 5e-12
 Identities = 15/73 (20%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ-PKGYAYVEFLQSEAVQEALH 106
           + +FVG +        ++ +F+  G +  + I TD+     +G+A+V F   ++V + + 
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 107 LNESELHGRQLKV 119
                ++G   +V
Sbjct: 63  QKYHTVNGHNCEV 75

>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 = 57.2 bits (137), Expect = 5e-12
 Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 3/93 (3%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNR-VTIRTDKFGQPKGYAYVEFLQSEAVQEA 104
                 + N+ +S T  +V Q  +        V +  D  GQ  G A V+F   +  +++
Sbjct: 7   AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKS 66

Query: 105 LHLNESELHGRQLKVTVKRTNVPGMKQHRPRRP 137
             L+  +L+GR+    V    +  M++     P
Sbjct: 67  ERLHRKKLNGREAF--VHVVTLEDMREIEKNPP 97

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 5e-12
 Identities = 17/80 (21%), Positives = 36/80 (45%), Gaps = 2/80 (2%)

Query: 45  VDSRSVFVGNVDYSCTPEEVQQHFQSCGT-VNRVTIRTDKFGQPKGYAYVEFLQSEAVQE 103
           +   +++V  +  + T +E++Q F   G  +    +     G  +G  ++ F +    +E
Sbjct: 4   IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEE 63

Query: 104 AL-HLNESELHGRQLKVTVK 122
           A+  LN  +  G    +TVK
Sbjct: 64  AIKGLNGQKPSGATEPITVK 83

>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 = 57.0 bits (137), Expect = 5e-12
 Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 2/84 (2%)

Query: 37  SSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFL 96
           SS  +  +   + + V N+ +     +++Q F   G +  V I  ++    KG+ +V F 
Sbjct: 1   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFE 59

Query: 97  QSEAVQEAL-HLNESELHGRQLKV 119
            S     A   L+ + + GR+++V
Sbjct: 60  NSADADRAREKLHGTVVEGRKIEV 83

>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 = 56.9 bits (137), Expect = 6e-12
 Identities = 16/87 (18%), Positives = 38/87 (43%), Gaps = 6/87 (6%)

Query: 38  SLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQ 97
            + N+    + +V+ G +    T + ++Q F   G +  + +  +K      Y++V F  
Sbjct: 9   DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG-----YSFVRFST 63

Query: 98  SEAVQEAL-HLNESELHGRQLKVTVKR 123
            E+   A+  +N + + G  +K    +
Sbjct: 64  HESAAHAIVSVNGTTIEGHVVKCYWGK 90

>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 = 56.2 bits (135), Expect = 8e-12
 Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 51  FVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK----FGQPKGYAYVEFLQSEAVQEAL- 105
           F+ N+++S T E ++  F   G +   TI   K         G+ +VE+ + E  Q+AL 
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 106 HLNESELHGRQLKV 119
            L    + G +L+V
Sbjct: 62  QLQGHTVDGHKLEV 75

>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 = 56.1 bits (134), Expect = 1e-11
 Identities = 17/90 (18%), Positives = 43/90 (47%)

Query: 35  GGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVE 94
           G   +   E     ++F+GN++ + +  E++         N + +   + G  + + YV+
Sbjct: 1   GSHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVD 60

Query: 95  FLQSEAVQEALHLNESELHGRQLKVTVKRT 124
           F  +E +++AL L   ++ G ++K+   + 
Sbjct: 61  FESAEDLEKALELTGLKVFGNEIKLEKPKG 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 = 55.8 bits (134), Expect = 1e-11
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 43  EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQ 102
           ++   R+++VGN+    T   + Q F   G      + T+       Y +VEF +     
Sbjct: 4   DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH-TSNDPYCFVEFYEHRDAA 62

Query: 103 EAL-HLNESELHGRQLKV 119
            AL  +N  ++ G+++KV
Sbjct: 63  AALAAMNGRKILGKEVKV 80

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 2e-11
 Identities = 21/85 (24%), Positives = 42/85 (49%), Gaps = 2/85 (2%)

Query: 41  NREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSE 99
           NR   D+ ++ V N+       ++Q+ F+  G+++R+ +  DK  GQ KG+A++ F + E
Sbjct: 2   NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 61

Query: 100 AVQEAL-HLNESELHGRQLKVTVKR 123
               A+  ++        L V   +
Sbjct: 62  DAARAIAGVSGFGYDHLILNVEWAK 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 = 54.6 bits (131), Expect = 4e-11
 Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL 105
           +  +F+G +      ++V++   S G +    +  D   G  KGYA+ E++      +A+
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 106 -HLNESELHGRQLKV 119
             LN  +L  ++L V
Sbjct: 61  AGLNGMQLGDKKLLV 75

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.7 bits (131), Expect = 5e-11
 Identities = 20/101 (19%), Positives = 42/101 (41%), Gaps = 7/101 (6%)

Query: 40  ANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQS 98
            ++++     +FVG + Y  T   ++++F+  G +    + TD+  G+ +GY +V     
Sbjct: 3   GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 62

Query: 99  EAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNP 139
            A + A       + GR+  V +           +PR    
Sbjct: 63  AAAERACKDPNPIIDGRKANVNLAY------LGAKPRSLQT 97

>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 = 54.3 bits (130), Expect = 6e-11
 Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 2/79 (2%)

Query: 43  EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNR-VTIRTDKFGQPKGYAYVEFLQSEAV 101
           E     +V+VG +D   +   + + F   G V      +    GQ +GY +VEFL  E  
Sbjct: 5   ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 64

Query: 102 QEAL-HLNESELHGRQLKV 119
             A+  ++  +L+G+ ++V
Sbjct: 65  DYAIKIMDMIKLYGKPIRV 83

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.3 bits (130), Expect = 7e-11
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ-PKGYAYVEFLQSEAVQEA 104
            S  +FV N+ Y+ + E++++ F + G ++ +    D   + PKG+A+V F+  E   +A
Sbjct: 7   GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66

Query: 105 L-HLNESELHGRQLKV 119
              ++     GR L V
Sbjct: 67  YAEVDGQVFQGRMLHV 82

>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 = 53.4 bits (128), Expect = 7e-11
 Identities = 9/80 (11%), Positives = 22/80 (27%), Gaps = 7/80 (8%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
           D   V V     +     +   F   G + +             + ++ +      ++AL
Sbjct: 3   DDTWVTVFGFPQASA-SYILLQFAQYGNILKH-----VMSNTGNWMHIRYQSKLQARKAL 56

Query: 106 HLNESELHGRQLKVTVKRTN 125
             +        + + VK   
Sbjct: 57  SKDGRIFGESIM-IGVKPCI 75

>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 = 53.9 bits (129), Expect = 8e-11
 Identities = 24/94 (25%), Positives = 42/94 (44%), Gaps = 12/94 (12%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG-QPKGYAYVEFLQSEAVQEA 104
             R ++VG +      + +   F   G +  + I  D    + +G+A+VEF  +E    A
Sbjct: 4   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63

Query: 105 L-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRP 137
           + ++NESEL GR ++V             +P R 
Sbjct: 64  IDNMNESELFGRTIRV----------NLAKPMRI 87

>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 = 53.0 bits (127), Expect = 1e-10
 Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 6/74 (8%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL- 105
              +FVGN+    T EE+++ F+  G    V I  DK      + ++        + A  
Sbjct: 8   RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG-----FGFIRLETRTLAEIAKV 62

Query: 106 HLNESELHGRQLKV 119
            L+   L G+QL+V
Sbjct: 63  ELDNMPLRGKQLRV 76

>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 = 55.4 bits (132), Expect = 1e-10
 Identities = 22/115 (19%), Positives = 49/115 (42%), Gaps = 1/115 (0%)

Query: 6   KEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQ 65
             +EE   A+     KV   +   +   +   S      +  + +FVG +        ++
Sbjct: 56  ATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLR 115

Query: 66  QHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV 119
            +F+  G +  + I TD+  G+ +G+A+V F   ++V + +      ++G   +V
Sbjct: 116 DYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 170

>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 = 51.9 bits (123), Expect = 2e-09
 Identities = 19/102 (18%), Positives = 42/102 (41%), Gaps = 1/102 (0%)

Query: 42  REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRV-TIRTDKFGQPKGYAYVEFLQSEA 100
           +E    R +F+G + +  T E ++ HF+  GT+     +R     + +G+ +V +   E 
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 101 VQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNPFMV 142
           V  A++    ++ GR ++     +     +           V
Sbjct: 61  VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFV 102

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.1 bits (127), Expect = 1e-10
 Identities = 16/79 (20%), Positives = 35/79 (44%), Gaps = 2/79 (2%)

Query: 42  REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEA 100
           R    +  + V  + +  T ++++++F + G V  V ++ D   G  KG+ +V F + E 
Sbjct: 3   RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 62

Query: 101 VQEALHLNESELHGRQLKV 119
             + +      + GR    
Sbjct: 63  QVKVMS-QRHMIDGRWCDC 80

>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 = 53.7 bits (128), Expect = 1e-10
 Identities = 21/100 (21%), Positives = 44/100 (44%), Gaps = 3/100 (3%)

Query: 36  GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVE 94
           GSS  + +  +   V +  + + C+ EE+ Q F     V         F G+  G A+V+
Sbjct: 4   GSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQ 63

Query: 95  FLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRP 134
           F   E  ++AL  ++  +  R   + + +++   ++   P
Sbjct: 64  FASQEIAEKALKKHKERIGHRY--IEIFKSSRAEVRTSGP 101

>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 = 53.1 bits (127), Expect = 2e-10
 Identities = 18/92 (19%), Positives = 32/92 (34%), Gaps = 10/92 (10%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
            S  VFVG      T +E+++ F   G V  V          + +A+V F   +  Q   
Sbjct: 4   GSSGVFVGRCTGDMTEDELREFFSQYGDVMDV----FIPKPFRAFAFVTFADDQIAQSLC 59

Query: 106 HLNESELHGRQLKVTVKRTNVPGMKQHRPRRP 137
              +  + G  + ++         K +    P
Sbjct: 60  G-EDLIIKGISVHISNAEP-----KHNSNSGP 85

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 52.8 bits (126), Expect = 2e-10
 Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 2/79 (2%)

Query: 43  EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG-QPKGYAYVEFLQSEAV 101
             V+   +FV ++      +E+Q+ F   G +  + +  D+     KGYA VE+   +  
Sbjct: 3   RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQA 62

Query: 102 QEAL-HLNESELHGRQLKV 119
             A   LN +E+ G+ ++V
Sbjct: 63  LAAKEALNGAEIMGQTIQV 81

>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 = 2e-10
 Identities = 20/98 (20%), Positives = 44/98 (44%), Gaps = 5/98 (5%)

Query: 28  SKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNR-VTIRTDKFGQ 86
           ++Q   A GS    +E  +  ++F+ ++      +++ Q F   G V         +   
Sbjct: 2   TQQSIGAAGSQ---KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNL 58

Query: 87  PKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR 123
            K + +V +    + Q A+  +N  ++  ++LKV +KR
Sbjct: 59  SKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR 96

>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 = 52.8 bits (126), Expect = 2e-10
 Identities = 12/78 (15%), Positives = 29/78 (37%), Gaps = 3/78 (3%)

Query: 45  VDSRSVFVGNVDYSCTPEEVQQHF---QSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAV 101
           ++ R + + N+      E + +             +     +       A++ F   ++ 
Sbjct: 2   LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSA 61

Query: 102 QEALHLNESELHGRQLKV 119
           + AL +N S L  R++ V
Sbjct: 62  ERALQMNRSLLGNREISV 79

>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 = 52.8 bits (126), Expect = 2e-10
 Identities = 16/76 (21%), Positives = 28/76 (36%), Gaps = 6/76 (7%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTI---RTDKFGQPKGYAYVEFLQSEAVQEA-- 104
           +F+G +      EE+ +            I         + +G+A+VE+    A   A  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 105 -LHLNESELHGRQLKV 119
            L     +L G Q+ V
Sbjct: 64  KLMPGRIQLWGHQIAV 79

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 2e-10
 Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 3/73 (4%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTI--RTDKFGQPKGYAYVEFLQSEAVQEAL-H 106
           +F+GN+D     + +   F + G + +     R    G  KGYA++ F   +A   A+  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 107 LNESELHGRQLKV 119
           +N   L  R + V
Sbjct: 61  MNGQYLCNRPITV 73

>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 = 52.0 bits (124), Expect = 3e-10
 Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL- 105
             ++F+ N+D S   + +   F + G +    +  D+ G  KGY +V F   EA + A+ 
Sbjct: 8   VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIE 66

Query: 106 HLNESELHGRQLKVTVKRT 124
            +N   L+ R++ V   ++
Sbjct: 67  KMNGMLLNDRKVFVGRFKS 85

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 4e-10
 Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 2/78 (2%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCG-TVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL- 105
            ++ V  +  + T EE +  F S G   +   +R    GQ  GY +V ++  +  ++A+ 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 106 HLNESELHGRQLKVTVKR 123
            LN   L  + +KV+  R
Sbjct: 63  TLNGLRLQTKTIKVSYAR 80

>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 = 50.9 bits (121), Expect = 1e-09
 Identities = 17/76 (22%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCG-TVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEA 104
           D   +FVG + +    + ++Q F   G     V ++  +  + +G+ +V F   +  ++A
Sbjct: 4   DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 63

Query: 105 LH-LNESELHGRQLKV 119
           +  +N   + GRQ++V
Sbjct: 64  MMAMNGKSVDGRQIRV 79

>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 = 50.4 bits (120), Expect = 1e-09
 Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 6/74 (8%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL- 105
            + ++V N+  S + E +++ F +           ++  + + YA+V F   E   EA+ 
Sbjct: 8   VKILYVRNLMLSTSEEMIEKEFNNI-----KPGAVERVKKIRDYAFVHFSNREDAVEAMK 62

Query: 106 HLNESELHGRQLKV 119
            LN   L G  ++V
Sbjct: 63  ALNGKVLDGSPIEV 76

>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 = 50.5 bits (120), Expect = 2e-09
 Identities = 31/99 (31%), Positives = 46/99 (46%), Gaps = 4/99 (4%)

Query: 43  EEVDSRSVFVGNVDYSCTPEEVQQHFQSCG-TVNRVTIRTDKFGQPKGYAYVEFLQSEAV 101
            +   RSVFVGN+ Y  T E+++  F   G  V+   +   + G+PKGY + E+   E  
Sbjct: 4   VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63

Query: 102 QEAL-HLNESELHGRQLKVT--VKRTNVPGMKQHRPRRP 137
             A+ +LN  E  GR L+V       N   +K      P
Sbjct: 64  LSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102

>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 = 49.6 bits (118), Expect = 4e-09
 Identities = 17/96 (17%), Positives = 33/96 (34%), Gaps = 9/96 (9%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 108
           + V N+ Y  T + + Q F   GTV ++   T      +  A +++    + Q A   L+
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLD 66

Query: 109 ESELHGRQLKVTV-----KRTNVPGMKQHRPRRPNP 139
              ++     + +        NV            P
Sbjct: 67  GQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRP 102

>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 = 49.4 bits (117), Expect = 4e-09
 Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 8/82 (9%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ-PKGYAYVEFLQSEAVQEA 104
           + ++VF+ N+ +    E + +  Q  G +  V +      +  KG A+ +F+  EA Q+ 
Sbjct: 7   EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKC 66

Query: 105 L-------HLNESELHGRQLKV 119
           L            +L GRQLKV
Sbjct: 67  LAAASLEAEGGGLKLDGRQLKV 88

>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 = 48.9 bits (116), Expect = 5e-09
 Identities = 10/82 (12%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSC--GTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEA 104
           + ++++ N++     +E+++   +        + I   +  + +G A+V F +  +   A
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62

Query: 105 L-HLNESELHGRQLKVTVKRTN 125
           L  +     + + +++   +T+
Sbjct: 63  LRSMQGFPFYDKPMRIQYAKTD 84

>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 = 47.9 bits (113), Expect = 2e-08
 Identities = 15/88 (17%), Positives = 34/88 (38%), Gaps = 1/88 (1%)

Query: 37  SSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFL 96
           + +A ++E D  ++++ N+  S   +E++   +  G V    I  D  G  +G  +    
Sbjct: 8   AQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARME 67

Query: 97  QSEAVQEAL-HLNESELHGRQLKVTVKR 123
            +E  +  + H N   +           
Sbjct: 68  STEKCEAVIGHFNGKFIKTPPGVSAPTE 95

>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 = 46.8 bits (110), Expect = 2e-08
 Identities = 14/72 (19%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 49  SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLN 108
           +V V N+  S    +V ++F+ CG +  V +      +   +A +EF + +    A+   
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK-KNFRFARIEFARYDGALAAITKT 60

Query: 109 ESELHGRQLKVT 120
              +   ++ V+
Sbjct: 61  HKVVGQNEIIVS 72

>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 = 46.6 bits (110), Expect = 3e-08
 Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 8/78 (10%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL- 105
             +++V       TP  ++  F   G +  +         P+  A+V + + E+  +A+ 
Sbjct: 5   GNTLYVYG--EDMTPTLLRGAFSPFGNIIDL-----SMDPPRNCAFVTYEKMESADQAVA 57

Query: 106 HLNESELHGRQLKVTVKR 123
            LN +++   QLKV + R
Sbjct: 58  ELNGTQVESVQLKVNIAR 75

>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 = 45.9 bits (108), Expect = 6e-08
 Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 2/71 (2%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL-HL 107
           +++  +    T +++ +  Q  G +       DK   + KGY +V+F    A Q+A+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 108 NESELHGRQLK 118
             S +  +  K
Sbjct: 61  KASGVQAQMAK 71

>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 = 46.2 bits (109), Expect = 6e-08
 Identities = 12/77 (15%), Positives = 31/77 (40%), Gaps = 6/77 (7%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL- 105
           +  ++VG +  + +   + + F   G++  +            +AY+++   +A Q A  
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS-----FAYIQYESLDAAQAACA 71

Query: 106 HLNESELHGRQLKVTVK 122
            +    L G   ++ V 
Sbjct: 72  KMRGFPLGGPDRRLRVD 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 = 46.3 bits (109), Expect = 6e-08
 Identities = 16/81 (19%), Positives = 29/81 (35%), Gaps = 7/81 (8%)

Query: 46  DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
            S  + V N+      +EV    +                + K  A+V  L  E  Q A+
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYDLKYC------YVDRNKRTAFVTLLNGEQAQNAI 57

Query: 106 -HLNESELHGRQLKVTVKRTN 125
              ++    G+ L V ++ T+
Sbjct: 58  QMFHQYSFRGKDLIVQLQPTD 78

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 45.6 bits (107), Expect = 7e-08
 Identities = 13/74 (17%), Positives = 31/74 (41%), Gaps = 2/74 (2%)

Query: 48  RSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL- 105
            ++++ N   S T   ++   Q    V   + + + +F   + +AY++    E  +  + 
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 106 HLNESELHGRQLKV 119
            LN  ++ G  L  
Sbjct: 62  KLNGLKIEGYTLVT 75

>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 = 45.6 bits (107), Expect = 9e-08
 Identities = 22/88 (25%), Positives = 35/88 (39%), Gaps = 8/88 (9%)

Query: 40  ANREEVDSRSVFVGNVDYSCTPEEVQQHFQ---SCGTVNRVTIRTDKFG----QPKGYAY 92
           A+   V    VFV  +       EV +  +     G +++V I           P   AY
Sbjct: 1   ASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAY 60

Query: 93  VEFLQSEAVQEAL-HLNESELHGRQLKV 119
           V +++SE    A+  +N   + GR LK 
Sbjct: 61  VTYIRSEDALRAIQCVNNVVVDGRTLKA 88

>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 = 45.9 bits (108), Expect = 1e-07
 Identities = 21/109 (19%), Positives = 39/109 (35%), Gaps = 12/109 (11%)

Query: 34  AGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYV 93
           + GSS ++ +   S  V V  +  S    ++ +  +  GT+  V +   K       A V
Sbjct: 2   SSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR-----QALV 56

Query: 94  EFLQSEAVQEA---LHLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNP 139
           EF   ++ +E           + G+Q       +     +  RP    P
Sbjct: 57  EFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK----RITRPGNSGP 101

>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 = 44.8 bits (105), Expect = 2e-07
 Identities = 15/80 (18%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL 105
           ++ +++ N+    T  ++   F          I+     G+ +G A++ F   E   +AL
Sbjct: 18  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 77

Query: 106 -HLNESELHGRQLKVTVKRT 124
             +N  +L+G+ L +   + 
Sbjct: 78  HLVNGYKLYGKILVIEFGKN 97

>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 = 44.6 bits (105), Expect = 3e-07
 Identities = 16/91 (17%), Positives = 33/91 (36%), Gaps = 2/91 (2%)

Query: 30  QDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKG 89
           ++P    S  A+        V +         E   +  +  G V  + +  +      G
Sbjct: 11  RNPQNS-SQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVG 69

Query: 90  YAYVEFLQSEAVQEAL-HLNESELHGRQLKV 119
             YV+F + E  ++A+  LN    +G+ +  
Sbjct: 70  NVYVKFRREEDAEKAVIDLNNRWFNGQPIHA 100

>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 = 43.9 bits (103), Expect = 3e-07
 Identities = 16/72 (22%), Positives = 34/72 (47%), Gaps = 7/72 (9%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 108
           +++GN+  + T ++++Q F              +     GYA+V++        A+  L+
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRK-----LPLAGQVLLKSGYAFVDYPDQNWAIRAIETLS 58

Query: 109 ES-ELHGRQLKV 119
              ELHG+ ++V
Sbjct: 59  GKVELHGKIMEV 70

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.4 bits (104), Expect = 3e-07
 Identities = 20/105 (19%), Positives = 42/105 (40%), Gaps = 9/105 (8%)

Query: 33  AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAY 92
            + GSS           V V  +  S + ++++ H +  G V    ++ D          
Sbjct: 1   GSSGSSGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGM------GM 54

Query: 93  VEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRR 136
           VE+L+ E ++ AL  L++++    + + +  R  V   +   P  
Sbjct: 55  VEYLRKEDMEYALRKLDDTKFRSHEGETSYIR--VYPERSSGPSS 97

>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 = 44.4 bits (104), Expect = 4e-07
 Identities = 13/99 (13%), Positives = 32/99 (32%), Gaps = 11/99 (11%)

Query: 47  SRSVFVGNVDYS-----CTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAV 101
           S  +     +        T  + +  F++               +      + F    + 
Sbjct: 5   SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-----KSFKRVRINFSNPLSA 59

Query: 102 QEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNP 139
            +A   L+++E  G+++K+   +T   G     P  P+ 
Sbjct: 60  ADARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDK 98

>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 = 43.6 bits (102), Expect = 7e-07
 Identities = 23/99 (23%), Positives = 40/99 (40%), Gaps = 6/99 (6%)

Query: 47  SRSVFVGNVD-YSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 105
           +  + V N++    TP+ +   F   G V RV I        K  A V+       Q A+
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKI----LFNKKENALVQMADGNQAQLAM 57

Query: 106 -HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNPFMVY 143
            HLN  +LHG+ +++T+ +     + +           Y
Sbjct: 58  SHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDY 96

>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 = 42.4 bits (99), Expect = 2e-06
 Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 5/82 (6%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL- 105
           S ++ + N+  S + E+++  F S G    V      F + +  A ++    E   +AL 
Sbjct: 10  SATLHLSNIPPSVSEEDLKVLFSSNGG---VVKGFKFFQKDRKMALIQMGSVEEAVQALI 66

Query: 106 -HLNESELHGRQLKVTVKRTNV 126
              N        L+V+  ++ +
Sbjct: 67  DLHNHDLGENHHLRVSFSKSTI 88

>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 = 42.2 bits (99), Expect = 2e-06
 Identities = 11/59 (18%), Positives = 21/59 (35%), Gaps = 4/59 (6%)

Query: 62  EEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV 119
           E+++      G + ++ +         G A V F   E     +  L+     GRQ+  
Sbjct: 34  EDLRVECSKFGQIRKLLLFDRHP---DGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 89

>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 = 43.0 bits (100), Expect = 2e-06
 Identities = 21/113 (18%), Positives = 45/113 (39%), Gaps = 7/113 (6%)

Query: 27  ASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQS-CGTVNRVTIRTDKFG 85
             +Q       +  N E    R++ V  +  +    +++Q F+      +   +   +  
Sbjct: 22  LQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETR 81

Query: 86  QPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRP 137
           Q +GY +V+F    + Q+A+  LN   +  ++LKV +  +        RP   
Sbjct: 82  QSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAAS-----GHQRPGIA 129

>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 = 41.0 bits (95), Expect = 8e-06
 Identities = 15/89 (16%), Positives = 33/89 (37%), Gaps = 1/89 (1%)

Query: 32  PAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHF-QSCGTVNRVTIRTDKFGQPKGY 90
           P+    S +         V++  + +    + V   F +     + + I     G+  G 
Sbjct: 3   PSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGE 62

Query: 91  AYVEFLQSEAVQEALHLNESELHGRQLKV 119
            +VEF      + AL  ++  +  R ++V
Sbjct: 63  GFVEFRNEADYKAALCRHKQYMGNRFIQV 91

>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 = 38.3 bits (88), Expect = 5e-05
 Identities = 13/76 (17%), Positives = 24/76 (31%), Gaps = 8/76 (10%)

Query: 47  SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL- 105
           SR + +  +    T  EV       G V  + +   K       A++E    EA    + 
Sbjct: 8   SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKN-----QAFLELATEEAAITMVN 62

Query: 106 --HLNESELHGRQLKV 119
                   L  + + +
Sbjct: 63  YYSAVTPHLRNQPIYI 78

>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 = 37.6 bits (86), Expect = 6e-05
 Identities = 16/77 (20%), Positives = 30/77 (38%), Gaps = 7/77 (9%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 108
           + +  +    T +EV                     + KG A+V  L  E  + A+   +
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINTFH 54

Query: 109 ESELHGRQLKVTVKRTN 125
           +S L  R+L V ++ T+
Sbjct: 55  QSRLRERELSVQLQPTD 71

>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 = 38.0 bits (87), Expect = 8e-05
 Identities = 22/94 (23%), Positives = 35/94 (37%), Gaps = 9/94 (9%)

Query: 35  GGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVE 94
           G S  + R       +   N+       E+Q+ F   G++ RV        +    A VE
Sbjct: 1   GSSGSSGR---SKTVILAKNLPAGTLAAEIQETFSRFGSLGRV-----LLPEGGITAIVE 52

Query: 95  FLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVP 127
           FL+    ++A  HL  S+ H   L +      V 
Sbjct: 53  FLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVF 86

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.6 bits (86), Expect = 8e-05
 Identities = 18/89 (20%), Positives = 34/89 (38%), Gaps = 12/89 (13%)

Query: 50  VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 108
           V V  +  S + ++++ H +  G V              G   VEF++ E +  A+  L+
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVCY------ADVYRDGTGVVEFVRKEDMTYAVRKLD 56

Query: 109 ESELHGRQLKVTVKRTNVPGMKQHRPRRP 137
            ++    + +    R      K   PR P
Sbjct: 57  NTKFRSHEGETAYIRV-----KVDGPRSP 80

>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 = 37.9 bits (87), Expect = 9e-05
 Identities = 17/95 (17%), Positives = 34/95 (35%), Gaps = 7/95 (7%)

Query: 43  EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFL--QSEA 100
           E++     F G++D     E++   F + G +  +        +      + F     EA
Sbjct: 7   EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV-----RGAKEGIILFKEKAKEA 61

Query: 101 VQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPR 135
           + +A   N   L  R  +VT +       K+   +
Sbjct: 62  LGKAKDANNGNLQLRNKEVTWEVLEGEVEKEALKK 96

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 34.4 bits (78), Expect = 0.001
 Identities = 10/82 (12%), Positives = 26/82 (31%), Gaps = 4/82 (4%)

Query: 40  ANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSE 99
           A  E+  ++ +F+ N+        +   F        V +  ++          E    +
Sbjct: 1   AQTEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTE---LQ 57

Query: 100 AVQEALHLNESEL-HGRQLKVT 120
           +      L   ++     +K+T
Sbjct: 58  SNAAKEALQGFKITPTHAMKIT 79

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {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: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.3 bits (76), Expect = 0.004
 Identities = 16/79 (20%), Positives = 30/79 (37%), Gaps = 9/79 (11%)

Query: 45  VDSRSVFVGNV-DYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQE 103
           + S ++   N        E +Q    S GT+  V I   +         V F  S +   
Sbjct: 22  LQSPTLEEKNEFPEDLRTELMQT-LGSYGTIVLVRINQGQ-------MLVTFADSHSALS 73

Query: 104 ALHLNESELHGRQLKVTVK 122
            L ++  ++ GR +K++  
Sbjct: 74  VLDVDGMKVKGRAVKISGP 92

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	176
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.91
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.9
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.9
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.9
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.9
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.9
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.9
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.9
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.9
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.89
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.89
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.89
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.89
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.89
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.89
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.89
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.89
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.89
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.89
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.89
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.89
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.88
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.88
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.88
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.88
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.88
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.88
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.88
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.88
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.88
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.87
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.87
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.87
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.87
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.87
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.86
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.86
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.86
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.86
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.86
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.85
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.85
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.85
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.85
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.84
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.84
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.84
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.84
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.83
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.83
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.83
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.83
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.83
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.82
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.82
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.82
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.82
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.81
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.81
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.81
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.81
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.81
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.81
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.81
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.81
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.8
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.8
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.8
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.8
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.8
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.79
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.79
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.78
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.77
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.77
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.74
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.74
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.7
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	99.69
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.63
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.62
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.62
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.59
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.52
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.43
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.89
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.82
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.67
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.45

>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=99.91  E-value=1.5e-23  Score=136.19  Aligned_cols=83  Identities=20%  Similarity=0.423  Sum_probs=77.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ..+++|||+|||+++|+++|+++|++||+|.+|.|+.++ ++.++|||||+|.+.++|+.|+ .||+..|+|+.|+|+++
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            457899999999999999999999999999999999988 7999999999999999999999 69999999999999999


Q ss_pred             cCCCC
Q 030488          123 RTNVP  127 (176)
Q Consensus       123 ~~~~~  127 (176)
                      .+...
T Consensus        85 ~~~~~   89 (93)
T d1h2vz_          85 AGFKE   89 (93)
T ss_dssp             SCCCT
T ss_pred             CCCCC
Confidence            75443

>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=99.90  E-value=9.8e-24  Score=134.54  Aligned_cols=78  Identities=22%  Similarity=0.499  Sum_probs=74.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEecc
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKR  123 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~  123 (176)
                      ..++|||+|||+++|+++|+++|++||.|..+.|++++ +++++|||||+|.+.++|++||+++++.|+|+.|+|..|.
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            45789999999999999999999999999999999998 7999999999999999999999889999999999999875

>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=99.90  E-value=1.8e-23  Score=137.25  Aligned_cols=82  Identities=26%  Similarity=0.496  Sum_probs=76.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ...++|||+|||+++|+++|+++|.+||.|.+|.|+.++ +++++|||||+|.+.++|+.|| .||+..|+|+.|+|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            346789999999999999999999999999999999987 7999999999999999999999 79999999999999999


Q ss_pred             cCCC
Q 030488          123 RTNV  126 (176)
Q Consensus       123 ~~~~  126 (176)
                      ....
T Consensus        86 ~~~~   89 (99)
T d1whwa_          86 TIKK   89 (99)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8643

>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=99.90  E-value=9.3e-24  Score=134.04  Aligned_cols=78  Identities=28%  Similarity=0.435  Sum_probs=74.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      +++|||+|||+++|+++|+++|++||.|.++.|++++ ++.++|||||+|.+.++|++|| .||+..+.|+.|+|++|++
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            4689999999999999999999999999999999987 7999999999999999999999 7999999999999999974

>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=99.90  E-value=2.1e-23  Score=134.17  Aligned_cols=81  Identities=26%  Similarity=0.448  Sum_probs=75.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      ..+..+|||+|||.++|+++|+++|++||.|.+|+|++++ +|+++|||||+|.+.++|+.|+ .||+..|.|+.|+|++
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3457899999999999999999999999999999999987 7999999999999999999999 7999999999999999


Q ss_pred             ccC
Q 030488          122 KRT  124 (176)
Q Consensus       122 a~~  124 (176)
                      |.+
T Consensus        84 a~~   86 (88)
T d1rk8a_          84 CFV   86 (88)
T ss_dssp             SEE
T ss_pred             ecC
Confidence            875

>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=99.90  E-value=2.5e-23  Score=134.36  Aligned_cols=81  Identities=23%  Similarity=0.416  Sum_probs=76.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      .+..+|||+|||.++|+++|+++|++||.|.+|.|+.++ ++.++|||||+|.+.++|++|| .||+..|+|+.|+|++|
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            456789999999999999999999999999999999988 7999999999999999999999 69999999999999999


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      ++.
T Consensus        86 kp~   88 (90)
T d2cq0a1          86 KPS   88 (90)
T ss_dssp             SCC
T ss_pred             eCC
Confidence            854

>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=99.90  E-value=4.1e-23  Score=130.96  Aligned_cols=78  Identities=27%  Similarity=0.491  Sum_probs=74.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      .++|||+|||+++++++|+++|++||.|.+|+|+.+. ++.++|||||+|.+.++|+.|+ .||+..|.|+.|+|++|++
T Consensus         2 ~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           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            4679999999999999999999999999999999987 6899999999999999999999 7999999999999999974

>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=99.90  E-value=1.8e-23  Score=135.81  Aligned_cols=81  Identities=26%  Similarity=0.475  Sum_probs=76.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ...++|||+|||.++|+++|+++|++||.|.+|.|+.++ ++.++|||||+|.+.++|++|+ .||+..|+|+.|+|.+|
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            345799999999999999999999999999999999987 7999999999999999999999 79999999999999999


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      ++.
T Consensus        87 ~~~   89 (93)
T d1x5ua1          87 SAH   89 (93)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            764

>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=99.90  E-value=3.1e-23  Score=131.00  Aligned_cols=75  Identities=24%  Similarity=0.475  Sum_probs=72.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           49 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        49 ~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      +|||+|||+++|+++|+++|++||+|.+|+|++++ +++++|||||+|.+.++|+.|+ .|++..+.|+.|+|.+++
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            69999999999999999999999999999999988 6999999999999999999999 799999999999999986

>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=99.89  E-value=1.1e-23  Score=135.67  Aligned_cols=80  Identities=28%  Similarity=0.522  Sum_probs=75.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      ..++|||+|||+++|+++|+++|++||.|.+|.|+.++ ++.++|||||+|.+.++|++|+ .||+..|+|+.|+|++|+
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            46899999999999999999999999999999999988 6999999999999999999999 799999999999999997


Q ss_pred             CC
Q 030488          124 TN  125 (176)
Q Consensus       124 ~~  125 (176)
                      +.
T Consensus        84 p~   85 (89)
T d2cqba1          84 PM   85 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.89  E-value=9.8e-23  Score=141.59  Aligned_cols=81  Identities=25%  Similarity=0.442  Sum_probs=75.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ...++|||+|||+++|+++|+++|++||.|.+|.|+.++ +++++|||||+|.+.++|+.|| .||++.|+|+.|+|+++
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            345789999999999999999999999999999999987 7999999999999999999999 69999999999999999


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      +..
T Consensus       120 ~~~  122 (139)
T d1u6fa1         120 ASG  122 (139)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            753

>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=99.89  E-value=2.6e-23  Score=130.72  Aligned_cols=76  Identities=24%  Similarity=0.490  Sum_probs=73.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           49 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        49 ~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      +|||+|||+++|+++|+++|++||.|.+++|+.+++++++|||||+|.+.++|+.|+ .||+..++|+.|+|+++.+
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 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            699999999999999999999999999999999999999999999999999999999 6999999999999999853

>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=99.89  E-value=8.3e-23  Score=134.79  Aligned_cols=82  Identities=21%  Similarity=0.342  Sum_probs=76.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      .+.++|||+|||+++|+++|+++|++||.|.++.++.++ ++.++|||||+|.+.++|+.|| .||+..|.|+.|+|+++
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            456789999999999999999999999999999999987 7999999999999999999999 79999999999999999


Q ss_pred             cCCC
Q 030488          123 RTNV  126 (176)
Q Consensus       123 ~~~~  126 (176)
                      ++..
T Consensus        96 ~~k~   99 (102)
T d2cpza1          96 RSKN   99 (102)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            7643

>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=99.89  E-value=1e-22  Score=134.60  Aligned_cols=82  Identities=22%  Similarity=0.466  Sum_probs=74.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      +...++|||+|||+++|+++|+++|++||.|.+|.|+.++ +++++|||||+|.+.++|++||+..+..|+|+.|.|.++
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~V~~a   86 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLA   86 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEES
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEc
Confidence            3456789999999999999999999999999999999998 799999999999999999999953445899999999998


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      ...
T Consensus        87 ~~~   89 (103)
T d2cqda1          87 YLG   89 (103)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            753

>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=99.89  E-value=6.3e-24  Score=133.25  Aligned_cols=75  Identities=21%  Similarity=0.483  Sum_probs=72.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      ++|||+|||+++|+++|+++|++||.|.++.|++|+ +++++|||||+|.+.++|++||+++++.|+|+.|.|..|
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            579999999999999999999999999999999998 699999999999999999999988999999999999886

>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=99.89  E-value=4.1e-23  Score=136.45  Aligned_cols=80  Identities=18%  Similarity=0.416  Sum_probs=75.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccC
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~  124 (176)
                      ..++|||+|||+++|+++|+++|++||.|..+.|++++ ++.++|||||+|.+.++|++||+++++.|+|+.|.|.+|.+
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECcc
Confidence            35799999999999999999999999999999999988 68999999999999999999999999999999999999875


Q ss_pred             C
Q 030488          125 N  125 (176)
Q Consensus       125 ~  125 (176)
                      .
T Consensus        99 k   99 (103)
T d1x4ba1          99 R   99 (103)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.89  E-value=1.9e-23  Score=137.59  Aligned_cols=80  Identities=30%  Similarity=0.486  Sum_probs=75.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEecc
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKR  123 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~  123 (176)
                      .+.++|||+|||+++|+++|+++|+.||.|.+|.|+.+. +|+++|||||+|.+.++|++|++||+..|.|+.|.|.++.
T Consensus        16 ~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          16 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHH
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECC
Confidence            345799999999999999999999999999999999987 7999999999999999999999999999999999999875


Q ss_pred             C
Q 030488          124 T  124 (176)
Q Consensus       124 ~  124 (176)
                      +
T Consensus        96 ~   96 (101)
T d2cq4a1          96 A   96 (101)
T ss_dssp             H
T ss_pred             C
Confidence            3

>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=99.89  E-value=1.2e-22  Score=127.98  Aligned_cols=76  Identities=21%  Similarity=0.472  Sum_probs=72.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      .++|||+|||+++|+++|+++|++||.|..+.++.++ ++.++|||||+|.+.+++++|++++++.|+|+.|+|+.|
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            4789999999999999999999999999999999988 789999999999999999999999999999999999876

>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=99.89  E-value=3.5e-23  Score=132.24  Aligned_cols=78  Identities=23%  Similarity=0.453  Sum_probs=74.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccCC
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTN  125 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~~  125 (176)
                      .+|||+|||+++|+++|+++|++||+|.+|+|++|+ +|.++|||||+|.+.++|+.|+ .||+..|+|+.|.|++|.+.
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            479999999999999999999999999999999988 7999999999999999999999 69999999999999999753

>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=99.89  E-value=2.7e-23  Score=129.74  Aligned_cols=74  Identities=24%  Similarity=0.554  Sum_probs=70.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           49 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        49 ~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      +|||+|||+++|+++|+++|++||.|.++.|++++ +++++|||||+|.+.++|++||+++++.|+|+.|.|..|
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            59999999999999999999999999999999988 799999999999999999999998999999999999754

>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=99.89  E-value=1.9e-22  Score=130.09  Aligned_cols=80  Identities=19%  Similarity=0.403  Sum_probs=73.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEecc
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKR  123 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~  123 (176)
                      ....+|||+|||+++|+++|+++|++||.|.+|.|++|+ +|.++|||||+|.+.++|++||+ +.+.|+|+.|.|.++.
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~-~~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEECCC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh-cCCccCCEEeEEEeCC
Confidence            456789999999999999999999999999999999998 79999999999999999999996 3458999999999987


Q ss_pred             CC
Q 030488          124 TN  125 (176)
Q Consensus       124 ~~  125 (176)
                      +.
T Consensus        85 ~k   86 (90)
T d2cqga1          85 SK   86 (90)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>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=99.88  E-value=1.3e-22  Score=129.54  Aligned_cols=79  Identities=28%  Similarity=0.504  Sum_probs=73.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCC--eeeEE
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHG--RQLKV  119 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g--~~i~v  119 (176)
                      ....++|||+|||+++|+++|+++|++||.|.+++|++++ +++++|||||+|.+.++|+.|| .||+..+.|  ++|.|
T Consensus         3 ~~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V   82 (85)
T d1b7fa2           3 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV   82 (85)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEE
Confidence            3456789999999999999999999999999999999987 7999999999999999999999 799999976  88999


Q ss_pred             Eec
Q 030488          120 TVK  122 (176)
Q Consensus       120 ~~a  122 (176)
                      ++|
T Consensus        83 ~~A   85 (85)
T d1b7fa2          83 RLA   85 (85)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            986

>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=99.88  E-value=1.2e-22  Score=129.13  Aligned_cols=74  Identities=26%  Similarity=0.414  Sum_probs=70.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEE
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV  119 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v  119 (176)
                      +.++|||+|||+++|+++|+++|++||.|.+|.|+.++ +++++|||||+|.+.++|+.|+ .||+..|+|+.|+|
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            35789999999999999999999999999999999988 6999999999999999999999 79999999999987

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=1.6e-22  Score=129.09  Aligned_cols=78  Identities=22%  Similarity=0.412  Sum_probs=72.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCC--eeeEEE
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHG--RQLKVT  120 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g--~~i~v~  120 (176)
                      ..+++|||+|||+++|+++|+++|++||.|.+++|+.++ ++.++|||||+|.+.++|++|+ .||+..+.|  ++|.|.
T Consensus         4 ~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEE
Confidence            346789999999999999999999999999999999988 6999999999999999999999 799999987  558888


Q ss_pred             ec
Q 030488          121 VK  122 (176)
Q Consensus       121 ~a  122 (176)
                      +|
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>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=99.88  E-value=9.2e-23  Score=131.58  Aligned_cols=81  Identities=22%  Similarity=0.540  Sum_probs=75.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      .+.++|||+|||+++|+++|+++|++||.|..+.++.+. ++.++|||||+|.+.++|+.|| .|+++.|+|+.|+|+++
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            456789999999999999999999999999999988877 7899999999999999999999 79999999999999998


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      .+.
T Consensus        83 ~~~   85 (90)
T d1x5sa1          83 GKS   85 (90)
T ss_dssp             ECC
T ss_pred             CCC
Confidence            754

>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=99.88  E-value=1.4e-22  Score=131.80  Aligned_cols=81  Identities=20%  Similarity=0.499  Sum_probs=75.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC--CCCceeEEEEEecCHHHHHHHH-Hh-CCCeeCCeeeEEE
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK--FGQPKGYAYVEFLQSEAVQEAL-HL-NESELHGRQLKVT  120 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~--~g~~~g~afv~f~~~~~a~~a~-~l-~~~~~~g~~i~v~  120 (176)
                      ....+|||+|||+++++++|+++|++||.|.+|.|+++.  +|.++|||||+|.+.++|+.|| .| |+..|+|+.|.|+
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            456789999999999999999999999999999998875  6899999999999999999999 67 8999999999999


Q ss_pred             eccCC
Q 030488          121 VKRTN  125 (176)
Q Consensus       121 ~a~~~  125 (176)
                      +|++.
T Consensus        86 ~A~~~   90 (94)
T d2cpha1          86 WADSE   90 (94)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            99764

>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=99.88  E-value=2.1e-23  Score=130.10  Aligned_cols=74  Identities=18%  Similarity=0.430  Sum_probs=70.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           49 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        49 ~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      +|||+|||+++|+++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|++||+.+++.|+|+.|.|..|
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            59999999999999999999999999999999998 799999999999999999999987889999999999875

>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=99.88  E-value=4.1e-22  Score=128.52  Aligned_cols=82  Identities=24%  Similarity=0.428  Sum_probs=74.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ..+.++|||+|||.++|+++|+++|++||+|.+|.|+.++... ++||||+|.+.++|+.|+ .+++..|.|+.|+|.+|
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~-~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS-CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc-ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            3456899999999999999999999999999999999887433 789999999999999999 69999999999999999


Q ss_pred             cCCC
Q 030488          123 RTNV  126 (176)
Q Consensus       123 ~~~~  126 (176)
                      +++.
T Consensus        84 ~~~~   87 (90)
T d2cqia1          84 TTPS   87 (90)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            7643

>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=99.88  E-value=7.1e-22  Score=128.13  Aligned_cols=81  Identities=22%  Similarity=0.431  Sum_probs=74.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ....++|||+|||+++++++|+++|++||+|.+|.++.++.+ ++|||||+|.+.++|++|| .||+..|+|+.|+|++|
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            455678999999999999999999999999999999988644 5899999999999999999 79999999999999999


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      ++.
T Consensus        87 ~~r   89 (93)
T d2cq3a1          87 TAR   89 (93)
T ss_dssp             CSS
T ss_pred             CcC
Confidence            864

>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=99.88  E-value=4.2e-22  Score=127.15  Aligned_cols=78  Identities=18%  Similarity=0.294  Sum_probs=74.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEecc
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKR  123 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~  123 (176)
                      ..++|||+|||.++|+++|+++|+.||+|..|.|..+.++.++|||||+|.+.++|++||++++..+.|+.|.|.++.
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 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            468999999999999999999999999999999999889999999999999999999999989999999999999875

>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=99.87  E-value=1.7e-22  Score=127.84  Aligned_cols=77  Identities=18%  Similarity=0.292  Sum_probs=67.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      ++|||+|||+++|+++|+++|++||.|..+.++.+. +++++|||||+|.+.++|++|+ .||+..++|+.|.|+++++
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            689999999999999999999999999888777666 7899999999999999999999 7999999999999999975

>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=99.87  E-value=1.6e-22  Score=129.39  Aligned_cols=80  Identities=18%  Similarity=0.411  Sum_probs=71.5

Q ss_pred             CCCCEEEEcCCCCCCC-HHHHHHHhhhCCCeeEEEEeeCC--CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEe
Q 030488           45 VDSRSVFVGNVDYSCT-PEEVQQHFQSCGTVNRVTIRTDK--FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTV  121 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t-~~~l~~~f~~~G~i~~~~~~~~~--~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~  121 (176)
                      .+.++|||+|||+++| +++|+++|++||.|.+|.|+.+.  +++++|||||+|.+.++|++||++|++.|+|+.|+|++
T Consensus         2 ~e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           2 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSL   81 (86)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEE
Confidence            4578999999999876 56699999999999999997754  68999999999999999999999999999999999999


Q ss_pred             ccC
Q 030488          122 KRT  124 (176)
Q Consensus       122 a~~  124 (176)
                      +.+
T Consensus        82 a~~   84 (86)
T d2ghpa3          82 ADK   84 (86)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            875

>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=99.87  E-value=2e-23  Score=135.05  Aligned_cols=82  Identities=20%  Similarity=0.379  Sum_probs=76.0

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      +.....+|||+|||+++|+++|+++|++||.|..+.|+.+.+|+++|||||+|.+.++|++||+||+..|.|+.|+|++|
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECC
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEec
Confidence            34556799999999999999999999999999988887777899999999999999999999999999999999999998


Q ss_pred             cC
Q 030488          123 RT  124 (176)
Q Consensus       123 ~~  124 (176)
                      ++
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=99.87  E-value=2.2e-22  Score=133.13  Aligned_cols=79  Identities=37%  Similarity=0.664  Sum_probs=74.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      .++|||+|||+++|+++|+++|++||.|.+|.|+.++ +|+++|||||+|.+.++|+.|+ .||+..|.|+.|+|+++.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4789999999999999999999999999999999987 7999999999999999999999 7999999999999999865


Q ss_pred             C
Q 030488          125 N  125 (176)
Q Consensus       125 ~  125 (176)
                      .
T Consensus        88 ~   88 (104)
T d1p1ta_          88 E   88 (104)
T ss_dssp             T
T ss_pred             C
Confidence            3

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.87  E-value=7.4e-22  Score=125.93  Aligned_cols=75  Identities=28%  Similarity=0.555  Sum_probs=69.6

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCC-C---CceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           50 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-G---QPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        50 i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~-g---~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      |||+|||+++|+++|+++|++||.|.+|.|++++. +   .++|||||+|.+.++|++|+ .||+..|+|+.|.|++++.
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            79999999999999999999999999999998763 2   47899999999999999999 7999999999999999853

>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=99.87  E-value=2.3e-22  Score=125.30  Aligned_cols=74  Identities=22%  Similarity=0.468  Sum_probs=70.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           49 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        49 ~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      +|||+|||+++|+++|+++|++||.|..+.++.++ ++.+++||||+|.+.++|++|+++|++.|+|+.|+|..|
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            59999999999999999999999999999998888 689999999999999999999999999999999999875

>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=99.86  E-value=4.5e-22  Score=128.08  Aligned_cols=78  Identities=24%  Similarity=0.417  Sum_probs=72.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccCC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTN  125 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~~  125 (176)
                      ..+|||+|||+++|+++|+++|++||.|..+.|+.++. .++|||||+|.+.++|++|| .||+..|+|+.|+|+++++.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT-BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC-CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            46799999999999999999999999999999998764 36899999999999999999 79999999999999999764

>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=5.9e-22  Score=125.85  Aligned_cols=76  Identities=26%  Similarity=0.478  Sum_probs=70.4

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhCCCeeEE-EEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccCC
Q 030488           50 VFVGNVDYSCTPEEVQQHFQSCGTVNRV-TIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTN  125 (176)
Q Consensus        50 i~v~~lp~~~t~~~l~~~f~~~G~i~~~-~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~~  125 (176)
                      |||+|||+++|+++|+++|++||.|.++ .+++++ +++++|||||+|.+.++|+.|| .|++..++|+.|+|+++.+.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            7999999999999999999999999664 778777 7999999999999999999999 69999999999999998753

>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=99.86  E-value=2.3e-21  Score=128.11  Aligned_cols=80  Identities=26%  Similarity=0.511  Sum_probs=72.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC--CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK--FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~--~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      .+.++|||+|||+++|+++|+++|++|| |..+.++.+.  +++++|||||+|.+.++|++|++||++.|.|+.|+|.++
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3568999999999999999999999998 7777777765  688999999999999999988899999999999999998


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      .+.
T Consensus        92 ~~~   94 (104)
T d1wi8a_          92 DQA   94 (104)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

>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=99.86  E-value=9.5e-22  Score=129.30  Aligned_cols=85  Identities=29%  Similarity=0.591  Sum_probs=75.5

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCee--------EEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCee
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVN--------RVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESEL  112 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~--------~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~  112 (176)
                      ++.+..+|||+|||+++|+++|+++|++||.|.        .+.+..++ ++++++||||+|.+.++|+.|| .||+..|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            345678999999999999999999999999874        45666666 6899999999999999999999 7999999


Q ss_pred             CCeeeEEEeccCCCC
Q 030488          113 HGRQLKVTVKRTNVP  127 (176)
Q Consensus       113 ~g~~i~v~~a~~~~~  127 (176)
                      .|+.|+|+++++..|
T Consensus        84 ~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          84 QGSKLKVSLARKKPP   98 (101)
T ss_dssp             TTEECEEECSSCCCC
T ss_pred             CCEEEEEEEcCCCCC
Confidence            999999999987543

>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=99.86  E-value=9.1e-22  Score=129.49  Aligned_cols=82  Identities=17%  Similarity=0.317  Sum_probs=75.7

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      .+.+.++|||+|||+++|+++|+++|++||.|..+.+..+.++.++|||||+|.+.++|++|| .||+..|.|+++.|..
T Consensus        14 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~   93 (101)
T d1x5oa1          14 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP   93 (101)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCC
Confidence            345568999999999999999999999999999999999888999999999999999999999 7999999999998877


Q ss_pred             ccC
Q 030488          122 KRT  124 (176)
Q Consensus       122 a~~  124 (176)
                      +++
T Consensus        94 ~~P   96 (101)
T d1x5oa1          94 TEP   96 (101)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            654

>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=99.85  E-value=2.9e-21  Score=126.18  Aligned_cols=81  Identities=28%  Similarity=0.493  Sum_probs=73.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhC------CCeeCCee
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLN------ESELHGRQ  116 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~------~~~~~g~~  116 (176)
                      .+.++|||+|||+++|+++|+++|++||.|..+.++.+. ++.++|||||+|.+.++|.+|| .++      +..++|+.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~   85 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   85 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEE
Confidence            456899999999999999999999999999999999888 6889999999999999999999 576      56789999


Q ss_pred             eEEEeccCC
Q 030488          117 LKVTVKRTN  125 (176)
Q Consensus       117 i~v~~a~~~  125 (176)
                      |+|+++.+.
T Consensus        86 l~v~~a~~k   94 (98)
T d1x4ha1          86 LKVDLAVTR   94 (98)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEECCCC
Confidence            999999764

>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=99.85  E-value=4.4e-21  Score=126.40  Aligned_cols=82  Identities=21%  Similarity=0.319  Sum_probs=74.8

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      ......+|||+|||+++|+++|+++|..|| +..|.++.+.++.++|||||+|.+.++|++|+++|++.|+|+.|+|.++
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLN   89 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            345568999999999999999999999997 4578888888999999999999999999999999999999999999998


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      ...
T Consensus        90 ~~~   92 (102)
T d1weza_          90 STA   92 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=1e-20  Score=123.04  Aligned_cols=79  Identities=18%  Similarity=0.405  Sum_probs=71.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      .+.++|||+|||+++|+++|+++|++||.|..+.+..  +..+++||||+|.+.++|+.|| .||++.|.|+.|+|++++
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~--~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~   89 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN--RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   89 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC--SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecc--cccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecc
Confidence            4567899999999999999999999999999988754  3456899999999999999999 799999999999999997


Q ss_pred             CC
Q 030488          124 TN  125 (176)
Q Consensus       124 ~~  125 (176)
                      +.
T Consensus        90 ~~   91 (95)
T d1x4aa1          90 SG   91 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.85  E-value=4.3e-21  Score=125.09  Aligned_cols=76  Identities=21%  Similarity=0.444  Sum_probs=71.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      ...++|||+|||.++++++|+++|++||.|.+|+|+.+     +|||||+|.+.++|+.|| .||+..|.|+.|+|++++
T Consensus        16 ~~~~~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          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            34578999999999999999999999999999999977     789999999999999999 799999999999999997


Q ss_pred             CC
Q 030488          124 TN  125 (176)
Q Consensus       124 ~~  125 (176)
                      +.
T Consensus        91 ~~   92 (96)
T d1x4ga1          91 ES   92 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.84  E-value=9.4e-21  Score=127.14  Aligned_cols=77  Identities=23%  Similarity=0.368  Sum_probs=71.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      .+++|||+|||.++|+++|+++|++||.|.+|.+..  ++.++|||||+|.+.++|..|| .||+..|+|+.|.|.++..
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~--~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC--STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc--cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            468999999999999999999999999999999875  4566899999999999999999 7999999999999999854

>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=99.84  E-value=9.2e-21  Score=117.99  Aligned_cols=74  Identities=19%  Similarity=0.294  Sum_probs=68.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      .+|||+|||+++++++|+++|+.||.|..|.|+.++.+. ++||||+|.+.++|++|+.+++..|+|+.|.|+.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~-~~~afV~F~~~~~a~~Al~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            479999999999999999999999999999999888654 47999999999999999999999999999999864

>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=99.84  E-value=1.8e-20  Score=122.47  Aligned_cols=75  Identities=19%  Similarity=0.446  Sum_probs=67.8

Q ss_pred             CCCCCEEEEcCCC-CCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEe
Q 030488           44 EVDSRSVFVGNVD-YSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp-~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~  121 (176)
                      .....+|||+||| ..+++++|+++|++||.|.+|.|.       +|||||+|.+.++|++|| .||++.|.|+.|+|++
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~-------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE-------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe-------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3445789999997 578899999999999999999984       799999999999999999 6999999999999999


Q ss_pred             ccCC
Q 030488          122 KRTN  125 (176)
Q Consensus       122 a~~~  125 (176)
                      ++..
T Consensus        85 a~~~   88 (98)
T d1wf2a_          85 AAEP   88 (98)
T ss_dssp             TTSC
T ss_pred             CCCC
Confidence            9753

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.84  E-value=1.2e-20  Score=119.71  Aligned_cols=76  Identities=16%  Similarity=0.243  Sum_probs=69.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCee-CCeeeEEEe
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESEL-HGRQLKVTV  121 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~-~g~~i~v~~  121 (176)
                      ..++++|||+|||.++|+++|+++|++||.|..|+++.++    +|||||+|.+.++|+.|+ .||+..| +|+.|+|++
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~   80 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITF   80 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEE
Confidence            3457899999999999999999999999999999998654    789999999999999999 7999998 468999999


Q ss_pred             cc
Q 030488          122 KR  123 (176)
Q Consensus       122 a~  123 (176)
                      |+
T Consensus        81 ak   82 (83)
T d2b0ga1          81 AK   82 (83)
T ss_dssp             CC
T ss_pred             ec
Confidence            86

>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=3.4e-20  Score=122.44  Aligned_cols=82  Identities=22%  Similarity=0.362  Sum_probs=72.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEE-EEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRV-TIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~-~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      ..+...|||+|||+++|+++|+++|..+|.|..+ .+..+.+++++|||||+|.+.++|++|+++|+..|.|+.|.|..+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEEC
Confidence            3456789999999999999999999999998764 444455899999999999999999999999999999999999998


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      ...
T Consensus        92 ~~~   94 (104)
T d1wg5a_          92 SRA   94 (104)
T ss_dssp             CTT
T ss_pred             CHH
Confidence            754

>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=99.83  E-value=1.1e-20  Score=120.60  Aligned_cols=75  Identities=28%  Similarity=0.490  Sum_probs=69.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      ..++|||+|||.++++++|+++|++||.|.+|.+..+     ++||||+|.+.++|+.|+ .||+..|+|+.|+|++|..
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~   81 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   81 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            3568999999999999999999999999999999866     789999999999999999 7999999999999999975


Q ss_pred             C
Q 030488          125 N  125 (176)
Q Consensus       125 ~  125 (176)
                      .
T Consensus        82 ~   82 (86)
T d2cpja1          82 S   82 (86)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.83  E-value=3.9e-20  Score=118.03  Aligned_cols=75  Identities=24%  Similarity=0.397  Sum_probs=68.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      ..++|||+|||+++|+++|+++|++||.|..+.+...     +|||||+|.+.++|..|+ .||+..|.|+.|.|+++++
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~-----rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP   81 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-----RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   81 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-----SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccc-----cEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccC
Confidence            4578999999999999999999999999988877554     889999999999999999 7999999999999999985


Q ss_pred             C
Q 030488          125 N  125 (176)
Q Consensus       125 ~  125 (176)
                      .
T Consensus        82 ~   82 (86)
T d2cpda1          82 V   82 (86)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=4.3e-21  Score=126.35  Aligned_cols=81  Identities=19%  Similarity=0.297  Sum_probs=75.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      .++++|||+|||.++++++|+++|++||.|..+.+..+. ++++++||||+|.+.++|+.|| .||+..|.|+.|+|+++
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            356899999999999999999999999999988888776 7899999999999999999999 79999999999999999


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      ++.
T Consensus        96 k~k   98 (102)
T d2cpxa1          96 KNK   98 (102)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            864

>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=99.83  E-value=1.6e-20  Score=119.83  Aligned_cols=77  Identities=21%  Similarity=0.396  Sum_probs=70.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeE-EEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNR-VTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~-~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ...+|||+|||+++++++|+++|+.||.|.. +.+..+.+++++|+|||+|.+.++|++|| .||+..|.|+.|+|+++
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            3467999999999999999999999999865 56777778999999999999999999999 79999999999999875

>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=99.82  E-value=1.1e-20  Score=121.45  Aligned_cols=75  Identities=28%  Similarity=0.492  Sum_probs=67.8

Q ss_pred             CCCEEEEcCCCCCCCHHHH---HHHhhhCCCeeEEEEeeCC-CC---CceeEEEEEecCHHHHHHHH-HhCCCeeCCeee
Q 030488           46 DSRSVFVGNVDYSCTPEEV---QQHFQSCGTVNRVTIRTDK-FG---QPKGYAYVEFLQSEAVQEAL-HLNESELHGRQL  117 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l---~~~f~~~G~i~~~~~~~~~-~g---~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i  117 (176)
                      ..++|||+|||+++++++|   .++|++||.|.+|.|++++ ++   ..+|||||+|.+.++|++|+ .||+..|+|+.|
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            4568999999999999999   7789999999999999887 33   34599999999999999999 799999999999


Q ss_pred             EEE
Q 030488          118 KVT  120 (176)
Q Consensus       118 ~v~  120 (176)
                      +|+
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            985

>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=99.82  E-value=1.1e-20  Score=121.15  Aligned_cols=76  Identities=22%  Similarity=0.368  Sum_probs=67.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccC
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~  124 (176)
                      ...++|||+|||+++|+++|+++|++||.|.+|++..+    +++||||+|.+.++|++||. +++.|+|+.|.|+++++
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~----~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~~a~~   77 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG-EDLIIKGISVHISNAEP   77 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEECCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec----cCceEEEEECCHHHHHHHHh-CCCEECCEEeEEEeCCC
Confidence            34689999999999999999999999999999877543    48899999999999999986 77899999999999865


Q ss_pred             C
Q 030488          125 N  125 (176)
Q Consensus       125 ~  125 (176)
                      .
T Consensus        78 k   78 (88)
T d1wf0a_          78 K   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.82  E-value=7.9e-20  Score=121.54  Aligned_cols=75  Identities=31%  Similarity=0.503  Sum_probs=69.1

Q ss_pred             CCEEEEcCCCC-CCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           47 SRSVFVGNVDY-SCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        47 ~~~i~v~~lp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      +.+|||+|||+ .+|+++|+++|+.||.|..|.|++++    +|||||+|.+.++|++|| .||+..|.|+.|+|++++.
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~~   77 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   77 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            57899999965 59999999999999999999998875    789999999999999999 7999999999999999864


Q ss_pred             C
Q 030488          125 N  125 (176)
Q Consensus       125 ~  125 (176)
                      .
T Consensus        78 ~   78 (109)
T d2adca1          78 Q   78 (109)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.82  E-value=3.7e-20  Score=120.57  Aligned_cols=79  Identities=22%  Similarity=0.314  Sum_probs=70.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCC-eeEEEEeeCC--CCCceeEEEEEecCHHHHHHHH-HhC--CCeeCCeeeEEE
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGT-VNRVTIRTDK--FGQPKGYAYVEFLQSEAVQEAL-HLN--ESELHGRQLKVT  120 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~-i~~~~~~~~~--~g~~~g~afv~f~~~~~a~~a~-~l~--~~~~~g~~i~v~  120 (176)
                      +++|||+|||.++|+++|+++|++||+ |..+.|+.+.  +++++|||||+|.+.++|..|+ .|+  +..+.|+.|+|+
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            368999999999999999999999996 8999998875  5889999999999999999999 675  456689999999


Q ss_pred             eccCC
Q 030488          121 VKRTN  125 (176)
Q Consensus       121 ~a~~~  125 (176)
                      +|++.
T Consensus        81 ~A~p~   85 (96)
T d2disa1          81 WAEPE   85 (96)
T ss_dssp             ESCSS
T ss_pred             EcCCC
Confidence            99754

>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=99.81  E-value=3.7e-20  Score=120.57  Aligned_cols=78  Identities=22%  Similarity=0.417  Sum_probs=69.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ..+.++|||+|||+++|+++|+++|++||.|..+..    ++.+++||||+|.+.++|++|+ .||+..|+|+.|+|.++
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a   88 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            344689999999999999999999999998866542    5778999999999999999999 79999999999999999


Q ss_pred             cCC
Q 030488          123 RTN  125 (176)
Q Consensus       123 ~~~  125 (176)
                      .+.
T Consensus        89 ~~k   91 (96)
T d1fjca_          89 GEK   91 (96)
T ss_dssp             SSS
T ss_pred             CCC
Confidence            764

>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=99.81  E-value=6.5e-21  Score=117.74  Aligned_cols=69  Identities=23%  Similarity=0.385  Sum_probs=65.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeE
Q 030488           50 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLK  118 (176)
Q Consensus        50 i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~  118 (176)
                      |||+|||+++|+++|+++|++||.|..+.+.+++ ++.++|||||+|.+.++|++|+ .||+..|+|+.|+
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            7999999999999999999999999999999888 7899999999999999999999 7999999998764

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=1.7e-20  Score=118.17  Aligned_cols=74  Identities=22%  Similarity=0.405  Sum_probs=66.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCC-eeCCeeeEEEeccCC
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNES-ELHGRQLKVTVKRTN  125 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~-~~~g~~i~v~~a~~~  125 (176)
                      ++|||+|||+++|+++|+++|++||.|..+.+...     +|||||+|.+.++|+.|+ .||+. .++|+.|+|+++.+.
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-----rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k   76 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   76 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE-----TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc-----cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCc
Confidence            47999999999999999999999999877666654     789999999999999999 79985 699999999999864


Q ss_pred             C
Q 030488          126 V  126 (176)
Q Consensus       126 ~  126 (176)
                      .
T Consensus        77 ~   77 (80)
T d2cqha1          77 K   77 (80)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=3.8e-20  Score=116.29  Aligned_cols=74  Identities=23%  Similarity=0.440  Sum_probs=68.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      ..+++|||+||+  +|+++|+++|++||.|.+|.+..+     ++||||+|.+.++|+.|+ +||+..++|+.|+|++++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~-----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC-----CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            356899999996  899999999999999999999765     689999999999999999 799999999999999997


Q ss_pred             CC
Q 030488          124 TN  125 (176)
Q Consensus       124 ~~  125 (176)
                      +.
T Consensus        76 ~~   77 (79)
T d2bz2a1          76 KQ   77 (79)
T ss_dssp             SS
T ss_pred             CC
Confidence            53

>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=99.81  E-value=3.3e-20  Score=122.30  Aligned_cols=79  Identities=24%  Similarity=0.328  Sum_probs=71.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeE-EEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEecc
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNR-VTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKR  123 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~-~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~  123 (176)
                      ....+|||+|||+++|+++|+++|..||.|.. +.+..+.+|+++|||||+|.+.++|++||.+|+..|+|+.|.|..+.
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEEC
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEECC
Confidence            34578999999999999999999999999875 56666668999999999999999999999999999999999999874

>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=99.81  E-value=7.2e-20  Score=119.60  Aligned_cols=75  Identities=20%  Similarity=0.360  Sum_probs=69.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      ....+|||+|||+++++++|+++|++||.|+.+.|..      +|||||+|.+.++|++|| .||+..|.|+.|+|.+++
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEe
Confidence            4567899999999999999999999999999999864      589999999999999999 799999999999999986


Q ss_pred             CC
Q 030488          124 TN  125 (176)
Q Consensus       124 ~~  125 (176)
                      ..
T Consensus        87 ~~   88 (98)
T d1wg4a_          87 VY   88 (98)
T ss_dssp             EE
T ss_pred             cC
Confidence            53

>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=99.81  E-value=8.1e-20  Score=117.05  Aligned_cols=77  Identities=21%  Similarity=0.313  Sum_probs=68.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCee-CCeeeEEEecc
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESEL-HGRQLKVTVKR  123 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~-~g~~i~v~~a~  123 (176)
                      ++++|||+|||+++|+++|+++|++||.|..+.+...   ++++||||+|.+.++|.+|+ .||+..| +|+.|+|++++
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~---~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk   85 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK   85 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS---SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee---cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCC
Confidence            4689999999999999999999999999988776543   34789999999999999999 7999988 58999999998


Q ss_pred             CC
Q 030488          124 TN  125 (176)
Q Consensus       124 ~~  125 (176)
                      +.
T Consensus        86 ~~   87 (88)
T d2adca2          86 ST   87 (88)
T ss_dssp             SC
T ss_pred             CC
Confidence            63

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.81  E-value=4.9e-20  Score=122.92  Aligned_cols=75  Identities=24%  Similarity=0.323  Sum_probs=68.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      ..++|||+|||+++++++|+++|++||.|..|.|..     +++||||+|.+.++|++|| .||+..|.|+.|.|+++..
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~-----~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~   83 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec-----cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCC
Confidence            357899999999999999999999999999998854     3789999999999999999 7999999999999999865


Q ss_pred             C
Q 030488          125 N  125 (176)
Q Consensus       125 ~  125 (176)
                      .
T Consensus        84 ~   84 (111)
T d1whxa_          84 G   84 (111)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.81  E-value=8.9e-21  Score=121.38  Aligned_cols=71  Identities=20%  Similarity=0.337  Sum_probs=65.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      ++|||+|||+++|+++|+++|++||.|.++.+..      .|||||+|.+.++|++|| .||+..|.|+.|+|.+++.
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~   72 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   72 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT------TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc------cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEec
Confidence            3699999999999999999999999999999865      479999999999999999 7999999999999988754

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=1e-19  Score=116.57  Aligned_cols=74  Identities=22%  Similarity=0.377  Sum_probs=64.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccC
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~  124 (176)
                      ...+|||+|||+++++++|+++|++|| +..+.+.     .+++||||+|.+.++|++|| .||++.|.|+.|+|++++.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~-----~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee-----ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            357899999999999999999999999 3333333     34899999999999999999 7999999999999999965


Q ss_pred             C
Q 030488          125 N  125 (176)
Q Consensus       125 ~  125 (176)
                      .
T Consensus        78 ~   78 (88)
T d1wg1a_          78 D   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.80  E-value=9.6e-20  Score=131.27  Aligned_cols=82  Identities=20%  Similarity=0.443  Sum_probs=76.2

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEe
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTV  121 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~  121 (176)
                      .....++|||+|||+.+|+++|+++|+.||.|..+.|+.+. ++.++|||||+|.+.++|++||.++++.|+|+.|+|.+
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            44567899999999999999999999999999999999988 68999999999999999999998899999999999998


Q ss_pred             ccC
Q 030488          122 KRT  124 (176)
Q Consensus       122 a~~  124 (176)
                      |.+
T Consensus       173 A~~  175 (183)
T d1u1qa_         173 ALS  175 (183)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            854

>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=99.80  E-value=5.5e-20  Score=123.03  Aligned_cols=80  Identities=18%  Similarity=0.274  Sum_probs=71.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeE-EEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEec
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNR-VTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVK  122 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~-~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a  122 (176)
                      .....+|||+|||+++|+++|+++|+.||.|.. +.+..+.+|.++|||||+|.+.++|++|+.+|+..|+|+.|.|..+
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEc
Confidence            345779999999999999999999999999865 4455556899999999999999999999999999999999999877


Q ss_pred             c
Q 030488          123 R  123 (176)
Q Consensus       123 ~  123 (176)
                      .
T Consensus        95 ~   95 (112)
T d1wela1          95 T   95 (112)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=2.2e-19  Score=117.08  Aligned_cols=76  Identities=18%  Similarity=0.408  Sum_probs=69.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCC--eeeEEEe
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHG--RQLKVTV  121 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g--~~i~v~~  121 (176)
                      .+.++|||+|||+++++++|+++|++||.|..+++.++     ++||||+|.+.++|+.|+ .||+..|.|  +.|+|++
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            45789999999999999999999999999999999765     789999999999999999 799999976  5899999


Q ss_pred             ccCC
Q 030488          122 KRTN  125 (176)
Q Consensus       122 a~~~  125 (176)
                      +++.
T Consensus        90 ak~~   93 (97)
T d1whya_          90 AKSG   93 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9864

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=5.6e-20  Score=118.56  Aligned_cols=78  Identities=14%  Similarity=0.363  Sum_probs=69.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHH----HhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEE
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQ----HFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT  120 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~----~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~  120 (176)
                      ++++|||+|||+++++++|++    +|++||.|.+|.+.  ++++++|||||+|.+.++|..|+ .+|+..++|+.|.|.
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~--~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~   79 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS--RSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   79 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECC--HHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEe--eeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            468999999999999999864    57999999998874  35677899999999999999999 799999999999999


Q ss_pred             eccCC
Q 030488          121 VKRTN  125 (176)
Q Consensus       121 ~a~~~  125 (176)
                      +|++.
T Consensus        80 ~ak~~   84 (91)
T d1nu4a_          80 YAKTD   84 (91)
T ss_dssp             ECSSC
T ss_pred             EeCCC
Confidence            99764

>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=99.79  E-value=3e-19  Score=110.99  Aligned_cols=70  Identities=23%  Similarity=0.406  Sum_probs=62.9

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEeccCC
Q 030488           50 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTN  125 (176)
Q Consensus        50 i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~~~  125 (176)
                      |||+|||+++++++|+++|++|| +..+.+.     +++|||||+|.+.++|++|+ .||+..+.|+.|+|++++..
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~-----~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD-----KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE-----TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec-----ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 5555553     34899999999999999999 79999999999999999754

>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=99.79  E-value=1.5e-18  Score=114.38  Aligned_cols=78  Identities=19%  Similarity=0.176  Sum_probs=69.8

Q ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-Hh--CCCeeCCeeeEE
Q 030488           43 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HL--NESELHGRQLKV  119 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l--~~~~~~g~~i~v  119 (176)
                      ...++++|||+|||.++|+++|.++|++||.|..+.+.++     +++|||+|.+.++|+.|+ .+  ++..+.|+.|+|
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~-----k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v   85 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec-----ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEE
Confidence            3456889999999999999999999999999999999765     789999999999999999 55  567889999999


Q ss_pred             EeccCC
Q 030488          120 TVKRTN  125 (176)
Q Consensus       120 ~~a~~~  125 (176)
                      .+++..
T Consensus        86 ~~s~~~   91 (104)
T d1wexa_          86 NYSTSK   91 (104)
T ss_dssp             EECSSS
T ss_pred             EEcCCC
Confidence            999653

>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=99.78  E-value=1.2e-18  Score=111.56  Aligned_cols=76  Identities=17%  Similarity=0.188  Sum_probs=69.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-H--hCCCeeCCeeeEEE
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-H--LNESELHGRQLKVT  120 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~--l~~~~~~g~~i~v~  120 (176)
                      ..++++|||+|||.++++++|+++|++||.|.++.+..+     ++||||+|.+.++|++|+ .  +++..++|+.|+|.
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~   79 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   79 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEE
Confidence            457889999999999999999999999999999998865     689999999999999999 4  46789999999999


Q ss_pred             eccC
Q 030488          121 VKRT  124 (176)
Q Consensus       121 ~a~~  124 (176)
                      +++.
T Consensus        80 ~sk~   83 (88)
T d2cq1a1          80 YSNH   83 (88)
T ss_dssp             ECSC
T ss_pred             ECCC
Confidence            9974

>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=99.77  E-value=7.2e-19  Score=114.98  Aligned_cols=78  Identities=17%  Similarity=0.214  Sum_probs=69.6

Q ss_pred             cCCCCCEEEEcCCCCC-CCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH---HhCCCeeCCeeeE
Q 030488           43 EEVDSRSVFVGNVDYS-CTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL---HLNESELHGRQLK  118 (176)
Q Consensus        43 ~~~~~~~i~v~~lp~~-~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~---~l~~~~~~g~~i~  118 (176)
                      ....+++|||+|||.+ +|+++|.++|++||.|.++.+..+     +++|||+|.+.++|..|+   .+++..+.|+.|+
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-----CCcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            3456789999999985 899999999999999999999866     689999999999999998   3788899999999


Q ss_pred             EEeccCC
Q 030488          119 VTVKRTN  125 (176)
Q Consensus       119 v~~a~~~  125 (176)
                      |.+++..
T Consensus        89 V~~s~~~   95 (99)
T d1x4fa1          89 VDLSEKY   95 (99)
T ss_dssp             EEEECSC
T ss_pred             EEEcCCc
Confidence            9999643

>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=99.77  E-value=7.5e-19  Score=116.64  Aligned_cols=78  Identities=19%  Similarity=0.258  Sum_probs=69.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCee--CCeeeEEEe
Q 030488           45 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESEL--HGRQLKVTV  121 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~--~g~~i~v~~  121 (176)
                      ....+|||+|||+++|+++|+++|++||.|..|.|..++   ++|||||+|.+.++|+.|| .||+..|  .+..|+|.+
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~---~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET---TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC---CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            345789999999999999999999999999999998764   4899999999999999999 7999998  578899998


Q ss_pred             ccCC
Q 030488          122 KRTN  125 (176)
Q Consensus       122 a~~~  125 (176)
                      ++..
T Consensus        82 s~~~   85 (108)
T d2adba1          82 SKLT   85 (108)
T ss_dssp             CSSC
T ss_pred             cCCc
Confidence            8653

>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=99.74  E-value=5e-18  Score=108.78  Aligned_cols=77  Identities=16%  Similarity=0.222  Sum_probs=68.7

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-Hh--CCCeeCCeeeEE
Q 030488           44 EVDSRSVFVGNVDYS-CTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HL--NESELHGRQLKV  119 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~-~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l--~~~~~~g~~i~v  119 (176)
                      ...+++|||+|||.. +|+++|.++|++||.|.+|.+..+     +++|||+|.+.++|+.|+ .+  ++..+.|++|+|
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            345789999999986 889999999999999999999866     679999999999999999 44  678999999999


Q ss_pred             EeccCC
Q 030488          120 TVKRTN  125 (176)
Q Consensus       120 ~~a~~~  125 (176)
                      ++++..
T Consensus        80 ~~s~~~   85 (89)
T d1x4da1          80 HLSQKY   85 (89)
T ss_dssp             EEECCC
T ss_pred             EECCCc
Confidence            999753

>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=99.74  E-value=2.3e-20  Score=120.17  Aligned_cols=77  Identities=22%  Similarity=0.433  Sum_probs=67.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEee------CCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEe
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRT------DKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTV  121 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~------~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~  121 (176)
                      ++|||+|||+++|+++|+++|++||.|..+.+..      ..+++++|||||+|.+.++|++|++||++.+.|+.|+|..
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            6899999999999999999999999876655432      2357889999999999999999999999999999999976


Q ss_pred             ccC
Q 030488          122 KRT  124 (176)
Q Consensus       122 a~~  124 (176)
                      ++.
T Consensus        82 ~k~   84 (90)
T d1u2fa_          82 PHD   84 (90)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            543

>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=99.70  E-value=1.9e-17  Score=109.00  Aligned_cols=77  Identities=12%  Similarity=0.164  Sum_probs=67.8

Q ss_pred             CCCCEEEEcCCCCCC-CH----HHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeE
Q 030488           45 VDSRSVFVGNVDYSC-TP----EEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLK  118 (176)
Q Consensus        45 ~~~~~i~v~~lp~~~-t~----~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~  118 (176)
                      ....+|||+||+.++ ++    ++|+++|++||.|.++.+.+.     ++||||+|.+.++|++|+ .||+..|.|+.|+
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~-----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC-----CCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            346789999999875 33    569999999999999999854     789999999999999999 7999999999999


Q ss_pred             EEeccCCC
Q 030488          119 VTVKRTNV  126 (176)
Q Consensus       119 v~~a~~~~  126 (176)
                      |.+++...
T Consensus        78 v~~a~~~~   85 (104)
T d1weya_          78 LYFAQTLH   85 (104)
T ss_dssp             EECCCCSS
T ss_pred             EeecccCC
Confidence            99997543

>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=99.69  E-value=2.5e-18  Score=113.31  Aligned_cols=75  Identities=17%  Similarity=0.233  Sum_probs=70.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ..++|.+++.++++++|+++|++||.|.+|.|+++.+++++|||||+|.+.++|.+|+ .||+..++|+.|+|+++
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 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            4588899999999999999999999999999998889999999999999999999999 79999999999999875

>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=99.63  E-value=1.4e-15  Score=109.13  Aligned_cols=78  Identities=22%  Similarity=0.502  Sum_probs=72.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-CCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEeccC
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKRT  124 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~~  124 (176)
                      .++|||+|||+++|+++|+++|++||.|.++.++.+. ++.++|||||+|.+.++|++|+.+++..+..+.+.+.....
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhh
Confidence            4789999999999999999999999999999999987 79999999999999999999998888999999888887643

>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=99.62  E-value=6e-16  Score=101.16  Aligned_cols=63  Identities=19%  Similarity=0.433  Sum_probs=57.0

Q ss_pred             CCCCEEEEc--CCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCee
Q 030488           45 VDSRSVFVG--NVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESEL  112 (176)
Q Consensus        45 ~~~~~i~v~--~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~  112 (176)
                      .+..+|||.  |||.++|+++|+++|++||.|..|.+..+     ++||||+|.+.++|+.|+ .||+..|
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            346788885  59999999999999999999999988765     689999999999999999 7999987

>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=99.62  E-value=3.5e-16  Score=104.35  Aligned_cols=71  Identities=17%  Similarity=0.231  Sum_probs=61.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCH-HHHHHHH-HhCCCeeCCeeeEEEec
Q 030488           47 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQS-EAVQEAL-HLNESELHGRQLKVTVK  122 (176)
Q Consensus        47 ~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~-~~a~~a~-~l~~~~~~g~~i~v~~a  122 (176)
                      ...+||||||.++|+++|+++|++||+|.+|.|+.+     ++||||.|.+. ++|..|+ .+++..+.++.+.|.++
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-----kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-----CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC-----CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            345699999999999999999999999999999865     79999999985 6788888 79998887766666654

>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=99.59  E-value=1.4e-15  Score=95.29  Aligned_cols=72  Identities=11%  Similarity=0.102  Sum_probs=62.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCe-eeEEEecc
Q 030488           46 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGR-QLKVTVKR  123 (176)
Q Consensus        46 ~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~-~i~v~~a~  123 (176)
                      +.+.|+|+++|++++++.| ++|++||.|.++.+..+     ++||||+|.+.++|++||.+|+..|+|+ .|.|..+.
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~-----~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS-----SSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC-----CCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCC
Confidence            4567999999999986655 57999999999987544     7999999999999999999999999997 46787764

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=2.7e-14  Score=92.79  Aligned_cols=79  Identities=19%  Similarity=0.308  Sum_probs=67.0

Q ss_pred             CCCCCEEEEcCC--CCCC---------CHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCe
Q 030488           44 EVDSRSVFVGNV--DYSC---------TPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESE  111 (176)
Q Consensus        44 ~~~~~~i~v~~l--p~~~---------t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~  111 (176)
                      ....++|+|.||  |.++         .+++|++.|++||.|..|.+..+.   .+|||||+|.+.++|.+|+ .||+..
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~---~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH---PDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC---TTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC---CccEEEEEECCHHHHHHHHHHhCCcE
Confidence            355789999999  5542         136789999999999999887553   4789999999999999999 799999


Q ss_pred             eCCeeeEEEeccCC
Q 030488          112 LHGRQLKVTVKRTN  125 (176)
Q Consensus       112 ~~g~~i~v~~a~~~  125 (176)
                      ++|+.|.|++..+.
T Consensus        82 ~~gr~i~v~~~~g~   95 (99)
T d2dita1          82 FGGRQITAQAWDGT   95 (99)
T ss_dssp             ETTEECEEEECCSC
T ss_pred             ECCEEEEEEEeCCc
Confidence            99999999998643

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=9.1e-14  Score=91.02  Aligned_cols=78  Identities=18%  Similarity=0.167  Sum_probs=66.8

Q ss_pred             CCCEEEEcCC--CCCCC--------HHHHHHHhhhCCCeeEEEEeeCCC---CCceeEEEEEecCHHHHHHHH-HhCCCe
Q 030488           46 DSRSVFVGNV--DYSCT--------PEEVQQHFQSCGTVNRVTIRTDKF---GQPKGYAYVEFLQSEAVQEAL-HLNESE  111 (176)
Q Consensus        46 ~~~~i~v~~l--p~~~t--------~~~l~~~f~~~G~i~~~~~~~~~~---g~~~g~afv~f~~~~~a~~a~-~l~~~~  111 (176)
                      +++.|.|.||  |.++.        .++|++.|++||.|++|.|+++..   ....|++||+|.+.++|.+|+ .||+..
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            5788999999  55443        357899999999999999988663   345689999999999999999 799999


Q ss_pred             eCCeeeEEEecc
Q 030488          112 LHGRQLKVTVKR  123 (176)
Q Consensus       112 ~~g~~i~v~~a~  123 (176)
                      ++|+.|.|.+..
T Consensus        83 f~gR~v~v~f~~   94 (104)
T d1o0pa_          83 FANRVVVTKYCD   94 (104)
T ss_dssp             SSSSCCEEEEEC
T ss_pred             ECCeEEEEEEcC
Confidence            999999999874

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.89  E-value=1.3e-05  Score=49.21  Aligned_cols=55  Identities=25%  Similarity=0.373  Sum_probs=49.1

Q ss_pred             HHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHHhCCCeeCCeeeEEEecc
Q 030488           62 EEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTVKR  123 (176)
Q Consensus        62 ~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~i~v~~a~  123 (176)
                      ++|.+.|..||+|.-|+++.+       ...|+|.+-++|.+|+.+++.+++|+.|+|....
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            367888999999999999855       5899999999999999999999999999998653

>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=97.82  E-value=7e-05  Score=46.36  Aligned_cols=75  Identities=15%  Similarity=0.145  Sum_probs=59.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCC-C-C-CceeEEEEEecCHHHHHHHH-HhCCCeeCCe-----eeE
Q 030488           48 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-F-G-QPKGYAYVEFLQSEAVQEAL-HLNESELHGR-----QLK  118 (176)
Q Consensus        48 ~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~-g-~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~-----~i~  118 (176)
                      ++|.|.+||++.|++++.+.+...+.+........+ + + ..-.-|+|.|.+.+++.... ..+++.+.+.     .-.
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            578999999999999999999999988877776655 2 2 33567999999999999988 6999988432     345


Q ss_pred             EEec
Q 030488          119 VTVK  122 (176)
Q Consensus       119 v~~a  122 (176)
                      |++|
T Consensus        82 VE~A   85 (91)
T d1uw4a_          82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            5555

>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=97.67  E-value=0.00021  Score=41.65  Aligned_cols=60  Identities=18%  Similarity=0.229  Sum_probs=51.0

Q ss_pred             HHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHH-HhCCCeeCCeeeEEEecc
Q 030488           62 EEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR  123 (176)
Q Consensus        62 ~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~i~v~~a~  123 (176)
                      +.|...|.+++.|.++.|.....+..  .|-|...+..+|.-|+ .|+...|+.++|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            34667789999999999875544544  5899999999999999 799999999999999874

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.45  E-value=0.0074  Score=37.22  Aligned_cols=56  Identities=21%  Similarity=0.292  Sum_probs=45.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhhCCCeeEEEEeeCCCCCceeEEEEEecCHHHHHHHHH
Q 030488           44 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH  106 (176)
Q Consensus        44 ~~~~~~i~v~~lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~g~~~g~afv~f~~~~~a~~a~~  106 (176)
                      .....-||.-..|..+...||.++|+.||.|. |.++.+.      -|||...+.++|+.++.
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT------Sa~V~L~~~e~~~~v~~   67 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT------SAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT------EEEEECSCHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc------eEEEEecCHHHHHHHHH
Confidence            34456688889999999999999999999873 3344332      59999999999998883